{"id":15906,"date":"2021-12-09T20:02:33","date_gmt":"2021-12-09T20:02:33","guid":{"rendered":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/?p=15906"},"modified":"2021-12-09T20:24:14","modified_gmt":"2021-12-09T20:24:14","slug":"profiling-antimicrobial-resistance-with-next-generation-sequencing","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/profiling-antimicrobial-resistance-with-next-generation-sequencing\/","title":{"rendered":"Profiling Antimicrobial Resistance with NGS"},"content":{"rendered":"

\"ProfilingWidespread, easily available antimicrobial agents have shaped the modern world, severely reducing the incidence of deadly microbial infections and diseases and making surgery and other invasive procedures far safer. Unfortunately, antimicrobial agents exist in an arms race with the microbes they control, and improper use of antimicrobial agents speeds that process along. Studying and tracking antimicrobial resistance (AMR) to understand which species are becoming resistant, which genes are involved, and which agents are becoming less effective is the first step toward combating it, and the Ion AmpliSeq Antimicrobial Resistance Research Panel<\/a> for AMR surveillance is proving to be a key tool in a variety of situations.<\/p>\n

Wastewater surveillance of antimicrobial resistance<\/h2>\n

Wastewater treatment facilities receive waste, and with it excreted bacteria and antimicrobial agents, from whole communities. This cell-culture stew provides what would seem like an ideal environment for one of the most dangerous things that antibiotic-resistant bacteria can do: horizontal gene transfer, in which non-resistant bacteria can acquire resistance genes from their neighbors. On the other hand, antimicrobial resistance genes tend to be expensive or even deleterious when their associated antimicrobial agents are not present, so the environment of a wastewater treatment facility could have the opposite effect, removing these genes naturally from the bacterial gene pool.<\/p>\n

Seeking to find out which possibility was true and whether different styles of wastewater treatment behaved differently, Agrawal et al.1<\/sup> examined antimicrobial resistance in a Namibian pond-based water treatment system versus an advanced wastewater treatment facility in Germany<\/a> by sequencing samples with the Ion AmpliSeq AMR Research Panel on Ion GeneStudio S5<\/a>. Antimicrobial resistance genes were more diverse in the Namibian system (277) compared to the German system (93), but resistance to several common antibiotics was present at far lower levels in the Namibian ponds, suggesting that pond-based systems, with their more natural environment, might provide a way to reduce antimicrobial resistance in bacterial populations.<\/p>\n

Antimicrobial resistance in space<\/h2>\n

Outer space might be one of the most hostile conceivable environments for life, but human-crafted space vehicles are far less so. These self-contained habitats lack the kinds of circulation that can be protective against infections and the stresses of spaceflight weaken astronauts\u2019 immune systems, increasing the hazards posed to astronauts by bacteria and other microbes, especially ones that resist common antimicrobials.<\/p>\n

Urbaniak et al.2<\/sup> used the Ion AmpliSeq AMR Research Panel on Ion PGM to study antimicrobial resistance in microbes from eight surfaces on the International Space Station<\/a>. A key advantage of the Ion AmpliSeq AMR Research Panel is that it can generate data from environmental DNA without the need for cell culture, which can be time-consuming, challenging and incomplete, and Urbaniak et al. were able to realize this advantage with their study. They found that 23 resistance genes were present on the ISS and that beta-lactam and trimethoprim resistance were the most abundant and widespread. Their data will contribute to the implementation of better mitigation procedures on future spaceflights.<\/p>\n

Community surveillance with Ion AmpliSeq NGS panels<\/h2>\n

The gut microbiota is a natural reservoir of antibiotic resistance genes and can provide a place for these genes to migrate between bacterial species. Surveying the gut microbiota of a population, then, can provide insight into which resistance genes are propagating in that population. Guernier-Cambert et al.3<\/sup> examined AMR genes in fecal samples of seven pregnant women and two healthy infants in Australia<\/a> by sequencing them with the Ion AmpliSeq AMR Research Panel on the Ion GeneStudio S5. They also used Ion AmpliSeq Pan-bacterial Research Panel and metagenomic sequencing in this study. These tools were ideal because the gut microbiota contains many species that do not respond to cell culture. By directly studying DNA, Guernier-Cambert et al. were able to study the genes present regardless of which species contained them and to detect rare variants that would have been difficult to spot with other methods. The researchers found that the profile of resistance genes in their samples reflected antibiotic use in Australia, with genes for resistance to tetracycline, \u03b2-lactams and MLSB (macrolide, lincosamide, streptogramin B) being particularly abundant. These findings can inform future antibiotic selections and otherwise improve the efficacy of antimicrobial treatments.<\/p>\n

Conclusion<\/h2>\n

Next-generation sequencing using the Ion AmpliSeq Antimicrobial Resistance Panel is a robust way to study antimicrobial resistance, which is a key first step toward mitigating antimicrobial spread and protecting human health.<\/p>\n

For research use only. Not for use in diagnostic procedures.<\/p>\n

References:<\/strong><\/p>\n

1. Agrawal S, L Orschler, J Sinn, et al. (2020) High-throughput profiling of antibiotic resistance genes in wastewater: comparison between a pond system in Namibia and an activated sludge treatment in Germany. J. Water Health<\/em> 18(6):867\u2013878.<\/p>\n

2. Urbaniak C, AC Sielaff, KG Frey, et al. (2018) Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces. Sci. Rep.<\/em> 8(1):814.<\/p>\n

3. Guernier-Cambert V, A Chamings, F Collier, et al. (2021) Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia\u2014A Descriptive Pilot Study. Front. Microbiol.<\/em> 12:2617.<\/p>\n","protected":false},"excerpt":{"rendered":"

Widespread, easily available antimicrobial agents have shaped the modern world, severely reducing the incidence of deadly microbial infections and diseases and making surgery and other invasive procedures far safer. Unfortunately, antimicrobial agents exist in an arms race with the microbes they control, and improper use of antimicrobial agents speeds that process along. Studying and tracking<\/p>\n","protected":false},"author":120,"featured_media":15908,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[67],"tags":[2221,2230],"division":[],"class_list":{"0":"post-15906","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-infectious-diseases","8":"tag-csd","9":"tag-popular","10":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nProfiling 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