AMR dissemination in the environment Professor Liz Wellington The - PowerPoint PPT Presentation

AMR dissemination in the environment Professor Liz Wellington

The connectivity of potential sources of antibiotic- resistant bacteria

Antibiotic resistance in the environment: soil, sediments, water bodies Environment acts as an reservoir for antibiotic resistance genes: -associated with antibiotic biosynthesis clusters - in closely related non-producers - in unrelated non-producers indigenous soil bacteria - in unrelated non-producers exotic bacteria = pathogens/commensals added to soil • Potential for selection of resistance -pollution • HGT of resistance genes- mobilome • Pathogens can survive in soil -Acquire integrons/plasmids -Act as source of antibiotic resistance

Reservoirs of antibiotic resistance genes in diverse environments: survey Non-producers Prevalence Soil Rhizosphere Manure Sewage Seawater Streptomycin aph3 aph6-Id ant3 adenylase aph6-Ic aph6-Ic (deg) Streptomycin Producers strA aphD strB1 stsC Non-producers aac(3)-I Gentamicin aac(3)-II/VI aac(3)-III/IV aac(6 ’) -II/Ib ant(2 ”) -I aph(2 ”) -I tetA tetB tetC tetD Non-producers Tetracycline tetE tetG tetH tetK tetL tetM tetO tetT Soil Rhizosphere Manure Sewage Seawater

Streptomycin biosynthetic cluster and mobility of resistance gene strA in soil Substitution rate in housekeeper genes vs. streptomycin resistance strA (APH II) Substitution rate Laskaris et al., 2010. Env Micro 12, 783 – 796

The connectivity of potential sources of antibiotic- resistant bacteria

Sewage treatment and disposal Application of sewage sludge /biosolids/ manure to land: what is the impact on antibiotic resistance in soil?

Occurrence of antibiotics in the natural environment, fish, crops and drinking water from published studies Antibiotic class General Sewage River Groundwat Drinking Fish Soil Crops Example compounds behaviour sludge water er water monitored impersistent/  Chloramphenicol - X - - - - - mobile persistent/ 2,4-     immobile X X - trimethoprim diaminopyridines persistent/ ciprofloxacin, norfloxacin,    Fluoroquinolones X X - - ofloxacin immobile amoxicillin, cloxacillin, impersistent dicloxacillin, methicillin,  -lactams - X X X - - - nafcillin, oxacillin, penicillin mobile G, penicillin V slightly azithromycin, clarithromycin, lincomycin, persistent/   Macrolides X - - - - roxithromycin, spyramycin, tylosin slightly mobile persistent/ sulfamethoxazole,      Sulfonamides X - sulfadiazine, sulfamerazine, mobile sulfamethazine, sulfapyridine persistent/ chlortetracycline,     Tetracyclines - X X doxycycline, oxytetracycline, immobile tetracycline A tick means that it has been monitored for and detected and a cross means that it has been monitored for and not detected. No entry means that no monitoring has been done yet (Alistair Boxall)

Schematic map of the complex class 1 integron carrying the bla CTX-M-14 gene on plasmid pAJE0508 gene on plasmid pAJE0508 Bae et al., AAC, Aug 2007, 3017-19

Class 1 integron prevalence in sewage sludge, pig slurry and following application to land RB, Reed bed sediment from textile mill; + Pig slurry SS, Fully digested sewage sludge; PS, Pig slurry; CW, Fallowed agricultural soil 9 0.016 8 intI1 0.014 intI1 qacE∆1 7 0.012 prevalence % 6 qacE 0.01 prevalence (%) qacG 5 0.008 qacH 4 0.006 3 0.004 2 0.002 1 0 pre- day 1 day 21 day 90 day 289 0 RB SS PS CW application sample site days after slurry application • 90 million tons animal faecal slurry added to UK soils per year Gaze et al., 2011 ISME J ; Bailey-Byrne et al 2011 AEM

Low cost AMR carriage gives selection with very low exposure Gulleberg et al., 2014 mBio

Waste water treatment plants as a reservoir for antibiotic resistance Waste Water treatment plants Hotspot for Horizontal Gene Transfer (HGT) as waste received from various sources Little is known about the impacts of effluent further downstream in the river or the possible role of co-selection of antibiotic resistant determinants via quaternary ammonium compounds (QACs) (Gaze et al., AAC 2005, ISMEJ 2011)

The risk of consuming 3GC resistant coliforms equal to or greater than the dose needed for colonization can be calculated using the inverse cumulative Poisson distribution 𝑙 λ i P = 1 − 𝑓 −𝜇 i! 𝑗=100 P= probability of being colonized by a 3GC resistant coliform. λ = average number of 3GC coliforms consumed, which is equal to number of 3GC coliforms multipled by the amount of water consumed (ml). i = 100, the number of coliforms needed for colonization. The volume of water consumed for > 99% probability of transient colonization of a 3GC resistant coliform at minimum levels of sediment disturbance was 12 · 5 ml downstream and 58 ml upstream, and under high levels of sediment disturbance, will decrease to 1 · 3 ml downstream and 5 · 8 ml upstream. Children swimming (37 ml of water consumed on average) downstream of treatment plants have a P > 99 % chance of being transiently colonized by a 3GC resistant coliform. Upstream of the WWTP, even under high levels of sediment disturbance, only swimming carried risks of colonization by 3GC resistant coliforms.

Contribution of WWTP effluent to integron levels in a whole river system River Thames catchment area: Collaboration with Wallingford CEH, meta-data available 13 sites samples every 3 months for a year: analysed for integron prevalence and 3GC resistance counts

In Integron pre revalence 3.5 Significant difference between summer months (May and August, and Winter months November and February P = 0.004 t -test 3 May 2.5 August Integron Prevalence / (%) 2 February 1.5 November 1 0.5 0 Sample site

All metadata included Output WWTP only 0.5 0.5 Actual log integron prevalence actual log integron prevalence 0.0 0.0 -0.5 -0.5 -1.0 -1.0 -1.5 -1.5 -2.0 -2.0 0.0 0.5 1.0 1.5 2.0 2.5 -2.0 -1.5 -1.0 -0.5 0.0 0.5 Predicted log integron prevalence Predicted log integron prevalence Explained 49 % of variance: Explained 82. 9 % of variance : R 2 adjusted  (0.49) P < 0.01 R 2 adj (0.83) P < 0.01 Amos et al., 2015 ISME J

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Acknowledgements Past: Present: Rothamsted Research Gemma Hill William Gaze Andrew Mead Hayley King Greg Amos Jennie Holden Lihong Zhang CEH Wallingford Severine Rangama Kathy Byrn-Bailey Andrew Singer Chiara Borsetto Paris Laskaris Leo Calvo-Bado University of Birmingham Helen Green Professor Peter Hawkey Claire Murray Katie Hardy