USA300: multiple imports and decline

Transcription

1 USA300: multiple imports and decline Patrícia Martins Simões, PhD Hospices Civils de Lyon, CIRI-INSERM U1111, University of Lyon, National Reference Center for Staphylococci

2 Community Acquired (CA-)MRSA: historical clones Western Australia, USA400 European clone USA300 clone Taiwan clone South West Pacific clone Global distribution of CA-MRSA (ST) Deleo et al. Lancet (2010) Dotted lines indicated = possible route of dissemination. +, PVL-positive;, PVL-negative; ±, combination of PVL-positive and PVL-negative strains isolated from the region. Historical pandemic CA-MRSA are from distinct clonal lineages

3 CA-MRSA: USA300 clone USA300 clone 1. skin and soft tissues infections (SSTIs) ++ in the early 2000's USA300 clone 2. Prevalence > 50% in the US 3. PVL+, MSLT ST8, spa t008, sek, seq, SCCmec IV 4. PFGE typing : USA300 clone Deleo et al. Lancet (2010)

4 CA-MRSA: pandemic USA300 clone USA300 clone 1. skin and soft tissues infections (SSTIs) ++ in the early 2000's 2. Prevalence > 50% in the US USA300 clone 3. PVL+, MSLT ST8, spa t008, sek, seq, SCCmec IV 4. PFGE typing : USA300 clone Deleo et al. Lancet (2010) Nimmo CMI (2014) USA300 pandemic clone: multiple reports of its presence worldwide

5 USA300 CA-MRSA clone: what makes it special? USA300 clone 1. skin and soft tissues infections (SSTIs) ++ in the early 2000's USA300 clone 2. Prevalence > 50% in the US 3. PVL+, MSLT ST8, spa t008, sek, seq, SCCmec IV 4. PFGE typing : USA300 clone Deleo et al. Lancet (2010) 5. Transmission ++ : arginine catabolic mobile element (ACME) with arcabcd and speg fitness advantage/survival (human skin acid environment) Thurlow et al. Cell Host and Microbes (2013) arc protects from organic acids arc diverts L-arginine from NO production speg confers resistance to toxic polyamines

6 USA300 CA-MRSA clone: what makes it special? USA300 clone 1. skin and soft tissues infections (SSTIs) ++ in the early 2000's 2. Prevalence > 50% in the US USA300 clone 3. PVL+, MSLT ST8, spa t008, sek, seq, SCCmec IV 4. PFGE typing : USA300 clone 5. Transmission ++ : arginine catabolic mobile element (ACME) with arcabcd and speg fitness advantage/survival (human skin acid environment) Deleo et al. Lancet (2010) BUT the PFGE USA300 encompasses multiple variants : Canada, USA, South America...

7 USA300 CA-MRSA clone: what makes it special? Planet et al. JID (2015) Planet et al. JID (2016) USA300 clone : at least 2 variants with a parallel evolution in the American continent since 1980's (ACME not conserved but copb yes)

8 USA300 CA-MRSA clone: a pandemic in evolution Nimmo CMI (2014) Is the USA300 clone in an inter-continental expansion phase?

9 USA300 CA-MRSA: the European continent USA300 clone Stegger et al. MBio (2014) European Continent: Köck Euro Surv. (2010) Grundmann et al.plos Med. (2010) Brauner et al. Eur J Clin Microbiol Infect Dis. (2013) Rolo et al.plos One (2012) Von Dach et al. JID (2016) The most prevalent CA-MRSA in Europe: ST80-IV, pvl+ ST80-IV, pvl+ is starting to decline and co-exists with other CA-MRSA at low prevalences Reports of USA300-NA in multiple countries has been increasing with local epidemics and multiple imports USA300 in Europe: is it replacing the European clone ST80?

10 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 67 USA300 CA-MRSA strains reported in the last decade ( ) 431 ST8 MSSA and MRSA strains from the US [Uhleman et al. PNAS (2014) + Tewhey et al. BMC Genomics (2012)]

11 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 67 USA300 CA-MRSA strains reported in the last decade ( ) 431 ST8 MSSA and MRSA strains from the US [Uhleman et al. PNAS (2014) + Tewhey et al. BMC Genomics (2012)] Red branches = US USA300-NA genomes Blue branches = FR USA300-NA genomes Strains isolated in France (blue) in the last decade are interleaved with USA300-NA strains from US (red) USA300 clone in France: multiple introductions of USA300-NA lineage in the last decade as early as the onset of this lineage

12 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 28 USA300 CA-MRSA strains reported between Outbreak? USA300 clone in France: multiple introductions of USA300-NA lineage in the last decade as early as the onset of this lineage

13 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 28 USA300 CA-MRSA strains reported between outbreaks from a same subclonal lineage of USA300-NA Same lineage was also responsible for sporadic cases scattered in French territor Dating froman introduction event occurring ~1998 USA300 clone in France: some introductions of the USA300-NA MRSA clone can be successful but to a limited extent

14 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 67 USA300 CA-MRSA strains reported in the last decade ( ) 431 ST8 MSSA and MRSA strains from the US [Uhleman et al. PNAS (2014) + Tewhey et al. BMC Genomics (2012)] Bayesian Skyline plot = inference of population dynamics using coalescence theory and estimation of effective population sizes Rise of USA300-NA: around 1996 with the acquisition of ACME and SCCmec Second weaker expansion of USA300-NA lineage coincides with Fluoroquinolone resistance Apparent decline of the USA300-NA lineage after 2008

15 USA300 CA-MRSA: a French snapshot of 14 years Genome wide comparison: 67 USA300 CA-MRSA strains reported in the last decade ( ) 431 ST8 MSSA and MRSA strains from the US [Uhleman et al. PNAS (2014) + Tewhey et al. BMC Genomics (2012)] Bayesian Skyline plot = inference of population dynamics using coalescence theory and estimation of effective population sizes Rise of USA300-NA: around 1996 with the acquisition of ACME and SCCmec Second weaker expansion of USA300-NA lineage coincides with Fluoroquinolone resistance Apparent decline of the USA300-NA lineage after 2008 USA300 clone: USA300-NA lineage seems to be in the decline phase

16 USA300 CA-MRSA: success in the European continent CONCLUSION(S) USA300-NA does not seem to have a higher intrinsic success than the ST80 European clone USA300 lineages show a trend to multiple introductions in Europe with a failure to spread an establish endemic transmissions USA300-NA CA-MRSA lineage seems to be in decline WHY? Competition? Selection? Random Stochastic processes? Glaser et al. Mbio (2016) Von Dach et al. JID (2016) Toleman et al. JID (2016)

17 CA-MRSAs: Pending Questions What are the driving forces for the simultaneous worldwide emergence of CA-MRSA clones? Does the PVL acquisition play(ed) an advantageous evolutionary role? Why the large success of USA300-NA in the US? Why the predicted decline of CA-MRSAs (ST80 and USA300-NA)? Glaser et al. Mbio (2016) Stegger et al. Mbio (2014)

18 CA-MRSA: Pending Questions Some answers... Claude-Alexandre GUSTAVE Dr. Anne TRISTAN

19 CA-MRSA USA300: Expansion and Virulence Do expanding phases associate with increased expression of virulence factors? Approach: qrt-pcr of virulence associated genes from the USA300 ancestral and derived lineages Derived ACME + FluorR Ancestral ACME FluorS Derived ACME + FluorS

20 CA-MRSA USA300: Expansion and Virulence Do expanding phases associate with increased expression of virulence factors? RNAIII LukS-PVL hla HlgC psmα No significant difference in virulence genes expression between the USA300 ancestral and derived USA300-NA strains

21 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Approach: 1. assessment of doubling time (BHI, 24h) 2. competitive fitness in vitro (qrt-pcr for ACME and CGG + ATB for Fluor) Derived ACME + FluorR Ancestral ACME FluorS Derived ACME + FluorS

22 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Doubling Time and the acquisition of the ACME element Ancestral ACME FluorS Derived ACME + FluorS Doubling time (min) 30 *** *** or S or S AC M E- Fl u Fl u E+ AC M AC M E+ Fl u or S 22 Acquisition of ACME may be related to a decreased doubling time between ancestral USA300 and derivate USA300-NA lineage

23 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Doubling Time and the acquisition of Fluoroquinolones resistance Derived ACME + FluorR Doubling time (min) Ancestral ACME FluorS 30 *** *** or R Fl u or S AC M E+ Fl u E+ AC M AC M E+ Fl u or S 22 Resistance to fluoroquinolones increased the doubling time between derivate USA300-NA lineages

24 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Competitive fitness in vitro of ACME- and ACME+ USA300 lineages Ancestral ACME FluorS Derived ACME + FluorS ACME acquisition seems to increase the fitness of the derived USA30NA lineage

25 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Competitive fitness in vitro of USA300 derived lineages FluorS and FluorR Derived ACME + FluorR Derived ACME + FluorS No ATB pressure Acquisition of Fluoroquinolones resistance seems to be a mutation with a deleterious fitness cost on the USA300-NA lineage

26 CA-MRSA USA300: Expansion and Fitness Do expanding phases associate with increased fitness? Competitive fitness in vitro of USA300 derived lineages FluorS and FluorR Derived ACME + FluorR ¼ MIC Derived ACME + FluorS 1/32 With ATB pressure (MIC = 0,38 µg/ml) Acquisition of Fluoroquinolones resistance seems to confer an increased fitness even at very low sub-inhibitory ATB concentrations MIC

27 CA-MRSA USA300: Fitness and Virulence CONCLUSION(S) Expression of core-genome encoded virulence genes do not seem to play a role in the USA300-NA CA-MRSA clone success Acquisition of the ACME element seems to have been a driving force to the USA300-NA CA-MRSA clone success Acquisition of a Fluoroquinolones resistance is costly and slightly deleterious without ATB pressure BUT plays a pivotal role in the fitness of the derived USA300-NA CA-MRSA lineage even at very low subinhibitory MICs

28 Thank you for your attention CIRI Team staphylococcal pathogenesis Philippe GLASER Prof. François VANDENESCH All colleagues at the CIRI's team Thierry WIRTH All the CNR Staph : ingeniers, biologists, technicians USA300 paper Michele BES Dr. Anne TRISTAN Prof. Frederic LAURENT Prof. Jerome ETIENNE Claude-Alexandre GUSTAVE All the colleagues at the CX Rouss (HCL)