Module 2.2 - Healthcare cluster transmission

Summary

In Module 2.2 of the COVID-19 Genomic Epidemiology Toolkit, Dr. Nicholas Lehnertz examines two outbreaks in skilled nursing facilities. Through whole genome sequencing, it's revealed that a single introduction of SARS-CoV-2 led to extensive outbreaks in both facilities. The presentation underscores the importance of infection prevention and early detection through universal testing to mitigate future outbreaks.

Takeaways

• 🦠 Whole genome sequencing is used as an investigative tool in outbreak settings, particularly for COVID-19.
• 🏥 Two separate COVID-19 outbreaks were identified in skilled nursing facilities in an urban area, prompting the Minnesota Department of Health to get involved.
• 📊 Facility-wide testing revealed extensive outbreaks in both Facility A (66% residents, 35% healthcare workers) and Facility B (63% residents, 33% healthcare workers).
• 😷 Many healthcare workers did not agree to be tested, which suggests the actual number of positive cases may have been higher.
• 🔍 Hypothesis 1: All outbreak cases were related, and SARS-CoV-2 rapidly spread throughout the facility unnoticed.
• 🔍 Hypothesis 2: Multiple virus introductions occurred due to various breaches in safety protocols.
• 🧬 Whole genome sequencing revealed that the outbreaks in both facilities likely stemmed from a single introduction of the virus.
• 🧪 The phylogenetic tree demonstrated that cases in both facilities were closely related at the genetic level.
• 📉 There were several limitations, including unsampled cases and untested healthcare workers, which could mean missing transmission links.
• 📈 Continued vigilance with infection prevention and control practices, as well as early detection through testing, were strongly recommended to prevent further outbreaks.

Q & A

What is the main focus of this module in the COVID-19 Genomic Epidemiology Toolkit?

The main focus of this module is identifying transmission in healthcare clusters using whole genome sequencing as an investigative tool during COVID-19 outbreaks.

What role did the Minnesota Department of Health (MDH) play in assisting the nursing facilities during the outbreaks?

The MDH helped both facilities implement system-wide serial testing, known as point prevalence surveys, to understand the magnitude of transmission and provide information on mitigation strategies like cohorting.

What were the testing results in Facility A and Facility B?

In Facility A, 66% of residents and 35% of healthcare workers who agreed to be tested were positive for COVID-19. In Facility B, 63% of residents and 33% of healthcare workers who agreed to be tested were positive.

What challenges did the nursing facilities face during the outbreaks?

Both facilities were short-staffed, which worsened with multiple healthcare workers testing positive. Overworked staff, inconsistent training, PPE shortages, and the difficulty of caring for residents in memory care units further contributed to viral transmission.

What were the two hypotheses regarding the outbreak origin?

Hypothesis one was that all cases were related, with SARS-CoV-2 spreading unnoticed throughout the facility. Hypothesis two was that multiple virus introductions contributed to the outbreak.

How did whole genome sequencing help in understanding the outbreaks?

Whole genome sequencing was used to determine if the outbreak cases shared a common ancestor. The findings supported the conclusion that all cases in both facilities descended from a single introduction of the virus.

What did the phylogenetic tree reveal about the outbreak in Facility A?

The phylogenetic tree showed that all cases in Facility A clustered into a single clade, with many genetically identical cases. This suggests that the cases likely originated from a common source.

What did the phylogenetic analysis show about the outbreak in Facility B?

Similar to Facility A, the cases in Facility B clustered into a single clade with a common ancestor. This suggests that the outbreak likely resulted from a single introduction of the virus.

What recommendations did MDH make after the genomic analysis?

MDH recommended continued vigilance in infection prevention and control practices, with a low threshold for testing residents and staff. Screening and universal testing were advised to identify and isolate cases early.

What limitations were identified in using whole genome sequencing in this outbreak investigation?

Limitations included the unavailability of some samples for sequencing, the inability to test over 80% of healthcare workers, and the possibility of missing cases. Additionally, two cases with identical genomes could still represent separate introduction events.