ST1478 bloodstream infections

From 2013 to 2018, 115 ST1478 BSI VRE isolates among 111 patients were identified in 19 CNISP hospitals (Table 1), ^{Reference McCracken, Mitchell and Smith2} with increasing incidence over the study period. Infections were largely concentrated in central and western Canada (Table 1 and Fig. 1). The most common pre-existing comorbidities were active malignancy (37%), liver disease (27%), kidney disease (26%), and cardiac disease (21%) (Table 1). Surgical procedures, particularly those involving manipulation of the gastrointestinal tract, were frequent among patients with an ST1478 VRE BSI (Table 1). The 30-day all-cause mortality was 32.4%. (Table 1).

Table 1. Geographic Location and Characteristics of Patients Identified With ST1478 VRE BSI, 2013–2018

Note. VRE, vancomycin-resistant Enterococcus; BSI, bloodstream infection; GI, gastrointestinal.

^a All procedures include and surgeries or endoscopic procedures that took place in the 3 months prior to the positive VRE blood culture.

Fig. 1. Both figures plot the hospital location of patients who developed ST1478 bloodstream infections. Colors represent hospitals, dots represent date of blood culture positivity, x-axis represents time of hospitalization and positive blood culture, and the left-hand column contains isolate or patient identifiers. (A) Hospitalizations of ST1478 patients along with date of blood culture positivity in central Canada. (B) Hospitalizations of ST1478 patients along with date of blood culture positivity in western Canada. Hospital 1 only began sending VRE bloodstream isolates to the National Microbiology Laboratory in 2018.

Figure 1 displays hospitalizations and the date of positive blood culture for central and western Canada. Central Canada (Fig. 1A) had a large burden of infection concentrated in 2 hospitals, whereas western Canada (Fig. 1B) had infections distributed in multiple hospitals, though with a large concentration at “hospital 1.”

Transmission analysis of hospital clusters

We identified 4 clusters within 2 hospitals in central Canada that had repeated interhospital transfers, 2 of which are shown (Fig. 2A and B), and 3 clusters in 3 separate hospitals in western Canada, 2 of which are shown (Fig. 2C and D).

Fig. 2. These figures show the inpatient location of patients who developed ST1478 infection, date of blood culture positivity, and the SNV difference between different isolates within each cluster. Patients are identified by letters; patients who developed 2 infections are identified by A(1) and A(2). Colors represent different wards dots represent date of blood culture positivity, and the x-axis represents time. The right contains an SNV matrix containing SNV differences between isolates, with groups of isolates with few SNV differences highlighted. (A–B) Two clusters within 2 hospitals in central Canada, hospital 1 and hospital 2, with repeated interhospital transfers. Most isolates within hospitals vary by <20 SNV, suggesting intrahospital transmission. (A) First cluster in central Canada hospitals. Patient B was hospitalized in hospital 2 shortly before hospitalization in hospital 1; their isolate varied from another in hospital 2 (isolate A) by 1 SNV and was within 16 SNVs of isolates C through K at hospital 1. (B) Third cluster in central Canada. Patient A had a short previous hospitalization in Hospital prior to a longer one in Hospital 2 with ST1478 BSI. (2C–D) Two clusters identified in separate hospitals in western Canada. (C) Cluster in a western Canada hospital. Highlighted isolates in the SNV matrix show closely related isolates, suggesting intrahospital transmission of these isolates. (D) Cluster in another western Canada hospital. Although all patients developed infections at similar times and spent time on the bone marrow transplant ward, there is significant SNV variation between most isolates, suggesting repeated introduction of this strain.

All epidemiologic defined clusters contained some isolates that appeared genetically related when comparing WGS SNV analysis. The central clusters spanned 2 hospitals (hospital 1 and hospital 2, in Fig. 2A and 2B) and had cases clustered on transplant, leukemia, bone marrow transplant, and the intensive care units. In Fig. 2A and in hospital 2 in Fig. 2B, most isolates were within 20 SNVs of each other. These suggest a major role for intrahospital transmission in propagating ST1478 within these hospitals.

Interestingly, in Fig. 2A, the first patient with a ST1478 BSI in hospital 1 (labelled B in Fig. 2A) was in hospital 2 two months earlier. This patient’s isolate had an SNV difference of 1 from the other ST1478 isolate found in hospital 2 (labelled A) and was within 15 SNV of most ST1478 cases at hospital 1 in the cluster (ie, clusters C–L in Fig. 2A). Given these genetically similar isolates in hospital 1 appeared after the patient labelled B arrived, it is possible that patient B was the source of ST1478 that caused the cluster at hospital 1.

Similarly, a major cluster at hospital 2 may have been initiated by a patient previously hospitalized at hospital 1. In Figure 2B, patient A had a short stay at hospital 1 followed by a longer hospitalization on the leukemia ward of hospital 2, with development of a ST1478 BSI. This BSI was followed by multiple ST1478 BSI (Fig. 2B patients B–D) within 4 SNV of A, along with another BSI in hospital 1 (E in Fig. 2B) within 7 SNV of the BSI at hospital 2. Although patient A’s stay at hospital 1 was short, the close relatedness between isolates at both hospitals suggests interhospital transmission; patient A was a plausible ST1478 source of introduction to hospital 2 in our data set.

In the Figure 2C cluster, which represents a single hospital, 3 groups of patients vary by 4 SNV or less on similar wards, suggesting transmission. However, within wards, there was evidence of multiple introductions of ST1478; however, patient C’s infection occurred in ICU at a similar time as patient I’s and patient K’s infections (Fig. 2C), SNV variation suggests 2 unrelated introductions. Figure 2D shows a separate western Canada hospital with high variability between many isolates despite many patients spending on the bone marrow transplant units.

Clusters predicted from sequence data

In addition to using WGS to better understand epidemiologic clusters, we sought to use WGS to analyze transmission of ST1478 across Canada. We used WGS data from the whole data set to generate an SNV matrix containing all isolates, and we identified clusters of isolates containing <20. Most clusters were in individual hospitals, some of which are explored in the previous section. However, 2 clusters spanned multiple hospitals, and they highlight the clonal spread of VRE ST1478 across Canada particularly well. The first cluster (not shown) identified 33 closely related isolates in 5 hospitals across 3 provinces; most occurred at a single hospital in central Canada. The second cluster, shown in Figure 3, spans 7 hospitals in multiple cities in western Canada.

Fig. 3. Phylogeny of a cluster of isolates, with 35 SNV between, spanning 7 western Canada hospitals. Phylogeny was determined using 88.44% of the core genome. The reference genome used was the E. faecium 26G17009 pseudogenome. SNV variation is more than the <20 SNV used to identify isolates within the larger SNV matrix that contains all isolates, with the smaller sample sizes allowing more core genome to be compared.

The cluster in Figure 3 highlights that there can be dispersion of this pathogen across hospitals regionally and that seemingly unrelated isolates epidemiologically can be very closely related through sequence data. However, as the precise patient movement that transmitted these strains between hospitals cannot be identified from our patient movement data, the exact mechanism by which this pathogen spread is difficult to elucidate.