Author(s): Muna F Anjum [*]
genotypes; microarrays; microbiome; phenotypes; whole-genome sequencing
Antimicrobial resistance (AMR) is a growing problem in the 21st century. The use, overuse and misuse of antibiotics, as well as their inappropriate disposal, have led to widespread dissemination of antibiotics in various environments, which has resulted in a disproportionate rise in antimicrobial-resistant bacteria that is affecting the treatment of bacterial infections in both humans and animals worldwide. In a recent review on AMR commissioned by the UK Prime Minister David Cameron, the chair of the report Jim O'Neill, an eminent economist, said that AMR is a more certain threat in the short term than climate change [1 ]. AMR in bacteria can result both from mutations arising in chromosomal genes and acquisition of mobile genetic elements (MGEs), which harbor AMR genes [2,3 ]. Screening of AMRs present in bacteria is an important first step to administration of the correct antibiotics to treat bacterial infection.
There is currently a diversity of screening methods available that involve both phenotypic and genotypic characterization of AMRs present in bacterial isolates. Some are being used routinely in diagnostic laboratories while others are still as research tools being used by academicians and specialists, which are in different stages of development. What are the pros and cons of using these different tools? Is one approach better than the other?
The conventional approach of screening for AMRs involves plating samples (e.g., feces and sputum) on nonselective or antibiotic-selective agar plates, purifying bacterial colonies and using disc diffusion, broth dilution, gradient strip and other similar methods to determine the MIC for resistance to a panel of antibiotics [4 ]; the MIC values are assessed against clinical breakpoints (e.g., those available from Clinical and Laboratory Standards Institute [5 ] or European Committee on Antimicrobial Susceptibility Testing [6 ]) or epidemiological cut-off values to determine if a bacterial isolate is sensitive or resistant to different antibiotics. Although this method is very informative, yet it is time consuming, often taking several days to perform the full panel of MICs on isolates, following purification. Automated bacterial characterization systems, such as Vitek 2 (bioMerieux, USA) or MicroScan (Siemens Healthcare Diagnostics Ltd, UK), which also perform antimicrobial sensitivity testing, are high throughput and increasingly being used in large hospitals to characterize the resistance phenotype of bacteria to different antimicrobial compounds. These automated methods are relatively rapid taking approximately 12 h following initial isolation of bacteria. Although treatment of patients usually precedes receiving the antibiotic sensitivity results, it can nevertheless alert clinicians about the presence of multidrug-resistant bacteria and the best therapeutic options.
However, phenotypic susceptibility relates only to the concentration of an antimicrobial that inhibits bacterial growth in vitro to breakpoints used to infer clinical success during treatment. It gives no indication of the mechanisms of resistance which may disseminate to other bacterial species via MGEs; for this molecular or genotypic characterization is required. Currently, there are a plethora of PCRs, including standard, real-time and multiplex PCRs that are used to look for the...