As we hear about rises in iGAS, the issue of antibiotic allergy – and specifically penicillin allergy – labelling comes to the fore. A good review here outlines some of the issues in this complex space, and makes some helpful suggestions about how this could be improved.
Continue readingAntibiotic resistance
Three key headlines from ESPAUR 2022
Great to see another fantastic annual ESPAUR report. It really is marvellous to have such a clear picture of HCAI and AMR related trends. As ever, there is some good news and some not so good news. Here three key headlines:
- Trends in bloodstream infection, antimicrobial resistance, and antimicrobial prescribing have changed during the pandemic.
- Tackling deprivation is tackling HCAI and AMR.
- We need to keep an eye on CPE
The role of IPC, vaccination, and OTC distribution in AMR
I had the privilege of chairing a session in the BSAC Spring Conference webinars yesterday about the role of IPC, vaccination, and OTC distribution in AMR. The session had a talk from Professor Andreas Voss on IPC as a cornerstone of successful stewardship, Dr Elizabeth Klemm on prevention through vaccination, and Dr Abdul Ghafur on community pharmacy and the challenge of over-the-counter (OTC) distribution.
Continue readingUsing machine learning to super-charge anti-infective drug discovery: the case of Halicin
Yes, it’s true. There is more to HCAI & AMR (and this blog) than COVID-19! To prove it, I’m posting on something different today – the use of AI to streamline the anti-infective drug discovery process. Scientists at MIT have used machine learning (aka “deep learning”) to improve the drug discovery process, by predicting antimicrobial activity in molecules that are different from known antibiotics. This process has yielded Halicin, a promising candidate molecule for a broad-spectrum antimicrobial agent – which is, of course, a long way from clinical trials!
On the origin of multidrug-resistant Gram-negative bacteria (MDR-GNB)
The colour of the global crisis of antibiotic resistance is red (if te Gram stain is your reference). In rich countries we have ESBL-producing Enterobacterales (mainly E. coli), but the real problem are carbapenemase-producing strains (Klebsiella, Pseudomonas and Acinetobacter) that are already endemic in lower and middle-income countries. The unanswered question is “where did these resistant bacteria come from”? Animals or bathrooms? Continue reading
ESPAUR 2019: a snazzy facelift
The 2019 edition of the ESPAUR report has recently been published, including data up to and including 2018. The report is an excellent read – here’s a few summary points.
- There’s a series of lovely infographics at the start of the report. I gave myself a challenge: to select the one infographic that told the story of the report. I toyed with the one about a small but increasing number of CPE BSIs (aghhhhh!), and the stark grave-stone themed image of mortality related to carbapenemase-producers, but ended up with this one: alarmingly, the rate of BSI for the seven priority bacterial pathogens rose 22% between 2014 and 2018 to 145 per 100,000 population. (Around half of these were coli). And there’s a certain inexorability about the antimicrobial resistance trends included in this report, with a 32% increase in AMR BSIs comparing 2014 to 2018.
Figure: Trends in BSIs (blue line) and AMR BSIs (green line).
- There were more than 60k antibiotic resistant severe infections in 2018, <150 per day.
- Confirmed CPEs have topped 4k (but this is a gross underestimate of true prevalence). The report makes the case that the rarity of CPE BSIs (142 reported nationally) represents a success of prevention. This is probably true if we compare across the pond and towards the southern reaches of Europe. But difficult to be sure without a control (i.e. what would have happened without the national initiatives etc)? Also, reporting of CPE BSIs to PHE is voluntary and not mandatory, so there will be some degree of under-reporting.
- Related to this, only 50% of diagnostic labs have introduced methods to detect CPE locally. Which links closely with the change in surveillance system for CPEs going forwards – rather than manual voluntary reporting, locally confirmed CPEs will be reported automatically to PHE. However, if only 50% of diagnostic labs have appropriate methods, we’ll still end up under-reporting (but it will be more a more accurate picture than the current process provides).
- 30 day all-cause mortality of invasive CPE infections is 24% (along with the arresting gravestone-themed infographic)! Not sure how helpful it is to make a big point based on unadjusted mortality data…
- Overall consumption of antibiotics continues to decline. Consumption fell from 20 to 18 DDDs per 1,000 population per day between 2014 and 2018. However, consumption increased by 3% in hospitals over this period.
- There’s a nice section on Candida auris
- ESPAUR reports some good work and outcomes related to training, education, and awareness (e.g. Keep Antibiotics Working and Antibiotic Guardian).
- What a wonderful resource the AMR Fingertips module is: automated data from >90% of NHS laboratories on a range of AMR indicators at our…ahem…fingertips. I am one of the 15k users over the past three years. (As an aside, the volume of traffic is fairly low by popular website standards – but I guess it is somewhat niche!)
ESPAUR is a fantastic resource – it seems that this is the last ESPAUR report related to the UK AMR Strategy from 2013-2018, but I’m confident that ESPAUR will continue to report the successes and challenges of implementing the new five year action plan (from 2019-2024).
The infinite trio from South Africa
Last week I had the pleasure of attending the 8th FIDSSA Congress in Johannesburg (Federation of Infectious Diseases Societies of Southern Africa). I was invited to talk on infection control in the Netherlands, SDD and empiric antibiotic strategies in ICU. I never felt more distance between my habitat and that of my hosts. It surpassed the 3732 miles in the air. I learned a lot; from how it is to go into military conflict areas to identify Ebola cases, fighting a cholera outbreak after a tropical cyclone in Mozambique to the infinite trio, which stands for carbapenem resistant Klebsiella, Pseudomonas and Acinetobacter. Continue reading
A pore way of dying (for MDR-GNB)
The lack of new antibiotics for Gram-negative bacteria is one of the cornerstones of the global crisis of antibiotic resistance. The quest is finding a molecule with antibacterial activity that can pass the double-layered cell wall and that manages to remain in the cell long enough to kill. New lab-based studies suggest that such antibiotics may already exist, and that the solution to activate them is widely available, and for free. As these findings were published in not-so-well-known-and-hardly-read journals for clinicians, such as EMBO journal and Scientific Reports, here follows the summary for dummies (written by a dummy). Continue reading
Summer break – don’t go near the water?
I trust you are enjoying a well-deserved summer break or packing your bags to take off. In case you missed this paper in the daily list of new ones on biorxiv, it tells you where to swim safely and where not. Elena Buelow, from Germany, a former PhD student in our lab in Utrecht and now post-doc in Limoges, France, reported. So, if you are floating quietly in a pittoresque small river and you see a hospital building on the hill near the next bend in the river, are you still in safe waters? Continue reading
Are the robots taking over? The role of machine learning and AI in tackling infectious diseases
I attended a brilliant seminar at Imperial College last week on the role of machine learning and artificial intelligence (AI) in infectious management, and to a lesser extent, infection prevention and control. There’s so much potential for this exciting technology to revolutionise the way we identify, treat, and prevent the spread of infectious diseases. But, there’s also some risks – some are already asking whether the robots are taking over, and whether that is an entirely good thing!
Reflections on Infection Prevention and Control 