table 1. Influence of Whole-Genome Sequencing (WGS) Results on Infection Prevention and Control Measures Phase 1 (June 2–11) Pre-WGS
Strains sent for WGS: June 17, 2016 WGS results: July 8, 2016
Summary 1. There were potential transmissions of S. pyogenes involving wards A and C. 2. S. pyogenes colonization and transmission were probably mediated by chronic skin lesions. 3. Staff, visitors, and volunteers were ruled out as potential sources of infection as their throat swabs were all negative. 4. Infection control recommendationsa were prescribed by the outbreak control team. Pre-WGS Hypotheses and Planning Parameters 1. A typing method was needed to determine whether it was large cluster of genetically linked S. pyogenes isolates or multiple small clusters. 2. WGS is accepted as a typing method by the outbreak control team.
Post-WGS
WGS Results 1. Isolates from wards A and C were genetically linked (Figure 1, cluster 1). 2. Pairwise SNP distances suggested transmissions involving wards A and C. 3. The pairwise SNP distances also suggested this strain may have been circulating for ~2 years. Post-WGS Conclusions and Recommendations by the Outbreak Control Team 1. Ward A appears to be the epicenter of the outbreak, most likely due to the extensive chronic skin lesions observed among most patients and patients’ psychosocial behavior patterns. 2. Ward C is potentially involved due to the extensive physical contacts between patients from wards A and C in the common areas. 3. To continue the focus on patient and environmental hygienemeasures to prevent further transmission of GAS. 4. Patient referral to external dermatologist for management of skin conditions. 5. Enhanced hospital-wide surveillance for skin lesions. If present, screen for GAS by wound culture.
Phase 2 (July 27–August 31)
Strains sent for WGS: August 18, 2016 WGS results: September 5, 2016
Summary 1. More cases of S. pyogenes from wound cultures were identified from ward A. 2. New cases of S. pyogenes were identified from 4 other wards (wards B, D, E, and F). 3. Infection prevention and control measures.a 4. Oropharyngeal carriage of S. pyogenes was identified in 2 staff at the institution. The staff were taken off clinical duty and referred for eradication therapy. Pre-WGS Hypotheses and Planning Parameters 1. The outbreak control team was concerned that this might be an institution-wide clonal outbreak of S. pyogenes and recommended WGS of all isolates until the outbreak settled. 2. The outbreak team was concerned about whether this might be a scenario of staff-to-patient transmission. 3. Possible WGS results and actions considered:
WGS Results 1. All isolates from ward A and 1 isolate from ward D were genetically linked to cluster 1. 2. All other S. pyogenes were genetically diverse, ruling out a hospital-wide clonal outbreak (Figure 1). 3. The S. pyogenes strains identified in 2 staff members were genetically distinct from all patient isolates, ruling out staff-to-patient transmissions (Figure 1). Post-WGS Conclusions and Recommendations by the Outbreak Control Team 1. Decision was made against prescribing institution- wide antibiotics treatment. 2. Additional epidemiological investigation was conducted to study the relationship between the isolate from ward D and cluster 1. 3. A visiting dermatologist was appointed to review patients on site weekly to manage their chronic skin conditions.
1. WGS results were available in a timely manner and prevented the use of institution-wide antibiotics treatment. 2. Detailed and targeted epidemiological investigation was conducted based on the WGS results. 3. Resources were pooled to contain the ongoing transmissions in ward A.
Remarks
1. WGS confirmed person-to-person transmission of S. pyogenes involving wards A and C. 2.WGS results did not significantly change the outbreak management at this time.
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