FMM/RAS/298: Strengthening capacities, policies and national action plans on prudent and responsible use of antimicrobials in fisheries Workshop 2 in cooperation with Malaysia Department of Fisheries and INFOFISH 7-9 August 2017, Kuala Lumpur, Malaysia Complexities involved in source attribution of AMR genes found in aquaculture products Iddya Karunasagar Iddya.Karunasagar@gmail.com
Environmental Microbiology (2006) 8(7), 1137 1144 doi:10.1111/j.1462-2920.2006.01054.x Minireview Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment Felipe C. Cabello Department of Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA. Summary many developed and developing countries. It is expected that this growth will increase at an even faster rate in the future, stimulated by the depletion of fisheries and the market forces that globalize the sources of food supply (Goldburg et al., 2001; Goldburg and Naylor, 2005). The
Personal View Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance Felipe C Cabello, Henry P Godfrey, Alejandro H Buschmann, Humberto J Dölz Aquaculture uses hundreds of tonnes of antimicrobials annually to prevent and treat bacterial infection. The passage of these antimicrobials into the aquatic environment selects for resistant bacteria and resistance genes and stimulates bacterial mutation, recombination, and horizontal gene transfer. The potential bridging of aquatic and human pathogen resistomes leads to emergence of new antimicrobial-resistant bacteria and global dissemination of them and their antimicrobial resistance genes into animal and human populations. Efforts to prevent antimicrobial overuse in aquaculture must include education of all stakeholders about its detrimental effects on the health of fish, human beings, and the aquatic ecosystem (the notion of One Health), and encouragement of environmentally friendly measures of disease prevention, including vaccines, probiotics, and bacteriophages. Adoption of these measures is a crucial supplement to efforts dealing with antimicrobial resistance by developing new therapeutic agents, if headway is to be made against the increasing problem of antimicrobial resistance in human and veterinary medicine. Lancet Infect Dis 2016; 16: e127 33 Published Online April 12, 2016 http://dx.doi.org/10.1016/ S1473-3099(16)00100-6 Department of Microbiology and Immunology and Department of Pathology, New York Medical College, Valhalla, New York, NY, USA (Prof F C Cabello MD, Prof H P Godfrey MD); Centro
RESISTANT MICROORGANISMS SELECTED IN OTHER SECTORS COULD REACH WATER SOURCE USED IN AQUACULTURE Antimicrobial use in humans Antimicrobial use in agriculture Antimicrobial use in farm animals Sewage Farm wastes sludge Effluent Storm Effluent sludge water Ground water storm water Aquatic environment: lakes, rivers, coastal waters storm water Ground water
AMR data Using microorganisms isolated from fish at retail level o Changes in microflora during handling and processing o It may not be possible to pick up indicators that represents aquaculture environment at this point. o Large amount of data on aquaculture products at retail level
Aspects not considered in many publications on AMR associated with aquaculture o Intrinsic resistance in many aquatic bacteria Aeromonas to ampicillin. o Selection of antibiotic resistant bacteria due to exposure to chemical pollutants, heavy metals. o AMR introduced into aquaculture environment from other sectors
AMR not related to use of antibiotics in aquaculture o Culture-independent studies in the Baltic sea show presence of resistance genes encoding resistance to sulphonamides, trimethoprim, tetracycline, aminoglycoside, chloramphenicol and also genes encoding multidrug efflux pumps in sediments below fish farms, though some antibiotics like tetracyclines, aminoglycosides and chloramphenicol are not used in this area (Muziasari et al., 2017). o Most Vibrio vulnificus strains isolated from Dutch eel farms showed resistance to cefoxitin, though this antibiotic was not used in eel aquaculture (Haenen et al., 2014).
Singer et al. Relevance of AMR to Regulators Singer et al., 2016 FIGURE 1 Schematic of the hot-spots and drivers of antimicrobial resistance (AMR). The environmental compartments that are currently monitored or regulated by the Environment Agency (EA; England) are denoted by an asterisk in red. WFD, Water Framework Directive. It is an unfortunate historical convention to label all these genes antimicrobial resistance genes (ARGs), when in fact they can potentially confer resistance to many more resistance gene can offer protection from multiple toxic chemicals (Curiao et al., 2016). Co-resistance is analogous to bringing a toolbox to a worksite; one might only need one or two tools from
Table 1. Details for the 50 Most Prevalent Resistance Classes Found in All Metagenomes Resistance Class Mechanism of Resistance Antibiotic Specificity mexef, ceo, mexvw, acr, mexhi, mexcd, RND class transporter multidrug resistance efflux mexab, mdtnop, amr, adeabc, smeabc, smedef, mdtef, mexxy, mdtk macab RND class transporter: macrolide multidrug resistance efflux bcr, bcr_mfs ABC class transporter system: bacitracin multidrug resistance efflux mls_abc ABC class transporter: macrolide multidrug resistance efflux mls_mfs, mls_hdr MFS class transporter: macrolide multidrug resistance efflux cml MFS class transporter: chloramphenicol multidrug resistance efflux rosab potassium antiporter system multidrug resistance efflux mepa, norm MATE transporter multidrug resistance efflux tcma, mdr, qac MFS transporter multidrug resistance efflux vana, vanb, vanc, vand, vane, vang vancomycin resistance operon genes (vanh, vans, vanr, vanx, vancomycin and vany) for each vancomycin resistance operon: VanA, VanB, VanC, VanD, VanE, and VanG types tet_rpp tetracyline ribosomal protection protein tetracycline tet_efflux tetracyline-specific efflux pump tetracycline tet_flavo flavoproteins resistance to tetracyline tetracycline bla_a, bla_b class A and class B b-lactamases b-lactams pbp penicillin-binding protein b-lactams baca bacitracin resistance bacitracin cata chloramphenicol acetyltransferase chloramphenicol ksga kasugamycin resistance kasugamycin arna polymixin resistance polymixin pur8 puromycin resistance puromycin vat virginiamycin resistance streptogramin sul sulfonamide resistance sulfonamide dfra trimethoprim resistance trimethoprim Source: Nesme et al., 2014
Phenotypic resistance and mechanisms of resistance o When same phenotypic resistance is detected in two isolates eg one from aquatic environment and another from a clinical case, the two isolates may have different resistance genes. o Eg tetracycline resistance could be due to (a) over production of efflux proteins or (b) production of ribosomal protection proteins or (c) production of tetracycline inactivating proteins
Common multidrug resistant infections in hospitals o Vancomycin resistant enterococci o Methicillin resistant Staphylococcus aureus o Extended spectrum beta-lactamase producing gram negative bacteria o Carbapenemase producing Klebseilla pnuemoniae o MultiDrug-Resistant gram negative rods (MDR GNR) bacteria such as Enterobacter species, E.coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa
PERSPECTIVES OPINION What is a resistance gene? Ranking risk in resistomes José L. Martínez, Teresa M. Coque and Fernando Baquero Abstract Metagenomic studies have shown that antibiotic resistance genes are ubiquitous in the environment, which has led to the suggestion that there is a high risk that these genes will spread to bacteria that cause human infections. If this is true, estimating the real risk of dissemination of resistance genes from environmental reservoirs to human pathogens is therefore very difficult. In this Opinion article, we analyse the current definitions of antibiotic resistance and antibiotic resistance genes, and we describe the bottlenecks that affect the transfer of antibiotic resistance genes to human pathogens. We propose rules for estimating the risks associated with genes that are present in environmental resistomes by evaluating the likelihood of their introduction into human pathogens, and the consequences of such events for the treatment of infections. resistance gene in a given ecosystem. This framework could function as the basis for interpretative guidelines and interventions, which are urgently required for both scientific and public health reasons. Antibiotic resistance can result from mutations 15, as is the case of resistance to fluoroquinolones, or by the acquisition of antibiotic resistance genes by horizontal gene transfer (HGT). Whereas a mutation is relevant only for the bacterium that harbours it, the presence of a potentially transferable antibiotic resistance gene in a bacterium might be important for the dissemination of resistance among a population. In this article, we focus on antibiotic resistance genes that can spread among a population, and we do not provide a detailed discussion of the relevance of mutations for the acquisition of resistance. What is antibiotic resistance? Different antibiotic resistance studies generate different results because the definition of resistance depends on the objectives of each
Box 2 Transfer bottlenecks for antibiotic resistance genes Functional metagenomic analyses have documented the presence of novel resistance genes that are capable of conferring resistance following their transfer to a susceptible host. However, the number and variety of antibiotic resistance genes acquired by human pathogens, and particularly those that lead to therapeutic failures, is extremely low compared to the number of sequences classified as resistance genes in metagenomic studies 4,49,67. This implies the existence of extremely stringent bottlenecks that modulate the transfer of resistance determinants from their original hosts to human pathogens 68,69. Consequently, these bottlenecks affect the risks that are associated with the presence of a functionally defined resistance gene in a given ecosystem (see the figure). The first bottleneck is ecological connectivity: a gene transfer event only occurs when donor and recipient populations come into contact. This usually means that they are able to reach a critical population size in the same, or neighbouring, ecological space. Genetic transfer ensures the connectivity of th investigations ha acquisition of ant the metabolic bu translation of the resistance gene. Only those deter those that are ba may successfully The figure show antibiotic resista harbour resistanc population densi and water, anima (some of which a populations from
Transfer bottleneck o Ecological connectivity: Gene transfer occurs when donor and recipient bacteria come in contact. They should be able to reach critical population size in the same or neighboring ecological niche. o Founder effect: when a microorganism harbours a resistance gene, it is rare to acquire another that has similar substrate profile. o Fitness cost of the acquired genes: Only those determinants that present substantial fitness advantage is likely to be acquired.
Summary o Antibiotic resistant bacteria can be found in many aquaculture systems. o Some of them may be intrinsic resistance, some may be selected due to antibitoic use, some of them may be derived from antibiotic use in other sectors. o It is difficult to trace the source of AMR found in aquatic bacteria o There is very little evidence that human pathogenic bacteria have acquired resistance from AMR coming out of antibiotic use in aquaculture.
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