Reducing the incidence of healthcare-associated infections, and the antimicrobial resistance they can trigger, is critical for patient care. Nanopore sequencing can more quickly and accurately identify these infections.
By Jonathan Edgeworth, MRCP, FRCPath, PhD
Summary: New genomic sequencing technologies enable clinical labs to quickly identify and prevent bacterial outbreaks in hospitals, crucial for combating healthcare-associated infections and antimicrobial resistance.
Takeaways:
- Technological Advancements: The latest DNA sequencers provide detailed genomic information rapidly, facilitating effective bacterial typing and outbreak tracing within clinical labs.
- Proactive Surveillance: Prospective surveillance using whole genome sequencing can prevent outbreaks, save healthcare costs, and improve patient outcomes by identifying and addressing community and hospital transmission routes early.
- Real-World Applications: Successful implementations in various global laboratories demonstrate the effectiveness of new sequencing technologies in detecting, managing, and preventing bacterial outbreaks, significantly enhancing infection control efforts.
Between the dangers of healthcare-associated infections and the growing threat of antimicrobial resistance (AMR), clinical laboratory teams are under more pressure than ever to identify bacterial outbreaks within the walls of a hospital. Finding the culprit is not enough; it also has to be done quickly enough to trace the source of infections and to target infection-prevention interventions to avoid an even wider outbreak.
Reducing the incidence of healthcare-associated infections, and the antimicrobial resistance they can trigger, is clearly critical for patient care. It’s also important for the hospital leadership team, particularly knowing whether the reservoir and routes of transmission are in the community rather than in the healthcare facility.
In the past, tracing the phylogeny of an outbreak within a hospital or other healthcare setting was far beyond the capabilities of clinical labs. Simple culture-based testing and even molecular tests designed to detect specific pathogens do not provide the genomic detail required for an investigation, and the cost of large high-throughput sequencers was prohibitive for most hospital-based laboratories.
They therefore relied on reference laboratories or regional public health laboratories to invest in sequencing capability to generate detailed typing data. Unfortunately, batching up samples and waiting for results can take weeks—far too long to make a difference for current patients. In the meantime, hospital infection control teams have to decide whether to wait for typing results and risk continued transmission, or to intervene early and then have to stand-down what would have been a costly and unnecessary program of screening patients, staff, and the environment.
New Technologies to Detect Healthcare-Associated Infections
New technologies now make it possible to generate higher-resolution genomic information from pathogens, and at least some of these tools are quick and easy to set up and run in the routine clinical lab, applied to small or large numbers of bacteria. Unlike the traditional short-read sequencing platforms found in human genetics laboratories, a new generation of DNA sequencers capable of generating long reads quickly and with richer data is a strong fit for bacterial typing and phylogenetic investigations.
Their unique data makes it possible to characterize genomes completely and accurately, allowing for pathogen identification while also capturing single nucleotide changes that can help trace the path of transmission. They also fully resolve plasmids, which can carry drug-resistance genes and move between different bacterial species. This latest generation of sequencing technology is being used in clinical labs today to prevent the spread of healthcare-associated infections.
Look Ahead or Look Back?
Broadly speaking, two approaches are taken for applying sequencing in response to suspected nosocomial bacterial outbreaks: the more common reactive approach, which kicks in when an outbreak is clinically suspected based on more infections being observed in a time and place than would normally be expected, and a prospective surveillance approach designed to prevent outbreaks before they are clinically recognized and can get a foothold.
This prospective approach routinely sequences all laboratory isolates of the dominant selected AMR organisms such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci, carbapenem-resistant Enterobacterales, or Clostridioides difficile and alerts clinicians when a cluster of isolates is genetically related.
Bursting the Conventional Wisdom Bubble
Conventional wisdom might predict that the reactive approach uses fewer resources, applying sequencer time only when an outbreak is suspected. But health economic studies indicate that proactive surveillance approaches may actually have the biggest impact preventing infection and reducing costs.
Critically, proactive surveillance studies have shown that many clinically suspected hospital outbreaks were, in fact, community outbreaks, and that other true hospital outbreaks were missed early on because the first few patients were on different wards at different times. These findings fundamentally change our understanding of routes of transmission underpinning hospital outbreaks, and the critical importance of genomic surveillance for cost-effective outbreak investigation.
In one detailed study of bacterial healthcare-associated infections, a team in the UK modeled the economic impact of a surveillance approach based on whole genome sequencing.1 They found that, in England, implementing a surveillance model could save approximately £478 million in healthcare costs while also preventing nearly 75,000 healthcare-associated infections and more than 1,000 deaths. In the U.S., the same change would support net savings of $3.2 billion, preventing nearly 170,000 healthcare-associated infections and saving nearly 5,000 lives.
In addition to enabling better patient care, the information generated should be broadly useful to antimicrobial and diagnostic stewardship teams within the healthcare facility. But this only works if the data can be produced quickly and locally, rather than being sent out to a reference lab.
Healthcare-Associated Infections: The Real-World Evidence
The new generation of sequencers can produce reads that stretch kilobases or even megabases, allowing for the representation of full plasmids in individual reads to capture critical drug resistance data. Recent protocol updates have made it easier for users to streamline the sequencing process, moving from microbial isolate extraction to comprehensive analysis in a simplified 24-hour workflow.
This kind of protocol can be used to sequence as many as two dozen genomes in a single sequencer run while generating sufficient coverage for whole genome and plasmid assembly, profiling of antimicrobial resistance markers, sequence typing, and SNP typing.
By now, long-read sequencing technologies have been available for enough time that many teams have reported their experience using them to manage bacterial outbreaks or set up surveillance programs.
One useful example comes from scientists at Wellington Southern Community Laboratories in New Zealand, where the microbiology and molecular biology lab runs about 300,000 samples per year.2 Three years ago they incorporated nanopore sequencing, which was the team’s first non-Sanger sequencing technology. The nanopore platform is used to investigate possible outbreaks and to perform surveillance sequencing for hospital-associated organisms such as Klebsiella pneumoniae and Staphylococcus aureus, generating data in less than 24 hours for many cases without needing a dedicated bioinformatician to analyze results. “This workflow is flexible and scalable and could easily be adapted to other purposes such as antimicrobial resistance (AMR) or virulence gene detection,” the scientists report.
Since implementing the approach, the Wellington Southern Community Laboratories team detected an outbreak of C. difficile that they say would not have been found any other way. In addition, their infection prevention and control team “used the results several times to rule out suspected transmission events, meaning further widespread screening of patients could be avoided.” In a separate report, the same team used this approach to identify a neonatal intensive care unit outbreak with an unusual MRSA strain that their surveillance program identified when only two cases were known, enabling prompt action and rapid outbreak resolution.3
In another recent study, scientists in China collected nearly 300 samples with suspected links to infectious diseases from 10 clinical centers and analyzed them with conventional culture tests and nanopore sequencing.4 “Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts,” they note. “Consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii.”
In a final example, scientists in Norway conducted a study at Akershus University Hospital using nanopore whole genome sequencing to support faster and more accurate outbreak investigations with their own internally developed protocol.5 Genome assemblies were available within 24 hours, allowing the team to quickly disprove an outbreak or provide supporting evidence of it. “During the real-time S. aureus outbreak investigation, the protocol was able to identify two outbreaks in less than 31 [hours],” they report.
What’s Next in the Fight Against Healthcare-Associated Infections?
Clinicians take a zero-tolerance approach to preventing hospital-acquired infections, which are caused by a wide range of organisms, only a proportion of which are antimicrobial-resistant. Infection rates and priorities also vary between institutions. Infections can be acquired from diverse sources including other colonized patients, the hospital environment, equipment and products, staff, or even food. Clinicians must therefore remain constantly vigilant and willing to investigate the unusual or novel, as well as focusing on their familiar AMR culprits.6
Taken together, it is likely that there will be increasing implementation of prospective surveillance programs tailored to selected local or regional AMR priorities, which then provides the flexibility to undertake rapid, on-demand reactive sequencing of a few concerning organisms outside the chosen surveillance list when something unusual occurs. This would be particularly useful when investigating potential hospital reservoirs for infection such as sinks, the fixed ward environment, endoscopes, theater heater-coolers, or even contaminated infusions and other commercial products.
Detection relies on heightened awareness of front-line staff and would be significantly enhanced by availability of rapid, local sequencing capability to immediately target interventions and limit what traditionally have been reported as prolonged and often devastating outbreaks that can affect many patients and hospitals.
As more studies are published from clinical laboratories around the world, it is clear that new sequencing technologies that are capable of rapidly generating richer data are empowering labs and clinical teams to track bacterial infections with ever greater confidence. It can help to more accurately distinguish community and hospital outbreaks of dominant AMR bacteria, so scarce resources are appropriately targeted. It can also be rapidly deployed to identify reservoirs of more unusual but potentially serious and protracted outbreaks that hitherto have gone hidden or been slow to identify.
As new streamlined protocols with automated analysis become available, these sequencing technologies are within reach of any routine microbiology laboratory, helping to improve the service they provide to their clinical colleagues conducting outbreak investigation and bacterial surveillance programs.
ABOUT THE AUTHOR
Jonathan Edgeworth, MD, PhD, is a professor of clinical infectious diseases at King’s College London and consultant microbiologist at Guy’s and St. Thomas’ NHS Foundation Trust. He also serves as vice president of medical affairs at Oxford Nanopore Technologies.
References
- Fox JM, Saunders NJ, Jerwood SH. Economic and health impact modelling of a whole genome sequencing-led intervention strategy for bacterial healthcare-associated infections for England and for the USA. Microb Genom. 2023 Aug;9(8):mgen001087. doi: 10.1099/mgen.0.001087.
- Bloomfield M, Hutton S, Velasco C, Burton M, et al. Oxford nanopore next generation sequencing in a front-line clinical microbiology laboratory without on-site bioinformaticians. Pathology. 2024 Apr;56(3):444-447. doi: 10.1016/j.pathol.2023.07.014.
- White RT, Bakker S, Burton M, Castro ML, et al. Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing. Microb Genom. 2024 Jul;10(7):001273. doi: 10.1099/mgen.0.001273.
- Zhao M, Zhang Y, Chen L, Yan X, et al. Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario. Front Cell Infect Microbiol. 2024 Jan 30;14:1330788. doi: 10.3389/fcimb.2024.1330788.
- Ferreira FA, Helmersen K, Visnovska T, Jørgensen SB, Aamot HV. Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation. Microb Genom. 2021 Apr;7(4):000557. doi: 10.1099/mgen.0.000557.
- Eyre DW. Infection prevention and control insights from a decade of pathogen whole-genome sequencing. J Hosp Infect. 2022 Apr;122:180-186. doi: 10.1016/j.jhin.2022.01.024.