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Carbapenemase-Producing Enterobacterales (CPE) Quarterly Surveillance Report – Q3, 2020 28 June – 26 September 2020 (Epidemiological Weeks 27–39, 2020)

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Carbapenemase-Producing Enterobacterales (CPE) Quarterly Surveillance Report – Q3, 2020 28 June – 26 September 2020 (Epidemiological Weeks 27–39, 2020) Carbapenemase-producing Enterobacterales (CPE) Quarterly Surveillance Report – Q3, 2020 28 June – 26 September 2020 (Epidemiological weeks 27–39, 2020) Summary “Carbapenemase- producing Enterobacterales (CPE) infection and colonisation” was added to the list of laboratory notifiable conditions in New South Wales on 28 February 2019. This CPE surveillance report summarises characteristics of patients who were notified with CPE infection or colonisation in NSW by laboratories during the third quarter of 2020 (28 June–26 September 2020; epidemiological weeks 27–39). In summary: Notifications • 64 unique notifications of carbapenemase-producing Enterobacterales (CPE) infection or colonisation in a total of 61 patients were received during this reporting period. Patients • 61 patients were identified as having CPE, three of whom had more than one notification of CPE (two notifications each). • The median age of patients at notification was 63 years (range: 2 months to 94 years). Five patients (8%) were under 10 years of age (including four infants under 12 months of age), 45 (74%) were 10-79 years, and 11 (18%) were 80 years or over. • 34 (56%) patients were male, and 27 (44%) patients were female. Specimens Of the 64 notifications, specimens collected included: • 22 (34%) for screening; • 22 (34%) from urine; • 17 (27%) from non-sterile sites, excluding urine; and • 3 (5%) from sterile sites, consistent with CPE infection. Bacteriology • Eleven different Enterobacterales species were detected, mostly: o Enterobacter cloacae complex (24, 37.5%); o Klebsiella pneumoniae (15, 23.4%); o Escherichia coli (10, 15.6%); o Citrobacter freundii (6, 9.4%); and o Klebsiella oxytoca (3, 4.7%). Genetics • Four different carbapenemase-producing resistance genes were detected (IMP, NDM, OXA-48, OXA-23), as follows: o IMP (46, 71.9%); o NDM (8, 12.5%); SHPN: (HP NSW) 210082 ISSN: 2652-4155 o OXA-48 like (4, 6.3%); o OXA-23 like (3, 4.7%); o IMP and OXA-23 like (2, 3.1%); and o IMP and OXA-48 like (1, 1.5%). • This includes two notifications which reported a single bacterial species (Enterobacter cloacae complex, n = 1 and Klebsiella oxytoca, n = 1) each harbouring two carbapenemase-producing resistance genes (IMP and OXA-23 like); and one notification reporting another bacterial species (Klebsiella aerogenes) harbouring a different combination of carbapenemase-producing resistance genes (IMP and OXA-48 like). Introduction Multi-resistant organisms are a growing threat internationally. Following expert review, NSW Health identified carbapenemase-producing Enterobacterales (CPE) as a high priority pathogen. The NSW Public Health Act 2010 was amended to require laboratory notification of ‘carbapenemase- producing Enterobacterales infection or colonisation’ from 28 February 2019. An aim of implementation of a state-wide surveillance program was to assist with identification of cases and increase our understanding of the epidemiology of CPE in NSW. Management of CPE is supported by the NSW Health Guideline for Surveillance and Management of CPE in NSW Health Facilities. Carbapenemase-producing Enterobacterales (CPE) Enterobacterales are an order of Gram-negative bacilli that occur naturally in the gastro-intestinal tract. They can spread outside the gastro-intestinal tract and cause serious infections such as bacteraemia, pneumonia, urinary tract infections and wound infections. Carbapenems are an important class of broad spectrum β-lactam antibiotics which are highly effective against most Gram-negative infections. Enterobacterales can acquire resistance to carbapenem antibiotics by a number of mechanisms. Enterobacterales which are resistant to carbapenem antibiotics, by one of a number of mechanisms, are called carbapenem-resistant Enterobacterales (CRE). Carbapenemase-producing Enterobacterales (CPE) describe Enterobacterales which are resistant to carbapenem antibiotics through production of carbapenemase enzymes encoded by plasmid-mediated carbapenemase genes. The carbapenemase enzymes hydrolyse carbapenems (as well as other β-lactams, such as penicillins and cephalosporins). This means that CPE infections are difficult to treat. Several different carbapenemase genes have been reported in Enterobacterales. Five of the most important types globally are: 1. Imipenemase (IMP) 2. Klebsiella pneumoniae carbapenemase (KPC) 3. New Delhi metallo-β-lactamase (NDM) 4. Verona integron-encoded metallo-β-lactamase (VIM) 5. Oxacillinases (OXA) Individuals who have acquired CPE can either carry it harmlessly in their gut, like other Enterobacterales, termed colonisation, or may develop an infection with the CPE. A person who is colonised will not have any symptoms. Here we report on the characteristics of patients who were notified in the third quarter of 2020 (epidemiological weeks 27–39, 2020). 2 | P a g e NSW CPE surveillance: epidemiological weeks 27–39, 2020 SHPN: (HP NSW) 210082 CPE infection or colonisation in NSW: 29 March – 27 June 2020 Notifications Between 28 June and 26 September 2020, 64 unique notifications have been received relating to specimens collected from 61 patients. Figure 1: Notifications of carbapenemase-producing Enterobacterales, by date of specimen collection and date of notification, NSW, 28 June–26 September 2020 5 Specimen collection date Notification date 4 3 2 1 Number of notifications of Number 0 16-Jul-20 01-Jul-20 04-Jul-20 07-Jul-20 10-Jul-20 13-Jul-20 19-Jul-20 22-Jul-20 25-Jul-20 28-Jul-20 31-Jul-20 07-Jun-20 10-Jun-20 13-Jun-20 16-Jun-20 19-Jun-20 22-Jun-20 25-Jun-20 28-Jun-20 11-Sep-20 02-Sep-20 05-Sep-20 08-Sep-20 14-Sep-20 17-Sep-20 20-Sep-20 23-Sep-20 26-Sep-20 03-Aug-20 06-Aug-20 09-Aug-20 12-Aug-20 15-Aug-20 18-Aug-20 21-Aug-20 24-Aug-20 27-Aug-20 30-Aug-20 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 Date and epidemiological week, 2020 Notes on Figure 1: • Displays all notifications received between 28 June and 26 September 2020 (epidemiological weeks 27–39) (n = 64); date of specimen collection may precede the surveillance reporting period specified. • Where multiple Enterobacterales species are cultured from a single isolate, each species is counted as a separate CPE notification (but a single case). • Where molecular testing has identified multiple carbapenemase genes from a single Enterobacterales species, this will be counted as one notification. Demographics Of the 61 patients, the median age of patients at notification was 63 years (range: 2 months to 94 years). Five patients (8%) were under 10 years of age (including four infants under 12 months of age), 45 (74%) were 10-79 years, and 11 (18%) were 80 years or over. In terms of gender distribution, 34 (56%) patients were male, and 27 (44%) patients were female. 3 | P a g e NSW CPE surveillance: epidemiological weeks 27–39, 2020 SHPN: (HP NSW) 210082 Figure 2: Carbapenemase-producing Enterobacterales cases, by gender and ten-year age group, NSW, 28 June– 26 September 2020 16 Female Male 14 12 10 8 Cases 6 4 2 0 0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 Age group Specimen type Of the 64 notifications (excluding duplicates and confirmatory testing), 22 (34%) were specimens collected for screening purposes; and 22 specimens (34%) were collected from urine, which could represent either infection or colonisation. Seventeen specimens (27%) were collected from non-sterile sites, excluding urine (e.g. wound culture, sputum, unspecified sites). Three (5%) specimens were collected from sterile sites, consistent with CPE infection. 4 | P a g e NSW CPE surveillance: epidemiological weeks 27–39, 2020 SHPN: (HP NSW) 210082 Figure 3: Daily notifications of carbapenemase-producing Enterobacterales by specimen type and date of specimen collection in NSW, 28 June–26 September 2020 5 Screening Non-sterile site Urine Sterile site 4 3 2 Number of specimens of Number 1 0 03-Jul-20 06-Jul-20 09-Jul-20 12-Jul-20 15-Jul-20 18-Jul-20 21-Jul-20 24-Jul-20 27-Jul-20 30-Jul-20 27-Jun-20 21-Jun-20 24-Jun-20 30-Jun-20 01-Sep-20 04-Sep-20 07-Sep-20 10-Sep-20 13-Sep-20 16-Sep-20 19-Sep-20 22-Sep-20 25-Sep-20 14-Aug-20 02-Aug-20 05-Aug-20 08-Aug-20 11-Aug-20 17-Aug-20 20-Aug-20 23-Aug-20 26-Aug-20 29-Aug-20 26 27 28 29 30 31 32 33 34 35 36 37 38 39 Date and epidemiological week Notes on Figure 3: • Duplicate notifications and confirmations are excluded. • Date of specimen collection may precede the surveillance reporting period specified. Figure 4: Notifications of carbapenemase-producing Enterobacterales by specimen type and gender in NSW, 28 June–26 September 2020 Screening Non-sterile site Urine Sterile site 16 14 12 10 8 6 Number of specimens of Number 4 2 0 Female Male Gender Notes on Figure 4: • Duplicate notifications and confirmations are excluded. • A specimen marked “screening” or some variation is considered to be part of a deliberate screen for CPE. The two remaining categories, namely non-sterile site and urine, could represent either an infection or colonisation. 5 | P a g e NSW CPE surveillance: epidemiological weeks 27–39, 2020 SHPN: (HP NSW) 210082 Bacteriology Eleven different Enterobacterales species were detected in the notified cases, as follows: Enterobacter cloacae complex (24, 37.5%); Klebsiella pneumoniae (15, 23.4%); Escherichia coli (10, 15.6%); Citrobacter freundii (6, 9.4%); Klebsiella oxytoca (3, 4.7%); Enterobacter gergoviae (1, 1.6%); Escherichia hermannii (1, 1.6%); Klebsiella aerogenes (1, 1.6%); Klebsiella variicola (1, 1.6%); Morganella morganii (1, 1.6%); and Proteus mirabilis (1, 1.6%). Figure 5: Notifications of carbapenemase-producing Enterobacterales by host bacterial species and carbapenemase gene type in NSW, 28 June–26 September 2020 IMP NDM OXA23 OXA48 Proteus mirabilis Morganella morganii Klebsiella variicola Klebsiella pneumoniae Klebsiella oxytoca Klebsiella aerogenes Organism Escherichia hermannii Escherichia coli Enterobacter gergoviae Enterobacter cloacae complex Citrobacter freundii 0 10 20 30 Number of notifications Note on Figure 5: • Duplicate notifications and confirmations are excluded.
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