© 2015 PLOS ONE.According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnos

Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens - eScholarship

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The emergence and spread of mobile colistin (COL) resistance (mcr) genes jeopardize the efficacy of COL, a last resort antibiotic for treating deadly infections. COL has been used in livestock for decades globally. Bacteria have mobilized mcr genes (mcr-1 to mcr-9). Mcr-gene-containing bacteria (MGCB) have disseminated by horizontal/lateral transfer into diverse ecosystems, including aquatic, soil, botanical, wildlife, animal environment, and public places. The mcr-1, mcr-2, mcr-3, mcr-5, mcr-7, and mcr-8 have been detected in isolates from and/or directly in environmental samples. These genes are harboured by Escherichia coli, Enterobacter, Klebsiella, Proteus, Salmonella, Citrobacter, Pseudomonas, Acinetobacter, Kluyvera, Aeromonas, Providencia, and Raulotella isolates. Different conjugative and non-conjugative plasmids form the backbones for mcr in these isolates, but mcr have also been integrated into the chromosome of some strains. Insertion sequences (IS) (especially ISApl1) located upstream or downstream of mcr, class 1–3 integrons, and transposons are other drivers of mcr in the environment. Genes encoding multi-/extensive-drug resistance and virulence are often co-located with mcr on plasmids in environmental isolates. Transmission of mcr to/among environmental strains is clonally unrestricted. Contact with the mcr-containing reservoirs, consumption of contaminated animal-/plant-based foods or water, international animal-/plant-based food trades and travel, are routes for transmission of MGCB.

/pdf/occurrence-and-characteristics-of-mobile-colistin-resistance-5a4t11glgx.pdf

Occurrence and Characteristics of Mobile Colistin Resistance (mcr) Gene-Containing Isolates from the Environment: A Review.

The proliferation of antibiotic-resistant bacteria in the environment has potential negative economic and health consequences. Thus, previous investigations have targeted wild animals to understand the occurrence of antibiotic resistance in diverse environmental sources. In this critical review and synthesis, we summarized important concepts learned through the sampling of wildlife for antibiotic-resistant indicator bacteria. These concepts are helpful for understanding dissemination of resistance through environmental pathways and helping to guide future research efforts. Our review begins by briefly introducing antibiotic resistance as it pertains to bacteria harbored in environmental sources such as wild animals. Next, we differentiate wildlife from other animals in the context of how diverse taxa provide different information on antibiotic resistance in the environment. In the third section of our review, we identify representative research and seminal works that illustrate important associations between the occurrence of antibiotic-resistant bacteria in wildlife and anthropogenic inputs into the environment. For example, we highlight numerous investigations that support the premise that anthropogenic inputs into the environment drive the occurrence of antibiotic resistance in bacteria harbored by free-ranging wildlife. Additionally, we summarize previous research demonstrating foraging as a mechanism by which wildlife may be exposed to anthropogenic antibiotic resistance contamination in the environment. In the fourth section of our review, we summarize molecular evidence for the acquisition and dissemination of resistance among bacteria harbored by wildlife. In the fifth section, we identify what we believe to be important data gaps and potential future directions that other researchers may find useful toward the development of efficient, informative, and impactful investigations of antibiotic-resistant bacteria in wildlife. Finally, we conclude our review by highlighting the need to move from surveys that simply identify antibiotic-resistant bacteria in wildlife toward hypothesis-driven investigations that: 1) identify point sources of antibiotic resistance; 2) provide information on risk to human and animal health; 3) identify interventions that may interrupt environmentally mediated pathways of antibiotic resistance acquisition and transmission; and 4) evaluate whether management practices are leading to desirable outcomes.

Antibiotic resistant bacteria in wildlife: perspectives on trends, acquisition and dissemination, data gaps, and future directions

The presence of bacteria carrying antimicrobial resistance (AMR) genes in wildlife is an indicator that resistant bacteria of human or livestock origin are widespread in the environment. In addition, it could represent an additional challenge for human health, since wild animals could act as efficient AMR reservoirs and epidemiological links between human, livestock and natural environments. The aim of this study was to investigate the occurrence and the antibiotic resistance patterns of several bacterial species in certain wild animals in Germany, including wild boars (Sus scrofa), roe deer (Capreolus capreolus) and wild ducks (family Anatidae, subfamily Anatinae) and geese (family Anatidae, subfamily Anserinae). In the framework of the German National Zoonoses Monitoring Program, samples from hunted wild boars, roe deer and wild ducks and geese were collected nationwide in 2016, 2017, and 2019, respectively. Fecal samples were tested for the presence of Salmonella spp. (in wild boars and wild ducks and geese), Campylobacter spp. (in roe deer and wild ducks and geese), Shiga toxin-producing Escherichia (E.) coli (STEC), commensal E. coli and extended-spectrum beta-lactamase- (ESBL) or ampicillinase class C (AmpC) beta-lactamase-producing E. coli (in wild boars, roe deer and wild ducks and geese). In addition, the presence of methicillin-resistant Staphylococcus aureus (MRSA) was investigated in nasal swabs from wild boars. Isolates obtained in the accredited regional state laboratories were submitted to the National Reference Laboratories (NRLs) for confirmation, characterization and phenotypic resistance testing using broth microdilution according to CLSI. AMR was assessed according to epidemiological cut-offs provided by EUCAST. Salmonella spp. were isolated from 13 of 552 (2.4%) tested wild boar fecal samples, but absent in all 101 samples from wild ducks and geese. Nine of the 11 isolates that were submitted to the NRL Salmonella were susceptible to all tested antimicrobial substances. Campylobacter spp. were isolated from four out of 504 (0.8%) roe deer fecal samples, but not from any of the samples from wild ducks and geese. Of the two isolates received in the NRL Campylobacter, neither showed resistance to any of the substances tested. From roe deer, 40.2% of the fecal samples (144 of 358) yielded STEC compared to 6.9% (37 of 536) from wild boars. In wild ducks and geese, no STEC isolates were found. Of 150 STEC isolates received in the NRL (24 from wild boars and 126 from roe deer), only one from each animal species showed resistance. Of the 219 isolates of commensal E. coli from wild boars tested for AMR, 210 were susceptible to all 14 tested substances (95.9%). In roe deer this proportion was even higher (263 of 269, 97.8%), whereas in wild ducks and geese this proportion was lower (41 of 49, 83.7%). Nevertheless, selective isolation of ESBL-/AmpC-producing E. coli yielded 6.5% (36 of 551) positive samples from wild boars, 2.3% (13 of 573) from roe deer and 9.8% (10 of 102) from wild ducks and geese. Among the 25 confirmed ESBL-/AmpC-producing isolates from wild boars, 14 (56.0%) showed resistance up to five classes of substances. This proportion was lower in roe deer (3 of 12, 25%) and higher in wild ducks and geese (7 of 10, 70%). None of the 577 nasal swabs from wild boars yielded MRSA. Results indicate that overall, the prevalence of resistant bacteria from certain wild animals in Germany is low, which may reflect not only the low level of exposure to antimicrobials but also the low level of resistant bacteria in the areas where these animals live and feed. However, despite this low prevalence, the patterns observed in bacteria from the wild animals included in this study are an indicator for specific resistance traits in the environment, including those to highest priority substances such as 3rd generation cephalosporins, fluoroquinolones and colistin. Therefore, also continuous monitoring of the occurrence of such bacteria in wildlife by selective isolation is advisable. Furthermore, the possible role of wildlife as reservoir and disperser of resistant bacteria would need to be assessed, as wild animals, and in particular wild ducks and geese could become spreaders of resistant bacteria given their capacity for long-range movements.

/pdf/wildlife-as-sentinels-of-antimicrobial-resistance-in-germany-3fnkx45fbr.pdf

Wildlife as Sentinels of Antimicrobial Resistance in Germany

Anthropogenic environmental drivers of antimicrobial resistance in wildlife

Abstract The effect of a novel consensus bacterial 6-phytase variant (PhyG) on apparent ileal digestibility (AID) of amino acids (AA) and phosphorus (P) utilization in young broilers when added to diets with high phytate-P (PP) content without added inorganic phosphate (Pi) and deficient in digestible (dig) AA and metabolizable energy (ME) was investigated. A total of 256 Ross 308 male broilers were assigned to 4 treatments (8 birds/cage, 8 cages/treatment) in a completely randomized design. Treatments comprised a positive control (PC, 2,975 kcal/kg ME, 3.7 g/kg dig P, 2.83 g/kg PP, 8.4 g/kg Ca, 10.6 g/kg dig lysine), a negative control (NC) without added Pi (ME −68 kcal/kg, crude protein −10 g/kg, dig AA −0.1 to −0.4 g/kg, Ca −2.0 g/kg, dig P −2.2 g/kg, Na −0.4 g/kg vs. PC), and NC plus 500 or 1,000 FTU/kg of PhyG. Test diets were corn/soy/rapeseed-meal/rice-bran-based and fed from 5 to 15 d of age. Ileal digesta and tibias were collected on day 15. Excreta was collected during days 12 to 15 to determine P retention. The NC (vs. PC) reduced (P < 0.05) P retention (−10.4% units), tibia ash (−14.3% units), weight gain (−109 g), feed intake (−82 g) and increased FCR (from 1.199 to 1.504), confirming that the NC was extremely deficient in nutrients and energy. Phytase addition to the NC linearly (P < 0.001) improved performance, but did not fully recover it to the level of the PC due to the severe nutrients/energy reduction in NC. Phytase linearly increased P retention (P < 0.001), tibia ash (P < 0.001), AID of dry matter (P < 0.05), nitrogen (P < 0.01), gross energy (P < 0.05), and all 17 individual AA (P < 0.01). At 1,000 FTU/kg, phytase increased (P < 0.05) P retention vs. PC and NC (+14.5 and +24.9% units, respectively) and increased tibia ash vs. NC (+13.8% units), equivalent to PC. The NC decreased AID of Cys, Gly, Thr, and Met vs. PC (P < 0.05). At 1,000 FTU/kg, phytase increased AID of all 17 AA vs. NC (P < 0.01), equivalent to PC. At 1,000 FTU/kg, AID AA responses (above NC) ranged from +4.5% (Met) to +15.0% (Cys), being maximal for essential Thr (+10.4%) and Val (+8.2%) and non-essential Cys (+15.0%) and Gly (+10.4%). The results highlight the efficacy of PhyG at a dose level of 500 to 1,000 FTU/kg in young broilers for improving the ileal digestibility of nitrogen, AA, and energy alongside P retention and tibia ash. The performance data emphasize the need to consider digestible nutrient intake as a response variable in exogenous enzyme studies.

/pdf/effects-of-a-novel-consensus-bacterial-6-phytase-variant-on-3bp59kri.pdf

Effects of a novel consensus bacterial 6-phytase variant on the apparent ileal digestibility of amino acids, total tract phosphorus retention, and tibia ash in young broilers

Handle everyday research tasks with reliable, citation-backed results

Your personal Research Agent to handle research tasks with citation-backed results

Popular Tasks used by Researchers

How can I help with your research?

Meet SciSpace

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Katie Waller

Author Tools

Chat about Author

Papers

Anthropogenic environmental drivers of antimicrobial resistance in wildlife

Effects of a novel consensus bacterial 6-phytase variant on the apparent ileal digestibility of amino acids, total tract phosphorus retention, and tibia ash in young broilers