Antibiotic resistant bacteria as contaminants of emerging concern. Célia M. Manaia Catholic University of Portugal

Transcription

1 Antibiotic resistant bacteria as contaminants of emerging concern Célia M. Manaia Catholic University of Portugal

2 ~75 YEARS OF ANTIBIOTHERAPY Clatworthy etal. (2007) Nature Chemical Biology 3,

3 ANTIBIOTICS TARGET SPECIFIC STRUCTURES IN THE BACTERIAL CELL THREE MAJOR TARGETS Cell wall DNA Ribosomes Lewis (2013) Nature Reviews Drug Discovery 12,

4 FIVE GENERAL RESISTANCE MECHANISMS HUNDREDS OF GENES Adaptado de: (Julho 2016)

5 HORIZONTAL GENE TRANSFER /MUTATION Andersson & Hughes (2010) Nature Reviews Microbiology, 8,

6 HORIZONTAL GENE TRANSFER MUTATION SELECTION Resistant bacteria Susceptible bacteria SELECTIVE PRESSURE SUSCEPTIBLE BACTERIA: DIE + RESISTANT BACTERIA: MULTIPLY RESISTANCE BECOMES PREDOMINANT Adapted: (Julho 2016)

7 ~75 YEARS OF ANTIBIOTHERAPY = 75 YEARS OF ANTIBIOTIC RESISTANCE Clatworthy etal. (2007) Nature Chemical Biology 3,

8 ANTIBIOTIC RESISTANCE FI NO SE IE UK DK LT PT ES FR NL BE CH DE IT CZ AU SI HR PL SK HU RO BU GR CY

9 ANTIBIOTIC CONSUMPTION

10 ANTIBIOTIC RESISTANCE IS NATURAL AND ALSO CONTAMINANT CONTAMINANT Top superbugs NATURAL Vaz-Moreira et al., FEMS Microbiol Rev. 38:761-78

11 CONTAMINANTS OF (SPECIAL) EMERGING CONCERN PROPAGATION Selection HGT Vaz-Moreira et al., FEMS Microbiol Rev. 38:761-78

12 WATER AS A MAJOR ROUTE OF PROPAGATION WATER HABITAT TRANSPORT Davies and Davies Microbiol. Mol. Biol. Rev. 2010;74:

13 WASTEWATER TREATMENT IS ESSENTIAL TO REMOVE 10 6 CFU/100 ml ANTIBIOTIC RESISTANCE 10 4 CFU/100 ml 20% Resistance prevalence

14 % of resistance Escherichia coli Quinolone-resistant Raw and treated wastewater p < Raw inflow Final effluent 100% due to mutation in chromosomal genes (gyra and parc) AML CIP SXT TET CP GEN Ferreira da Silva, et al FEMS Microbiology Ecology, 60: Figueira et al Science of the Total Environment, 409:

15 Gene copy number per day It is estimated that more than to copies of genes encoding for tetracycline or beta-lactam resistance are released per minute to the surrounding environment bla OXA bla sul1 sul2 SHV bla CTX-M bla TEM teta tetc tetg tetm tetq tetwtetx qnra,b,s ES FI EE EE FI EE EE ES FI EE EE ES ES PT ES FI EE EE FI EE EE CN US CN FI EE EE US US FI EE EE US US US ES US ES ES ES ES Manaia et al., Applied Microbiology and Biotechnology. 100:

16 WASTEWATER TREATMENT IS ESSENTIAL TO REMOVE ANTIBIOTIC RESISTANCE OPERATIONAL CONDITIONS (oxygen, organic matter, sludge age, etc) SELECTIVE PRESSURES (antibiotic residues, metals, nanoparticles, etc) INFLUENT QUALITY (hospital, animal production, etc)

17 Axis 2 (6.5%) SELECTIVE PRESSURES Total bacteria vs. Antimicrobial residues vs. ARG vs. ARB mfccip GSPCIP PCACIP Antimicrobial Residues Bacterial Communities Antibiotic Resistant Bacteria Antibiotic Resistance Genes B20 B10 B21 (AX1-0.22, AX2 0.53) B16 B11 B14 OFX PEN (AX1-0.15, AX2 0.11) (AX2 0.31) B9 B19 CIP B2 B18 B17 B5 B12 B23 B1 AS B22 B13 B3 B4 B8 (AX1 0.20, AX2 0.49) B24 Clostridia Bacteroidia B1 5B6 Clostridia Gammaproteobacteria (B25) Clostridia TET SUL (AX1 0.68, AX2 0.11) (B7) Bacteroidia Gammaproteobacteria (AX1 0.43, AX2-0.14) inti1 bla TEM vana B Axis 1 (11.4%) 1.0 Varela et al., Water Research, 54, ; Narciso da Rocha et al., Journal of Global Antimicrobial Resistance, 2:

18 INFLUENT QUALITY HOSPITAL EFFLUENT VS. THE MUNICIPAL WWTP inti1/mara/bla TEM /vana - Prevalence / 16S rrna (~2%) m 3 /day m 3 /dia Narciso da Rocha et al., Journal of Global Antimicrobial Resistance, 2:

19 INFLUENT QUALITY HOSPITAL EFFLUENT VS. THE MUNICIPAL WWTP inti1/mara/bla TEM /vana Narciso da Rocha et al., Journal of Global Antimicrobial Resistance, 2:

20 Quinolone resistant Escherichia coli birds of prey, water environments and gulls Portugal, Spain and Sweden Gulls Wastewater Surface water Birds of prey Natural reserve WA20 TWW SVu32 Columbidae WA23 stream WZ5 stream SG20 Larus fuscus SG16 Larus fuscus (Ile80Ala84) WA7 RWW SG15 Larus fuscus (Ile80Ala84) SG7 Larus fuscus SG5 Larus fuscus 100 WA24 RWW (aac(6')-ib-cr, qnrs) SG3 Larus fuscus SP480 Larus michaelis 69 WZ2 stream SP281 Larus michaelis SP422 Larus michaelis (Leu83Asn87) BR8 Hieraaetus pennatus BR6 Buteo buteo BR7 Hieraaetus pennatus BR1 Buteo buteo WA12 TWW SP367 Larus michaelis SP254 Larus michaelis (Leu83Asn87) BR5 Buteo buteo BR4 Hieraaetus pennatus BR3 Buteo buteo WA8 RWW (Leu83, Arg80) BR9 Milvus migrans SG6 Larus fuscus SG12 Larus fuscus SG9 Larus fuscus (aac(6')-ib-cr) SG8 Larus fuscus (aac(6')-ib-cr) SG11 Larus fuscus (aac(6')-ib-cr) SG10 Larus fuscus (aac(6')-ib-cr) SG4 Larus fuscus (aac(6')-ib-cr) WA9 TWW SP238 Larus michaelis (Leu83, qnrs) WZ6 RWW SVu22 Laridae UR2 stream WZ3 stream A WA19 RWW WA15 TWW WA5 TWW SP444 Larus michaelis WA18 RWW WZ10 TWW (Leu83) WA2 stream (Leu83) SP418 Larus michaelis WA16 RWW WZ4 stream SG17 Larus fuscus WZ9 TWW (Ile80Gly84) WA10 TWW UP2 stream SG14a Larus fuscus (aac(6')-ib-cr) WZ11 TWW WA6 TWW (Ile80Gly84) SV32 Larus argentatus (aac(6')-ib-cr, Ile80Gly84) SV83 Larus argentatus (Ile80Gly84) SV230 Larus argentatus (Ile80Gly84) SG1 Larus fuscus (aac(6')-ib) SG19 Larus fuscus (aac(6')-ib-cr) vana Hospital blactxm-15 Effluent 100 WZ7 RWW WA21 TWW SG2 Larus fuscus (Leu83Tyr87, Arg80) SG18 Larus fuscus (aac(6')-ib-cr) BR19 Bubo bubo (Leu83Gly87) BR12 Aegypius monachus (Leu83Gly87) BR15 Accipiter nisus (Leu83Gly87) BR17 Hieraaetus fasciatus (Leu83Gly87) BR16 Buteo buteo (Leu83Gly87) BR18 Bubo bubo (Leu83Gly87) BR10 Aegypius monachus (Leu83Gly87) BR11 Aegypius monachus (Leu83Gly87) BR13 Strix aluco (Leu83Tyr87) Vredenburg et al., Environ Microbiology, 16(4): ; Varela et al., J Global Antimicrobial Resistance, 3: Varela et al FEMS Microbiol Ecol. 91(5). B Hospital Effluent Hospital Effluent ST131 Hospital Effluent E F C D

21 Mitigation measures

22 I. ASSESS THE RISKS OF TRANSMISSION FROM ENVIRONMENT TO HUMANS METHODS HARMONIZATION LOWER THE QUANTIFICATION LIMITS EXPAND ARG DATABASES ENVIRONMENT + ANIMAL + HUMAN Davies and Davies Microbiol. Mol. Biol. Rev. 2010;74: Berendonk et al Nature Reviews Microbiology. 13(5):310-7.

23 II. IDENTIFICATION OF CRITICAL CONTROL POINTS INCOME OF ANTIBIOTIC RESISTANT BACTERIA BACTERIAL GROWTH BIOFILM/CELL AGGREGATES SELECTIVE PRESSURES ADAPTATIVE MUTATIONS HORIZONTAL GENE TRANSFER Davies and Davies Microbiol. Mol. Biol. Rev. 2010;74: Berendonk et al Nature Reviews Microbiology. 13(5):310-7.

24 Log (gene copy number/100 ml) LOQ LOQ LOQ LOQ Log (gene copy number/100 ml) LOQ LOQ WASTEWATER DISINFECTION Antibiotic resistance genes Ozonation UV S rrna inti1 blatem qnrs sul S rrna inti1 blatem qnrs sul1 Untreated control Treated Three days storage J Hazard Mater ;323(Pt A):

25 % of reads REGROWTH AFTER DISINFECTION 100% A Classes Phyla 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% C0 C3 T3 C0 C3 T3 C0 C3 T3 C0 C3 T3 TM7-1 TM7 Gammaproteobacteria Deltaproteobacteria Proteobacteria Betaproteobacteria Alphaproteobacteria Clostridia Firmicutes Sphingobacteriia Flavobacteriia Bacteroidetes Bacteroidia [Saprospirae] Actinobacteria Actinobacteria Acidimicrobiia Other classes with abundance < 5 % reads Unclassified at class level WW1-UV WW1UV 254 nm WW1-O WW1O3 3 WW2-PO WW2PO SW-PO SWPO Besides treatment, also storage and transport are key issues in wastewater reuse Sci Total Environ ;573:

26 WASTEWATER TREATMENT IS ESSENTIAL TO REMOVE ANTIBIOTIC RESISTANCE Improved wastewater treatment processes Bacterial removal (disinfection) Environmental friendly (low impact on the environment in particular on the microbiota) Cost effective Wastewater plumbing/storage

27 StARE Stopping Antibiotic Resistance Evolution 2013 Water JPI Pilot Call focused on Emerging water contaminantsanthropogenic pollutants and pathogens National Funding Agencies Portugal Spain Cyprus Germany Ireland Norway Finland December 2014 December 2017

28 Partners 7 countries, 10 institutions National University of Ireland, Maynooth (NUIM) Norwegian School of Veterinary Science (NSVS) University of Helsinki (UHel) Aquantec GmbH Universidade Católica Portuguesa (UCP) University of Aveiro (UA) Fundació Institut Català de Recerca de l Aigua (ICRA Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC) Technische Universität Dresden (TUD) Nireas International Water Research Center, Univesity of Cyprus (Nireas- IWRC)

29 On-going projects on antibiotic resistance in wastewater (and its reuse) EU EU WG5 NORMAN HEARD US EU Asia StARE EU OVERSEAS ANSWERS NEREUS EU US Australia Asia

30 Partners (EU) Olga Nunes (Portugal) Paulo Costa (Portugal) Manuela Caniça (Portugal) Adrian Silva (Portugal) Sérgio Silva (Portugal) Isabel Henriques (Portugal) Despo Fatta-Kassinos (Cyprus) Thomas Berendonk (Germany) Thomas Schwartz (Germany) José Luis Martinez (Spain) Sara Rodriguez (Spain) Marko Virta (Finland) Fiona Walsh (Ireland) Henning Sörum (Norway) Eddie Cytryn (Israel) Christophe Merlin (France) Luigi Rizzo (Italy) Norbert Kreuzinger (Austria) UID/Multi/50016/2013-CBQF Stopping Antibiotic Resistance Evolution COST-European Cooperation in Science and Technology, to the COST Action ES1403: New and emerging challenges and opportunities in wastewater reuse (NEREUS) - ANtibioticS and mobile resistance elements in WastEwater Reuse applications: risks and innovative solutions ANSWERS. European Commission Horizon MSCA-ITN-2015-ETN: Marie Sklodowska- Curie Innovative Training Networks (ITN-ETN) OVERSEAS (FLAD 298/2015) Network of reference laboratories, research centres and related organisations for monitoring of emerging environmental substances -

31 Bacterial diversity group ESB-UCP, Porto, Portugal