Clinical Microbiologist Dr Max Bloomfield
One of the challenges for pathologists and laboratories is identifying and preventing the spread of bacteria, such as Staphylococcus aureus, which can pose a serious health risk within both local communities and hospitals.
S. aureus is transmitted by humans and animals, causing skin and soft tissue infections in patients, through to more serious conditions such as blood and bone infection and pneumonia. It can also be resistant to several types of antibiotics including penicillin, amoxicillin, and flucloxacillin, among others. S. aureus that is resistant to flucloxacillin is known as MRSA.
A recent scientific study sought to demonstrate the value of Oxford Nanopore Technologies for a proactive and pre-emptive approach to the surveillance of pathogens found in hospitals, in particular, S. aureus transmission within hospital Neonatal Intensive Care Units (NICU).
Transmission within a NICU is a concern for pathologists and medical professionals. Newborn babies, particularly those who born premature or underweight, face a higher risk of S. aureus infection due to their underdeveloped protective microbiota and immune systems. They also face transmission risks from parents, and even health staff, who may unknowingly be carrying the pathogen but are not showing symptoms.
After Awanui Labs established its genomic surveillance programme in 2022, our Microbiology Team in Wellington began using Oxford Nanopore Technologies to target several common hospital pathogens, including monitoring for MRSA outbreaks at hospitals in the region.
Last year, the lab detected the presence of the ST97 MRSA pathogen in two infants from a routine sequencing run of all swabs collected from the NICU at the Regional Hospital.
Normally this would go unnoticed, but because of the genomic surveillance program we could see these two infants were carrying the same bug meaning it spread from one to the other. This led to further screening of infants on the unit, which confirmed an outbreak had occurred. Because it was detected so quickly, it could be contained quickly with minimal disruption to the NICU, and no infants developed serious infection.
Such incidents can potentially disrupt and compromise the ability of the hospital to safely deliver care to this vulnerable patient group, especially if case numbers increase, and the outbreak is prolonged.
However, while genomics has improved the understanding and control of MRSA transmission, investigations into outbreaks have tended to be retrospective or reactive. These are often only undertaken when outbreaks have reached sufficient size to be detected based on standard surveillance techniques.
Our research went beyond the case study to provide a greater understanding the phylogeny and evolution of ST97 MRSA which resulted in the transmission at the Wellington NICU.
Phylogeny is the history and relationships between groups of organisms, examining how distinct types of MRSA have evolved, and the varying types of strains. Our team studied 679 unique S. aureus genomes in total, sequenced using different technologies, and data on the genome types sourced from different libraries including bovine genomes from livestock trials.
The team were able to build a detailed picture of the DNA of each type of the S. aureus strains, including ST97 MRSA found in the swabs from the infants in the NICU, and pathogens from swabs sequenced by Awanui Labs since the genome programme started in 2022.
By mapping the lineages of the pathogens, we could assess the genomic characteristics and variations of S. aureus strains found in neonatal hosts in New Zealand, compared with those recorded overseas.
The team examined any alignments or commonalities of the variants (SNVs) which make up the strains, the differences in how they had evolved when using nanopore and non-nanopore sequencing, how quickly they could be detected and how resistant to antibiotic treatment.
The results showed integrating genomics into standard hospital epidemiological methods can identify transmission of infection and nanopore sequencing is a practical, proactive platform for studying outbreaks of MRSA before they escalate. Our team were also able to enhance our understanding of antibiotic resistance development and dissemination by examining the evolutionary history of MRSA strains.
The research underscores the importance of advanced genomic technologies as an alternative approach to the conventional sequencing used in New Zealand’s pathology laboratories. By increasing our knowledge and understanding of how pathogens develop and mutate, we are in a better position to detect and prevent transmission and increase the safety for patients, staff, and neonates within our healthcare settings.
The research paper titled Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing is published in Microbial Genomics journal.