1. About

Several comprehensive literature searches have been conducted to inform the IAM.AMR models. The first search was conducted in May of 2015, and was subsequently updated in June of 2016. A qualitative description of the included studies is available (see below).

As of May of 2019, the search is being repeated with a modified search string, designed to include addtional food-animal species and commodities, and additional bacterial species. Additionally, this search excludes human-related factors influencing resistance; human-related factors (e.g. AMU, immune status) will be identified in a seperate search at a later date.

1.1. Goal of the Literature Search

The goal of the literature search is to identify, from existing literature, factors that potentially influence antimicrobial resistance in the agri-food production system.

1.2. What is a ‘Factor’?

The general definition of a ‘factor’ is a “circumstance, fact, or influence that contributes to a result or outcome”. Similarly, the term ‘driver’ is defined as “a factor which causes a particular phenomenon to happen or develop”. Despite their near interchangeability, the terms ‘factor’ and ‘driver’ are often interpreted differently in an epidemiological context; the term ‘factor’ is used more loosely, while ‘driver’ is generally reserved for those ‘factors’ with a purported causative relationship with their outcome.

In the context of the IAM.AMR project, we have defined a ‘factor’ as a practice or circumstance which influences the occurrence of AMR. This is an intentionally broad definition that does not consider the concept of causality; we consider any relationship between an exposure and outcome as a factor, whether or not we can elucidate a causal pathway.

Tip

A factor may have a clear, causal relationship, like the relationship between antimicrobial use and resistance. A factor may also have a statistical relationship, but lack a clear causal relationship, like a purported relationship between vacuum packaging and resistance.

1.3. The 2015–16 Search

For a complete overview of the search strategy used in 2015–16, and a qualitative description of the captured literature, please see Murphy CP, Carson C, Smith BA, et al. Factors potentially linked with the occurrence of antimicrobial resistance in selected bacteria from cattle, chickens and pigs: A scoping review of publications for use in modelling of antimicrobial resistance (IAM.AMR Project). in Zoonoses and Public Health. 2018; 65:957–971. https://doi.org/10.1111/zph.12515.

The following extracts are provided by the authors:

1.3.1. Search strategy

Comprehensive literature search strings were developed and pretested in Medline to return records for both human and animal populations of (a) the frequency of antimicrobial use or resistance (results not presented) and (b) the factors potentially associated with antimicrobial use or resistance (results presented herein; Appendix 1). The characterization of associations was broad and was not limited to interpretations of statistical significance, but included non-significant, causal and correlative relationships, or possible spurious findings. The searches included multiple broad and specific search terms for antimicrobial susceptibility, antimicrobial use, and population (animal or human), and specific search terms for Campylobacter species, E. coli, and S. enterica, and searches were not limited to a particular study design (e.g., observational, experimental, field trials, mathematical models). Following the pre-test, Medline and three other databases were searched as follows: Agricola, Centre for Agriculture and Bioscience, and Cumulative Index to Nursing and Allied Health Literature, using database‐specific search strings adapted from the initial pretested Medline search string.

1.3.2. Search string

((((Antimicrobial[Title/Abstract] OR Antibiotic[Title/Abstract]) AND (Resistance[Title/Abstract] OR Susceptibility[Title/Abstract])) AND (Blactam$[ All Fields] OR (“cephalosporins”[MeSH Terms] OR “cephalosporins”[All Fields] OR “cephalosporin”[All Fields]) OR (“tetracycline”[MeSH Terms] OR “tetracycline”[All Fields]) OR (“quinolones”[MeSH Terms] OR “quinolones”[All Fields] OR “quinolone”[All Fields]) OR (“fluoroquinolones”[MeSH Terms] OR “fluoroquinolones”[All Fields] OR “fluoroquinolone”[All Fields]) OR (“macrolides”[MeSH Terms] OR “macrolides”[All Fields] OR “macrolide”[All Fields]) OR (“nalidixic acid”[MeSH Terms] OR (“nalidixic”[All Fields] AND “acid”[All Fields]) OR “nalidixic acid”[All Fields]) OR (“ciprofloxacin”[MeSH Terms] OR “ciprofloxacin”[All Fields] OR (“enrofloxacin” [MeSH Terms] OR “enrofloxacin” [All Fields])))) AND (cow$[Title/Abstract] OR cattle[Title/Abstract] OR beef[Title/Abstract] OR dairy[Title/Abstract] OR pig$[Title/Abstract] OR sow$[Title/ Abstract] OR piglet$[Title/Abstract] OR pork[Title/Abstract] OR chicken$[Title/Abstract] OR broiler$[Title/Abstract] OR chick$[Title/ Abstract] OR horse$[Title/Abstract] OR turkey$ss[Title/Abstract] OR human$[Title/Abstract] OR foal$[Title/Abstract] OR cat$[Title/ Abstract] OR dog$[Title/Abstract] OR sheep[Title/Abstract] OR lamb$[Title/Abstract] OR goat$[Title/Abstract] OR fish[Title/Abstract] OR rabbit$[Title/Abstract] OR people[Title/Abstract] OR adult$[Title/ Abstract] OR children[Title/Abstract] OR kid$[Title/Abstract])) AND (E. coli[Title/Abstract] OR Escherichia coli [Title/Abstract] OR Salmonella[Title/Abstract] OR Campylobacter[Title/Abstract])

1.4. The 2019 Search

The 2019 search is currently in progress. Please find the instructions for reviewers below.

1.4.1. Search strategy

To Be Updated.

1.4.2. Search string

To Be Updated.

1.4.3. Scope

To reduce the scope of the project to a manageable size, the three most common food-animal species and the three most commonly isolated enteric bacteria from those species were selected as the core areas of focus. These include chicken, cattle, and swine, and E. coli, Salmonella Spp. and Campylobacter Spp. for host species and bacterial species respectively. While the primary human exposure route is assumed to be consumption of the corresponding agri-food products (chicken, beef, and pork), additional focus has been placed on environmental exposure routes (e.g. through the consumption of leafy greens or root vegetables, grown in manure-amended soils).

Additional food-animal and bacterial species of interest include turkeys and Enterococcus Spp., which may be explored later as the project progresses.

1.5. Scope

The iAM.AMR project focuses on four [food-animal species | commodities]:

• broiler chicken | chicken
• swine | pork
• dairy cattle or beef cattle | beef
• turkey | turkey

The iAM.AMR project focuses on four microbes:

• E.coli
• Salmonella Spp.
• Campylobacter Spp.
• Enterococcus Spp.

The iAM.AMR project focuses on resistance to drugs of human importance, including:

• macrolides
• tetracyclines
• fluoroquinolones
• third-generation cephalosporins