scholarly journals Characterisation of the rumen resistome in Spanish dairy cattle

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Adrián López-Catalina ◽  
Raquel Atxaerandio ◽  
Aser García-Rodríguez ◽  
Idoia Goiri ◽  
Mónica Gutierrez-Rivas ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Dairy Cattle ◽  
Resistance Genes ◽  
One Health ◽  
Potential Effect ◽  
Ruminal Bacteria ◽  
Rumen Microorganisms ◽  
Rumen Ph ◽  
Antimicrobial Resistance Genes ◽  
Cattle Farms

Abstract Background Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to understand how they appear, their relationship with the host, how they behave as a whole in the ruminal ecosystem or how they spread to the environment or humans. We sequenced ruminal samples from 416 Holstein dairy cows in 14 Spanish farms using nanopore technology, to uncover the presence of resistance genes and their potential effect on human, animal and environmental health. Results We found 998 antimicrobial resistance genes (ARGs) in the cow rumen and studied the 25 most prevalent genes in the 14 dairy cattle farms. The most abundant ARGs were related to the use of antibiotics to treat mastitis, metritis and lameness, the most common diseases in dairy cattle. The relative abundance (RA) of bacteriophages was positively correlated to the ARGs RA. The heritability of the RA of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW), similar to the heritability of the RA of microbes that carried those ARGs. Even though these genes are carried by the microorganisms, the host is partially controlling their RA by having a more suitable rumen pH, folds, or other physiological traits that promote the growth of those microorganisms. Conclusions We were able to determine the most prevalent ARGs (macB, msbA, parY, rpoB2, tetQ and TaeA) in the ruminal bacteria ecosystem. The rumen is a reservoir of ARGs, and strategies to reduce the ARG load from livestock must be pursued.

scholarly journals Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens

2020 ◽  
Vol 8 (12) ◽  
pp. 2031
Author(s):  
Sian Marie Frosini ◽  
Ross Bond ◽  
Alex J. McCarthy ◽  
Claudia Feudi ◽  
Stefan Schwarz ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
One Health ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Tetracycline Resistance ◽  
Methicillin Resistant ◽  
Antimicrobial Resistance Genes ◽  
Resistance Transfer ◽  
Coagulase Positive Staphylococci

Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health.

scholarly journals Occurrence and Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Dairy Cattle, Milk, and Farm Environments in Peninsular Malaysia

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1007
Author(s):  
Emelia Aini Kamaruzzaman ◽  
Saleha Abdul Aziz ◽  
Asinamai Athliamai Bitrus ◽  
Zunita Zakaria ◽  
Latiffah Hassan
Keyword(s):  
Antimicrobial Resistance ◽  
Dairy Cattle ◽  
One Health ◽  
Antimicrobial Agents ◽  
Public Health Problem ◽  
Diffusion Method ◽  
Resistant Bacteria ◽  
E Coli ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes

The emergence and spread of antimicrobial resistance genes and resistant bacteria do not recognize animal, human, or geographic boundaries. Addressing this threat requires a multidisciplinary approach involving human, animal, and environmental health (One Health) sectors. This is because antimicrobial agents used in veterinary medicine have been reported to be the same or similar to those in human medicine use. Extended-spectrum β-lactamase (ESBL) E. coli is a growing public health problem worldwide, and the agri-food industry is increasingly becoming a source of clinically important ESBL bacteria. Accordingly, the aim of this study was to investigate the occurrence and characteristics of ESBL-producing E. coli from dairy cattle, milk, and the farm environment. E. coli isolates were identified by their 16sRNA, and their ESBL production was confirmed using ESBL–CHROMagar media and the double disk diffusion method. Genotypes of ESBL producers were characterized using multiplex polymerase chain reaction (mPCR) assay. It was found that 18 (4.8%) of the total samples were positive for ESBL-producing E. coli. Of these, 66.7% were from milk, and 27.8% and 5.5% were from the farm environment and faecal samples, respectively. Predominant ESBL genotypes identified were a combination of both TEM and CTX-M in eight out of 18 (44.4%) isolates. Four (22.2%) isolates produced the CTX-M gene, two (11.1%) isolates produced the TEM gene, and four (22.2%) remaining isolates produced the ESBL genes other than TEM, SHV, CTX-M, and OXA. The SHV and OXA gene were not detected in all 18 isolates. In all, there were four profiles of genetic similarity. The occurrence of these genotypes in indicator organisms from dairy cattle, milk, and the farm environment further re-enforced the potential of food-animals as sources of ESBL-producing E. coli infection in humans via the food chain. Thus, there is the need for the adoption of a tripartite One Health approach in surveillance and monitoring to control antimicrobial resistance.

scholarly journals One Health Genomic Surveillance ofEscherichia coliDemonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Catherine Ludden ◽  
Kathy E. Raven ◽  
Dorota Jamrozy ◽  
Theodore Gouliouris ◽  
Beth Blane ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
One Health ◽  
Core Genome ◽  
Bloodstream Infections ◽  
Mobile Genetic Elements ◽  
Human Infection ◽  
Content Type ◽  
E Coli ◽  
Antimicrobial Resistance Genes

ABSTRACTLivestock have been proposed as a reservoir for drug-resistantEscherichia colithat infect humans. We isolated and sequenced 431E. coliisolates (including 155 extended-spectrum β-lactamase [ESBL]-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1,517E. colibacteria associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, suggesting thatE. colicausing serious human infection had not directly originated from livestock. In contrast, we observed highly related isolates from the same animal species on different farms. Screening all 1,948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions in human and livestock isolates. Overall, we identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that within the confines of our sampling framework, there was limited evidence that antimicrobial-resistant pathogens associated with serious human infection had originated from livestock in our region.IMPORTANCEThe increasing prevalence ofE. colibloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources ofE. coliassociated with serious human disease.E. colifrom 1,517 patients with bloodstream infections were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was limited overlap in the mobile elements carrying these genes. Within the limitations of sampling, our findings do not support the idea thatE. colicausing invasive disease or their resistance genes are commonly acquired from livestock in our region.

Imported One-Day-Old Chicks as Trojan Horses for Multidrug-Resistant Priority Pathogens Harboring mcr-9 , rmtG and Extended-Spectrum β-Lactamase Genes.

2021 ◽  
Author(s):  
Nadia Coppola ◽  
Nicolás F. Cordeiro ◽  
Gustavo Trenchi ◽  
Fernanda Esposito ◽  
Bruna Fuga ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
One Health ◽  
Production Systems ◽  
Animal Health ◽  
Critical Issue ◽  
Multidrug Resistant ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes ◽  
Production Stages

Antimicrobial resistance is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving intensive animal production systems. In this study, we have performed a microbiological and molecular investigation of priority pathogens carrying transferable resistance genes to critical antimicrobials in one-day-old chickens imported from Brazil to Uruguay. Bacterial identification was performed by MALDI-TOF mass spectrometry and antibiotic susceptibility was determined by Sensititre. Antimicrobial resistance genes were sought by polymerase chain reaction and clonality was assessed by PFGE. Four multidrug-resistant (MDR) representative strains were sequenced by Illumina and/or Oxford Nanopore Technologies. Twenty-eight MDR isolates identified as Escherichia coli ( n = 14), Enterobacter cloacae ( n = 11) and Klebsiella pneumoniae ( n = 3). While resistance to oxyiminocephalosporins was due to bla CTX-M-2 , bla CTX-M-8 , bla CTX-M-15 , bla CTX-M-55 and bla CMY-2 , plasmid-mediated quinolone resistance was associated with qnrB19 , qnrE1 , and qnrB2 genes. Finally, resistance to aminoglycosides and fosfomycin was due to the presence of 16S rRNA methyltransferase rmtG and fosA -type genes, respectively. Short and long-read genome sequencing of E. cloacae ODC-Eclo3 strain revealed the presence of IncQ/ rmtG (pUR-EC3.1, 7400-pb), IncHI2A/ mcr-9.1 / bla CTX-M-2 [pUR-EC3.2, ST16 (pMLST), 408,436-bp] and IncN2/ qnrB19 / aacC3 / aph(3’’)-Ib (pUR-EC3.3) resistance plasmids. Strikingly, the bla CTX-M-2 gene was carried by a novel Tn 1696 -like composite transposon designated Tn 7337 . In summary, we report that imported one-day-old chicks can act as Trojan horses for the hidden spread of WHO critical priority MDR pathogens harboring mcr-9 , rmtG and extended-spectrum β-lactamase genes in poultry farms, which is a critical issue within a One Health perspective. Importance section Antimicrobial resistance is considered a significant problem for global health, including within the concept of "One Health", therefore, the food chain is a link that connects human and animal health directly. In this work, we searched for microorganisms resistant to antibiotics considered critical for human health in intestinal microbiota of one-day-old baby chicks imported to Uruguay from Brazil. We described antibiotic-resistant genes to antibiotics named as to watch or reserve for the WHO, such as rmtG or mcr9.1 , which confers resistance to all the aminoglycosides and colistin, respectively, among others genes, and their presence in new mobile genetic elements that favor its dissemination. The sustained entry of these microorganisms evades the sanitary measures implemented by the countries and production establishments to reduce the selection of resistant microorganisms. These silently imported resistant microorganisms could explain a considerable part of the antimicrobial resistance problems found in the production stages of the system.

scholarly journals Occurrence and Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Dairy Cattle, Milk and Farm Environment in Peninsular Malaysia

2020 ◽  
Author(s):  
Emelia Aini Kamaruzzaman ◽  
Saleha Abdul-Aziz ◽  
Asinamai Athliamai Bitrus ◽  
Zunita Zakaria ◽  
Latiffah Hassan
Keyword(s):  
Antimicrobial Resistance ◽  
Dairy Cattle ◽  
One Health ◽  
Antimicrobial Agents ◽  
Public Health Problem ◽  
Diffusion Method ◽  
Resistant Bacteria ◽  
E Coli ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes

.The emergence and spread of antimicrobial resistance genes and resistant bacteria does not recognized animal, human or geographic borders. Addressing this threat requires a combination of multidisciplinary approach involving human, animal and environmental health (One Health). Because antimicrobial agents used in veterinary medicine maybe the same or like those in human medicine. Extended-spectrum beta lactamase (ESBL) E. coli is a growing public health problem worldwide, and the Agri-Food industry is constantly becoming sources of clinically important ESBL bacteria. Accordingly, the aim of this study was to investigate the occurrence and characteristics of ESBL-producing E. coli from dairy cattle, milk, and the farm environment. E. coli isolates were identified by their 16sRNA and their ESBL production was confirmed by ESBL-CHROMagar media and double disk diffusion method. Genotypes of ESBL producers were characterised using mPCR assay. Among the examined samples, 18(4.8 %) were positive for ESBL-producing E. coli. Of these, 66.7% were from milk, 27.8% and 5.5% were from farm environment and faecal samples respectively. Predominant ESBL Genotype identified were a combination of both TEM and CTX-M in eight out of 18 (44.4%) isolates. Four (22.2%) isolates produced CTX-M gene, two (11.1%) isolates produced TEM gene and four (22.2%) remaining isolates produced ESBL genes other than TEM, SHV, CTX-M and OXA. The SHV and OXA gene were not detected in all 18 isolates. The occurrence of these genotype in indicator organisms from dairy cattle, milk, and farm environment further re-enforced the potentials of food-animals as sources of infection for humans via the food chain. Thus, consolidating the need for the adoption of tripartite One Health approach in surveillance and monitoring antimicrobial resistance

scholarly journals The fecal resistome of dairy cattle is associated with diet during nursing

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jinxin Liu ◽  
Diana H. Taft ◽  
Maria X. Maldonado-Gomez ◽  
Daisy Johnson ◽  
Michelle L. Treiber ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Dairy Cattle ◽  
Resistance Genes ◽  
Early Life ◽  
Dairy Calves ◽  
Health Concern ◽  
Metagenomic Sequencing ◽  
Global Public Health ◽  
Antimicrobial Resistance Genes

Abstract Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.

scholarly journals One Health genomic surveillance ofEscherichia colidemonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock

2018 ◽  
Author(s):  
Catherine Ludden ◽  
Kathy E. Raven ◽  
Dorota Jamrozy ◽  
Theodore Gouliouris ◽  
Beth Blane ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Bloodstream Infection ◽  
Resistance Genes ◽  
One Health ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
E Coli ◽  
Genetic Elements ◽  
Antimicrobial Resistance Genes ◽  
Livestock Farms

ABSTRACTLivestock have been proposed as a reservoir for drug-resistantEscherichia colithat infect humans. We isolated and sequenced 431E. coli(including 155 ESBL-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1517E. coliassociated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, indicating thatE. colicausing serious human infection do not directly originate from livestock. By contrast, we observed highly related isolates from the same animal species on different farms. Analysis of accessory (variable) genomes identified a virulence cassette associated previously with cystitis and neonatal meningitis that was only present in isolates from humans. Screening all 1948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions of humans and livestock isolates. We identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that in this setting, there was limited evidence to support the suggestion that antimicrobial resistant pathogens that cause serious infection in humans originate from livestock.ImportanceThe increasing prevalence ofE. colibloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources ofE. coliassociated with serious human disease.E. colifrom 1517 patients with bloodstream infection were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was little overlap in the mobile elements carrying these genes. In addition, a virulence cassette found in humans isolates was not identified in any livestock-associated isolate. Our findings do not support the idea thatE. colicausing invasive disease or their resistance genes are commonly acquired from livestock.

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