The power of genomics to tackle the threat of antibiotic resistance

Leila Luheshi

14 October 2013

In 2011 the UK Chief Medical Officer published a report highlighting the serious and growing threat posed to global health by the increased occurrence of bacterial infections that are resistant to treatment with antibiotics. The government has now published a strategy (see previous news) that aims to tackle this problem through a combination of educational, research and healthcare practice approaches. This article outlines where greater use of genomics may improve the ability of the healthcare system to meet the ambitious targets that the government has set.

One of the most pressing challenges facing healthcare practitioners is the need to prevent the spread of infections that have already become resistant to most antibiotics. These infections can be life threatening, particularly to the most vulnerable patients such as premature babies, and pose a significant threat to public health as they are close to becoming untreatable with currently available antibiotics.

A number of government-funded clinical research initiatives have now demonstrated that sequencing the whole genomes of the bacteria causing antibiotic resistant infections can be more powerful than existing methods for detecting when outbreaks are occurring and identifying the source and potential routes of transmission of the infection. This knowledge enables infection control teams to intervene more rapidly and effectively to prevent further spread of the antibiotic resistant bacteria. It is vital that the government’s AMR strategy takes steps to ensure that such genomic approaches can be evaluated and then rapidly implemented in the healthcare system.

Using whole genome sequencing to understand better how the genomes of bacteria allow them to evade antibiotics and our immune system also has the potential to enable the discovery of new drugs, and the better selection of existing ones to use for treatment. The government should also ensure it learns and applies to antibiotic resistant bacterial infections the lessons successful initiatives like the UK HIV Drug Resistance Database which enables virologists to share and compare the DNA sequences of their patient’s HIV to enable prediction of its drug resistance. The power of this approach is that as each additional genome is added to the database, its power to identify causes of drug resistance increases for each individual and the population as a whole. As we start to sequence the genomes of bacterial infections routinely in clinical and public health practice, the government must ensure that these data are shared nationally and internationally to maximise patient benefit from the knowledge they will generate.

Perhaps the most significant opportunity to bring the power of genomics to bear in tackling the threat of antimicrobial resistance comes through the government’s own 100,000 genomes initiative. By sequencing the genomes of new TB infections (amongst others), this programme aims to demonstrate that this information can be used to identify which antibiotics each patient’s infection can be treated by, and reduce the threat of antibiotic resistant TB spreading in the population. Vitally, early scientific studies have indicated that whole genome sequencing of TB can identify drug resistance in weeks, a process which takes months using current standard practice. It is vital that the knowledge accrued through the sequencing of TB and other infectious diseases as part of the 100,000 Genomes Project is shared throughout the healthcare system and internationally, as antibiotic resistance can only be tackled effectively if best practices are followed nationwide and, where possible, internationally.