Scoping review to identify potential non-antimicrobial interventions to mitigate antimicrobial resistance in commensal enteric bacteria in North American cattle production systems

SUMMARYA scoping review was conducted to identify modifiable non-antimicrobial factors to reduce the occurrence of antimicrobial resistance in cattle populations. Searches were developed to retrieve peer-reviewed published studies in animal, human andin vitromicrobial populations. Citations were retained when modifiable non-antimicrobial factors or interventions potentially associated with antimicrobial resistance were described. Studies described resistance in five bacterial genera, species or types, and 40 antimicrobials. Modifiable non-antimicrobial factors or interventions ranged widely in type, and the depth of evidence in animal populations was shallow. Specific associations between a factor or intervention with antimicrobial resistance in a population (e.g. associations between organic systems and tetracycline susceptibility inE. colifrom cattle) were reported in a maximum of three studies. The identified non-antimicrobial factors or interventions were classified into 16 themes. Most reported associations between the non-antimicrobial modifiable factors or interventions and antimicrobial resistance were not statistically significant (P> 0·05 and a confidence interval including 1), but when significant, the results were not consistent in direction (increase or decrease in antimicrobial resistance) or magnitude. Research is needed to better understand the impacts of promising modifiable factors or interventions on the occurrence of antimicrobial resistance before any recommendations can be offered or adopted.

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Characterization of cefotaxime resistant Escherichia coli isolated from broiler farms in Ecuador

10.1101/462994 ◽

2018 ◽

Author(s):

Christian Vinueza-Burgos ◽

David Ortega-Paredes ◽

Cristian Narváez ◽

Lieven De Zutter ◽

Jeannete Zurita

Keyword(s):

Antimicrobial Resistance ◽

Latin American ◽

Production Systems ◽

Diffusion Method ◽

Poultry Production ◽

Disk Diffusion Method ◽

E Coli ◽

Resistance Patterns ◽

Latin American Countries

AbstractAntimicrobial resistance (AR) is a worldwide concern. Up to a 160% increase in antibiotic usage in food animals is expected in Latin American countries. The poultry industry is an increasingly important segment of food production and contributor to AR. The objective of this study was to evaluate the prevalence, AR patterns and the characterization of relevant resistance genes in Extended Spectrum β-lactamases (ESBL) and AmpC E. coli from large poultry farms in Ecuador. Sampling was performed from June 2013 to July 2014 in 6 slaughterhouses that slaughter broilers from 115 farms totaling 384 flocks. Each sample of collected caeca was streaked onto TBX agar supplemented with cefotaxime (3 mg/l). In total, 176 isolates were analyzed for antimicrobial resistance patterns by the disk diffusion method and for blaCTX-M, blaTEM, blaCMY, blaSHV, blaKPC, and mcr-1 by PCR and sequencing. ESBL and AmpC E. coli were found in 362 flocks (94.3%) from 112 farms (97.4%). We found that 98.3% of the isolates were multi-resistant to antibiotics. Low resistance was observed for ertapenem and nitrofurantoin. The most prevalent ESBL genes were the blaCTX-M (90.9%) blaCTX-M-65, blaCTX-M-55 and blaCTX-M-3 alleles. Most of the AmpC strains presented the blaCMY-2 gene. Three isolates showed the mcr-1 gene. Poultry production systems represent a hotspot for antimicrobial resistance in Ecuador, possibly mediated by the extensive use of antibiotics. Monitoring this sector in national and regional plans of antimicrobial resistance surveillance should therefore be considered.

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The characterization of ESBL genes in Escherichia coli and Klebsiella pneumoniae causing nosocomial infections in Vietnam

The Journal of Infection in Developing Countries ◽

10.3855/jidc.2938 ◽

2013 ◽

Vol 7 (12) ◽

pp. 922-928 ◽

Cited By ~ 15

Author(s):

Nguyen Hoang Thu Trang ◽

Tran Vu Thieu Nga ◽

James I Campbell ◽

Nguyen Trong Hiep ◽

Jeremy Farrar ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Nosocomial Infections ◽

Enteric Bacteria ◽

E Coli ◽

Plasmid Analysis ◽

Resistance Plasmids ◽

Genes Encoding ◽

Third Generation Cephalosporins

Background: Extended-spectrum β-lactamases (ESBLs) are enzymes capable of hydrolyzing oxyimino-β-lactams and inducing resistance to third generation cephalosporins. The genes encoding ESBLs are widespread and generally located on highly transmissible resistance plasmids. We aimed to investigate the complement of ESBL genes in E. coli and Klebsiella pneumoniae causing nosocomial infections in hospitals in Ho Chi Minh City, Vietnam. Methodology: Thirty-two non-duplicate isolates of E. coli and Klebsiella pneumoniae causing nosocomial infections, isolated between March and June 2010, were subjected to antimicrobial susceptibility testing. All isolates were PCR-amplified to detect the blaSHV, blaTEM and blaCTX-M ESBL genes and subjected to plasmid analysis. Results: We found that co-resistance to multiple antimicrobials was highly prevalent, and we report the predominance of the blaCTX-M-15 and blaCTX-M-27 genes, located on highly transmissible plasmids ranging from 50 to 170 kb in size. Conclusions: Our study represents a snap shot of ESBL-producing enteric bacteria causing nosocomial infections in this setting. We suggest that antimicrobial resistance in nosocomial E. coli and Klebsiella pneumoniae is rampant in Vietnam and ESBL organisms are widespread. In view of these data and the dramatic levels of antimicrobial resistance reported in Vietnam we advocate an urgent review of antimicrobial use in the Vietnamese healthcare system.

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Antimicrobials use and resistance on integrated poultry-fish farming systems in the Ayeyarwady Delta of Myanmar

Scientific Reports ◽

10.1038/s41598-020-73076-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Justine S. Gibson ◽

Honey Wai ◽

Shwe Sin May Lwin Oo ◽

Ei Moh Moh Hmwe ◽

Soe Soe Wai ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Production Systems ◽

Farming Systems ◽

Fish Farming ◽

Fish Ponds ◽

Fish Farms ◽

E Coli ◽

Livestock Species ◽

Poultry Farms ◽

Livestock Health

Abstract Antimicrobials are used to support livestock health and productivity, but might pose a risk for the development of antimicrobial resistance; in particular, when multiple livestock species are raised together in production systems. On integrated chicken-fish farms, chickens are raised over fish ponds and poultry faeces is excreted into the ponds. We investigated antimicrobial usage and the antimicrobial susceptibility of Escherichia coli cultured from poultry faeces on 301 integrated farms in Ayeyarwady Delta of Myanmar. Antimicrobials were used by 92.4% of farmers for chickens, but they were not applied to fish. The most common antimicrobials used were Octamix (amoxicillin and colistin sulfate) on 28.4%, enrofloxacin on 21.0% and amoxicillin on 16% of farms. Overall, 83.1% (152/183) of the E. coli were resistant to at least one antimicrobial. The highest level of resistance was to amoxicillin (54.6%), tetracycline (39.9%), sulfamethoxazole/trimethoprim (35.5%) and enrofloxacin (34.4%). Multidrug resistance was identified in 42.4% of isolates. In general, we found similar levels of antimicrobial resistance in non-users of antimicrobials as in users of antimicrobials for more commonly applied antimicrobials. Overall, antimicrobial resistance was lower in chickens on these integrated farms in Myanmar, compared to poultry farms in other countries of South East and East Asia.

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Zoonotic bacteria in the food chain: antimicrobial resistance and associated factors in Portugal

European Journal of Public Health ◽

10.1093/eurpub/ckaa166.237 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

M Costa ◽

A Cara d'Anjo ◽

M Cardo ◽

A Leite

Keyword(s):

Antimicrobial Resistance ◽

Associated Factors ◽

Laying Hens ◽

Control Measures ◽

Processing Plant ◽

Sample Type ◽

Bacterial Isolates ◽

Final Model ◽

E Coli ◽

Animal Populations

Abstract Antimicrobial resistance (AMR) poses a threat to public health and animal food-production plays a crucial role in AMR spread. We thus aimed to characterize AMR profiles and associated factors in zoonotic bacterial isolates in Portugal. Data from the Portuguese AMR surveillance program on animal populations and derived food, 2014-2018, was used. AMR frequency was described in E coli, Campylobacter and Salmonella isolates from poultry and pigs, according to antibiotic and samples tested. For Salmonella, AMR associated factors were studied: animal populations (broilers, laying hens, pigs) and derived meat, sampling stage (farm, slaughterhouse, processing plant), sample type (environmental, carcase, food), sampler (HACCP, industry, official, official and industry), sample context (control and eradication programmes, monitoring), year (2014-2018) and season. Logistic regression was applied to estimate crude (OR) and adjusted odds ratio (aOR) with 95% confidence intervals (95%CI). The final model was obtained using a backward stepwise method. We assessed 2157 E Coli, 561 Campylobacter and 826 Salmonella isolates. AMR rates were higher to cefepime (91-98%) in E coli in all sample types; cefotaxime (100%) in E coli in broiler's meat; nalidixic acid (79-96%) in E coli and Campylobacter in poultry and derived meat; ciprofloxacin (50-98%) in all bacteria isolates from poultry and derived meat. For Salmonella, AMR was more likely in pig's meat (OR 3.66; 95%CI:1.19-2.82), slaughterhouses (OR 10.18; 95%CI:4.69-26.70), carcases (OR 5.90;95%CI:3.74-9.69). The final model indicated a lesser chance of AMR in laying hens (aOR .21; 95%CI:.11-.37), industry sampling (aOR .25; 95%CI:.07-.73), 2018 (aOR .24; 95%CI:.13-.42), and a higher chance in summer (aOR 2.39; 95%CI:1.34-4.28). The findings support the need for control measures on the use of key antibiotics in veterinary medicine. AMR occurrence in Portugal seems to be related to summer, although less in laying hens and in 2018. Key messages AMR in bacterial isolates suggests the need for integrated actions to mitigate and control the use of 3rd and 4rd generation cephalosporins, fluoroquinolones and quinolones in animal production. AMR occurrence in Portugal seems to be further related to summer conditions, while comparing to other seasons.

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Antimicrobial Drug Resistance Genes Do Not Convey a Secondary Fitness Advantage to Calf-Adapted Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.72.1.443-448.2006 ◽

2006 ◽

Vol 72 (1) ◽

pp. 443-448 ◽

Cited By ~ 25

Author(s):

Artashes R. Khachatryan ◽

Dale D. Hancock ◽

Thomas E. Besser ◽

Douglas R. Call

Keyword(s):

Antimicrobial Resistance ◽

Resistance Genes ◽

Null Mutant ◽

Antimicrobial Drug Resistance ◽

E Coli ◽

Fitness Advantage ◽

Antimicrobial Resistance Genes ◽

Mutant Strains

ABSTRACT Maintenance of antimicrobial drug resistance in bacteria can be influenced by factors unrelated to direct selection pressure such as close linkage to other selectively advantageous genes and secondary advantage conveyed by antimicrobial resistance genes in the absence of drug selection. Our previous trials at a dairy showed that the maintenance of the antimicrobial resistance genes is not influenced by specific antimicrobial selection and that the most prevalent antimicrobial resistance phenotype of Escherichia coli is specifically selected for in young calves. In this paper we examine the role of secondary advantages conveyed by antimicrobial resistance genes. We tested antimicrobial-susceptible null mutant strains for their ability to compete with their progenitor strains in vitro and in vivo. The null mutant strains were generated by selection for spontaneous loss of resistance genes in broth supplemented with fusaric acid or nickel chloride. On average, the null mutant strains were as competitive as the progenitor strains in vitro and in newborn calves (in vivo). Inoculation of newborn calves at the dairy with antimicrobial-susceptible strains of E. coli did not impact the prevalence of antimicrobial-resistant E. coli. Our results demonstrate that the antimicrobial resistance genes are not responsible for the greater fitness advantage of antimicrobial-resistant E. coli in calves, but the farm environment and the diet clearly exert critical selective pressures responsible for the maintenance of antimicrobial resistance genes. Our current hypothesis is that the antimicrobial resistance genes are linked to other genes responsible for differential fitness in dairy calves.

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The Streptomycin-Sulfadiazine-Tetracycline Antimicrobial Resistance Element of Calf-Adapted Escherichia coli Is Widely Distributed among Isolates from Washington State Cattle

Applied and Environmental Microbiology ◽

10.1128/aem.01534-07 ◽

2007 ◽

Vol 74 (2) ◽

pp. 391-395 ◽

Cited By ~ 19

Author(s):

Artashes R. Khachatryan ◽

Thomas E. Besser ◽

Douglas R. Call

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Selective Advantage ◽

Washington State ◽

Resistance Pattern ◽

Genetic Element ◽

Dairy Calf ◽

Genetic Traits ◽

E Coli

ABSTRACT Association of specific antimicrobial resistance patterns with unrelated selective traits has long been implicated in the maintenance of antimicrobial resistance in a population. Previously we demonstrated that Escherichia coli strains with a specific resistance pattern (resistant to streptomycin, sulfadiazine, and tetracycline [SSuT]) have a selective advantage in dairy calf intestinal environments and in the presence of a milk supplement commonly fed to the calves. In the present study we identified the sequence of the genetic element that confers the SSuT phenotype and show that this element is present in a genetically diverse group of E. coli isolates, as assessed by macrorestriction digestion and pulsed-field gel electrophoresis. This element was also found in E. coli isolates from 18 different cattle farms in Washington State. Using in vitro competition experiments we further demonstrated that SSuT strains from 17 of 18 farms were able to outcompete pansusceptible strains. In a separate set of experiments, we were able to transfer the antimicrobial resistance phenotype by electroporation to a laboratory strain of E. coli (DH10B), making that new strain more competitive during in vitro competition with the parental DH10B strain. These data indicate that a relatively large genetic element conferring the SSuT phenotype is widely distributed in E. coli from cattle in Washington State. Furthermore, our results indicate that this element is responsible for maintenance of these traits owing to linkage to genetic traits that confer a selective advantage in the intestinal lumens of dairy calves.

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Antimicrobial Resistance and Sensitivity of Phytophthora agathidicida

10.26686/wgtn.15506373 ◽

2021 ◽

Author(s):

Kaitlyn Daley

Keyword(s):

Natural Products ◽

New Zealand ◽

Antimicrobial Resistance ◽

Plant Pathogens ◽

Keystone Species ◽

Resistance Mutations ◽

E Coli ◽

Oxysterol Binding Protein ◽

Significant Difference

Members of the oomycete genus Phytophthora are highly infectious plant pathogens. P. agathidicida affects the New Zealand native keystone species Agathis australis(kauri) and is the cause of kauri dieback. The complex oomycete lifecycle makes Phytophthora infections hard to manage. The current management of kauri dieback has been limited and antimicrobial resistance is a concern. Phosphite agrichemical preparations are commonly used in the control of Phytophthora diseases, including kauri dieback. However, phosphite is not the only option; the agrichemicals oxathiapiprolin, and the plant-derived natural products polygodial and falcarindiol, have also been shown to have activity against P. agathidicida. The overall goal of this thesis was to further explore aspects of sensitivity and resistance of P. agathidicidatowards these four compounds.In New Zealand, there are three commercially available phosphite preparations, Agri-Fos 600, Phosgard, and Foschek. All previous studies have used Agri-Fos 600, so the first aim was to determine whether the particular formulation altered anti-oomycete activity. No significant difference was found between the 50% inhibitory concentrations (EC50 values) for the three formulations. Interestingly, however, formulating polygodial and falcarindiol with the surfactants and other non-phosphite ingredients of Foschek led to a significant increase in their inhibitory effects. The second aim of this thesis was to implement a serial passaging protocol for P. agathidicida and attempt to isolate mutants with increased resistance to phosphite, polygodial or falcarindiol. Serial passaging was carried out on amended agar plated with increasing concentrations of each chemical. However, even after 7 passages, over 16-18 weeks of growth, no mutants with increased resistance were isolated. This could be due to the complicated modes of action of the polygodial, falcarindioland phosphite, which makes it likely that several specific mutations are required to effect resistance. <br>IIOxathiapiprolin is a highly potent, new anti-oomycete agrichemical. It targets the Phytophthora oxysterol binding protein (OSBP) related protein (ORP1). Mutations in this protein are known to give oxathiapiprolin resistance in other species of Phytophthora; however, the P. agathidicida protein (PaORP1) has never been studied. In this work, the gene for PaORP1 was partially sequenced from five P. agathidicida isolates. None contained any of the known resistance mutations. A new protocol for expressing PaORP1 in E. coli and purifying it using immobilised metal affinity chromatography was also developed. After optimisation, this protocol yielded up to 30 mg of purified protein per litre of E. coli culture and is the first successful example of heterologously expressing and purifying any P. agathidicida protein. In future, this will allow the biomolecular interaction between PaORP1 and oxathiapiprolin to be studied in more detail. Overall, the work presented in this thesis assessed commercial formulations of phosphite, established a directed evolution protocol for studying resistance in P. agathidicida, and reported the first in vitro characterisation of a P. agathidicidaprotein. This research suggests that commercial formulation of plant-derived natural products may be a powerful new approach for combatting kauri dieback and, promisingly, also suggests that the risk of developing resistance to these compounds might be low.

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Characteristics ofEscherichia coliIsolated from Bovine Mastitis Exposed to Subminimum Inhibitory Concentrations of Cefalotin or Ceftazidime

BioMed Research International ◽

10.1155/2018/4301628 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Gang Liu ◽

Laidi Ding ◽

Bo Han ◽

Sofie Piepers ◽

S. Ali Naqvi ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Morphological Changes ◽

Bovine Mastitis ◽

Clinical Mastitis ◽

Powdered Infant Formula ◽

Formula Milk ◽

Extended Spectrum Beta Lactamase ◽

E Coli

Escherichia coliis a major udder pathogen causing clinical mastitis in dairy cattle and its heat stable endotoxin in powdered infant formula milk is a potential risk factor in neonatal infections. Cephalosporins are frequently used for treatment of mastitis caused by mastitis; however, use of these antimicrobials may induce antimicrobial resistance inE. coli. The objective of this study was to explore thein vitroeffect of subminimum inhibitory concentrations (sub-MIC) of cefalotin (CF) and ceftazidime (CAZ) on the morphology, antimicrobial resistance, and endotoxin releasing characteristics of 3E. coliisolates recovered from bovine clinical mastitis. The parentE. coliisolates, which were susceptible to CF and CAZ, were exposed to CF or CAZ separately at sub-MIC levels to produce 9 generations of induced isolates. Colonies of the CAZ-induced isolates from all 3 parentE. coliwere smaller on blood agar and the bacteria became filamentous, whereas the CF-induced isolates did not demonstrate prominent morphological changes. After induction by CF or CAZ, many induced isolates showed resistance to cefoxitin, CAZ, CF, kanamycin, ampicillin, and amoxicillin/clavulanic acid while their parent isolates were susceptible to these antimicrobials. Notably, 5 CAZ-induced isolates from the same parent isolate were found to produce extended-spectrum beta-lactamase (ESBL) though none of the tested ESBL related genes could be detected. All CAZ-induced isolates released more endotoxin with a higher release rate, whereas endotoxin release of CF-inducedE. coliisolates was not different from parent isolates. The exposure of cephalosporins at sub-MIC levels induced resistantEscherichia coli.We inferred that cephalosporins, especially CAZ, should be used prudently for treatment of clinicalE. colimastitis.

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In Vitro Analytical System for Determining the Ability of Antibiotics at Residue Levels to Select for Resistance in Bacteria

Journal of AOAC INTERNATIONAL ◽

10.1093/jaoac/71.2.295 ◽

1988 ◽

Vol 71 (2) ◽

pp. 295-298

Author(s):

Marietta Suebrady ◽

Robert J Strobel ◽

Stanley E Katz

Keyword(s):

Analytical Procedure ◽

Inhibitory Concentration ◽

Enteric Bacteria ◽

E Coli ◽

Resistant Population ◽

Test Organisms ◽

Residue Levels ◽

Analytical System ◽

Selection Of

Abstract An analytical procedure, based on the concept that exposure of bacteria to antibiotics will result in the selection of a resistant population, was developed. Two strains of enteric bacteria, Escherichia coli CS-1 and Enterobacter cloacae B520, which are sensitive to a wide variety of antibiotics, were used as the test organisms. E. coli CS-1 were exposed to 1.00 μg antibiotic or antimicrobial/mL; E. cloacae B520 were exposed to 0.01, 0.10, 0.50,1.00, and 5.00 μg/mL. Both organisms developed increased resistance to other antibiotics after exposure to chlortetracycline and oxytetracycline, as measured by the minimum inhibitory concentration (MIC). E. cloacae B520 showed increased resistance to ampicillin, oxytetracycline, and chloramphenicol after exposure to levels as low as 0.10 μg/mL. Exposure to streptomycin, sulfamethazine, tylosin, bacitracin, flavomycin, virginiamycin, and monensin at levels of 1.00 μg/mL did not increase the MIC. Exposure to 5.00 *tg streptomycin, sulfamethazine, tylosin, and monensin/mL increased the MIC ofE. cloacae to one of the antibiotic markers. These increased MICs exceeded the 95% confidence limits of the MIC values of the unexposed organisms.

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Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection

Microorganisms ◽

10.3390/microorganisms8060827 ◽

2020 ◽

Vol 8 (6) ◽

pp. 827 ◽

Cited By ~ 1

Author(s):

Ana Carolina M. Santos ◽

Rosa M. Silva ◽

Tiago B. Valiatti ◽

Fernanda F. Santos ◽

José F. Santos-Neto ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Bloodstream Infection ◽

Galleria Mellonella ◽

Multidrug Resistant ◽

Coli Strain ◽

Pathogenic Potential ◽

E Coli ◽

Antimicrobial Resistance Genes

Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.

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