2.1.2 Different types of bacteria and their roles in AMR emergence

It is typical for animals to be exposed to bacteria in the environment. They also carry a substantial and diverse population of microbes on their skin and in their guts: the microbiota. The collection of all their genes is called the microbiome.

Bacteria can be classified as pathogenic or commensal. Some commensal bacteria can be opportunistic pathogens, causing disease when the immune system of the host is weakened. Some species of bacteria have both pathogenic and commensal strains.

Bacteria that can be transmitted between animals and humans and cause infection are called zoonotic bacteria and can cause zoonotic diseases in humans. Some zoonotic bacteria can be commensal in animals but pathogenic for humans, commensal in both, or pathogenic for both. Examples of these are illustrated in Table 1.

The digestive tracts of humans and animals contain thousands of millions of bacteria, most of them commensal. When antimicrobials are administered to animals, some of the commensal bacteria die. Certain commensal bacteria that are usually present in small numbers (such as Escherichia coli, Salmonella spp. or Campylobacter spp.) and that may contain resistance genes can survive and replicate, outnumbering the rest of the commensal bacteria, and becoming a dominant component of in the gut microbiota.

Both pathogenic and commensal bacteria can carry ARGs and can be transmitted to humans. Once resistant bacteria reach the human gut, resistance genes can be transferred between commensal and pathogenic bacteria. Commensal bacteria can act as significant reservoirs of AMR genes in the gut microbiome and the environment. Humans, animals and the environment can be reservoirs of resistant bacteria, which are themselves reservoirs of ARGs. Sources of resistant bacteria, residues and ARGs in the environment could be waste systems such as manure heaps, hospital or pharmaceutical plant waste, the soil and water courses (Toutain et al., 2016).

Note that a reservoir of AMR is defined as any component of a system that can contain resistant bacteria or ARGs.

The case of E. coli as commensal bacteria and indicator

Figure 6 Rod-shaped E. coli bacteria, taken using an electron microscope.

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A photograph of yellow rod-shaped bacteria on an uneven background.

Figure 6 Rod-shaped E. coli bacteria, taken using an electron microscope.

E. coli is considered a commensal zoonotic bacterium common to animals, humans and the environment, and commonly acquires AMR genes. Some of these genes control the production of an enzyme, called extended spectrum beta-lactamase (ESBL), that increases resistance to some antibiotics. This type of resistant E. coli is called ESBL-E. coli.

E. coli is usually a commensal for animals, but some strains may be pathogenic to humans. If those strains also have the ESBL enzyme, they will be much more difficult to treat. ESBL-E. coli has been used as a representative indicator organism, which means that its presence in different settings is monitored to give us an indication of the magnitude of the AMR problem.