Accredited official statistics

Quarterly epidemiological commentary: Mandatory Gram-negative bacteraemia, MRSA, MSSA and C. difficile infections (data up to January to March 2023)

Updated 6 November 2024

Applies to England

UK Health Security Agency and this report

Since the UK Health Security Agency (UKHSA) was created in April 2021, it has been responsible for protecting every member of every community from the effect of infectious diseases, chemical, biological, radiological, and nuclear incidents and other health threats. We provide intellectual, scientific, and operational leadership at national and local level, as well as on the global stage, to make the nation’s health secure.

The agency replaces Public Health England (PHE) and is an executive agency of the Department of Health and Social Care (DHSC). The transition to UKHSA included the integration of both staff and systems. Accordingly, the systems and processes responsible for the publication of the previous annual epidemiological commentaries were incorporated into UKHSA. The same methods of data capture, analysis and dissemination have been employed in the production of this report.

Data included in this quarterly epidemiological commentary

This document contains quarterly, national-level epidemiological commentaries for meticillin-resistant Staphylococcus aureus (MRSA), meticillin-susceptible Staphylococcus aureus (MSSA), Escherichia coli (E. coli), Klebsiella spp. and Pseudomonas aeruginosa (P. aeruginosa) bacteraemia and Clostridioides difficile infection (CDI). These include analyses on counts and incidence rates of all reported, hospital-onset (previously referred to as trust-apportioned) and community-onset (previously referred to as non-trust-apportioned) cases of MRSA, MSSA, E. coli, Klebsiella spp. and P. aeruginosa bacteraemia and CDI. All data tables associated with this report are included in an OpenDocument spreadsheet.

Revisions to data included are covered by a data-specific revisions and correction policy.

If these data are used for publication elsewhere, citation to UK Health Security Agency (UKHSA), healthcare associated infections (HCAI) and antimicrobial resistance (AMR) division is required, using the content below.

Citation: UK Health Security Agency. Quarterly epidemiology commentary: Mandatory Gram-negative bacteraemia, MRSA, MSSA and C. difficile infections in England (data up to January to March 2023) London: UK Health Security Agency, July 2023.

COVID-19 and this data

Marked differences in general trends of all the data collections were observed over the course of the SARS-CoV-2 (COVID-19) pandemic. In general, we observed a reduction in the number of counts, compared to what would have been expected, across all BSI and CDI cases in the initial stages, followed by various fluctuations.

Analysis of voluntary laboratory surveillance data from April 2020 to March 2022 mirrored the changes seen in the mandatory surveillance system during this period, albeit to different extents. Due to the similarities in trends across both systems, these changes do not appear to be a specific ascertainment problem in the mandatory programme.

Hospital activity changed radically over the course of the pandemic, with an influx of patients critically ill with respiratory infection, and cancellation or delays applied to elective procedures. A gradual staged return to normal activity occurred later. Various other general restrictions on movement and mixing were introduced nationally to limit spread of the virus. As a result, data and trends from the beginning of the pandemic onwards should be interpreted with caution and take into consideration these otherwise unprecedented changes.

Epidemiological analyses of Gram‑negative bacteraemia data

E. coli bacteraemia

Main findings

All reported cases of E. coli bacteraemia in January to March 2023 increased by 12.4% from 8,275 cases to 9,302 when compared to July to September 2011, with a corresponding increase in the incidence rate of 7.9% from 61.8 to 66.7 cases per 100,000 population. This increase was primarily driven by an increase in community-onset cases, the count of which increased by 17.8% from 6,279 to 7,399, with a 13.1% increase in incidence rate from 46.9 to 53.1 cases per 100,000 population. In contrast, the count of hospital-onset cases decreased by 4.7% from 1,996 to 1,903 cases, and the incidence rate of these cases decreased by 9.8% from 23.6 to 21.3 per 100,000 bed-days.

When comparing the same quarter to the previous year (2022), counts and incidence rates of all reported cases increased by 3.2%, respectively, from 9,011 to 9,302 and from 64.6 to 66.7 per 100,000 population (Figure 1a). This more recent increase is driven by an increase in hospital-onset cases: these increased by 7.8% from 1,765 to 1,903 compared to January to March 2022 (Figure 1b), which corresponded to an incidence rate increase of 1.9% from 20.9 to 21.3 per 100,000 bed-days. Over the same time period, the count and incidence rate of community-onset E. coli bacteraemia cases increased by 2.1%, respectively, from 7,246 to 7,399 and from 52.0 to 53.1 per 100,000 population (Table S1 in the accompanying data tables).

Detailed findings

The incidence rate of all reported E. coli bacteraemias increased each financial year between the initiation of the mandatory surveillance of E. coli bacteraemia in July 2011 and the start of the COVID-19 pandemic (January to March 2020, Figure 1a). This increase was primarily driven by community-onset cases (Table S1 in the accompanying data tables). A reduction in the count and incidence rates of all reported and community-onset cases was observed after the start of the pandemic, but they remained higher than they were at the start of this surveillance ( Figure 1a). In contrast, the incidence rate of hospital-onset cases remained relatively stable during the same period, except for a sharp reduction (20.7 cases per 100,000 bed days) observed in April to June 2021 (Figure 1b). This was followed by a steady return to pre-pandemic rates, which however remained lower than at the start of E. coli surveillance.

Overnight occupied bed-days were 20.3% higher in January to March 2023 when compared to the same quarter in 2021. There has been a slow return to more usual counts of overnight bed-days in the current quarter (January to March 2023), which is 5.9% higher than the same quarter in 2022. The incidence rate of hospital-onset E. coli bacteraemia increased more slowly than its count did; this may be due to a steady return to the typical number of overnight bed-days in January to March 2023, compared to the unusually low levels in October to December 2020.

When comparing January to March 2023 with the equivalent pre-COVID-19 pandemic period in 2019, there was a 9.3% decrease in total cases from 10,250 to 9,302, with a corresponding decrease of 9.7% in the incidence rate from 73.9 to 66.7 cases per 100,000 population (Figure 1a). Community-onset cases decreased by 11.9% from 8,395 to 7,399. Similarly, the incidence rate of community-onset cases also declined by 12.3% from 60.5 to 53.1 cases per 100,000 population. Finally, the total numbers of hospital-onset cases increased slightly by 2.6% compared to the same period from 1,855 to 1,903. The hospital-onset incidence rate remained substantially stable, increasing slightly from 21.1 to 21.3 cases per 100,000 bed-days (Figure 1b). These highlight the slow increase in reports of E. coli bacteraemia cases since the decline seen at the start of the COVID-19 pandemic, with community-onset counts and rates not yet returning to levels seen prior to the COVID-19 pandemic. There are uncertainties in why we still see lower levels of community-onset E. coli BSI post pandemic, with further investigative work ongoing.

A seasonality trend is visible with all reported E. coli bacteraemia, whereby the highest rates are observed between July to September of each year, although there was more fluctuation during the pandemic years. There is less evidence of the same seasonality among hospital-onset cases, though a summer peak is observed between April 2015 and March 2019.

Figure 1a. Quarterly rates of all reported E. coli bacteraemia: July 2011 to March 2023

Figure 1b. Quarterly rates of hospital-onset E. coli bacteraemia: July 2011 to March 2023

Since April 2020, community-onset E. coli bacteraemia cases have been further categorised into healthcare- or community- associated, based on whether each patient had been previously discharged from the same reporting acute trust in the preceding 28 days (see appendix).

Despite a slight decline in community-onset community-associated (COCA) cases between April to June 2020 and January to March 2023, these still accounted for the majority of reported community-onset E. coli bacteraemia by the end of this period, with the percentage of cases decreasing from 69.9% to 65.7%. The percentage of hospital-onset healthcare associated (HOHA) and community-onset healthcare-associated (COHA) cases increased from 15.9% to 20.5% and 12.5% to 13.4%, respectively, over the same period.

The distribution of cases across these categories remained relatively stable from the current quarter (January to March 2023) compared to the same quarter in the previous year (January to March 2022). The percentage of cases that were HOHA increased slightly from 19.6% to 20.5%, whereas for COHA and COCA, cases decreased slightly from 13.6% to 13.4% and 66.4% to 65.7%, respectively (Figure 1c and Table 1a in the accompanying data tables).

Figure 1c. Quarterly percentage of E. coli bacteraemia cases by prior trust exposure: April 2020 to March 2023

Klebsiella spp. bacteraemia

Main findings

All reported cases of Klebsiella species bacteraemia increased by 20.1% from 2,352 cases to 2,824 in January to March 2023 when comparing to April to June 2017. The incidence rate of all reported cases also increased by 19.4% from 17.0 to 20.3 cases per 100,000 population. These increases are most notable in hospital-onset cases, which increased by 36.2% from 671 to 914 cases and by 31.5% from 7.8 to 10.2 cases per 100,000 bed-days respectively (Figure 2b). Over the same period, the count of community-onset cases increased by 13.6% from 1,681 to 1,910, with a corresponding 13.0% increase in incidence rate from 12.1 to 13.7 cases per 100,000 population.

Comparing the same quarter to the previous year (2022), both counts and incidence rates of all reported cases increased by 6.3% from 2,657 to 2,824 and 19.1 to 20.3 per 100,000 population, respectively (Figure 2a). This was driven by a decrease in community-onset cases, however we continued to see increases in hospital-onset cases. Over this time period, community-onset Klebsiella species bacteraemia cases and rates increased by 3.6% from 1,844 to 1,910 cases and 13.2 to 13.7 per 100,000 population, Table S1 in the accompanying data tables). In January to March 2023, hospital-onset Klebsiella species bacteraemia cases increased by 12.4% from 813 to 914 when compared to January to March 2022 (Figure 2b), while the incidence rate increased by 6.2% from 9.6 to 10.2 per 100,000 bed-days (Table S2 in accompanying data tables).

Detailed findings

Counts and rates of hospital-onset Klebsiella spp. had a sustained peak between the July to September 2020 and January to March 2021 quarters, during the COVID-19 pandemic. Both counts and rates of hospital-onset cases reached their highest levels observed since the inception of mandatory Klebsiella spp. surveillance. The incidence rate of hospital-onset cases peaked at 15.5 cases per 100,000 bed-days in January to March 2021. The specific causes of this increase are not well understood; however, it coincided with a high incidence of COVID-19, with many cases identified as COVID-19 co-infections (1).

When comparing the most recent quarter (January to March 2023) with the equivalent pre-COVID-19 pandemic period in 2019, there was a 9.3% increase in total cases from 2,583 to 2,824, with a corresponding increase of 8.8% in the incidence rate from 18.6 to 20.3 cases per 100,000 population (Figure 2a, Table S2 in the accompanying data tables). Community-onset cases increased by 4.0% from 1,837 to 1,910. Similarly, the incidence rate of community-onset cases also increased by 3.5% from 13.2 to 13.7 cases per 100,000 population. Finally, the count and rate of hospital-onset cases increased by 22.5% and 20.1% from 746 to 914 and 8.5 to 10.2 cases per 100,000 bed-days (Figure 2b, Table S2 in the accompanying data tables), respectively. These highlight a gradual increase in total counts, signalling a return to pre COVID-19 levels. The all reported rates however, have now exceeded the pre COVID-19 levels, continuing on an upward trajectory and are at the highest since the start of surveillance.

During the January to March 2023 quarter, 72.2% of all reported Klebsiella spp. bacteraemias (2,039 of 2,824) were caused by Klebsiella pneumoniae, similar to the same quarter in the previous year (72.2%, January to March 2022). In January to March 2023, 17.0% of cases were identified as Klebsiella oxytoca (480 of 2,824), a marginal decrease from the 17.1% reported in January to March 2022.

The incidence rate of the majority of Klebsiella species increased at approximately the same pace (Figure 2a, Table S2 in the accompanying data tables). The exception to this was the incidence rate of K. oxytoca, which increased within hospital-onset cases around the start of the pandemic and subsequently stabilised from 1.9 to 2.1 per 100,000 bed days.

There is evidence of seasonality in the trend of all reported Klebsiella spp. bacteraemia cases, with the highest incidence rates normally observed in July to September of each year (Figure 2a).

Figure 2a. Quarterly rates of all reported Klebsiella spp. bacteraemia by species: April 2017 to March 2023

Figure 2b. Quarterly rates of hospital-onset Klebsiella spp. bacteraemia: April 2017 to March 2023

Between April to June 2020 and January to March 2023, COCA cases made up roughly half of all Klebsiella spp. bacteraemia (Figure 2c).

Since the start of surveillance, the proportion of HOHA cases peaked at 39.6% in January to March 2021 alongside a decline in COCA cases to 46.4%. The increase in HOHA cases coincided with the third lockdown (January 2021), where an increase in Klebsiella spp. BSI cases were observed in the hospital setting (1).

Comparing January to March 2023 to the same quarter in 2022, the percentage of HOHA cases of all cases increased slightly (from 30.6% to 32.4%), while COHA cases remained broadly the same (from 13.6% to 13.8%). The percentage of COCA cases decreased slightly from 55.4% to 53.4% of all Klebsiella spp. bacteraemia cases. (Figure 2c, Table S2a in the accompanying data tables).

Figure 2c. Quarterly percentage of Klebsiella spp. bacteraemia cases by prior trust exposure: April 2020 to March 2023

Pseudomonas aeruginosa bacteraemia

Main findings

Between April to June 2017 and January to March 2023, there was a slight increase of 1.3% in the count and in the incidence rate of all reported P. aeruginosa bacteraemia cases: from 1,016 to 1,029 and from 7.3 to 7.4 cases per 100,000 population, respectively (Figure 3a). This was driven by an increase in hospital-onset cases, which increased by 10.1% from 376 to 414 cases and by 6.3% from 4.3 to 4.6 cases per 100,000 bed-days, respectively. The count and the incidence rate of community-onset cases decreased by 3.9% from 640 to 615 cases and by 4.4% from 4.6 to 4.4 cases per 100,000 population, respectively. Over the same period, the count and the incidence rate of hospital-onset cases (Figure 3b, Table S3 in the accompanying data tables).

Comparing January to March 2023 with the same period in the previous year (January to March 2022), the total reported counts and rates increased by 9.1% from 943 to 1,029, and from 6.8 to 7.4 cases per 100,000 population, respectively. A 15% increase was observed in the hospital-onset counts, 360 to 414, with an 8.7% increase in the hospital-onset incidence rate from 4.3 to 4.6 cases per 100,000 bed-days. Community-onset cases displayed a 5.5% increase in both counts and rates from 583 in January to March 2022 to 615 in January to March 2023 and 4.2 to 4.4 per 100,000 population.

Detailed findings

Similarly to Klebsiella spp. cases, increases in counts and rates of hospital-onset P. aeruginosa were observed during the second wave of the COVID-19 pandemic. The counts and rates of hospital-onset P. aeruginosa increased between July 2020 and March 2021 to levels not seen since the start of the mandatory surveillance of P. aeruginosa bacteraemia. The incidence rate of hospital-onset cases peaked at 7.0 cases per 100,000 bed-days in the January to March 2021 period. The reasons for this increase have been investigated and it was observed that this increase coincided with a rise in the percentage of hospital-onset bacteraemia cases who were also positive for COVID-19 (1).

Compared to the same period in 2019 (January to March 2019), which was a more typical year before the COVID-19 pandemic, there was a 6.6% increase in the count of all reported cases from 965 to 1,029, with a similar increase in incidence rate of 6.2%, from 7.0 to 7.4 per 100,000 population. (Figure 3a, Table S3 in the accompanying data tables). During the same period, counts of community-onset P. aeruginosa cases saw a similar increase of 1.8% from 604 to 615, with a marginal increase in the community-onset incidence rate of 1.4% (Table S3 in the accompanying data tables). In addition, a rise in counts and rates of hospital-onset P. aeruginosa cases of 14.7% from 361 to 414 in counts and 12.4% increase from 4.1 to 4.6 per 100,000 bed-days was observed (Figure 3b, Table S3 in the accompanying data tables). This suggests that the general trend seen in the all reported and community onset P. aeruginosa cases has broadly remained unaffected by the COVID-19 pandemic, and that, following the initial peak in hospital onset cases seen at the start of the COVID-19 pandemic (Figure 3b), the hospital-onset counts have returned to expected pre-pandemic levels.

There is evidence of seasonality in the incidence of all reported P. aeruginosa bacteraemia cases, with the highest rates normally observed in the July to September quarter of each year (Figure 3a).

Figure 3a. Quarterly rates of all reported P. aeruginosa bacteraemia: April 2017 to March 2023

Figure 3b. Quarterly rates of hospital-onset P. aeruginosa bacteraemia: April 2017 to March 2023

Similar to E. coli and Klebsiella spp., COCA cases tend to make up around 45% of all P. aeruginosa bacteraemia cases between the April to June 2020 and January to March 2023 quarters. However, in the January to March 2021 quarter, HOHA cases (48.2% of total) surpassed COCA cases (36.8%) for the first time since April 2020, coinciding with the peak of the second wave of the COVID-19 pandemic.

Comparing January to March 2023 to the same quarter in 2022, COHA and COCA cases decreased from 16.9% to 15.6% and 44.9% to 43.4% of all P. aeruginosa bacteraemia cases, respectively. The percentage of HOHA cases increased from 38.2% to 40.2% (Figure 3c, Table S3a in the accompanying data tables).

Figure 3c. Quarterly percentage of P. aeruginosa bacteraemia cases by prior trust exposure: April 2020 to March 2023

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

Main findings

Comparing January to March 2023 to the same period in 2022 (January to March 2022), a 17.3% increase was seen in the count and rate of all reported cases from 179 to 210 cases, and from 1.3 to 1.5 per 100,000 population (Figure 4a, Table S4 in the accompanying data tables). The increase was more pronounced in hospital-onset cases, which increased by 48.1% from 54 to 80, with a corresponding 40.0% increase in incidence rate from 0.6 to 0.9 per 100,000 bed-days. Community-onset MRSA bacteraemia counts showed a slight increase of 4.0% from 125 to 130. However the rate remained unchanged at 0.9 cases per 100,000 population. (Table S4 in the accompanying data tables).

Detailed findings

A considerable decrease in the incidence rate of all reported MRSA bacteraemia cases has been observed since the enhanced mandatory surveillance began in April 2007 (Figure 4a, Table S4 in the accompanying data tables). The incidence rate of all reported cases fell by 86.9% from 10.2 in the April to June 2007 quarter to 1.3 cases per 100,000 in the April to June 2014 quarter. The rate has fluctuated between 1.0 and 1.8 since then and is currently at 1.5 cases per 100,000 population in the most recent quarter (January to March 2023).

A similar trend was observed with the incidence rate of hospital-onset cases (Figure 4b, Table S4 in the accompanying data tables). There was a steep decrease of 83.3%, from 4.9 cases per 100,000 bed-days in the April to June 2008 period to 0.8 case per 100,000 bed-days in the April to June 2014 period. Subsequently, between April to June 2014 and January to March 2023, the rate has increased to 0.8 cases per 100,000 bed-days. Since April to June 2014, there have been fluctuations in both the number of hospital-onset infections, ranging between 48 and 107, and the hospital-onset incidence rate, ranging between 0.6 and 1.4 cases per 100,000 population.

Similarly to Klebsiella spp. and P. aeruginosa, between January and March 2021 there was a peak in the incidence rate of hospital-onset MRSA bacteraemia, at 1.4 cases per 100,000 bed-days (Figure 4b, Table S4 in the accompanying data tables). This was the highest rate seen for hospital-onset MRSA bacteraemia since April to June 2011. The reasons for this increase are still being investigated, although it has been observed that this increase coincided with a rise in the percentage of hospital-onset bacteraemia cases who were also positive for COVID-19 (1).

Comparing January to March 2023 with the same period in 2019 (January to March 2019), which represents a more typical year before the COVID-19 pandemic, a 17.3% increase was seen in all reported counts of cases from 179 to 210 cases, with a corresponding increase in rate of 16.8% from 1.3 to 1.5 per 100,000 population (Figure 4a, Table S4 in the accompanying data tables). Community-onset MRSA bacteraemia counts increased by 9.2% from 119 to 130 and rates remained the same at 0.9 cases per 100,000 population (Table S4 in the accompanying data tables). The count of hospital-onset MRSA bacteraemia cases also increased more by 33.3% from 60 to 80, with a 30.7% increase in incidence rate from 0.7 to 0.9 per 100,000 bed-days (Figure 4b, Table S4 in the accompanying data) tables). These trends suggest a return to pre COVID-19 levels in hospital-onset counts and rates.

Figure 4a. Quarterly rates of all reported MRSA bacteraemia: April 2007 to March 2023

Figure 4b. Quarterly rates of hospital-onset MRSA bacteraemia: April 2008 to March 2023

MSSA bacteraemia

Main findings

The count of all reported cases of MSSA bacteraemia increased by 48.7% from 2,199 to 3,269 between January to March 2011 and January to March 2023. This was accompanied by a 39.6% increase in incidence rate from 16.8 to 23.4 per 100,000 population (Figure 5a, Table S5 in the accompanying data tables). Increases have been driven by community-onset cases. Between the January to March 2011 and January to March 2023 quarters, the count and the incidence rate of community-onset cases increased by 59.4% and 49.7% respectively from 1,464 to 2,333 cases and from 11.2 to 16.7 cases per 100,000 population (Table S5 in the accompanying data tables). Over the same period, the count of hospital-onset cases increased by 27.3% from 735 to 936 cases, while the hospital-onset incidence rate increased by 25.4% from 8.3 to 10.5 cases per 100,000 bed-days (Figure 5a and Figure 5b, Table S5a in the accompanying data tables). Counts and rates of MSSA bacteraemia remain the highest since the beginning of the surveillance programme in 2011.

Comparing the most recent quarter (January to March 2023) to the same period in the previous year (January to March 2022) shows a 4.8% increase in the count and rates of all reported cases from 3,120 to 3,269, and from 22.4 to 23.4 per 100,000 bed-days, respectively. Hospital-onset MSSA bacteraemia cases remained nearly unchanged declining from 937 to 936, with a 5.6% decrease in incidence rate from 11.1 to 10.5 per 100,000 bed-days. The count and incidence rate for community-onset MSSA bacteraemia cases increased 6.8% from 2,183 to 2,333 cases and 15.7 to 16.7 per 100,000 population.

Detailed findings

There has been a general trend of increasing count and incidence rate of cases since the mandatory reporting of MSSA bacteraemia began in January 2011. This trend was not inverted despite a temporary reduction (2,753 and 19.6 cases per 100,000 population, respectively) during the COVID-19 pandemic: the latest quarterly MSSA count and rate are still higher than at the beginning of the MSSA surveillance. Since April 2021, all reported cases and rates have returned to a more steadily increasing trend. Between April to June 2021 and the most recent quarter, a 9.0% increase in all counts of MSSA bacteraemia has been observed (2,998 to 3,269). This coincides with an 10.3% increase in incidence rate from 21.3 to 23.4 per 100,000 population.

Since the April to June 2020 quarter, there has been an increase in the incidence rate of hospital-onset MSSA bacteraemia cases. The increase in hospital-onset rate is, in part, a result of reduced hospital activity, resulting in reduced occupied overnight bed-days (Table S5 in the accompanying data tables), the denominator used for the hospital-onset rates. The increasing rate culminated in a peak during the January to March 2021 quarter, when it was 13.4 cases per 100,000 bed-days and 1,000 cases reported. This was the highest MSSA hospital-onset rate and count that has been observed since the inception of MSSA surveillance. This pattern is comparable to that observed in both Klebsiella spp. and P. aeruginosa.

When comparing the current quarter to the pre-pandemic period of January to March 2019, a 7.9% increase in the counts of all reported cases was observed, rising from 3,029 to 3,269 cases, along with a 7.4% increase in the rate from 21.8 to 23.4 cases per 100,000 population. Over this same period, hospital-onset MSSA bacteraemia cases have increased by 10.9% from 844 to 936, which corresponds to an 8.7% increase in the incidence rate from 9.6 to 10.5 per 100,000 bed-days. Community-onset MSSA bacteraemia cases displayed the least change, with an increase in counts of 6.7% from 2,185 to 2,333, and 6.3% increase in incidence rate from 15.7 to 16.7 per 100,000 population, over the same period. Although there was an initial drop in all reported cases at the start of the COVID-19 pandemic, the all reported count and incidence rate have generally remained high since the inception of the MSSA surveillance (Figure 5a). The reasons behind these observed increases are still under investigation.

Figure 5a. Quarterly rates of all reported MSSA bacteraemia: January 2011 to March 2023

Figure 5b. Quarterly rates of hospital-onset MSSA bacteraemia: January 2011 to March 2023

Epidemiological analyses of Clostridioides difficile infection data

Main findings

When comparing the most recent quarter to the same period in the previous year (January to March 2022), there has been a 10.5% increase in the count and rate of all reported cases from 3,274 to 3,619 and 23.5 to 26.0 cases per 100,000 population (Figure 6a, Table S6 in the accompanying data tables), respectively. These changes were driven by an increase in hospital-onset cases, which increased by 19.1% from 1,359 to 1,618 which corresponds to an incidence rate increase of 12.5% from 16.1 to 18.1 cases per 100,000 bed-days. Community-onset CDI counts and rates increased by 5%, changing from 1,915 to 2,001 and 13.7 to 14.4 cases per 100,000 population (Figure 6b, Table S6 in the accompanying data tables).

Detailed findings

Since the initiation of C. difficile infection (CDI) surveillance in April 2007, there has been an overall decrease in the count and incidence rate of both all reported and hospital-onset cases (Figure 6a, Figure 6b and Table S6 in the accompanying data tables).

The greatest decrease in CDI cases and incidence rate occurred between the April to June 2007 and January to March 2012 quarters. During this time, there was a large 78.0% reduction in all reported cases of CDI, dropping from 16,864 to 3,711 cases, with an associated 78.8% decrease in incidence rate from 131.6 to 27.9 cases per 100,000 population. Following this notable decline, CDI cases and incidence rate remained stable. Subsequently, between January to March 2012 and the same period in 2023, the count of all reported cases decreased by 2.5% from 3,711 to 3,619 cases; with a corresponding 7.0% reduction in the incidence rate from 27.9 to 26.0 cases per 100,000 population. This is, in part, due to an absolute population increase of 4.8%.

There were similar, but greater, reductions among hospital-onset CDI cases between April to June 2007 and January to March 2012, with an 84.5% reduction in count of cases (from 10,436 to 1,613 cases) and an 83.9% reduction in the incidence rate (from 112.5 to 18.1 per 100,000 bed-days). This was followed by a 1.9% increase in the count of cases between January to March 2012 and January to March 2023, from 1,613 to 1,618 cases, and no change in incidence rate, which remained 18.1 cases per 100,000 bed-days.

When comparing the most recent quarter with January to March 2019, which was a more typical period prior to the COVID-19 pandemic, there has been a 39.0% increase in the count of all reported cases from 2,604 to 3,619, corresponding to an 38.4% increase in the incidence rate, from 18.8 to 26.0 cases per 100,000 population (Figure 6a, Table S6 in the accompanying data tables). Community-onset CDI cases increased by 21.0% from 1,654 to 2,001 while the rate increased by 20.4% from 11.9 to 14.4 per 100,000 population (Table S6 in the accompanying data tables). The greatest rise can be seen in the hospital-onset CDI cases, which increased by 70.3% from 950 to 1,618 which corresponds to an incidence rate increase of 67.0% from 10.8 to 18.1 cases per 100,000 bed-days (Figure 6b, Table S6 in the accompanying data tables).

Figure 6a. Quarterly rates of all reported C. difficile: April 2007 to March 2023

Figure 6b. Quarterly rates of hospital-onset C. difficile: April 2007 to March 2023

Between January to March 2018 and January to March 2023 the largest percentage of cases were HOHA, however, this percentage increased from approximately 43.9% of all cases to 48.7%. Over the same period, the percentage of COCA cases decreased from 26.9% to 26.1% (although primarily in the early quarters), as did the COHA cases, which decreased from 18.0% to 15.7% of all CDI. Community Onset Indeterminate Association (COIA) cases increased from 8.8% to 9.3% of all CDI. Much of the increase observed is likely due to improved data quality as shown by the sharp decline of cases with missing or not reported data (Figure 6c, Table S6c in the accompanying data tables).

Figure 6c. Percentage of CDI cases by prior trust exposure April 2017 to March 2023

Appendix

Bed-day data

For bacteraemia and CDI, the average bed-day activity reported by acute trusts via KH03 returns is used to derive the bed-day denominator for acute trust incidence rate rates (assigned and apportioned). As of Q1 2010 to 2011, bed-day data has been available on a quarterly basis and has been used as such for Q2 2011 to 2012, to Q3 2022 to 2023.

However, UKHSA has reviewed its policy for processing KH03 data. Data irregularities identified have been flagged with colleagues at NHS England (data owners of the KH03 data set). Until we receive confirmation that any identified change in the occupied overnight bed-days for an acute trust is anomalous, UKHSA now uses the data as published in the KH03 data set. This affects all reports published since 1 December 2015 and incidence rate rates published prior that time will differ slightly as a result.

For the KH03 data used to calculate rates included in this report to be consistent over the full-time period, previously amended KH03 data for trust United Lincolnshire Hospitals (RWD) for financial year 2014 to 2015, has been altered to reflect that published in the KH03 data set. Please note that this could lead to slight differences in hospital-onset assigned rates when compared with publications prior to 1 December 2015.

KH03 data can be found on the NHS England website.

Missing data for acute trusts in the KH03 returns will continue to be processed as before, where the KH03 return for the same quarter from the previous year will be used as a proxy. The following acute trusts were therefore affected:

• Moorfields Eye Hospital NHS Foundation Trust (RP6) 2007 to 2008, and 2008 to 2009 KH03 figures: replaced with 2006 to 2007 KH03 figure

• Rotherham NHS Foundation Trust (RFR): 2009 to 2010 and from April to June 2010, to April to June 2011 KH03 figures: replaced with 2008 to 2009 KH03 figure

• Sheffield Teaching Hospitals NHS Foundation Trust (RHQ) from April to June 2010, to April to June 2011 KH03 figures: replaced with 2009 to 2010 KH03 data

• The Princess Alexandra Hospital NHS Trust (RQW) April to June 2014, and October to December 2014 KH03 figures: replaced with April to June 2013, to October to December 2013 KH03 figures, respectively

• Ipswich Hospital NHS Trust (RGQ) January to March 2016 KH03 figure: replaced with January to March 2015 figures

• West Suffolk NHS Foundation Trust (RGR) April to June 2016, to October to December 2016 and April to June 2017 KH03 figures: replaced with April to June 2015, to October to December 2015 KH03 figures

• Gloucestershire Hospitals NHS Foundation Trust (RTE) October to December 2016, to January to March 2017 KH03 figures: replaced with October to December 2015, to January to March 2016 KH03 figures

The KH03 data used for this report were published on 25 May 2023. This may include revisions of previously published KH03 data used in earlier reports.

Population data

National incidence rates are calculated using 2007 to 2020 mid-year resident population estimates which are based on the 2011 census for England (2022 and 2023 estimates are based on 2021 mid-year estimates).

Definitions

Bacteraemia hospital-onset (trust-apportioned) cases

Include patients who are (i) in-patients, day-patients, emergency assessment patients or not known, and (ii) have had their specimen taken at an acute trust or not known, and (iii) specimen was taken on or after day 3 of the admission (admission date is considered day ‘one’). Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

CDI hospital-onset (trust-apportioned) cases

Include patients who are (i) in-patients, day-patients, emergency assessment patients or not known, and (ii) have had their specimen taken at an acute trust or not known, and (iii) specimen was taken on or after day 4 of the admission (admission date is considered day ‘one’). Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

Historically, reports published before September 2017 have used the term ‘trust- apportioned’ to describe cases meeting the above conditions for apportionment and ‘not trust-apportioned’ for those that do not. Moving forward, these terminologies have been updated to ‘hospital-onset’ and ‘community-onset’ respectively. Please note that this is simply a change in terminology and does not constitute a change in the methodology for apportionment.

Prior trust exposure

From April 2017, reporting trusts were asked to provide information on whether patients with CDI had been admitted to the reporting trust within the 3 months prior to the onset of the current case. This allows a greater granulation of the healthcare association of cases. This was extended to all other data collections in 2019.

Cases are split into one of 6 groups for CDI and 5 groups for the bacteraemias.

CDI prior trust exposure categories

1. Hospital-onset healthcare-associated (HOHA): date of onset is greater than 2 days after admission (where day of admission is day 1).
2. Community-onset healthcare-associated (COHA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the date of discharge).
3. Community-onset indeterminate association (COIA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust between 29 and 84 days prior to the specimen date (where day 1 is the date of discharge).
4. Community-onset community-associated (COCA): is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 84 days prior to the specimen date (where day 1 is the date of discharge)
5. Unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the 3 months prior to CDI case.
6. No Information: the reporting trust did not provide any answer for questions on prior admission.

Bacteraemia prior trust exposure categories

In addition, in April 2020, the HCAI DCS has included questions relating to prior trust exposure to the same acute trust reporting Gram-negative bacteraemia cases. These additional mandatory items were developed to assist the UK governments ambition to reduce healthcare-associated Gram-negative BSI and CDI from a 2019 baseline to threshold levels. This supports the intention to reduce Gram-negative BSI by 25% by March 2022, and by 50% by March 2024.

Cases since April 2020 have also been categorised as:

1. Hospital-onset healthcare-associated (HOHA): date of onset is greater than 2 days after admission (where day of admission is day 1).
2. Community-onset healthcare-associated (COHA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the specimen date).
3. Community-Onset, Community Associated (COCA): is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 28 days prior to the specimen date (where day 1 is the specimen date).
4. Unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the month prior to the current episode.
5. No Information: the reporting trust did not provide any answer for questions on prior admission.

Total reported cases

This is the total count of infections for each organism as of the date of extraction. Please note that for C. difficile, this count excludes those from patients less than 2 years old.

Episode duration

The length of an infection episode is defined as 14 days (28 days for CDI) from the earliest case’s specimen date (day ‘one’).

Incidence rate calculations

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa bacteraemia, and CDI population incidence rate (episodes per 100,000)

This incidence rate is calculated using the number of episodes and the mid-year population for England:

That is: the number of episodes is multiplied by 100,000, then multiplied by the number of days in the year, then divided by the mid-year of population for the same year for England, then divided by the number of days in the quarter.

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa and CDI hospital-onset incidence

This incidence rate is calculated using the number of episodes and the KH03 average bed-day activity (see bed-day data above) and is calculated as follows:

That is: the number of episodes is multiplied by 100,000, then divided by the average number of beds occupied-overnight in a quarter, then divided by the number of days in the same quarter.

Graphs and percentage change calculation

Please note that percentage changes in rate have been calculated using raw rate figures while those presented in the tables and commentary have been rounded to one decimal place. Similarly, graphs included in this report were plotted using raw rates figures. The raw rate figures are included in the Quarterly Epidemiological Commentary’s accompanying data.

Quarters

In publications prior to March 2016, all references to quarterly data are based on calendar year definitions and not financial year definitions, that is:

• Quarter 1: January to March
• Quarter 2: April to June
• Quarter 3: July to September
• Quarter 4: October to December

However, for all subsequent publications, including this one, all references to quarterly data are based on financial year definitions and not calendar year definitions, that is:

• Quarter 1 2014 to 2015: April to June 2014
• Quarter 2 2014 to 2015: July to September 2014
• Quarter 3 2014 to 2015: October to December 2014
• Quarter 4 2014 to 2015: January to March 2015

References

1. Sloot R, Nsonwu O, Chudasama D, Rooney G, Pearson C, Choi H, Mason E, Springer A, Gerver S, Brown C, Hope R. 2022, ‘Rising rates of hospital-onset Klebsiella spp. and Pseudomonas aeruginosa bacteraemia in NHS acute trusts in England: a review of national surveillance data, August 2020 to February 2021.’ Journal of Hospital Infection, 119, 175-181

Further information

This publication forms part of the range of National Statistics outputs routinely published by UKHSA which include monthly and annual reports on the mandatory surveillance of MRSA, MSSA and E. coli, Klebsiella spp. and P. aeruginosa bacteraemia and CDI.

Annual report output

Further epidemiological analyses by financial year can be found in UKHSA’s annual epidemiological commentary.

Monthly report outputs

The following reports are produced by UKHSA monthly.

MRSA bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MRSA bacteraemia by organisation.

MSSA bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MSSA bacteraemia by organisation.

E. coli bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated E. coli bacteraemia by organisation.

Klebsiella spp. bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated Klebsiella spp. bacteraemia by organisation.

P. aeruginosa bacteraemia – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated P. aeruginosa bacteraemia by organisation.

CDI – counts of all reported, hospital-onset cases, community-onset cases, healthcare associated and community associated CDI by organisation.

Data for this report were extracted from UKHSA’s HCAI data capture system (DCS) on 09 May 2023.

Enquiries and feedback

For any enquiries or feedback on this report, or to request copies of this report in PDF format, please contact [email protected]