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Quarterly laboratory surveillance of acquired carbapenemase-producing Gram-negative bacteria in England: October 2020 to March 2021 Health Protection Report Volume 15 Number 13 27 July 2021 1
Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Contents
Introduction ....................................................................................................................... 3
First 2 quarters of notification data (October 2020 to March 2021)................................... 5
Geographic distribution ..................................................................................................... 6
Regional differences in resistance mechanism................................................................. 8
Distribution of species and resistance mechanism ........................................................... 9
Age and sex distribution ................................................................................................. 11
Acknowledgements ........................................................................................................ 12
2Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Introduction
From 1 October 2020, all diagnostic laboratories in England have a duty to notify the
following via PHE’s Second Generation Surveillance System (SGSS):
• acquired carbapenemase-producing Gram-negative bacteria identified in human
samples
• the results of any antimicrobial susceptibility test and any resistance mechanism for any
of the causative agents listed in Schedule 2 of the Health Protection (Notifications)
Regulations 2010
This requirement was launched in conjunction with the national Framework of Actions to
contain carbapenemase-producing Enterobacterales (CPE), which sets out a range of
measures, that if implemented well, will help health and social care providers minimise the
impact of CPE.
These analyses are based on data relating to notifications of confirmed acquired
carbapenemase-producing Gram-negative bacteria between October 2020 and March
2021 in England. The data were extracted on 1 July 2021 from both Public Health
England’s voluntary surveillance database, SGSS, and Public Health England’s
Antimicrobial Resistance and Healthcare-Associated Infections (AMRHAI) Reference Unit
database.
Rates of acquired carbapenemase-producing Gram-negative bacteria were calculated
using mid-year resident population estimates for the respective year and geography.
Geographical analyses were based on the patient’s residential postcode. Where this
information was unknown, the postcode of the patient’s General Practitioner was used.
Failing that, the postcode of the reporting laboratory was used. Cases in England were
further assigned to 1 of 9 local PHE Centres (PHECs), formed from the administrative
local authority boundaries.
As patients may have more than one positive specimen taken, specimens taken from the
same patient that yielded growth of the same pathogen and carbapenemase within a 52-
week period from the initial positive sterile site specimen, screening site specimen or other
specimen type (grouped together), were regarded as comprising the same episode of
infection and were de-duplicated. Carbapenemase-producing Gram-negative bacteria
referred isolates and local laboratory isolates were combined for this de-duplication
process, with resistance mechanism results from the AMRHAI Reference Unit retained
preferentially where patient specimen overlap occurred. This method differs slightly from
the weekly causative agent notification data, where data are not de-duplicated
incorporating specimen type. In addition, the data presented in the weekly notification
reports are utilising SGSS reports only.
3Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
The following report summarises trends and geographical distribution of
carbapenemase mechanisms identified from Gram-negative bacteria in human
samples. Species, mechanism, sample type, and age and sex of patients are also
described. For the purposes of this report, quarters are calendar quarters, as such
October to December is referred to as 'Q4' and January to March is referred to as 'Q1’
alongside relevant years. When reporting on the combined 6-month period, this is referred
to as October 2020 to March 2021.
4Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
First 2 quarters of notification data
(October 2020 to March 2021)
Between October 2020 and March 2021, there were 1,042 acquired carbapenemase-
producing Gram negative bacteria notifications. The majority were identified in
screening samples, accounting for 68.4% of carbapenemase notifications, with only
6.7% reported in sterile site specimens (Table 1).
Table 1. Number and percentage of acquired carbapenemase-producing Gram-
negative reports by specimen type (England): Q4 2020 and Q1 2021
All reports From AMRHAI ǂ
Specimen type
No. % No. %
Sterile site samples 70 6.7 40 45.7
Screening samples 713 68.4 112 16.3
Other samples * 259 24.9 93 38.0
All samples 1,042 100.0 245 100.0
* Samples that do not fall into either ‘invasive’ or ‘screening’ samples, for example, urine and
lower respiratory tract specimens.
ǂ The AMRHAI reference unit actively encourages submission of sterile site isolates for
carbapenemase confirmation; the distribution of specimen type will reflect this.
The remaining data summaries in this report consider all samples grouped together.
5Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Geographic distribution
Between October 2020 and March 2021, the overall rate of acquired carbapenemase-
producing Gram-negative bacteria reports was 0.92 per 100,000 population across
England. The overall rate was slightly higher in the first quarter of notifications compared
to the second (1.05 versus 0.80 per 100,000 population, respectively).
Figure 1. Geographical distribution of acquired carbapenemase-producing Gram-
negative bacteria rates per 100,000 population (England): October 2020 to March
2021
The rate of acquired carbapenemase-producing Gram-negative reports varied by region
(Figure 1), with the highest overall rate for both quarters combined being in the North
West (1.91 per 100,000 population), closely followed by the London region (1.77 per
100,000 population). The lowest incidence across the time period was reported in the
South West at 0.20 per 100,000 population.
6Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Comparing the regional case numbers and rates across the first 2 quarters, all
regions noted a decrease between Q4 2020 and Q1 2021, with the exception of
the Yorkshire and Humber and North East regions, where the rate per 100,000
population increased from 0.42 to 0.49 (23 to 27 reports) and 0.34 to 0.71 (9 to 19
reports), respectively (Table 2)
Table 2. Number and rate per 100,000 population of acquired
carbapenemase-producing Gram-negative reports by region (England): Q4
2020 and Q1 2021
Q4 2020 Q1 2021
PHE
Region Rate per Rate per
Centre Number Number
100,000 100,000
of reports of reports
population population
North East 9 0.34 19 0.71
North West 164 2.23 118 1.60
North of England
Yorks and
23 0.42 27 0.49
Humber
East
47 0.97 32 0.66
Midlands
Midlands and East of
23 0.37 19 0.30
East of England England
West
88 1.48 81 1.36
Midlands
London London 191 2.12 127 1.41
South East 32 0.35 18 0.20
South of England South
16 0.28 7 0.12
West
England overall 593 1.05 448 0.80
While the London region recorded the highest number of acquired carbapenemase-
producing Gram-negative bacteria in each quarter (191 and 127 in Q4 2020 and Q1
2021, respectively), the North West had the highest rate in each quarter at 2.23 and
1.60 reports per 100,000 population, respectively.
7Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Regional differences in resistance mechanism
Table 3. Regional distribution of reports by resistance mechanism (England):
Q4 2020 and Q1 2021
Reports by resistance mechanism
Region
IMP KPC NDM OXA48 VIM Other Total
East Midlands 1 11 13 53 1 0 79
East of England 3 0 9 27 3 0 42
London 13 7 144 135 14 5 318
North East 12 8 3 4 1 0 28
North West 2 169 11 84 14 2 282
South East 5 1 24 13 7 0 50
South West 0 1 11 9 1 1 23
West Midlands 0 33 28 107 1 0 169
Yorkshire and
7 11 19 7 5 1 50
Humber
England overall 43 241 262 439 47 9 1041
Similar to the incidence variation by region, the carbapenemase family identified also
varied (Table 3). Between October 2020 and March 2021, the most common
carbapenemase families reported from the North West region were KPC and OXA-48-
like, accounting for 60% and 30% of cases respectively. In the London region, the most
common carbapenemase families were NDM (45%) and OXA-48-like (42%). The South
West and South East had the lowest rates of confirmed carbapenemase-positive
isolates, and in both regions the most common resistance mechanism was NDM (48%
of isolates in both regions).
8Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume 15 number 13
Distribution of species and resistance
mechanism
The most frequently isolated Gram-negative bacterial species with a confirmed
carbapenemase mechanism in the first 2 quarters was Klebsiella pneumoniae, accounting
for 33.2% (346/1,042) of all specimens. This was followed by Escherichia coli and
Enterobacter cloacae complex, which accounted for 25.0% (261) and 18.7% (195) of all
specimens respectively (Table 4).
Among K. pneumoniae and Enterobacter cloacae complex isolates, the most common
resistance mechanisms were OXA-48-like (51.7% and 36.4%, respectively), KPC (27.7%
and 35.4%, respectively) and NDM (17.9 and 20.5%, respectively). Whilst among E. coli
isolates, the most common resistance mechanisms were OXA-48-like (45.6%), NDM
(39.1%) and KPC (13.0%).
Aside from the 'big 5' carbapenemase families (KPC, OXA-48-like, NDM, VIM and IMP),
the AMRHAI Reference Unit also screens for rarer carbapenemase families. In England
between October 2020 and March 2021, there were 5 reports of a GES carbapenemase,
3 in Pseudomonas aeruginosa, and 1 each in Acinetobacter spp. and E. coli. There were
4 Enterobacter spp. reports positive for an IMI carbapenemase. None of the rarely
identified carbapenemase families were from invasive specimens.
9Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021 Health Protection Report volume, 15
number 13
Table 4. Reports of acquired carbapenemase-producing Gram-negative bacteria by species and resistance
mechanism (England): Q4 2020 and Q1 2021)
IMP KPC NDM OXA-48-like VIM Other Total
Species
No. % No. % No. % No. % No. % No. % No. %
Acinetobacter spp. 2 25.0 0 0.0 5 62.5 0 0.0 0 0.0 1 12.5 8 100.0
Citrobacter spp. 1 1.8 12 21.4 13 23.2 25 44.6 5 8.9 0 0.0 56 100.0
Coliform 0 0.0 0 0.0 0 0.0 3 100.0 0 0.0 0 0.0 3 100.0
Enterobacter spp. 20 9.0 74 33.2 48 21.5 76 31.1 1 0.4 4 1.8 223 100.0
Escherichia coli 1 0.4 34 13.0 102 39.1 119 45.6 4 1.5 1 0.4 261 100.0
Other Escherichia spp. 0 0.0 0 0.0 1 100.0 0 0.0 0 0.0 0 0.0 1 100.0
Hafnia spp. 0 0.0 0 0.0 1 100.0 0 0.0 0 0.0 0 0.0 1 100.0
Klebsiella oxytoca 0 0.0 10 40.0 1 4.0 11 44.0 3 12.0 0 0.0 25 100.0
Klebsiella pneumoniae 5 1.4 96 27.7 62 17.9 179 51.7 4 1.2 0 0.0 346 100.0
Other Klebsiella species 1 2.5 7 17.5 16 40.0 14 35.0 2 5.0 0 0.0 40 100.0
Kluyvera species 0 0.0 1 100.0 0 0.0 0 0.0 0 0.0 0 0.0 1 100.0
Morganella spp. 0 0.0 0 0.0 1 20.0 4 80.0 0 0.0 0 0.0 5 100.0
Pluralibacter gergoviae 0 0.0 1 100.0 0 0.0 0 0.0 0 0.0 0 0.0 1 100.0
Proteus mirabilis 0 0.0 0 0.0 0 0.0 2 100.0 0 0.0 0 0.0 2 100.0
Pseudomonas aeruginosa 10 19.2 3* 5.8 11 21.2 0 0.0 25 48.1 3 5.8 52 100.0
Other Pseudomonas species 2 22.2 3* 33.3 1 11.1 0 0.0 3 33.3 0 0.0 9 100.0
Raoultella spp. 1 33.3 0 0.0 0 0.0 2 66.7 0 0.0 0 0.0 3 100.0
Serratia spp. 0 0.0 0 0.0 1 20.0 4 80.0 0 0.0 0 0.0 5 100.0
* KPC in Pseudomonas spp are extremely rare, and results should be interpreted with caution.
10Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume, 15 number 13
Age and sex distribution
The rate of acquired carbapenemase-producing Gram-negative bacteria reports
generally increased with age. A similar pattern was noted for both sexes (Figure 3) and
overall the rate was higher in males compared to females (1.7 and 1.3 reports per
100,000 population, respectively).
Figure 2. Rates of acquired carbapenemase-producing Gram-negative bacteria
reports per 100,000 population by age and sex* (England): Q4 2020 and Q1 2021
* Information about patient sex is only recorded in 82% of cases.
Figure 2 shows the acquired carbapenemase-producing Gram-negative bacterial
incidence rates by age group, with the highest rate reported in those aged 75 years and
over (8.68 per 100,000 population) followed by the 50 to 74 year age group (7.60 per
100,000 population). The rate of confirmed carbapenemases was 3.10 per 100,000
population in infants less than one year.
11Laboratory surveillance of carbapenemase-producing Gram-negative bacteria (England): Oct 2020 to March 2021
Health Protection Report volume, 15 number 13
Acknowledgements
These reports are only possible thanks to the weekly contributions from microbiology
colleagues in laboratories across England, without whom there would be no surveillance
data. Support from colleagues within Public Health England and the PHE AMRHAI
Reference Unit, is particularly valued in the preparation of the report. Feedback and
specific queries about this report are welcome via hcai.amrdepartment@phe.gov.uk.
12www.gov.uk/phe
Twitter: @PHE_uk
www.facebook.com/PublicHealthEngland
© Crown copyright 2021
Version 2
Queries relating to this document should be directed to:
HCAI-AMR Department,
National Infection Service, PHE Colindale,
61 Colindale Avenue, London NW9 5EQ.
hcai.amrdepartment@phe.gov.uk
Published July 2021
PHE gateway number: GOV-9132
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