A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage.
Ontology highlight
ABSTRACT:
SUBMITTER: AbuOun M
PROVIDER: S-EPMC8627209 | biostudies-literature | 2021 Oct
REPOSITORIES: biostudies-literature
Publications
A genomic epidemiological study shows that prevalence of antimicrobial resistance in <i>Enterobacterales</i> is associated with the livestock host, as well as antimicrobial usage.
AbuOun Manal M Jones Hannah H Stubberfield Emma E Gilson Daniel D Shaw Liam P LP Hubbard Alasdair T M ATM Chau Kevin K KK Sebra Robert R Peto Tim E A TEA Crook Derrick W DW Read Daniel S DS Gweon H Soon HS Walker A Sarah AS Stoesser Nicole N Smith Richard P RP Anjum Muna F MF On Behalf Of The Rehab Consortium
Microbial genomics 20211001 10
Similar Datasets
Project description:Senecavirus A (SVA) infection was recently confirmed in pigs in Brazil, United States of America and Canada. To better understand the molecular characteristics of isolated SVA genomes, we first reported genome-wide comprehensive analyses of codon usage and various factors that have contribute to the molecular evolution in SVA. The effective number of codons (ENC) ranged from 54.51 to 55.54 with an average of 54.87 ± 0.285, which reveals a relatively stable nucleotide composition. We found that codon usage bias of the SVA was low. Mutational pressure acted as an increasingly dominant factor for the evolution of the virus compared with the natural selection. Notably, codon usage bias was also affected by the geographic distribution and isolated time. The first systemic analysis on the codon usage bias of the SVA provides important information for the understanding of the evolution of the SVA and has fundamental and theoretical benefits.
| S-EPMC7172466 | biostudies-literature
Project description:IntroductionThere are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections is becoming harder in humans and animals. The aim of this study was to evaluate factors, including usage, that affect antimicrobial resistance (AMR) on farm over time.MethodsA population of 14 cattle, sheep and pig farms within a defined area of England were sampled three times over a year to collect data on AMR in faecal Enterobacterales flora; AMU; and husbandry or management practices. Ten pooled samples were collected at each visit, with each comprising of 10 pinches of fresh faeces. Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes.ResultsSheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. AMR genes were detected persistently across pig farms at all visits, even on farms with low AMU, whereas AMR bacteria was consistently lower on cattle farms than pigs, even for those with comparably high AMU. MDR bacteria was also more commonly detected on pig farms than any other livestock species.DiscussionThe results may be explained by a complex combination of factors on pig farms including historic AMU; co-selection of AMR bacteria; variation in amounts of antimicrobials used between visits; potential persistence in environmental reservoirs of AMR bacteria; or importation of pigs with AMR microbiota from supplying farms. Pig farms may also be at increased risk of AMR due to the greater use of oral routes of group antimicrobial treatment, which were less targeted than cattle treatments; the latter mostly administered to individual animals. Also, farms which exhibited either increasing or decreasing trends of AMR across the study did not have corresponding trends in their AMU. Therefore, our results suggest that factors other than AMU on individual farms are important for persistence of AMR bacteria on farms, which may be operating at the farm and livestock species level.
| S-EPMC10043416 | biostudies-literature
Project description:Antimicrobial resistance is a global health concern; Enterobacterales resistant to third-generation cephalosporins (3GCs) and carbapenems are of the highest priority. Here, we conducted genome sequencing and standardized quantitative antimicrobial susceptibility testing of 4,195 isolates of Escherichia coli and Klebsiella pneumoniae resistant to 3GCs and Enterobacterales with reduced meropenem susceptibility collected across Japan. Our analyses provided a complete classification of 3GC resistance mechanisms. Analyses with complete reference plasmids revealed that among the blaCTX-M extended-spectrum β-lactamase genes, blaCTX-M-8 was typically encoded in highly similar plasmids. The two major AmpC β-lactamase genes were blaCMY-2 and blaDHA-1. Long-read sequencing of representative plasmids revealed that approximately 60% and 40% of blaCMY-2 and blaDHA-1 were encoded by such plasmids, respectively. Our analyses identified strains positive for carbapenemase genes but phenotypically susceptible to carbapenems and undetectable by standard antimicrobial susceptibility testing. Systematic long-read sequencing enabled reconstruction of 183 complete plasmid sequences encoding three major carbapenemase genes and elucidation of their geographical distribution stratified by replicon types and species carrying the plasmids and potential plasmid transfer events. Overall, we provide a blueprint for a national genomic surveillance study that integrates standardized quantitative antimicrobial susceptibility testing and characterizes resistance determinants.
| S-EPMC10698200 | biostudies-literature
Project description:BackgroundAntimicrobial resistance is one of the great challenges facing global health security in the modern era. Wildlife, particularly those that use urban environments, are an important but understudied component of epidemiology of antimicrobial resistance. We investigated antimicrobial resistance overlap between sympatric wildlife, humans, livestock, and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant antimicrobial resistance.Methods99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (ie, the household and its perimeter; n=849), 13 livestock species (n=656), and humans (n=333), and from the external environment (n=288). Escherichia coli, our sentinel organism, was cultured and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of antimicrobial resistant phenotypes was compared between urban wildlife, humans, livestock, and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of antimicrobial resistant phenotypes and multidrug-resistant E coli carriage in urban wildlife is linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of antimicrobial resistance between humans, wildlife, and livestock.FindingsE coli were isolated from 485 samples collected from wildlife between Sept 6,2015, and Sept 28, 2016. Wildlife carried a low prevalence of E coli isolates susceptible to all antibiotics tested (45 [9%] of 485 samples) and a high prevalence of clinically relevant multidrug resistance (252 [52%] of 485 samples), which varied between taxa and by foraging traits. Multiple isolates were resistant to one agent from at least seven antimicrobial classes tested for, and a single isolate was resistant to all antibiotics tested for in the study. The phenotypic diversity of antimicrobial-resistant E coli in wildlife was lower than in livestock, humans, and the environment. Within household compounds, statistical models identified two interfaces for exchange of antimicrobial resistance: between both rodents, humans and their rubbish, and seed-eating birds, humans and their rubbish; and between seed-eating birds, cattle, and bovine manure.InterpretationUrban wildlife carry a high burden of clinically relevant antimicrobial-resistant E coli in Nairobi, exhibiting resistance to drugs considered crucial for human medicine by WHO. Identifiable traits of the wildlife contribute to this exposure; however, compared with humans, livestock, and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that wildlife are a net sink rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock, and both human and livestock waste within households, are exposed to more antimicrobial resistant phenotypes, and could therefore act as conduits for the dissemination of clinically relevant antimicrobial resistance to the wider environment. These results provide novel insight into the broader epidemiology of antimicrobial resistance in complex urban environments, characteristic of lower-middle-income countries.FundingUK Medical Research Council and CGIAR Research Program on Agriculture for Nutrition and Health.
| S-EPMC6630895 | biostudies-literature
Project description: Not available
| S-EPMC7443702 | biostudies-literature
Project description:BackgroundPrevalence surveys are useful tools for assessing the appropriateness of antimicrobial therapy.ObjectivesThe primary objective was to assess patterns of antimicrobial utilization and appropriateness in New Brunswick hospitals. The secondary objective was to assess the impact of hospital size and the presence of a penicillin allergy label on antimicrobial appropriateness.MethodsA point prevalence survey was conducted of inpatients taking 1 or more systemic antimicrobials during admission to hospitals in New Brunswick. A structured protocol and web-based data collection tool (National Antimicrobial Prescribing Survey) were used for this survey. Data regarding hospital size and presence of a penicillin allergy label were also collected. Antimicrobial utilization was assessed in terms of guideline compliance and appropriateness. Results were summarized descriptively. A χ2 analysis was performed to describe secondary outcomes.ResultsTen hospitals participated, and a total of 2200 patients were admitted at the time of the survey. The overall prevalence of antimicrobial use was 22.7% (500/2200). A total of 648 antimicrobials were ordered. The most frequently prescribed antimicrobials by class were first-generation cephalosporins (14.0%, 91/648), third-generation cephalosporins (11.3%, 73/648), and piperacillin-tazobactam (10.2%, 66/648). The most common indications for antimicrobial therapy were respiratory tract infections (27.3%, 177/648), urinary tract infections (12.2%, 79/648), and intra-abdominal infections (11.4%, 74/648). Compliance with local or regional treatment guidelines, where applicable, was 66.2% (188/284). Provincially, 68.1% (441/648) of the antimicrobial orders were deemed appropriate. Larger centres had substantially higher rates of appropriateness (p < 0.001). The presence of a penicillin allergy label had no impact on appropriateness (p = 0.21).ConclusionsSeveral opportunities for targeted interventions were identified to improve antimicrobial prescribing, including decreasing the use of broad-spectrum antimicrobials, increasing guideline compliance, and ensuring documentation of antimicrobial duration by prescribers.
| S-EPMC8956466 | biostudies-literature
Project description:Antimicrobial resistance (AMR) is a current public health issue globally. To counter this phenomenon and prioritize AMR in the health sector, the World Health Organization (WHO) published a list of bacterial pathogens against which the development of new antimicrobial agents is urgently needed, designating the ESKAPE pathogens (i.e., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) with a 'priority status'. Moreover, the One Health High Level Expert Panel (OHHLEP) states that human health is closely linked to animal and environmental health, thus promoting a holistic One Health approach in order to be prepared to address possible emerging health threats from the human-animal-environment interface. Wild birds may host and spread pathogens, integrating the epidemiology of infectious diseases. The aim of this study was to examine the role of wild birds as a source of ESKAPE bacteria and other antibiotic-resistant enterobacterales. A total of fifty strains within the ESKAPE group were detected in 40/163 cloacal samples of examined birds (24.5%). Additionally, different strains of enterobacterales were detected in 88/163 cloacal samples (53.9%). Isolated strains exhibited antimicrobial resistance, including towards critically important antibiotics (e.g., third, fourth, fifth generation cephalosporins, fluoroquinolones) for human medicine. Our results confirm that wild birds are potential reservoirs of several pathogens and antimicrobial-resistant bacteria and that they could be involved in the dissemination of those bacteria across different environments, with resulting public health concerns.
| S-EPMC9774818 | biostudies-literature
Project description: Not available
| S-EPMC10817951 | biostudies-literature
Project description:Reducing antimicrobial use (AMU) in livestock is requested by Public Health authorities. Ideally, this should be achieved without jeopardizing production output or animal health and welfare. Thus, efficient measures must be identified and developed to target drivers of AMU. Veterinarians play a central role in the identification and implementation of such efficient interventions. Sixty-seven veterinarians with expertise in livestock production in Denmark, Portugal, and Switzerland participated in an expert opinion study aimed at investigating experiences and opinions of veterinarians about the driving forces and practices related to AMU in the main livestock sectors (broiler, dairy cattle, fattening/veal calf, and pig industry) of the aforementioned countries. Opinions on potential factors influencing the choice of antimicrobials and opportunities to reduce AMU were collected. Antibiograms are seldom used, mainly due to the time lag between testing and obtaining the results. The perceived percentage of treatment failures varied between countries and livestock sectors; however, little changes were reported over time (2005-2015). The animal health problems of each livestock sector most frequently leading to AMU did not vary substantially between countries. Mandatory official interventions (i.e., binding measures applied by national or international authorities) were highlighted as having the biggest impact on AMU. There was a variation in the experts' opinion regarding feasibility and impact of interventions both between countries and livestock sectors. Nevertheless, improved biosecurity and education of veterinarians frequently received high scores. Most veterinarians believed that AMU can be reduced. The median potential reduction estimates varied from 1% in Swiss broilers to 50% in Portuguese broilers and veal/fattening calves in all countries. We hypothesize that the differences in views could be related to disease epidemiology, animal husbandry, and socio-economic factors. A profound investigation of these disparities would provide the required knowledge for developing targeted strategies to tackle AMU and consequently resistance development. However, experts also agreed that mandatory official interventions could have the greatest impact on antimicrobial consumption. Furthermore, improvement of biosecurity and education of veterinarians, the use of zinc oxide (in pigs), improving vaccination strategies, and the creation of treatment plans were the measures considered to have the largest potential to reduce AMU. This paper can inform policymakers in Europe and countries with a similar animal production regarding their AMU policy.
| S-EPMC5837977 | biostudies-literature
Project description:BackgroundAntimicrobial usage in food producing animals is of major concern. A clear link between the extent of use and the development of antimicrobial resistance has already been demonstrated. To evaluate strategies that may reduce the antimicrobial usage while assuring pig health and welfare, it requires profound knowledge of factors that are associated with antimicrobial usage. Data on biosecurity and herd management practices are important parameters to identify risk factors which are related to a higher antimicrobial usage. To investigate between-farm variations of high and low usage the treatment incidence (TI) per age group in 60 German farrow-to-finish herds was qualitatively and quantitatively analysed and linked to biosecurity measures, and herd management characteristics.ResultsWeaned pigs received most of the treatments (median TI = 487.6), followed by suckling pigs (median TI = 138.9). Suckling pigs were treated with critically important antimicrobials (3rd and 4th generation cephalosporines) to a remarkable extent. The number of sows present at site (p < 0.01) and a low score for external biosecurity (p = 0.06) were associated with a higher antimicrobial usage in pigs from birth till slaughter. Herds with a higher treatment incidence in growing pigs (TI 200 days): i) were located in a region with a high pig density (p < 0.01), ii) had a less strict access check for visitors and personnel (p < 0.01) and iii) scored lower in the subcategory 'cleaning and disinfection' (internal biosecurity) (p < 0.01). Herds with a higher treatment incidence in breeding pigs weaned more piglets per sow and year and scored better in the internal biosecurity level (p = 0.02).ConclusionsWith the main focus on the treatment incidence in pigs from birth till slaughter and in breeding pigs risk factors for a high usage in these age groups were identified. The level of biosecurity of a herd was associated with the amount of antimicrobials used. Therefore, the findings in this study indicate possible points of action in the reduction and prudent use of antimicrobials in Germany. The active improvement of biosecurity measures could be a promising alternative to reduce antimicrobial usage on herd level.
| S-EPMC6293545 | biostudies-literature