scholarly journals A Bayesian latent class mixture model with censoring for correlation analysis in antimicrobial resistance across populations

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Min Zhang ◽  
Chong Wang ◽  
Annette M. O’Connor
Keyword(s):  
Antimicrobial Resistance ◽  
Mixture Model ◽  
Latent Class ◽  
National Level ◽  
Resistant Bacteria ◽  
Human Populations ◽  
Concentration Data ◽  
Animal Populations ◽  
Surveillance Programs ◽  
And Control

Abstract Background The emergence of antimicrobial resistance across populations is a global threat to public health. Surveillance programs often monitor human and animal populations to evaluate trends of emergence in these populations. Many national level antibiotic resistance surveillance programs quantify the proportion of resistant bacteria as a means of monitoring emergence and control measures. The reason for monitoring these different populations are many, including interest in similar changes in resistance which might provide insight into emergence and control options. Methods In this research, we developed a method to quantify the correlation in antimicrobial resistance across populations, for the conventionally unnoticed mean shift of the susceptible bacteria. With the proposed Bayesian latent class mixture model with censoring and multivariate normal hierarchy, we address several challenges associated with analyzing the minimum inhibitory concentration data. Results Application of this approach to the surveillance data from National Antimicrobial Resistance Monitoring System led to a detection of positive correlation in the central tendency of azithromycin resistance of the susceptible populations from Salmonella serotype Typhimurium across food animal and human populations. Conclusions Our proposed approach has been shown to be accurate and superior to the commonly used naïve estimation by simulation studies. Further implementation of this Bayesian model could serve as a useful tool to indicate the co-existence of antimicrobial resistance, and potentially a need of clinical intervention.

scholarly journals A Bayesian Latent Class Mixture Model With Censoring for Correlation Analysis in Antimicrobial Resistance Across Populations

2020 ◽  
Author(s):  
Min Zhang ◽  
Chong Wang ◽  
Annette O'Connor
Keyword(s):  
Antimicrobial Resistance ◽  
Mixture Model ◽  
Latent Class ◽  
National Level ◽  
Resistant Bacteria ◽  
Human Populations ◽  
Concentration Data ◽  
Animal Populations ◽  
Surveillance Programs ◽  
And Control

Abstract Background: The emergence of antimicrobial resistance across populations is a global threat to public health. Surveillance programs often monitor human and animal populations to evaluate trends of emergence in these populations. Many national level antibiotic resistance surveillance programs quantify the proportion of resistant bacteria as a means of monitoring emergence and control measures. The reason for monitoring these different populations are many, including interest in similar changes in resistance which might provide insight into emergence and control options. Methods: In this research, we developed a method to quantify the correlation in antimicrobial resistance across populations, for the conventionally unnoticed mean shift of the susceptible bacteria. With the proposed Bayesian latent class mixture model with censoring and multivariate normal hierarchy, we address several challenges associated with analyzing the minimum inhibitory concentration data. Results: Application of this approach to the surveillance data from National Antimicrobial Resistance Monitoring System led to a detection of positive correlation in the central tendency of azithromycin resistance of the susceptible populations from Salmonella serotype Typhimurium across food animal and human populations. Conclusions: Our proposed approach has been shown to be accurate and superior to the naïve frequentist estimation by simulation studies. Further implementation of this Bayesian model could serve as a useful tool to indicate the co-existence of antimicrobial resistance, and potentially a need of clinical intervention.

scholarly journals CON: COVID-19 will not result in increased antimicrobial resistance prevalence

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Peter Collignon ◽  
John J Beggs
Keyword(s):  
Antimicrobial Resistance ◽  
Infection Prevention ◽  
Developed Countries ◽  
International Travel ◽  
Infection Prevention And Control ◽  
Resistant Bacteria ◽  
Healthcare Facilities ◽  
Factors Associated ◽  
Resistance Rates ◽  
And Control

Abstract Antimicrobial resistance (AMR) is affected by many factors, but too much of our focus has been on antimicrobial usage. The major factor that drives resistance rates globally is spread. The COVID-19 pandemic should lead to improved infection prevention and control practices, both in healthcare facilities and the community. COVID-19 will also have ongoing and profound effects on local, national and international travel. All these factors should lead to a decrease in the spread of resistant bacteria. So overall, COVID-19 should lead to a fall in resistance rates seen in many countries. For this debate we show why, overall, COVID-19 will not result in increased AMR prevalence. But globally, changes in AMR rates will not be uniform. In wealthier and developed countries, resistance rates will likely decrease, but in many other countries there are already too many factors associated with poor controls on the spread of bacteria and viruses (e.g. poor water and sanitation, poor public health, corrupt government, inadequate housing, etc.). In these countries, if economies and governance deteriorate further, we might see even more transmission of resistant bacteria.

scholarly journals An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

2011 ◽  
Vol 279 (1733) ◽  
pp. 1630-1639 ◽  
Author(s):  
Alison E. Mather ◽  
Louise Matthews ◽  
Dominic J. Mellor ◽  
Richard Reeve ◽  
Matthew J. Denwood ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Ecological Approach ◽  
Human Populations ◽  
Ecological Diversity ◽  
Animal Population ◽  
Current Policy ◽  
Animal Populations ◽  
Two Populations ◽  
Animal Isolates

We examined long-term surveillance data on antimicrobial resistance (AMR) in Salmonella Typhimurium DT104 (DT104) isolates from concurrently sampled and sympatric human and animal populations in Scotland. Using novel ecological and epidemiological approaches to examine diversity, and phenotypic and temporal relatedness of the resistance profiles, we assessed the more probable source of resistance of these two populations. The ecological diversity of AMR phenotypes was significantly greater in human isolates than in animal isolates, at the resolution of both sample and population. Of 5200 isolates, there were 65 resistance phenotypes, 13 unique to animals, 30 unique to humans and 22 were common to both. Of these 22, 11 were identified first in the human isolates, whereas only five were identified first in the animal isolates. We conclude that, while ecologically connected, animals and humans have distinguishable DT104 communities, differing in prevalence, linkage and diversity. Furthermore, we infer that the sympatric animal population is unlikely to be the major source of resistance diversity for humans. This suggests that current policy emphasis on restricting antimicrobial use in domestic animals may be overly simplistic. While these conclusions pertain to DT104 in Scotland, this approach could be applied to AMR in other bacteria–host ecosystems.

scholarly journals Assessing Transmission of Antimicrobial-ResistantEscherichia coliin Wild Giraffe Contact Networks

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
Elizabeth A. Miller ◽  
Timothy J. Johnson ◽  
George Omondi ◽  
Edward R. Atwill ◽  
Lynne A. Isbell ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Wild Animal ◽  
Anthropogenic Sources ◽  
Resistant Bacteria ◽  
Wild Animals ◽  
Natural Ecosystems ◽  
Content Type ◽  
E Coli ◽  
Animal Populations

ABSTRACTThere is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistantEscherichia coliin wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistantE. colibetween giraffe. Of 195 giraffe sampled, only 5.1% harboredE. coliisolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistantE. coli, but this relationship was likely driven by a correlation between an individual’s social connectedness and age. Indeed, resistantE. coliwas most frequently detected in socially isolated neonates, indicating that resistantE. colimay have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCEAntimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems.

scholarly journals Endolysin, a Promising Solution against Antimicrobial Resistance

Antibiotics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1277
Author(s):  
Mujeeb ur Rahman ◽  
Weixiao Wang ◽  
Qingqing Sun ◽  
Junaid Ali Shah ◽  
Chao Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
High Efficiency ◽  
High Specificity ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Effective Prevention ◽  
Rapid Action ◽  
Promising Solution ◽  
Pathogen Diagnosis ◽  
And Control

Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.

scholarly journals Successful Prevention of Antimicrobial Resistance in Animals—A Retrospective Country Case Study of Sweden

Antibiotics ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 129
Author(s):  
Martin Wierup ◽  
Helene Wahlström ◽  
Björn Bengtsson
Keyword(s):  
Antimicrobial Resistance ◽  
National Level ◽  
Antibiotic Use ◽  
Eu Member States ◽  
Fundamental Factor ◽  
Endemic Diseases ◽  
Country Case Study ◽  
Access To Data ◽  
And Control

The misuse and overuse of antibiotics have resulted in an alarmingly high prevalence of antimicrobial resistance (AMR) in human and animal bacteria. European monitoring programmes show that AMR occurrence in food animals is lower in Sweden than in most other EU Member States and that the use of antibiotics for animals is among the lowest in Europe. In this retrospective country case study, we analysed published documents to identify factors contributing to this favourable situation. A fundamental factor identified was early insight into and sustained awareness of the risks of AMR and the need for the prudent use of antibiotics. Early and continuous access to data on antibiotic use and AMR made it possible to focus activities on areas of concern. Another factor identified was the long-term control and eradication of infectious animal diseases, including coordinated activities against endemic diseases, which reduced the need to use antibiotics. Structures and strategies for that purpose established at the national level have since proven useful in counteracting AMR as an integral part of disease prevention and control, guided by a “prevention is better than cure” approach. A third factor identified was consensus among stakeholders on the need to address AMR and their cooperation in the design and implementation of measures.

scholarly journals The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli

2020 ◽  
Vol 8 (4) ◽  
pp. 568 ◽  
Author(s):  
Lara Pérez-Etayo ◽  
David González ◽  
Ana Isabel Vitas
Keyword(s):  
Antimicrobial Resistance ◽  
Associated Factors ◽  
Wastewater Treatment Plants ◽  
Hospital Environment ◽  
Resistant Bacteria ◽  
E Coli ◽  
Extended Spectrum ◽  
Surveillance Programs ◽  
Reported Data ◽  
Good Environment

One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10−1 ± 5 × 10−1, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10−4 ± 2.85 × 10−4 and 9.61 × 10−4 ± 1.96 × 10−3, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.

scholarly journals Occurrence and antimicrobial resistance of enterococci isolated from goat’s milk

2021 ◽  
Vol 65 (4) ◽  
pp. 449-455
Author(s):  
Marlena Gołaś-Prądzyńska ◽  
Jolanta G. Rola
Keyword(s):  
Antimicrobial Resistance ◽  
Food Chain ◽  
Antimicrobial Agents ◽  
Bacterial Flora ◽  
Resistant Bacteria ◽  
Human Populations ◽  
Milk Samples ◽  
Goat’S Milk ◽  
Route Of Transmission ◽  
Goat's Milk

Abstract Introduction Enterococci are widespread, being part of the bacterial flora of humans and animals. The food chain can be therefore considered as the main route of transmission of antibiotic resistant bacteria between the animal and human populations. Milk in particular represents a source from which resistant bacteria can enter the human food chain. The aim of the study was to determine the occurrence and resistance to antimicrobial agents of Enterococcus spp. strains isolated from raw goat’s milk samples. Material and Methods A total of 207 goat’s milk samples were collected. Samples were cultivated on selective media and confirmed as E. faecium or E. faecalis and screened for selected resistance genes by PCR. Drug susceptibility determination was performed by microdilution on Sensititre EU Surveillance Enterococcus EUVENC Antimicrobial Susceptibility Testing (AST) Plates and Sensititre US National Antimicrobial Resistance Monitoring System Gram Positive CMV3AGPF AST Plates. Results Enterococcal strains totalling 196 were isolated, of which 40.8% were E. faecalis and 15.3% were E. faecium. All tested isolates were susceptible to linezolid, penicillin and tigecycline. For most other antimicrobials the prevalence of resistance was 0.5–6.6% while high prevalence of quinupristin/dalfopristin (51.5%), tetracycline (30%) and lincomycin (52%) resistance was observed. Conclusion This study affords better knowledge concerning the safety of raw goat’s milk in terms of the enterococci possible to isolate from this foodstuff. It seems that enterococci in milk are still mostly susceptible to antimicrobials of major concern as multiply resisted drugs, such as gentamycin and vancomycin. However, the presence of multi-resistant strains in goat milk is cause for apprehension.

scholarly journals A hierarchical Bayesian latent class mixture model with censorship for detection of linear temporal changes in antibiotic resistance

2019 ◽  
Author(s):  
Min Zhang ◽  
Chong Wang ◽  
Annette O’Connor
Keyword(s):  
Public Health ◽  
Mixture Model ◽  
Latent Variables ◽  
Latent Class ◽  
Temporal Changes ◽  
Right Censoring ◽  
Hierarchical Bayesian ◽  
Resistant Population ◽  
Surveillance Programs ◽  
The Mean

AbstractIdentifying and controlling the emergence of antimicrobial resistance (AMR) is a high priority for researchers and public health officials. One critical component of this control effort is timely detection of emerging or increasing resistance using surveillance programs. Currently, detection of temporal changes in AMR relies mainly on analysis of the proportion of resistant isolates based on the dichotomization of minimum inhibitory concentration (MIC) values. In our work, we developed a hierarchical Bayesian latent class mixture model that incorporates a linear trend for the mean log2MIC of the non-resistant population. By introducing latent variables, our model addressed the challenges associated with the AMR MIC values, compensating for the censored nature of the MIC observations as well as the mixed components indicated by the censored MIC distributions. Inclusion of linear regression with time as a covariate in the hierarchical structure allowed modelling of the linear creep of the mean log2MIC in the non-resistant population. The hierarchical Bayesian model was accurate and robust as assessed in simulation studies. The proposed approach was illustrated using Salmonella enterica I,4,[5],12:i:- treated with chloramphenicol and ceftiofur in human and veterinary samples, revealing some significant linearly increasing patterns from the applications. Implementation of our approach to the analysis of an AMR MIC dataset would provide surveillance programs with a more complete picture of the changes in AMR over years by exploring the patterns of the mean resistance level in the non-resistant population. Our model could therefore serve as a timely indicator of a need for antibiotic intervention before an outbreak of resistance, highlighting the relevance of this work for public health. Currently, however, due to extreme right censoring on the MIC data, this approach has limited utility for tracking changes in the resistant population.

scholarly journals A review of antimicrobial resistance in imported foods

2021 ◽  
Author(s):  
Dongyun Jung ◽  
Beverly J Morrison ◽  
Joseph E. Rubin
Keyword(s):  
Antimicrobial Resistance ◽  
Food Products ◽  
International Travel ◽  
Resistant Bacteria ◽  
New Delhi ◽  
Medical Sciences ◽  
Potential Source ◽  
Surveillance Programs ◽  
Imported Foods

Antimicrobial resistance is one of the most serious threats to the medical sciences. The food supply is recognized as a potential source of resistant bacteria, leading to the development of surveillance programs targeting primarily poultry, pork and beef. These programs are limited in scope not only in the commodities tested, but also in the organisms targeted (Escherichia coli, Salmonella and Campylobacter); consequently, neither the breadth of food products available nor the organisms which may harbour clinically relevant and/or mobile resistance genes are identified. Furthermore, there is an inadequate understanding of how the international trade in food products contributes to the global dissemination of resistance. This is despite the recognized role of international travel in dissemination disseminating antimicrobial-resistant organisms (ARO), notably the New Delhi Metallo-betalactamase. An increasing number of studies describing ARO in a variety of imported foods will be summarized in this review.

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