Update on resistance trends for HAIs and blood stream infections

ROSANNA PEELING: From the clinical case study in the last step, we’ve learned that during the COVID-19 pandemic, hospitalised patients can often be at risk of acquiring health care associated bloodstream infections. For more details on health care associated infections, please refer to our previous MOOC on the role of diagnostics in the AMR response, currently offered on the FutureLearn platform. We will also take a look at this step at the 2021 global antimicrobial resistance and use surveillance system report on the latest resistance trends for major bacterial pathogens causing bloodstream infections, such as Klebsiella pneumoniae, Acinetobacter species, E. coli, and Streptococcus pneumoniae.

Finally, we will provide an update on laboratory methods for the identification and antimicrobial susceptibility or resistance testing for bacteria that are common causes of bloodstream infections.

In this slide, you could see the common causes of health care associated infections, which are infections acquired during the course of receiving treatment for other conditions within the health care setting. If you recall, in the clinical case presented by Doctor Ram in the previous step, his patient had a central line put in as part of her COVID case management. On day 10 of her hospitalisation, she developed a fever, and Doctor Ram suspected a health care associated infection because of the central line that was inserted. A blood culture was performed and the laboratory identified Klebsiella pneumoniae from her blood culture, which was likely the cause of her fever.

Many of the common pathogens causing health care associated infections have become highly resistant to many first line antibiotics. This graph from the 2021 WHO Global Antimicrobial Resistance and Use Surveillance System report shows that the proportion of patients with bloodstream infections caused by resistant Klebsiella pneumoniae is indeed very high for commonly-used antibiotics, such as cephalosporins and quinolones. The median resistance frequency to third generation cephalosporins was about 60%, with 12 countries reporting 80% to 100% resistance to these broad spectrum antibiotics. The median frequency of carbapenem resistance was over 15%, with about 10 countries reporting an alarming 30% to 60% resistance to carbapenems for blood isolates of Klebsiella pneumoniae, further limiting our treatment options.

This graph shows the global distribution of different genes that encodes for carbapenem resistance. If you recall, the laboratory at Doctor Ram’s hospital was able to determine that the carbapenemase gene responsible for his patient’s infection was the OXA-48-like gene, shown here in green. This kind of data is important for tracking the spread of these resistance genes around the world, and can be used for optimising local treatment guidelines. Doctor Ram was able to use the locally recommended drug regimen for his patient, and fortunately, she recovered.

We want to take this opportunity to provide an update on the resistance trends for some of the other bacterial pathogens that cause bloodstream infections. Last week, in step 1.9, we noted that the 2021 WHO GLASS report showed extremely high proportions of patients with carbapenem resistant Acinetobacter species depicting a dire scenario for patients with health care associated infections. As you could see from this graph, the median carbapenem resistance frequency for this bacteria isolated from blood was over 60%. And a number of countries reported resistance frequencies well above 80%. We now have very limited options for the treatment of patients with health care associated infections due to Acinetobacter species.

Carbapenems, which are last line drugs, are effective also against pathogens that are resistant to third generation cephalosporins. They’re often used empirically when there is an urgent need to quickly initiate antibiotic therapy to increase the chances of survival. For example, in patients with bloodstream infections. High levels of resistance to these important antibiotics are therefore extremely worrying.

This slide shows the high proportion of patients with bloodstream infections caused by resistant E. coli. As you recall in week one, step 1.9, extended spectrum beta lactamase ESBL E. coli has now been designated as one of the two AMR indicators for the sustainable development goals. The other indicator is methicillin resistant Staphylococcus aureus or MRSA.

This graph shows the proportion of patients with bloodstream infections caused by resistant Streptococcus pneumoniae. The increasing proportion of patients with resistant infections to penicillin and co-trimoxazole has given us fewer treatment options for this pathogen. Next, we would like to provide an update on the diagnosis of bloodstream infections and subsequent testing to determine antibiotic susceptibility or resistance patterns. In a basic laboratory, the traditional method is to draw two blood samples and inoculate them onto separate agar plates or separate blood culture bottles and place them in an incubator. You must take care not to contaminate the samples with bacteria from the skin, which may cause a false positive result.

In our previous course on the role of diagnostics in the AMR response, we provided a mini lecture on how to collect a sample for blood culture. After about 12 hours of incubation, a sample from a blood culture bottle can be subcultured onto an agar plate. And if any bacteria grow on the plate, a gramme stain and biochemical tests would then be performed to identify the pathogen followed by antibiotic susceptibility testing. This whole process takes about 48 hours. Since blood is a sterile site in the body, any pathogen that grows from these blood cultures is considered a likely cause of a bloodstream infection.

Nowadays, there are faster methods to identify blood culture pathogens and their antibiotic susceptibility or resistance patterns, as shown here. There are three major methods for detecting carbapenem resistance, for example. The fastest method is to use molecular assays to detect the pathogen and whether it carries any genes encoding carbapenem resistance. The disadvantage of this method is that the presence of a resistance gene is not always correlated with expression of phenotypic resistance. The second method is to detect the presence of carbapenemase activity by detecting products from the hydrolysis of imipenem. A third method is the use of simple rapid immunoassays to detect different carbapenemases.

These methods can shorten the time for clinicians to be able to optimise treatment by as much as 30 to 40 hours. If a patient is already on therapy, escalation or de-escalation can be done rapidly as part of antimicrobial stewardship, saving health care costs as well as reducing the length of hospital stay and the risk of further selection for resistance. We note here that, although methods such as MALDI-Tof or whole genome sequencing can provide rapid identification of blood culture pathogens, the equipment is expensive and not widely available. These methods will not be discussed here.

This slide shows two examples of faster methods for culture identification and susceptibility testing within five to seven hours after sample inoculation. There are also flexible systems for either identification alone or susceptibility testing alone or a combination of both. And this is especially offered for carbapenem producing organisms, from pure culture of gramme negative bacteria. Both of these systems are automated methods that are USFDA approved. But there’s been very few independent evaluations of the performance of these systems, and they’re fairly costly.

There are manual and automated molecular systems for blood culture identification and resistance testing. The manual methods usually consist of nucleic acid amplification testing methods such as the Polymerase Chain Reaction, PCR. And these procedures are done on a variety of thermal cycler instruments. Shown here are three examples of automated multiplex systems for the rapid identification of clinically-relevant carbapenemase and extended spectrum beta lactamase producing organisms. These three examples are USFDA approved. And although more expensive than manual methods, they require much less hands-on time. They offer quality control reagents and random access testing, giving greater flexibility in running individual samples, when needed.

Rapid identification of carbapenemase-producing organisms is very important in the control of health care associated infections. This slide shows several examples of such rapid tests. There are tests that could detect the products of hydrolysis of imipenem. Hydrolysis of imipenem from a pathogen-producing carbapenemase acidifies the medium, which results in a colour change of a pH indicator. There are also rapid immunoassays that could directly detect different carbapenemases. The time to result for these rapid tests range from 15 minutes to two hours.