Antimicrobial resistance determinants in silage

Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. But resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer's body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 40 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 57 ARGs occurred 616 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. We believe that our results point to a substantial source of ARG in the food chain.

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Aquatic environments in the One Health context: modulating the antimicrobial resistance phenomenon

Acta Limnologica Brasiliensia ◽

10.1590/s2179-975x4719 ◽

2020 ◽

Vol 32 ◽

Cited By ~ 1

Author(s):

Juliana Alves Resende ◽

Vânia Lúcia da Silva ◽

Claudio Galuppo Diniz

Keyword(s):

Antimicrobial Resistance ◽

One Health ◽

Anthropogenic Activities ◽

Treatment Strategies ◽

Chemical Pollution ◽

Resistant Bacteria ◽

Aquatic Environments ◽

Antimicrobial Substances ◽

Antimicrobial Resistance Genes ◽

The One

Abstract: From an anthropocentric perspective, aquatic environments are important to maintain health and survival, however, as they are sometimes managed based on misconception, they are considered a convergent pathway for anthropogenic residues and sanitation. Thus, it is observed that these ecosystems have been threatened by chemical pollution due to xenobiotics, especially from a more contemporary approach, by the selective pressure associated with antimicrobials. There are several studies that report the enrichment of antimicrobial resistant bacteria and mobilizable antimicrobial resistance genes in aquatic and adjacent ecosystems. From the perspective of the emerging and reemerging number of diseases related to the interplay of human, animal, and environmental factors, a new conception arose to address these issues holistically, which is known as the One Health approach. Scientific and political discourse on this conception should lead to effective action plans for preventing and controlling the spread of infectious diseases in open environment, including those impacted by anthropogenic activities. Therefore, nowadays, discussions on antimicrobial resistance are becoming broader and are requiring a multi-disciplinary view to address health and environmental challenges, which includes aquatic environment management. Water may represent one of the most important ecosystems for the in antimicrobial resistance phenomenon that arises when a dynamic and singular microbial community may be influenced by several characteristics. As antimicrobial substances do not all degrade at the same time under the same treatment, strategies concerning their removal from the environment should consider their individualized chemical characteristics.

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Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02612-20 ◽

2021 ◽

Author(s):

Dominic Poulin-Laprade ◽

Jean-Simon Brouard ◽

Nathalie Gagnon ◽

Annie Turcotte ◽

Alexandra Langlois ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Efflux Pump ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Production Cycle ◽

Antimicrobial Use ◽

Resistance Determinants ◽

Extended Spectrum ◽

Antimicrobial Resistance Genes ◽

The Impact

Pigs are major reservoirs of resistant Enterobacteriaceae that can reach humans through consumption of contaminated meat or vegetables grown in manure-fertilized soil. Samples were collected from sows during lactation and their piglets at five time points spanning the production cycle. Cefotaxime-resistant bacteria were quantified and isolated from feed, feces, manures and carcasses of pigs reared with penicillin-using or antibiotic-free husbandries. The isolates were characterized by antibiotic susceptibility testing, whole genome sequencing and conjugation assays. The extended spectrum β-lactamase (ESBL) phenotype was more frequent in isolates originating from antibiotic-free animals, while the bacteria isolated from penicillin-using animals were on average resistant to a greater number of antibiotics. The ESBL-encoding genes identified were blaCTX-M-1, blaCTX-M-15 and blaCMY-2 and they co-localised on plasmids with various genes encoding resistance to ß-lactams, co-trimoxazole, phenicols and tetracycline, all antibiotics used in pig production. Groups of genes conferring the observed resistance and the mobile elements disseminating multidrug resistance were determined. The observed resistance to ß-lactams was mainly due to the complementary actions of penicillin-binding proteins, an efflux pump and ß-lactamases. Most resistance determinants were shared by animals raised with or without antimicrobials. This suggests a key contribution of indigenous enterobacteria maternally transmitted along the sow lineage, regardless of antimicrobial use. It is unclear if the antimicrobial resistance observed in the enterobacteria populations of the commercial pig herds studied were present before the use of antibiotics, or the extent to which historical antimicrobial use exerted a selective pressure defining the resistant bacterial populations in farms using penicillin prophylaxis. Importance: Antimicrobial resistance is a global threat that needs to be fought on numerous fronts along the One Health continuum. Vast quantities of antimicrobials are used in agriculture to ensure animal welfare and productivity, and are arguably a driving force for the persistence of environmental and food-borne resistant bacteria. This study evaluated the impact of conventional, organic and other antibiotic-free husbandry practices on the frequency and nature of antimicrobial resistance genes and multidrug resistant enterobacteria. It provides knowledge about the relative contribution of specific resistance determinants to observed antibiotic resistance. It also showed the clear co-selection of genes coding for extended-spectrum beta-lactamases and genes coding for the resistance to antibiotics commonly used for prophylaxis or in curative treatments in pig operations.

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A glimpse of antimicrobial resistance gene diversity in kefir and yoghurt

Scientific Reports ◽

10.1038/s41598-020-80444-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Adrienn Gréta Tóth ◽

István Csabai ◽

Gergely Maróti ◽

Ákos Jerzsele ◽

Attila Dubecz ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Pathogenic Bacteria ◽

Gene Diversity ◽

Fermented Food ◽

Practical Significance ◽

Fermented Foods ◽

Bacterial Strains ◽

Genetic Components ◽

Antimicrobial Resistance Genes ◽

Antimicrobial Resistance Gene

AbstractAntimicrobial resistance (AMR) is a global threat gaining more and more practical significance every year. The main determinants of AMR are the antimicrobial resistance genes (ARGs). Since bacteria can share genetic components via horizontal gene transfer, even non-pathogenic bacteria may provide ARG to any pathogens which they become physically close to (e.g. in the human gut). In addition, fermented food naturally contains bacteria in high amounts. In this study, we examined the diversity of ARG content in various kefir and yoghurt samples (products, grains, bacterial strains) using a unified metagenomic approach. We found numerous ARGs of commonly used fermenting bacteria. Even with the strictest filter restrictions, we identified ARGs undermining the efficacy of aminocoumarins, aminoglycosides, carbapenems, cephalosporins, cephamycins, diaminopyrimidines, elfamycins, fluoroquinolones, fosfomycins, glycylcyclines, lincosamides, macrolides, monobactams, nitrofurans, nitroimidazoles, penams, penems, peptides, phenicols, rifamycins, tetracyclines and triclosan. In the case of gene lmrD, we detected genetic environment providing mobility of this ARG. Our findings support the theory that during the fermentation process, the ARG content of foods can grow due to bacterial multiplication. The results presented suggest that the starting culture strains of fermented foods should be monitored and selected in order to decrease the intake of ARGs via foods.

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Merging Metagenomics and Spatial Epidemiology To Understand the Distribution of Antimicrobial Resistance Genes from Enterobacteriaceae in Wild Owls

Applied and Environmental Microbiology ◽

10.1128/aem.00571-20 ◽

2020 ◽

Vol 86 (20) ◽

Author(s):

Elizabeth A. Miller ◽

Julia B. Ponder ◽

Michelle Willette ◽

Timothy J. Johnson ◽

Kimberly L. VanderWaal

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Spatial Epidemiology ◽

Anthropogenic Sources ◽

Resistant Bacteria ◽

Metagenomic Sequencing ◽

Wild Animals ◽

Natural Ecosystems ◽

Content Type ◽

Antimicrobial Resistance Genes

ABSTRACT Antimicrobial resistance (AMR) is a well-documented phenomenon in bacteria from many natural ecosystems, including wild animals. However, the specific determinants and spatial distribution of resistant bacteria and antimicrobial resistance genes (ARGs) in the environment remain incompletely understood. In particular, information regarding the importance of anthropogenic sources of AMR relative to that of other biological and ecological influences is lacking. We conducted a cross-sectional study of AMR in great horned owls (Bubo virginianus) and barred owls (Strix varia) admitted to a rehabilitation center in the midwestern United States. A combination of selective culture enrichment and shotgun metagenomic sequencing was used to identify ARGs from Enterobacteriaceae. Overall, the prevalence of AMR was comparable to that in past studies of resistant Enterobacteriaceae in raptors, with acquired ARGs being identified in 23% of samples. Multimodel regression analyses identified seasonality and owl age to be important predictors of the likelihood of the presence of ARGs, with birds sampled during warmer months being more likely to harbor ARGs than those sampled during cooler months and with birds in their hatch year being more likely to harbor β-lactam ARGs than adults. Beyond host-specific determinants, ARG-positive owls were also more likely to be recovered from areas of high agricultural land cover. Spatial clustering analyses identified a significant high-risk cluster of tetracycline resistance gene-positive owls in the southern sampling range, but this could not be explained by any predictor variables. Taken together, these results highlight the complex distribution of AMR in natural environments and suggest that both biological and anthropogenic factors play important roles in determining the emergence and persistence of AMR in wildlife. IMPORTANCE Antimicrobial resistance (AMR) is a multifaceted problem that poses a worldwide threat to human and animal health. Recent reports suggest that wildlife may play an important role in the emergence, dissemination, and persistence of AMR. As such, there have been calls for better integration of wildlife into current research on AMR, including the use of wild animals as biosentinels of AMR contamination in the environment. A One Health approach can be used to gain a better understanding of all AMR sources and pathways, particularly those at the human-animal-environment interface. Our study focuses on this interface in order to assess the effect of human-impacted landscapes on AMR in a wild animal. This work highlights the value of wildlife rehabilitation centers for environmental AMR surveillance and demonstrates how metagenomic sequencing within a spatial epidemiology framework can be used to address questions surrounding AMR complexity in natural ecosystems.

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Metagenomics: aid to combat antimicrobial resistance in diarrhea

Gut Pathogens ◽

10.1186/s13099-019-0331-8 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 5

Author(s):

Rituparna De

Keyword(s):

Antimicrobial Resistance ◽

Antimicrobial Agents ◽

Genetic Recombination ◽

Molecular Taxonomy ◽

Ecological Niches ◽

Next Generation ◽

Genetic Determinants ◽

Antimicrobial Resistance Genes ◽

And Function ◽

Generation Sequencing

Abstract Antimicrobial resistance (AMR) has emerged as an obstacle in the supple administration of antimicrobial agents to critical diarrheal patients. Most diarrheal pathogens have developed resistance against the major classes of antibiotics commonly used for assuaging diarrheal symptoms. Antimicrobial resistance develops when pathogens acquire antimicrobial resistance genes (ARGs) through genetic recombination from commensals and pathogens. These are the constituents of the complex microbiota in all ecological niches. The recombination events may occur in the environment or in the gut. Containment of AMR can be achieved through a complete understanding of the complex and diverse structure and function of the microbiota. Its taxonomic entities serve as focal points for the dissemination of antimicrobial resistance genetic determinants. Molecular methods complemented with culture-based diagnostics have been historically implemented to document these natural events. However, the advent of next-generation sequencing has revolutionized the field of molecular epidemiology. It has revolutionized the method of addressing relevant problems like diagnosis and surveillance of infectious diseases and the issue of antimicrobial resistance. Metagenomics is one such next-generation technique that has proved to be a monumental advancement in the area of molecular taxonomy. Current understanding of structure, function and dysbiosis of microbiota associated with antimicrobial resistance was realized due to its conception. This review describes the major milestones achieved due to the advent and implementation of this new technique in the context of antimicrobial resistance. These achievements span a wide panorama from the discovery of novel microorganisms to invention of translational value.

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Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16244896 ◽

2019 ◽

Vol 16 (24) ◽

pp. 4896

Author(s):

Na Li ◽

Chong Liu ◽

Zhiguo Zhang ◽

Hongna Li ◽

Tingting Song ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

High Throughput Sequencing ◽

Animal Husbandry ◽

Control Measures ◽

Research Progress ◽

Future Research ◽

Resistant Bacteria ◽

Technological Advances ◽

Antimicrobial Resistance Genes

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

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Characterization of Multiple-Antimicrobial-Resistant Salmonella Serovars Isolated from Retail Meats

Applied and Environmental Microbiology ◽

10.1128/aem.70.1.1-7.2004 ◽

2004 ◽

Vol 70 (1) ◽

pp. 1-7 ◽

Cited By ~ 251

Author(s):

Sheng Chen ◽

Shaohua Zhao ◽

David G. White ◽

Carl M. Schroeder ◽

Ran Lu ◽

...

Keyword(s):

United States ◽

Antimicrobial Resistance ◽

Resistance Genes ◽

The United States ◽

People’S Republic Of China ◽

People's Republic Of China ◽

Republic Of China ◽

Resistance Determinants ◽

Antimicrobial Resistance Genes ◽

Retail Meats

ABSTRACT A total of 133 Salmonella isolates recovered from retail meats purchased in the United States and the People's Republic of China were assayed for antimicrobial susceptibility, the presence of integrons and antimicrobial resistance genes, and horizontal transfer of characterized antimicrobial resistance determinants via conjugation. Seventy-three (82%) of these Salmonella isolates were resistant to at least one antimicrobial agent. Resistance to the following antibiotics was common among the United States isolates: tetracycline (68% of the isolates were resistant), streptomycin (61%), sulfamethoxazole (42%), and ampicillin (29%). Eight Salmonella isolates (6%) were resistant to ceftriaxone. Fourteen isolates (11%) from the People's Republic of China were resistant to nalidixic acid and displayed decreased susceptibility to ciprofloxacin. A total of 19 different antimicrobial resistance genes were identified in 30 multidrug-resistant Salmonella isolates. The bla CMY-2 gene, encoding a class A AmpC β-lactamase, was detected in all 10 Salmonella isolates resistant to extended-spectrum β-lactams. Resistance to ampicillin was most often associated with a TEM-1 family β-lactamase gene. Six aminoglycoside resistance genes, aadA1, aadA2, aacC2, Kn, aph(3)-IIa, and aac(3)-IVa, were commonly present in the Salmonella isolates. Sixteen (54%) of 30 Salmonella isolates tested had integrons ranging in size from 0.75 to 2.7 kb. Conjugation studies demonstrated that there was plasmid-mediated transfer of genes encoding CMY-2 and TEM-1-like β-lactamases. These data indicate that Salmonella isolates recovered from retail raw meats are commonly resistant to multiple antimicrobials, including those used for treating salmonellosis, such as ceftriaxone. Genes conferring antimicrobial resistance in Salmonella are often carried on integrons and plasmids and could be transmitted through conjugation. These mobile DNA elements have likely played an important role in transmission and dissemination of antimicrobial resistance determinants among Salmonella strains.

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Antimicrobial resistance in United States retail ground beef with and without label claims regarding antibiotic use

Journal of Food Protection ◽

10.4315/jfp-20-376 ◽

2020 ◽

Author(s):

John W. Schmidt ◽

Amit Vikram ◽

Enrique Doster ◽

Kevin Thomas ◽

Margaret D Weinroth ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Production System ◽

Ground Beef ◽

Antibiotic Use ◽

Resistant Bacteria ◽

Antimicrobial Use ◽

Food Animal ◽

Antimicrobial Resistance Genes ◽

Human Health Impacts ◽

Beef Products

Antibiotics used during food-animal production account for approximately 77% of U.S. antimicrobial consumption by mass. Ground beef products labeled as raised without antibiotics (RWA) are perceived to harbor lower antimicrobial resistance (AMR) levels than conventional (CONV) products with no label claims regarding antimicrobial use. Retail ground beef samples were obtained from 6 U. S. cities. Samples with a RWA or USDA Organic claim ( N = 299) were assigned to the RWA production system. Samples lacking these claims ( N = 300) were assigned to the CONV production system. Each sample was cultured for the detection of five antimicrobial resistant bacteria. Genomic DNA was isolated from each sample and qPCR was used to determine the abundance of ten antimicrobial resistance genes (ARGs). Tetracycline-resistant Escherichia coli (CONV = 46.3%; RWA = 34.4%, P < 0.01) and erythromycin-resistant Enterococcus (CONV = 48.0%; RWA = 37.5%, P = 0.01) were more frequently detected in CONV. Salmonella were detected in 1.2% of samples. The ARG bla CTX-M (CONV = 4.1 log 10 normalized abundance, RWA = 3.8 log 10 normalized abundance, P < 0.01) was more abundant in CONV ground beef. The ARGs mecA (CONV = 4.4 log 10 normalized abundance, RWA = 4.9 log 10 normalized abundance, P = 0.05), tet (A) (CONV = 3.9 log 10 normalized abundance, RWA = 4.5 log 10 normalized abundance, P < 0.01), tet (B) (CONV = 3.9 log 10 normalized abundance, RWA = 4.5 log 10 normalized abundance, P < 0.01), and tet (M) (CONV = 5.4 log 10 normalized abundance, RWA = 5.8 log 10 normalized abundance, P < 0.01) were more abundant in RWA ground beef. Although these results suggest that antimicrobial use during U. S. cattle production does not increase human exposure to AMR via ground beef quantitative microbiological risk assessments are required for authoritative assessments regarding the human health impacts of antimicrobial uses during beef production.

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Seasonal resistome diversity and dissemination of WHO priority antibiotic-resistant pathogens in Lebanese estuaries

10.1101/2021.12.13.472353 ◽

2021 ◽

Author(s):

Wadad Hobeika ◽

Margaux Gaschet ◽

Marie-Cecile Ploy ◽

Elena Buelow ◽

Dolla Karam Sarkis ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Pathogenic Bacteria ◽

Anthropogenic Activities ◽

Resistant Bacteria ◽

Anthropogenic Pressure ◽

Significant Information ◽

Antibiotic Resistant ◽

Culture Techniques ◽

Antimicrobial Resistance Genes ◽

Key Drivers

Anthropogenic activities are demonstrated to be the key drivers of antimicrobial resistance (AMR) dissemination in the environment. Lebanese rivers that lead to the Mediterranean Sea were sampled at estuaries sites, under high anthropogenic pressure, in spring 2017 and winter 2018 to study seasonal variation of antimicrobial-resistant bacteria (ARBs) and antimicrobial resistance genes (ARGs). Methods: A combined approach using culture techniques and high throughput qPCR identified hotspots for antimicrobial resistance and anthropogenic pressure in particular locations along the Lebanese coast. Results: Multi-resistant Gram-negative (Enterobacterales and Pseudomonas spp) and Gram-positive bacterial pathogens were isolated. A high abundance of certain ARGs (vanB, blaBIC-1, blaGES, tetM, and mcr-1) was detected in 5 Lebanese estuaries. The relative abundance of ARGs was highest in winter and areas with high anthropogenic activities and population growth with an influx of refugees. Conclusion: Qualitative analysis of ARB and the analysis of the Lebanese estuaries resistome revealed critical levels of contamination with pathogenic bacteria and provided significant information about the spread of ARGs in anthropogenically impacted estuaries.

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Characterization and Horizontal Transfer of Antimicrobial Resistance Genes and Integrons in Bacteria Isolated from Cooked Meat Products in China

Journal of Food Protection ◽

10.4315/0362-028x.jfp-17-119 ◽

2017 ◽

Vol 80 (12) ◽

pp. 2048-2055 ◽

Cited By ~ 2

Author(s):

Tao Yu ◽

Xiaobing Jiang ◽

Yu Liang ◽

Yanping Zhu ◽

Jinhe Tian ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Meat Products ◽

Multidrug Resistant ◽

Resistant Bacteria ◽

Integrase Gene ◽

Antimicrobial Resistance Genes ◽

Class 1 ◽

Cooked Meat ◽

Cooked Meat Products

ABSTRACT The aim of this study was to investigate antimicrobial resistance and the presence and transferability of corresponding resistance genes and integrons in bacteria isolated from cooked meat samples in the People's Republic of China. A total of 150 isolates (22 species belonging to 15 genera) were isolated from 49 samples. Resistance of these isolates to antimicrobials was commonly observed; 42.7, 36.0, and 25.3% of the isolates were resistant to tetracycline, streptomycin, and ampicillin, respectively. Multidrug resistance was observed in 41 (27.3%) of the isolates. Sixteen resistance genes, i.e., blaTEM-1 and blaCTX-M-14 (β-lactams), aac(3)-IIa (gentamicin), strA and strB (streptomycin), qnrB and qnrS (fluoroquinolone), sul1, sul2, and sul3 (sulfamethoxazole), cat1 and cat2 (chloramphenicol), and tetM, tetA, tetS, and tetB (tetracycline), were found in 54 isolates. One isolate of Pseudomonas putida carried qnrB, and sequence analysis of the PCR product revealed 96% identity to qnrB2. The qnr genes were found coresiding and were cotransferred with bla genes in two isolates. Twelve isolates were positive for the class 1 integrase gene, and four isolates carried the class 2 integrase gene. However, no class 3 integrase gene was detected. One isolate of Proteus mirabilis carried dfrA32-ereA-aadA2, and this unusual array could be transferred to Escherichia coli. Nonclassic class 1 integrons lacking qacEΔ1 and sul1 genes were found in 2 of the 12 intI1-positive isolates. Our results revealed the presence of multidrug-resistant bacteria in cooked meats and the presence and transferability of resistance genes in some isolates, suggesting that cooked meat products may act as reservoirs of drug-resistant bacteria and may facilitate the spread of resistance genes.

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