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Diagnostics Clinical care, Biochemistry and molecular biology, Laboratory management, Microbiology and immunology, Genetics and epigenetics, Omics

Waging War on Pathogens

Very few procedures in modern medicine are possible without the administration of prophylactic antibiotics: chemotherapy, knee and hip replacements, heart surgery, and solid organ transplants all require treatment with one or more of these critically important drugs. However, the continuous rise in the frequency and range of antibiotic resistance is making the treatment and prevention of microbial infections challenging and in some cases impossible. The impact of antibiotic resistant organisms on the treatment of patients is undeniable – the question is: how do we respond?

In my view, it is imperative that we broaden the techniques available to the clinical microbiology laboratory such that we can identify not only the infection-associated pathogens but also any resistance-associated molecular mechanisms they may possess. Taking a molecular approach can both improve the sensitivity and specificity of testing and decrease the time required to evaluate the pathogen and its mode of antibiotic resistance. Indeed, molecular testing has for many years been a mainstay for the identification of viral and bacterial infections, including methicillin-resistant Staphylococcus aureus (MRSA). These techniques are also relevant to today’s major concerns – not least the detection of infections by those Gram-negative bacteria which are resistant to third generation cephalosporins and carbapenems by virtue of production of extended-spectrum β-lactamase (ESBLs) and carbapenemase enzymes. Given that β-lactams are the largest class of antibiotics prescribed today, the prospect of broad resistance to these drugs is singularly unwelcome. Accordingly,  these bacteria have been recognized by the Centers for Disease Control in the USA and the World Health Organization as serious threats to human health. This threat is implicitly recognized in the recent approval by the US Food and Drug Administration (FDA) of two new antibiotics which work in combination as β-lactam/β-lactamase inhibitors.

Molecular diagnostic approaches directed towards identifying the presence of ESBLs and carbapenemases have at least three benefits, as follows.

  • Infection control – tests which identify the type(s) of β-lactamase producing organisms circulating in a particular hospital or community will assist the development of infection control strategies.
  • Antibiotic stewardship – tests which reveal the molecular basis of drug resistance, in addition to the drug susceptibility profile, will aid in selecting the best options for antibiotic therapy for a given infection.
  • Monitoring resistance – tests which alert healthcare workers to the emergence of resistance mediated by a β-lactamase to a new or existing β-lactam drug will assist in developing a timely and appropriate response to such threats.
Adding molecular diagnostic tools into the workflow of the clinical laboratory will help to quickly identify any potential problems related to resistance, big or small.

That said, not all of the >1,000 different β-lactamases  demand routine application of a specific molecular diagnostic test. At present, the most clinically relevant β-lactamase genes are those that encode carbapenemases, ESBLs, and plasmid-encoded AmpC enzymes. Within this broad range of targets, a few are of particular importance. Thus, among the ESBLs, the CTX-M ESBLs – in particular, the CTX-M-15 and CTX-M-14 groups of enzymes – are the most prevalent group of ESBLs worldwide and also the most clinically significant. These are so commonly identified in isolates collected from patients in the community, mostly through urinary tract infections, that it is generally thought that no communities or hospitals are ESBL-free. Similarly, among the carbapenemase genes, we can focus on five families that are particularly important to target by molecular testing, namely the NDM, VIM, IMP, OXA-48, and KPC families. Last, but not least, are enzymes encoded by plasmid-located AmpC genes. Two of the six different families of plasmid-encoded AmpCs  are particularly important: the CMY-2 and DHA families. CMY-2 enzymes are significant in that they are the most prevalent plasmid-encoded AmpCs in the world. DHA family members are also important since treatment with a third generation cephalosporin can result in the emergence of resistance to that treatment regimen. Since there are no recommendations by the Clinical Laboratory Standards Institute (CLSI) for identifying plasmid-encoded AmpC β-lactamases, I recommend a molecular test to identify the genes encoding these enzymes in species of Enterobacteriaceae.

It is critical that we identify the types of resistant organisms circulating in hospitals and communities and their respective mechanisms of resistance. The need for molecular diagnostics to detect and define the β-lactamases that underpin resistance is evident, but the most appropriate molecular tests will vary according to the specific needs of different hospitals and the different patient populations they serve. For all pathogens, however, molecular surveillance is a key component in combating resistance. Adding molecular diagnostic tools into the workflow of the clinical laboratory will help to quickly identify any potential problems related to resistance, big or small, and thus will allow the medical institution to quickly manage emerging issues and decrease the rate at which these types of organisms can spread in the community.

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About the Author
Nancy Hanson

Nancy Hanson is Full Professor, Department of Medical Microbiology and Director of the Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, Omaha, USA.

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