Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics

Abstract

Background: Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. Objectives: To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the humanelivestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. Sources: Key articles investigating various aspects of AMR transmission at the humanelivestock interface are discussed, with a focus on Escherichia coli. Content: We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of welldesigned, high-resolution genome sequencing studies can improve our understanding of the human elivestock interface. Implications: A better understanding of the humanelivestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.

Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda

“…In addition, we encountered unanticipated resources (especially funding) required to explore the additional sites, including obtaining administrative and ethical clearance at the respective sites, materials and consumables, as well as other expenses. Third, although genomic data have been described as being better at providing closer insight into AMR transmission dynamics and acquisition, 34,47 we do not present these data, which could have affected our interpretation of AMR transmission dynamics and acquisition data.…”

“…32,33 The potential of using ESBL-PE from sewage as AMR detection markers that can then be used in monitoring and surveillance-particularly E. coli and K. pneumoniae-is supported by the fact that these are documented priority pathogens as a result of their widespread levels of AMR, distribution in the gastrointestinal tract of humans as well as animals, and involvement in the sharing of AMR gene carrying mobile genetic elements with other bacteria that are found in similar environments. 34,35 Regarding the abundance of ARB in the hospital environment (ward environment). Environmental sampling in our study revealed that hospital environments were mostly free of ARB except for the health-care worker handwashing sink, where these bacteria were isolated.…”

Landscape genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban city

“…The rapid expansion of urban environments into previously pristine or sparsely populated natural landscapes also increases the potential for greater contact between wildlife, humans and livestock which can provide conduits for microbiome sharing (14). Fundamental to whole genome sequencing studies is the availability of systematically sampled bacterial isolates obtained from humans, livestock and wildlife across overlapping geographical regions and time-frames, yet data are lacking (15). In this study, we sampled the bacterium Escherichia coli from humans, livestock and peri-domestic wildlife of 99 households and their environs across 33 sublocations in Nairobi, Kenya, in an epidemiologically structured study.…”

One Health: a multifaceted concept combining diverse approaches to prevent and control antimicrobial resistance

“…This special issue contains three reviews selected by the Scientific Committee of the 2nd ICOHAR to best represent the scientific perspective of the meeting. Each paper focuses on a specific feature of AMR prevention and control: surveillance [4], risk assessment [5] and alternative anti-infective strategies [6]. Nielsen et al [4] reviewed the strengths and weaknesses of three diverse tools for evaluating integrated AMR surveillance systems, providing guidance on how to choose a fit-for-purpose tool.…”

“…Nielsen et al [4] reviewed the strengths and weaknesses of three diverse tools for evaluating integrated AMR surveillance systems, providing guidance on how to choose a fit-for-purpose tool. Wee et al [5] highlighted the function of well-designed, high-resolution genome sequencing approaches to quantify transmission of AMR at the humaneanimal interface. Finally, Pollock et al [6] outlined the value of microbial and host genomics for developing alternative strategies for prevention and control of infectious diseases in livestock, namely microbiota modulation via faecal transplantation and probiotics, genetic manipulation of the host via selective breeding and gene editing, vaccines, antivirulence strategies and phage therapy.…”