Accredited official statistics

Quarterly epidemiological commentary: mandatory Gram-negative bacteraemia, MRSA, MSSA and C. difficile infections (data up to January to March 2025)

Updated 10 July 2025

Applies to England

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Main points

Escherichia coli (E. coli) bacteraemia

During the latest quarter, January to March 2025:

• the all-reported incidence rate of E. coli bacteraemia was 72.7 per 100,000 population
• this was a 1.0% increase compared with the same quarter last year and 1.6% lower when compared to the corresponding pre-COVID-19 pandemic quarter (January to March 2019)
• E. coli cases remain predominantly (79.5%) community-onset. Hospital-onset incidence rates have remained relatively stable with some fluctuations since the start of surveillance

Klebsiella species (spp.) bacteraemia

During the latest quarter, January to March 2025:

• the all-reported incidence rate of Klebsiella spp. bacteraemia was 22.3 per 100,000 population
• there was no substantial change compared with the same quarter last year and a 19.3% increase to the corresponding quarter in 2019
• K. pneumoniae is the most common cause of Klebsiella spp. bacteraemia, accounting for 75.6% of cases and has been the primary contributor to the recent increases, and predominantly due to community cases

Pseudomonas aeruginosa (P. aeruginosa) bacteraemia

During the latest quarter, January to March 2025:

• the all-reported incidence rate of P. aeruginosa bacteraemia was 6.8 per 100,000 population
• this was a 7.3% decrease compared with the same quarter last year and a 2.4% decrease compared to the equivalent quarter in 2019
• the rate remains relatively unchanged, despite observed fluctuations since the start of surveillance, with a notable spike in the hospital-onset incidence rate during the acute stages of the COVID-19 pandemic

MRSA bacteraemia

During the latest quarter, January to March 2025:

• the all-reported incidence rate of MRSA bacteraemia was 1.8 per 100,000 population
• this was a 4.1% increase compared with the same quarter last year and a 39.4% increase since the corresponding quarter in 2019
• the all-reported rate has been steadily increasing since the financial year 2021 to 2022 in community-onset cases and to a lesser degree for hospital-onset
• in the past year there were notable increases in the proportion of community-onset community-associated cases

MSSA bacteraemia

During the latest quarter, January to March 2025:

• the all-reported incidence rate of MSSA bacteraemia was 24.3 per 100,000 population during the latest quarter January to March 2025
• this was a 1.6% increase compared with the same quarter last year and a 11.2% increase since the corresponding quarter in 2019
• overall, cases remain at their highest with increases predominately attributed to community cases

Clostridioides difficile infection (CDI)

During the latest quarter, January to March 2025:

• the all-reported incidence rate of C. difficile infection was 29.1 per 100,000 population
• this was a 2.4% decrease compared with the same quarter last year and a 55.0% increase since the corresponding quarter in 2019
• both community and hospital-onset rates saw marked rises since 2023, with community-onset rates rising by 24.7% to a peak of 21.3 per 100,000 population in July to September 2024, compared to the corresponding quarter in 2023 (17.1 per 100,000 population). The latest quarter has observed a 5.8% decline to 15.2 per 100,000 compared to the same quarter in 2024
• for the same period, hospital-onset rates rose to a peak of 25.7 per 100,000 bed-days from 21.6 per 100,000 bed-days (18.9% increase). The latest quarter has observed a relatively smaller increase of 2.3% to 21.7 per 100,000 bed-days compared to the same quarter in 2024

Overview of long-term trends

Prior to the COVID-19 pandemic, MSSA, Klebsiella spp. and E. coli bacteraemia case counts were increasing, while MRSA bacteraemia and CDI counts fluctuated, but remained at relatively low levels and below 2012 levels. Case numbers from all data collections declined to varying degrees in 2020, coinciding with the beginning of the COVID-19 pandemic.

All collections returned to pre-pandemic levels relatively soon after, apart from E. coli which reached levels similar to pre-pandemic levels from July 2024.

From 2021 until the latest quarter, MRSA bacteraemia (particularly community-onset cases) and CDI see the highest percentage increases in 12-month rolling case counts, followed by MSSA, Klebsiella spp. and E. coli bacteraemia and lastly P. aeruginosa bacteraemia; all 6 organisms surpass records of counts since their respective data collections began. Both Klebsiella spp. and E. coli bacteraemia see lower sustained increases over this period followed by a sharp increase from January 2023 (Figure 1, Table S7 in the accompanying data tables).

Figure 1: CDI and bloodstream infections, 12-month rolling percent change since calendar year 2012 for MRSA, MSSA and E. coli bacteraemia and CDI, and from FY 2017 for Klebsiella spp. and P. aeruginosa bacteraemia, December 2012 to March 2025

Epidemiological analyses of Gram-negative bacteraemia (E. coli, Klebsiella spp. and P. aeruginosa) data

E. coli bacteraemia

Main findings

The total reported cases of E. coli bacteraemia in financial quarter (FQ) January to March 2025 increased by 34.4% from 7,698 to 10,347 cases when compared with January to March 2012, with an increase of 25.7% in the incidence rate from 57.9 to 72.7 cases per 100,000 population. This increase was primarily due to community-onset cases, which increased by 42.5% from 5,774 to 8,227, with a 33.3% increase in incidence rate from 43.4 to 57.8 cases per 100,000 population. The count of hospital-onset cases increased by 10.2% from 1,924 to 2,120 cases, and the incidence rate increased 7.8% from 21.6 to 23.3 per 100,000 bed-days.

When comparing the most recent quarter to last year’s corresponding quarter, counts of total reported cases showed no substantial change (from 10,325 to 10,347 cases), while incidence rates increased by 1.0%, from 72.0 to 72.7 per 100,000 population (Figure 2). The recent increase was due to an increase in hospital-onset cases; these increased by 4.2% from 2,034 to 2,120, compared with January to March 2024 (Figure 2), which corresponded to an increase of 5.7% in incidence rate, from 22.0 to 23.3 per 100,000 bed-days. Over the same period, counts (8,291 to 8,227) and incidence rate (57.8 to 57.8 per 100,000 population) of community-onset E. coli bacteraemia cases showed no substantial change (Table S1 in the accompanying data tables).

Figure 2: Quarterly rates of E. coli bacteraemia, total reported and hospital-onset cases, July 2011 to March 2025

Detailed findings

The incidence rate of total reported E. coli bacteraemia increased each financial year between the start of the mandatory surveillance of E. coli bacteraemia in July 2011 and the start of the COVID-19 pandemic (January to March 2020, Figure 2). This increase was primarily driven by community-onset cases (Table S1 in the accompanying data tables).

At the start of the pandemic, the total reported and community-onset cases declined sharply, reaching 60.1 and 50.5 per 100,000 population, respectively, in April to June 2020, but they remained higher than they were at the start of surveillance. While incidence rate of hospital-onset cases, except for a sharp reduction (20.7 cases per 100,000 bed-days) observed in April to June 2021 (Figure 2), remained relatively stable during the same period. This was followed by a steady return to pre-pandemic rates.

When comparing January to March 2025 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was no substantial change in total cases (10,251 to 10,347), with a decrease of 1.6% in the incidence rate from 73.9 to 72.7 cases per 100,000 population (Figure 2). Community-onset cases decreased by 2.0% from 8,396 to 8,227. Similarly, the incidence rate of community-onset cases also decreased by 4.5% from 60.6 to 57.8 cases per 100,000 population. However, the total number of hospital-onset cases increased by 14.3% compared with the same period, from 1,855 to 2,120. The hospital-onset incidence rate increased by 10.0% from 21.1 to 23.3 cases per 100,000 bed-days (Figure 2). In the latest quarter, the number of E. coli bacteraemia cases were at levels comparable to pre-pandemic.

A strong seasonality trend is visible with total reported E. coli bacteraemia, whereby the highest rates are observed between July to September of each year, although there were more fluctuations during the pandemic years. The same seasonal trend is apparent among hospital-onset rates since July 2011, excluding the period January 2020 to December 2021.

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 our quality and methodology information (QMI) report for more details).

Community-onset community-associated (COCA) cases accounted for the majority of reported community-onset E. coli bacteraemia from April 2020. While there have been some fluctuations, the proportion of COCA cases has remained similar at around two-thirds of all cases since.

The distribution of cases by these categories has remained broadly stable since 2020. In the current quarter, 65.5% of cases were COCA, 13.9% were community-onset healthcare-associated (COHA), and 20.5% were hospital-onset healthcare-associated (HOHA) (Figure 3, Table S1a in the accompanying data tables).

Figure 3: Percentage of E. coli bacteraemia cases by prior trust exposure, April 2020 to March 2025

Klebsiella spp. bacteraemia

Main findings

The total reported cases of Klebsiella spp. bacteraemia in January to March 2025 increased by 40.3% from 2,258 to 3,167 cases when compared with January to March 2018; this corresponded with an increase of 36.0% in the incidence rate from 16.4 to 22.3 cases per 100,000 population. The count of hospital-onset cases increased by 44.9% from 702 to 1,017 cases, and the incidence rate increased by 41.6% from 7.9 to 11.2 per 100,000 bed-days. The count of community-onset cases increased by 38.2% from 1,556 to 2,150, with a 33.9% increase in incidence rate from 11.3 to 15.1 cases per 100,000 population.

Comparing the most recent quarter to the same quarter in the previous year, counts (3,191 to 3,167 cases) and incidence rates (22.2 to 22.3 per 100,000 population) of total reported cases showed no substantial change (Figure 4). Community-onset case counts decreased by 3.0% and their rate by 2.2%, respectively, from 2,216 to 2,150 and from 15.4 to 15.1 per 100,000 population. Hospital-onset cases increased by 4.3% from 975 to 1,017, compared with January to March 2024 (Figure 4), which corresponded to an increase of 5.8% in incidence rate, from 10.5 to 11.2 per 100,000 bed-days (Table S2 in the accompanying data tables).

Figure 4: Quarterly rates of Klebsiella spp. bacteraemia, all-reported and hospital-onset cases, by species, April 2017 to March 2025

Detailed findings

Counts and rates of hospital-onset Klebsiella spp. reached the highest levels observed since the beginning of mandatory Klebsiella spp. surveillance during the acute stage of the COVID-19 pandemic. The incidence rate of hospital-onset cases peaked at 15.6 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 Sloot and colleagues 2022.

When comparing the most recent quarter (January to March 2025) with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was a 22.4% increase in total cases from 2,587 to 3,167, and a corresponding increase of 19.3% in the incidence rate from 18.7 to 22.3 cases per 100,000 population (Figure 4, Table S2 in the accompanying data tables). Community-onset cases increased by 17.0% from 1,837 to 2,150. Similarly, the incidence rate of community-onset cases also increased by 14.1% from 13.2 to 15.1 cases per 100,000 population. Finally, the count of hospital-onset cases increased by 35.6% from 750 to 1,017. The rate increased by 30.5% from 8.5 to 11.2 cases per 100,000 bed-days, respectively (Figure 4, Table S2 in the accompanying data tables). Trends returned to pre-pandemic levels at the start of 2022, continuing on an upward trajectory.

During January to March 2025, 75.6% of the total reported Klebsiella spp. bacteraemia were due to K. pneumoniae, 15.0% by K. oxytoca, and 3.4% by K. aerogenes (Figure 4, Table S2 in the accompanying data tables). During the COVID-19 pandemic, K. pneumoniae and K. aerogenes saw peaks at 10.8 and 1.8 per 100,000 bed-days, respectively.

There is evidence of seasonality in the trend of total reported Klebsiella spp. bacteraemia cases, with higher rates normally observed in July to December and lower rates observed from January to June of each year (Figure 4).

Since the addition of prior trust exposure classifications in April to June 2020, COCA cases have made up slightly more than half of all Klebsiella spp. bacteraemia. The proportion of HOHA cases peaked at 39.6% in January to March 2021; this coincided with the increase in COVID-19 cases and associated hospitalisations observed in January 2021, where an increase in Klebsiella spp. bacteraemia was observed in the hospital setting (Sloot and colleagues 2022). This proportion has since decreased and was 32.1% in the latest quarter. In the same period, the proportion of COHA cases was 14.2% (Figure 5, Table S2a in the accompanying data tables).

Figure 5: Percentage of Klebsiella spp. bacteraemia cases by prior trust exposure, April 2020 to March 2025

Pseudomonas aeruginosa bacteraemia

Main findings

Total reported cases of P. aeruginosa bacteraemia in January to March 2025 showed no substantial change when compared with January to March 2018 (from 965 to 966 cases); while the incidence decreased by 3.0% from 7.0 to 6.8 cases per 100,000 population. The count of hospital-onset cases decreased by 7.6% from 394 to 364 cases, and incidence rate decreased by 9.7% from 4.4 to 4.0 per 100,000 bed-days. Over the same period, the count of community-onset cases increased by 5.4% from 571 to 602, with a 2.2% increase in incidence rate from 4.1 to 4.2 cases per 100,000 population.

When comparing the most recent quarter to last year’s corresponding quarter, counts and incidence rates of total reported cases decreased by 8.1% and 7.3%, respectively, from 1,051 to 966 cases and 7.3 to 6.8 per 100,000 population (Figure 6). Hospital-onset cases decreased by 7.1% from 392 to 364, compared with January to March 2024 (Figure 6), which corresponded to a decrease of 5.8% in incidence rate, from 4.2 to 4.0 per 100,000 bed-days. Over the same period, the count and incidence rate of community-onset P. aeruginosa bacteraemia cases decreased by 8.6% and 7.9%, respectively, from 659 to 602 and from 4.6 to 4.2 per 100,000 population (Table S3 in the accompanying data tables).

Figure 6: Quarterly rates of P. aeruginosa bacteraemia, total reported and hospital-onset cases, April 2017 to March 2025

Detailed findings

Similar 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 in July to September 2020 and again in July to September 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 (Sloot and colleagues 2022).

When comparing January to March 2025 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was no substantial change in total cases (965 to 966), with a decrease of 2.4% in the incidence rate from 7.0 to 6.8 cases per 100,000 population (Figure 6). Community-onset cases (604 to 602) showed no substantial change. Similarly, the community-onset incidence rates also decreased by 2.9% from 4.4 to 4.2 cases per 100,000 population. Hospital-onset cases (361 to 364) showed no substantial change compared with the same period in 2019. The hospital-onset incidence rate decreased by 2.9% from 4.1 to 4.0 cases per 100,000 bed-days (Figure 6). Despite increase in counts, rates appear reduced due to an increase in bed-days denominator compared with the previous financial year. This suggests that the general trend seen in the total and community-onset P. aeruginosa cases has broadly remained unaffected by the COVID-19 pandemic. It also suggests that, following the initial peak in hospital-onset cases, there has been a return to pre-pandemic levels.

Similarly to E. coli and Klebsiella spp., COCA cases make up the highest proportion of P. aeruginosa bacteraemia cases; however, they do not constitute most cases. In the latest quarter, 43.5% of the total, 18.8% were COHA and 37.7% were HOHA. This contrasts with January to March 2021, when HOHA cases made up 48.1% of the total (Figure 7, Table S3a in the accompanying data tables).

Figure 7: Percentage of P. aeruginosa bacteraemia cases by prior trust exposure, April 2020 to March 2025

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

Main findings

Comparing the most recent quarter with last year’s corresponding quarter, counts and incidence rates of total reported cases increased by 3.2% and  4.1%, respectively, from 248 to 256 cases and from 1.7 to 1.8 per 100,000 population, reaching levels not seen since financial year (FY) 2011 to 2012 (Figure 8). The rise was more pronounced in the community-onset cases. The count and incidence rate of community-onset MRSA bacteraemia cases increased by 15.1% and 16.1%, respectively, from 152 to 175 and from 1.1 to 1.2 per 100,000 population. Over the same period, hospital-onset cases decreased by 15.6% from 96 to 81, compared with January to March 2024 (Figure 8), which corresponded to a decrease of 14.4% in incidence rate, from 1.0 to 0.9 per 100,000 bed-days (Table S4 in the accompanying data tables).

Of note, due to the low incidence of MRSA bacteraemia, proportions should be interpreted with caution.

Figure 8: Quarterly rates of MRSA bacteraemia, total reported cases (April 2007 to March 2025) and hospital-onset cases (April 2008 to March 2025)

Detailed findings

There has been a considerable decrease in the incidence rate of total reported MRSA bacteraemia since its enhanced mandatory surveillance began in April 2007 (Figure 8, Table S4 in the accompanying data tables). The incidence rate of total reported cases fell by 84.9% from 10.2 cases per 100,000 population in April to June 2007 to 1.5 cases per 100,000 in January to March 2014. Since then, where counts and rates remained stable until FY 2022 to 23, where an annual increasing trend was observed.

A similar trend was observed with the incidence rate of hospital-onset cases (Figure 8, Table S4 in the accompanying data tables). There was a steep decrease of 79.3% from 4.9 cases per 100,000 bed-days in April to June 2008 to 1.0 in January to March 2014 followed by several years of stability, until trends began increasing from FY 2022 to 23.

When comparing January to March 2025 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was a 43.0% increase in total cases from 179 to 256, with an increase of 39.4% in the incidence rate from 1.3 to 1.8 cases per 100,000 population (Figure 8). Community-onset MRSA bacteraemia counts increased by 47.1% from 119 to 175 and incidence rate increased by 43.3% from 0.9 to 1.2 cases per 100,000 population (Figure 8).

There was a growing proportion of COCA cases and a decline of HOHA cases, and to a lesser extent COHA in recent quarters. In the current quarter, 54.7% of cases were COCA; this is an increase from 44.8% in the same quarter in 2024. While HOHA and COHA have declined to 31.6% were 13.7%, respectively, from 38.7% and 16.5% in the same quarter in 2024 (Figure 9, Table S4a in the accompanying data tables).

Figure 9: Percentage of MRSA bacteraemia cases by prior trust exposure, April 2020 to March 2025

MSSA bacteraemia

Main findings

Counts and rates of MSSA bacteraemia remain higher than those seen at the beginning of the surveillance programme in 2011. The count of total reported cases increased by 57.2% from 2,199 in January to March 2011 to 3,456 in January to March 2025. This corresponded to an increase of 44.7% in incidence rate, from 16.8 to 24.3 per 100,000 population (Figure 10, Table S5 in the accompanying data tables).

These increases are primarily due to the increase in community-onset cases. Between these 2 quarters, the count and incidence rate of community-onset cases increased by 67.1% , from 1,464 to 2,446 cases and from 11.2 to 17.2 cases per 100,000 population. Over the same period, the count of hospital-onset cases increased by 37.4% from 735 to 1,010 cases, while the incidence rate increased by 32.9% from 8.3 to 11.1 cases per 100,000 bed-days.

Comparing the most recent quarter (January to March 2025) to the same period in the previous year (January to March 2024), there was no substantial change (3,430 to 3,456) in the count of total reported cases, while the incidence rate increased by 1.6% from 23.9 to 24.3 per 100,000 population. Hospital-onset MSSA bacteraemia cases increased by 1.2% from 998 to 1,010, which corresponds to an increase of 2.7% in incidence rate from 10.8 to 11.1 per 100,000 bed-days. Community-onset MSSA bacteraemia cases (2,432 to 2,446) showed no substantial change, while the community-onset incidence rate increased by 1.4% from 17.0 to 17.2 cases per 100,000 population.

Figure 10: Quarterly rates of MSSA bacteraemia, total reported and hospital-onset cases, January 2011 to March 2025

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, with the exception of a temporary decline in cases during the initial stages of the COVID-19 pandemic. Comparing the latest quarter with the corresponding quarter in 2019, the count and incidence rate of MSSA bacteraemia have increased by 14.1% and 11.2%, respectively, from 3,030 to 3,456 cases and from 21.9 to 24.3 cases per 100,000 population.

The incidence rate of hospital-onset MSSA bacteraemia cases peaked during the early stages of the COVID-19 pandemic. This was in part due to reduced hospital activity, resulting in reduced occupied overnight bed-days, the denominator used to calculate hospital-onset rates. These MSSA rates peaked in January to March 2021 at 13.4 cases per 100,000 bed-days. This was the highest MSSA hospital-onset rate and count observed since the introduction of MSSA surveillance. This pattern is similar to that observed in both Klebsiella spp. and P. aeruginosa.

When comparing the latest quarter to the pre-pandemic period of January to March 2019, counts of community-onset MSSA bacteraemia cases increased by 11.9% from 2,185 to 2,446. There was a 9.1% increase in incidence rate from 15.8 to 17.2 per 100,000 population, over the same period.

In the current quarter, 59.0% of cases were COCA, 11.6% COHA, and 29.2% HOHA (Figure 11, Table S5a in the accompanying data tables).

Figure 11: Percentage of MSSA bacteraemia cases by prior trust exposure, April 2020 to March 2025

Laboratory blood cultures

On a quarterly basis NHS acute trusts are mandated to report the total number of blood culture sets examined. The pooled blood culture positivity of E. coli, Klebsiella spp., P. aeruginosa, MRSA and MSSA bacteraemia reduced slightly from 3.5% at the start of the surveillance, in April to June 2017, to 3.3% in the latest quarter of January to March 2025, with some minor fluctuations in the intervening quarters (Figure 12, Table S8 in the accompanying data tables).

The rate of blood culture sets examined gradually increased from April to June 2010, rising by 18.2% from 30.3 to 35.8 blood culture sets examined per 1,000 population by April to June 2019. This was followed by a decline at the start of the COVID-19 pandemic, to 29.4 blood culture sets examined per 1,000 population in the corresponding quarter in 2020. Since then, the blood culture sampling rate has returned to an upward trajectory, increasing to 38.4 tests per 1,000 population in January to March 2025, which is 26.5% higher than the start of surveillance (Figure 13, Table S9 in the accompanying data tables). While the sampling rate has increased concurrently with the overall increase in bacteraemia incidence rates, this does not appear to have impacted positivity, which has remained relatively stable between 2.9 to 4.1% during the surveillance period. However, there may be variation by data collection or at trust-level.

Figure 12: Trends in pooled E. coli, Klebsiella spp., P. aeruginosa, MRSA and MSSA blood culture positivity, England, by financial year: April to June 2017 to January to March 2025

Figure 13: Trends in the rate of blood culture sets, England, by financial year: April to June 2010 to January to March 2025

Epidemiological analyses of Clostridioides difficile infection (CDI) data

Main findings

Comparing the most recent quarter (January to March 2025) to the same period in the previous year (January to March 2024), there was a 3.2% decrease in the count of total reported cases, from 4,278 to 4,141. Similarly, the incidence rate decreased by 2.4%, from 29.8 to 29.1 cases per 100,000 population (Figure 14, Table S6 in the accompanying data tables).

Hospital-onset CDI cases (1,959 to 1,975) showed no substantial change, with a 2.3% in incidence rate from 21.2 to 21.7 cases per 100,000 bed-days. Community-onset CDI cases decreased by 6.6% from 2,319 to 2,166, while the community-onset incidence rate decreased by 5.8% from 16.2 to 15.2 cases per 100,000 population (Figure 14, Table S6 in the accompanying data tables).

Figure 14: Quarterly rates of C. difficile infection, total reported and hospital-onset cases, April 2017 to March 2025

Detailed findings

Since the initiation of CDI surveillance in April 2007, there have been substantial decreases in the count and associated incidence rate of both all-reported and hospital-onset cases of CDI, with recent years noting an increasing trend.

Most of the decrease in counts and incidence rate of cases occurred between April to June 2007 and April to June 2012, with a 78.3% decrease in all-reported cases of CDI from 16,864 to 3,656 cases and an associated 79.1% reduction in incidence rate from 131.6 cases per 100,000 population to 27.5. Cases and rates were then stable until between January to March 2021 and January to March 2025. This is when the count of all-reported cases increased by 42.3% from 2,991 to 4,141 cases and the incidence rate increased by 35.7% from 21.4 to 29.1 cases per 100,000 population. Although this rate remains elevated, the most recent quarter shows that the rate of increase has slowed, with figures comparable to those observed in the corresponding quarter in 2024. This change in trend to a steadily increasing trajectory in CDI counts and rates is of major concern and it is the only organism among the six showing this major shift post pandemic. The underlying causes for this trend have been investigated further within this technical report.

Hospital-onset CDI cases, saw similar large reductions with an 83.5% decrease in count of cases between April to June 2007 and January to March 2012, from 10,974 to 1,808 cases, and an 82.8% reduction in the incidence rate, from 117.9 to 20.3 per 100,000 bed-days (Figure 14, Table S6 in the accompanying data tables). Since then, the number of cases has increased by 9.2%, rising from 1,808 to 1,975, while the rate has also increased, by 6.9%, reaching 21.7 cases per 100,000 bed-days. Most of the rise in hospital-onset cases was seen following the COVID-19 pandemic, whereas prior to this, rates were observed as generally declining with some fluctuations.

Community-onset rates reached a recent peak of 21.3 cases per 100,000 population in July to September 2024 and have not been this high since April to June 2010. In the latest quarter of January to March 2025, the rate has declined to 15.2 cases per 100,000 population, which is 5.8% lower than the same quarter in 2024 (16.2 cases per 100,000).

Figure 15: Percentage of C. difficile infection cases by prior trust exposure, April 2020 to March 2025

The largest proportion of cases in the latest quarter were HOHA accounting for 47.7% of the total (Figure 15, Table S6a in the accompanying data tables) which have steadily risen from 36.6% in July to September 2020. COCA cases in the latest quarter are 26.8% of the total which has gradually reduced from 31.9% over the same period. COHA and community-onset indeterminate-association (COIA) cases constituted 16.3% and 9.1% in the last quarter, respectively and remained relatively stable since July 2020.

Laboratory stool specimens

On a quarterly basis NHS acute trusts are mandated to report the total number of stool specimens examined and the total number of stool specimens examined for diagnosis of CDI. The overall stool specimen sampling rate declined from a rate of 30.0 per 1,000 population in April to June 2010, by 15.0% to 25.5 in the corresponding quarter in 2019. This was followed by a sharper 40.8% decline to 15.1 at the start of the pandemic in April to June 2020. Since then, the testing rate has steadily increased, surpassing 2010 levels to reach 35.2 tests per 1,000 population in January to March 2025 (Figure 16, Table S9 in the accompanying data tables).

At the start of surveillance, in April to June 2010, the sampling rate of stool specimens examined for C. difficile diagnosis was 12.9 per 1,000 population. By the same quarter in 2019, the rate saw a similar decline by 27.1% to 9.4. This downward trend continued into the start of the pandemic, with a further 28.5% decline to 6.8. Since then, the sampling rate has returned to an upward trend, increasing to 12.7 per 1,000 population in January to March 2025, levels similar to those seen in 2010. The CDI positivity was initially 3.5% in April to June 2010 before declining by 28.0% to 2.5% by the same quarter in 2012. Since then, the rate has been predominately stable, with a positivity of 2.3% in the latest quarter of January to March 2025 (Figure17, Table S8 in the accompanying data tables). While the sampling rate has increased concurrently with the increase in CDI incidence rates, this does not appear to have impacted positivity which has remained relatively stable between 2.0 to 3.2% during this period. However, there may be variation by data collection or at trust-level.

Figure 16: Trends in the rate of stool specimens examined for CDI diagnosis and overall stool specimens examined, England, by financial year: April to June 2010 to January to March 2025

Figure 17: Trends in CDI positivity, England, by financial year: April to June 2010 to January to March 2025

Data sources and methodology 

For detailed information about the data sources and methodology used to analyse data in this report, please refer to our QMI report. Some additional information related to this publication is summarised below.

Data sources

Numerator data

Infection episode data used in this report were extracted from UKHSA’s HCAI data capture system (DCS) on 26 February 2025.

Population data

Mid-year resident population estimates released by the Office for National Statistics and based on the 2021 census for England are used to derive the population denominator for the total reported incidence rates and the community-onset incidence rates.

Bed-day data

For bacteraemia and CDI, the average bed-day activity reported by NHS England’s KH03 returns is used to derive the bed-day denominator for hospital-onset incidence rates. As of Q1 FY 2010 to 2011, bed-day data has been available on a quarterly basis and has been used as such since Q2 FY 2011 to 2012.

The KH03 data used for this report were published by NHS England on 20 February 2025. This may include revisions of previously published KH03 data used in earlier reports.

On 1 December 2015, UKHSA has reviewed its policy for processing KH03 data. Data irregularities identified have been flagged with colleagues at NHS England. 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. Incidence rate rates published before December 2015 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 (trust code: RWD) for FY 2014 to 2015 has been altered to reflect that published in the KH03 data set. This could lead to slight differences in hospital-onset assigned rates when compared with publications prior to 1 December 2015.

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) FY 2007 to 2008, and FY 2008 to 2009 KH03 figures: replaced with FY 2006 to 2007 KH03 figure
• Rotherham NHS Foundation Trust (RFR): FY 2009 to 2010 and from April to June 2010, to April to June 2011 KH03 figures: replaced with FY 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 FY 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

COVID-19 and these 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 with what would have been expected, across all bloodstream infection 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 the spread of the virus. Post pandemic, many of these collections have now returned to normal pre-pandemic levels, except for E. coli and CDI.

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.

Background information

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.

Report summary

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 total 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. Data revisions are covered by a data-specific revisions and correction policy.

If this data is used for publication elsewhere, citation to UKHSA, healthcare-associated infections (HCAI) and antimicrobial resistance (AMR) division is required, using the content below.

Further information and contact details 

This publication forms part of the range of accredited official statistics outputs routinely published by UKHSA which include monthly and annual reports on the mandatory surveillance of MRSA, MSSA, 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:

• Gram-negative, MRSA and MSSA bacteraemia and CDI: monthly data trends
• E. coli, Klebsiella spp., P. aeruginosa, MRSA and MSSA bacteraemia – counts of total reported, hospital-onset healthcare-associated, community-onset healthcare-associated, community-onset community-associated for each bacteraemia by organisation
• CDI – counts of total reported, hospital-onset healthcare-associated, community-onset healthcare-associated, community-onset of indeterminate association, community-onset community-associated CDI by organisation

Feedback and contact information

For any enquiries or feedback on this report, or to request copies of this report in PDF format, please contact mandatory.surveillance@ukhsa.gov.uk.

Official statistics

These official statistics were independently reviewed by the Office for Statistics Regulation in May 2022. They comply with the standards of trustworthiness, quality and value in the Code of Practice for Statistics and should be labelled ‘accredited official statistics’. Accredited official statistics are called National Statistics in the Statistics and Registration Service Act 2007. Further explanation of accredited official statistics can be found on the Office for Statistics Regulation website.

Citation

Please cite this document as follows:

UK Health Security Agency. Quarterly epidemiology commentary: mandatory MRSA, MSSA and Gram-negative bacteraemia and C. difficile infection in England (up to January to March 2024). London: UK Health Security Agency, July 2025.