The prevalence and risk factors of Staphylococcus aureus carriage, analysis of antibiotic resistance and virulence factors ; Staphylococcus aureus nešiojimo paplitimas ir rizikos veiksniai, atsparumo antimikrobinėms medžiagoms ir virulentiškumo veiksnių analizė

VILNIUS UNIVERSITY




Agnė Kirkliauskienė





The prevalence and risk factors of Staphylococcus aureus carriage,
analysis of antibiotic resistance and virulence factors




Doctoral Dissertation

Biomedical Sciences, Medicine (07B)










Vilnius, 2011 VILNIAUS UNIVERSITETAS




Agnė Kirkliauskienė





Staphylococcus aureus nešiojimo paplitimas ir rizikos veiksniai,
atsparumo antimikrobinėms medžiagoms ir virulentiškumo veiksnių
analizė



Daktaro disertacija

Biomedicinos mokslai, medicina (07B)









Vilnius, 2011
2 The Doctoral Dissertation was prepared at the Department of Infectious
Diseases, Dermatovenereology and Microbiology of Vilnius University,
Lithuania and National Centre for Antimicrobials and Infection Control,
Statens Serum Institute, Copenhagen, Denmark in 2004–2011.



Scientific Supervisor
Prof. Habil. Dr. Arvydas Ambrozaitis (Department of Infectious Diseases,
Dermatovenereology and Microbiology, Vilnius University, Lithuania,
Medicine – 07B)



Scientific Consultant
Prof. Dr. Niels Frimodt-Møller MD, DMSc (National Centre for
Antimicrobials and Infection Control, Statens Serum Institute, Denmark,
Medicine – 07B)













3 CONTENTS

ABBREVIATIONS……………………………………………………… 7

1 INTRODUCTION………………………………………………….. 9
1.1. Aim of the study ……………………………………………... 12
1.2. Objectives of the study ………………………………………. 12
1.3. Scientific novelty of the study ……………………………….. 12
1.4. Practical value of the study…………………………………… 13
1.5. Defensive statements of the dissertation……………………… 14

2 LITERATURE REVIEW………………………………………….. 15
2.1. Diversity of S. aureus phenotypic characteristics…………….. 15
2.1.1. Virulence factors and encoding genes of S. aureus….. 16
2.1.1.1. Panton – Valentine leukocidin………………. 17
2.1.2 Molecular typing of S. aureus………………………... 19
2.2. Antimicrobial resistance in staphylococci……………………. 21
2.2.1. β-lactam antibiotics…………………………………... 23
2.2.2. Glycopeptides………………………… 30
2.2.3. Rifampin……………………………………………… 31
2.2.4. Fluoroquinolones……………………………………... 32
2.2.5. Aminoglycosides……………………... 33
2.2.6. Tetracyclines…………………………………………. 33
2.2.7. Macrolides-Lincosamides-Streptogramin B…………. 35
2.2.8. Fusidic acid…………………………………………... 38
2.2.9. Mupirocin…………………………………………….. 39
2.3. Colonization and carriage of S. aureus……………………….. 40
2.4. Risk factors for acquisition of S. aureus……………………… 45


4 3 MATERIALS AND METHODS…………………………………... 52
3.1. Study participants and selection ……………………………... 52
3.2. The study of risk factors influencing S. aureus carriage .......... 55
3.3. S. aureus isolation and detection of resistance to
antimicrobials by microbiological methods…………………... 58
3.3.1. Samples and culturing………………………………... 58
3.3.2. Identification of S. aureus……………………………. 59
3.3.3. Antimicrobial susceptibility testing………………….. 63
3.4. The identification of the resistance to some antimicrobials and
virulence gene detection by molecular methods……………… 68
3.4.1. Preparation of chromosomal DNA ……....................... 69
3.4.2. Multiplex PCR for ermA, ermC, tetK, tetM genes
detection……………………………………………… 69
3.4.3. Multiplex PCR for mecA, spa and pvl detection ……... 69
3.5. Study time and location ……………………………………… 70
3.6. The aspects of ethics …………………………………………. 71
3.7. Statistical analysis …………………………… 71

4. RESULTS OF THE STUDY………………………………………. 74
4.1. Characteristics of the respondents …………………………… 74
4.1.1. Community group characteristics……………………. 74
4.1.2. Hospitalized patients‘ group characteristics………….. 76
4.2. Isolation of S. aureus from participants of the study…………. 81
4.2.1. S. aureus carriage in the community groups…………. 81
4.2.2. S. aureus carriage in the hospitalized patients‘ group... 83
4.3. The resistance of S. aureus isolates to antibiotics analyzed …. 87
4.3.1. The resistance of S. aureus isolates to antibiotics
analysed in the community group……………………. 87
4.3.2. The resistance of S. aureus isolates to antibiotics
analyzed in the hospitalized patients‘ group ………… 89
5 4.4. Distribution of selected erm and tet genes among isolated S.
aureus ………………………………………………………... 94
4.4.1. The presence of resistance genes of S. aureus isolated
in the community group ……………………………... 94
4.4.2. The presence of resistance genes of S. aureus isolated
in the hospital group ………………………………… 96
4.5. The presence of Panton-Valentine leukocidin gene …………. 98
4.6. spa typing of isolated S. aureus strains ……………………… 100
4.7. The risk factors for colonization of S. aureus in upper
respiratory tract ………………………………………………. 103
4.7.1. The risk factors influencing the colonization of S.
aureus in upper respiratory tract in the community
group ………………………………………………… 103
4.7.2. The risk factors possibly influencing respiratory tract
colonization with S. aureus in the hospitalized
patients group ……………………………………….. 110

5. DISCUSSION ..…………………………………………………….. 114
6. CONCLUSSIONS …………………………………………………. 132
7. RECOMMENDATIONS . 134
8. LIST OF PUBLICATIONS ………………. 135
Acknowledgements ………..……………………………………….. 136
138 9. REFERENCES …………….
APPENDIX ………………………………………………………… 171
6 ABBREVIATIONS

– community associated methicillin–resistant Staphylococcus CA-MRSA
aureus
CA-SA – community associated Staphylococcus aureus
CDC – Centers for Disease Control
Cl – confidence interval
CLSI – Clinical Laboratory Standards Institute
C – coefficient of variation V
DNA – deoxyribonucleic acid
dNTP – deoxyribonucleotide triphosphate
EARSS – European Antimicrobial Resistance Surveillance System
– health care associated methicillin–resistant Staphylococcus HA-MRSA
aureus
HA-SA – health care associated Staphylococcus aureus
ICU – intensive care unit
IU – international unit
IDUs – injecting drug users
MIC – minimum inhibitory concentration
MLS – macrolide-lincosamide-streptogramin
MLST – multi locus sequence typing
MRSA – methicillin–resistant Staphylococcus aureus
MSSA – methicillin–sensitive Staphylococcus aureus
NHANE – National Health and Nutrition Examination Survey
OG – occupational group
OR – odds ratio
p – level of statistical significance
– statistical significance, based on Fishers exact test, when
pF number of cases in the cells of the contingency table is les
than 5
PBP2a – penicillin-binding protein 2a
PCR – polymerase chain reaction
PFGE – pulsed field gel electrophoresis
7 PVL – Panton-Valentine leukocidin
rpm – revolutions per minute
S. aureus – Staphylococcus aureus
SCCmec – staphylococcal cassette chromosome mec
SD – standard deviation
spa – gene encoding Staphylococcal Protein A
SSI – surgical site infection
SSTI – skin and soft tissue infections
ST – sequence type
VISA – vancomycin-intermediate S. aureus
VRSA – vancomycin-resistant S. aureus
VCUH – Vilnius City University Hospital
VUHSK – Vilnius University Hospital Santariškių Klinikos





8 1. INTRODUCTION

Staphylococcus aureus (S. aureus) was discovered in Aberdeen, Scotland
in 1883 by the surgeon Sir Alexander Ogston in pus from a surgical abscess
[1]. He introduced the name “staphylococcus” (from the Greek σταϕυλʊƞ,
“bunch of grapes”) to describe “micrococci” responsible for inflammation and
suppuration. Pasteur (1880), independently from Ogston, described small
spherical bacteria isolated from pus obtained from furuncles and osteomyelitis
and considered them to be pathogenic.
Members of the genus Staphylococcus form a coherent and well-defined
group of related species that is widely divergent from those of the genus
Micrococcus. The genus Staphylococcus consists of 36 species, 16 of which
are found in humans. [2]
Only a few of the staphylococci are pathogenic in the absence of
predisposing host conditions such as immunosuppresion or the presence of a
foreign body. The most virulent ones include S. aureus and S. lugdunensis in
humans. Although S. epidermidis and S. saprophyticus are commonly
responsible for devise-related and urinary tract infections, they produce
substantially less devastating disease syndromes than S. aureus. [2]
S. aureus is part of the usual bacterial flora of humans and can also be
found in other mammals as well as birds. Nevertheless, throughout the
recorded history this commensal has been a significant cause of infections in
humans. Even Egyptian mummies are known to have pathological changes
consistent with staphylococcal osteomyelitis. This microorganism has
exceptional ability of transforming itself and being one step ahead of
therapeutic novelties.
S. aureus is re-e