Antimicrobial resistance in humans, livestock and the wider environment

Abstract

Antimicrobial resistance (AMR) in humans is inter-linked with AMR in other populations, especially farm animals, and in the wider environment. The relatively few bacterial species that cause disease in humans, and are the targets of antibiotic treatment, constitute a tiny subset of the overall diversity of bacteria that includes the gut microbiota and vast numbers in the soil. However, resistance can pass between these different populations; and homologous resistance genes have been found in pathogens, normal flora and soil bacteria. Farm animals are an important component of this complex system: they are exposed to enormous quantities of antibiotics (despite attempts at reduction) and act as another reservoir of resistance genes. Whole genome sequencing is revealing and beginning to quantify the two-way traffic of AMR bacteria between the farm and the clinic. Surveillance of bacterial disease, drug usage and resistance in livestock is still relatively poor, though improving, but achieving better antimicrobial stewardship on the farm is challenging: antibiotics are an integral part of industrial agriculture and there are very few alternatives. Human production and use of antibiotics either on the farm or in the clinic is but a recent addition to the natural and ancient process of antibiotic production and resistance evolution that occurs on a global scale in the soil. Viewed in this way, AMR is somewhat analogous to climate change, and that suggests that an intergovernmental panel, akin to the Intergovernmental Panel on Climate Change, could be an appropriate vehicle to actively address the problem.

Keywords: Intergovernmental Panel on Climate Change; biota; governance; phylogenetics; reservoirs; sequencing.

Figure 1.

Diagrammatic representation of the routes of transmission of AMR between farm animals, the wider environment and humans. Reprinted with permission from [4] (Credit: P. Huey/Science).

Figure 2.

Sales of antibiotics for veterinary use in Europe, 2005–2009, for third and fourth generation cephalosporins (purple) and fluoroquinolones (blue). Units are milligram per population correction unit (=1 kg). In 2006, an EU-wide ban on the use of antibiotics as growth promoters was introduced. Data from [10].

Figure 3.

Discrete traits analysis of S. aureus CC398. Adapted and reprinted with permission from [26]. (a) Frequency of host jumps between human and livestock populations. (i) Staphylococcus aureus CC398 core genome BEAST maximum clade credibility tree with discrete-trait mapping by host. Branches are coloured according to inferred ancestral host (human or livestock). (ii) The inferred number of transitions between human and livestock hosts across 9000 BEAST phylogeny samples are plotted (95% highest posterior density intervals and medians shown as horizontal lines). (b) Frequency of gain and loss of mecA, a determinant of methicillin resistance for S. aureus CC398. (i) Staphylococcus aureus CC398 core genome BEAST maximum clade credibility tree with discrete-trait mapping for presence or absence of mecA. Branches are coloured according to inferred ancestral state (mecA absent or present). (ii) The inferred number of gains (transitions from absence to presence of mecA) or losses (transitions from presence to absence of mecA) across 9000 BEAST phylogeny samples are plotted (95% highest posterior density intervals and medians shown as horizontal lines).