The discovery of antibiotics was a milestone for the advancement of medicine throughout the world. Infections with pathogenic bacteria were causing severe diseases and several deadly epidemics before the diffusion of antibiotics. Furthermore, progress in modern medicine has been assured through the capacity to control infections in clinical settings. Without effective antimicrobials, modern medicine is at risk: minor and major surgeries, cancer chemotherapy, and transplants are all dependent on antimicrobials to prevent and treat infection in immunosuppressed patients. It has been estimated that up to 10 million people could die by 2050 due to the failure of antimicrobial treatments. Here, poorly treated bacterial infections can lead to failures of different organ systems, particularly in fragile patients, and excessive immune-mediated inflammatory responses during sepsis may occur more frequently https://www.sepsis.org/power-the-amrevolution/ (accessed on 3 November 2023). As in many other fields, the problems of AMR diffusion are often due to disequilibrium caused by human activity in the natural environment in which bacteria can immediately adapt due to their high genome plasticity. The prevalence and sometimes very rapid diffusion of MDR is largely due to the inappropriate use of drugs not only for clinical treatment in animals and humans but also for other purposes. Antibiotics were used in the past as growth promoters for livestock to increase food production and profit. Although this practice is now illegal in many countries, it is possible that this practice may be still be in place in some countries due to a lack of appropriate controls by public authorities. Antibiotic consumption is a key driver of antibiotic resistance. Antibiotics are often inappropriately prescribed for viral infections such as colds and influenza. The quantity and quality of antibiotic prescribing differs greatly among countries. For instance, a greater prevalence of resistant microorganisms exists in southern European countries where the amount of antibiotic consumption is about three times higher than in Scandinavian countries or the Netherlands ^[1]. After decades of antibiotic misuse, the result is that resistance is a huge problem for public health worldwide, as underlined by major international health organizations for humans and animals such as the WHO, FAO, and WOAH.

2. Antibiotics’ Primary Targets and Resistance Mechanisms

The discovery of penicillin in 1928 represented one of the great milestones in human medicine after centuries of periodically deadly epidemics due to bacterial infections amplified by wars, poverty, and poor hygienic conditions. Over time, antibiotics became very popular for their efficacy, specificity, and relatively low cost. Although some resistance was always possible, antibiotics were considered innocuous for humans and animals because their specific targets are present in bacteria and not in eucaryotes (Figure 1). In light of recent evidence of the great importance that the internal microbiota has for its respective host (animals, humans, and plants) this concept should be revisited, and a rational plan for the usage of antibiotics is important not only to control the resistance of pathogens but also to preserve the “good bacteria” to benefit the ecosystem and individuals’ health.

2.1. Lessons from Nature: From Intrinsic to Acquired Resistance

Antibiotic resistance is a natural and general phenomenon in many bacteria which carrying chromosomally located resistance genes (intrinsic resistance) to compete with other species in their environment and to be successful. Highly effective antibiotics have been derived from environmental microorganisms such as Streptomyces, Actinomycetes, and Fungi that produce antibiotics as secondary metabolites. The main molecular mechanisms of bacterial antibiotic resistance can be divided into (I) modifications to the target sites of antibiotics; (II) the alteration or degradation of the antibiotic; (III) antibiotic efflux via transporters; and (IV) reduced antibiotic penetration into bacteria through decreased membrane permeability (Figure 2).

2.1.1. Intrinsic Resistance

All microorganisms are trained through evolution to become the fittest and best adapted to a particular environment, but they are also capable of innovating when alterations to their natural habitats occur ^[2]. Intrinsic resistance (IR) is an intraspecies genetic and phenotypic resistance which is transmitted vertically and has been used for decades to prepare selective culture media for specific enrichment and to isolate bacteria from complex matrices such as food, soil, and tissue samples. IR is present in the majority of the most relevant opportunistic pathogenic and resistant bacteria in clinical settings, including some bacteria of the so-called ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), due to their capacity to escape or evade the action of antimicrobial agents ^[3]. Moreover, these opportunistic pathogens also have great capacity to acquire new resistance through horizontal transfer and to form biofilms. IR can exist for a single class of antibiotics, such as the resistance of Listeria monocytogenes to cephalosporins ^[4], but also for multiple drugs, such as the case of Enterococci (Gram-positive, monoderm), which have the potential for resistance to virtually all clinically useful antibiotics ^[5]. P. aeruginosa, among Gram-negative bacteria (diderm bacteria), represents well the phenomenon of intrinsic bacterial resistance since it carries practically all known mechanisms of antimicrobial resistance: the activation of chromosomal AmpC cephalosporinase; the production of plasmid- or integron-mediated b-lactamases from different molecular classes, diminished outer membrane permeability, and the overexpression of active efflux systems with wide substrate profiles, etc. ^[6] (Table 1).

2.1.2. Acquired Resistance

Acquired resistance is related mainly to two mechanisms:

(a)

Mutations in target genes located at chromosomal or extrachromosomal elements which are vertically transmitted in the same bacteria species. The mutation rate increases when bacteria are actively multiplying as, for example, during the acute phase of host infection.

(b)

Horizontal gene transfers occur through mobile elements that can be transmitted both intraspecies and among different bacteria genera, i.e., the vancomycin-resistant gene (vanA) from Enterococcus to S. aureus. Plasmids, prophages, pathogenicity islands, restriction and modification systems, transposons, and insertion sequences are able to move within the host genome as well as jump across genomes. Mobile elements can change their insertion location and copy number and produce frequent gene gain and loss, modifying and co-evolving with chromosomal genomes. The genetic modifications induced by mobile elements can deeply affect bacterial fitness, contributing to their adaptation to new environments and, ultimately, producing evolutionarily distinct species over time. Once the acquisition of resistance determinants is established in few strains, antibiotic misuse and pressure drive the positive selection of resistant over sensitive strains.

The paradigm for this phenomenon is represented by the fast antibiotic resistance acquisition of S. aureus from ampicillin to methicillin to vancomycin in less than 60 years. In contrast to other bacteria, S. aureus was naturally susceptible to virtually every antibiotic that was ever developed, starting from penicillin. However, by the mid-1940s, only a few years after the introduction of penicillin into daily clinical practice, penicillin-resistant S. aureus strains were encountered in hospitals and, within a decade, had become a significant problem in the community ^[10]. Considering its ubiquity in the environment and its pathogenicity for humans and animals, as well as its antibiotic resistance and biofilm capacity, S. aureus is a major concern in both hospital and community settings.

2.1.3. Acquired Resistance through Bacterial Cooperation

The study of biofilms as sources of persistent infection and contamination underpinned the importance of looking at microorganisms in natural conditions, as members of complex communities which modify their capacities. In contrast to laboratory conditions in which single colonies of the same strain are grown and analyzed in pure cultures, in natural external environments and internally in a host, bacterial cells are “compelled” to interact with many different components ^[11]. “Social structure” has been a fitness evolutionary advantage for “social animals” including humans passing from nomadism to settled communities. Individuals each gain a different “social role and activity”, and all work together for the wellness of the community. In bacteria, a cooperative resistance process has been observed when resistant bacteria producing beta-lactamases can help antibiotic-sensitive bacteria survive during antibiotic treatment ^[12]. Cooperative action has been observed in sensitive and resistant mixed cultures of Salmonella tiphymurium strains toward the antibiotic ceftriaxone with an increase in the MIC value upon an increase in cell density ^[13].