Challenges in identifying antibiotic resistance targets for point-of-care diagnostics in general practice

Mitsakakis, Konstantinos; Kaman, Wendy E; Elshout, Gijs; Specht, Mara; Hays, John P

The type of antibiotic resistance and antibiotic resistance mechanisms found in the primary care setting depends on several factors, including the availability and use of antibiotics by GPs and patients within a particular geographical location and community. Therefore, the types of resistances to be detected may be very diverse, including both intrinsic and acquired resistances. Intrinsic resistance is an inherent characteristic of microorganisms that makes them insensitive to particular antibiotics, with an example being the inherent resistance of Gram-negative microorganisms to the antibiotic vancomycin due to the inability of vancomycin to efficiently penetrate the Gram-negative bacterial outer membrane. Acquired antimicrobial resistance is, however, most relevant for antimicrobial prescribing in healthcare as they can generate resistance in previously nonintrinsically resistant (antibiotic susceptible) microorganisms. Further, this resistance can be readily transferred between different bacterial species (either in the presence or absence of antibiotics). Transferable antibiotic resistance genes may be present in different mobile genetic elements (MGE), carried for example in many different types of plasmids (via conjugation), or transferred by the uptake of naked DNA (transfection), or spread via bacteriophage-mediated transfer (transduction). Examples of antimicrobial resistance genes carried by MGE include genes coding for β-lactam-based antibiotic hydrolyzing proteins, such as extended spectrum β-lactamases (ESBL) and carbapenemases, for example, Klebsiella pneumoniae carbapenemase, Verona integron-encoded metallo-β lactamase, etc. Further, for each gene there may be many different variants, for example, >160 TEM (isolated from patient Temoneira) and >100 sulfhydryl variant (SHV) β-lactamase gene variants [10] . Antibiotic resistance may also originate via nontransferable genetic events, that is, genetic mutations. For example, mutations in the quinolone resistance-determining region of the gyrase A (gyrA) gene may result in bacterial resistance to quinolone-based antibiotics such as ciprofloxacin and nalidixic acid. Genetic mutations may also be associated with the downregulation of porins or the upregulation of efflux pumps [11, 12] . Further, many different resistance mechanisms may be present within a single isolate of a bacterium at the same time, resulting in multiresistant or even pan-resistant microorganisms [13, 14] . With particular respect to general practice, and as an example, community respiratory tract infections in the Netherlands are generally treated using amoxicillin and as a second or third choice tetracyclines and macrolides, while urinary tract infections are generally treated using nitrofurantoin, phosphomycin, trimethoprim and ciprofloxacin. Just some of the antibiotic resistances associated with these combinations of antibiotics include hyper production of penicillinases, plasmidal resistances, point mutations, efflux pumps, etc. [15] [16] [17] . Such a diversity of antimicrobial resistance mechanisms means that it is unlikely (or feasible) to develop a POC diagnostic that can detect all of the different antibiotic resistances described in the scientific literature. Instead, a 'targeted' approach may be required, whereby diagnostics are targeted to the antimicrobial resistance actually circulating within a given geographical location or community. This solution, however, generates two problems: diagnost