Accredited official statistics

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

Updated 9 October 2025

Applies to England

Main points

Escherichia coli (E. coli) bacteraemia

During the latest quarter, April to June 2025: 

• the total-reported incidence of E. coli bacteraemia was 78.3 per 100,000 population
• this was a 2.2% increase compared with the same quarter last year and a 5.1% decrease compared with the equivalent pre-COVID-19 pandemic quarter (April to June 2018)
• E. coli cases remain mainly community onset (73.8%); hospital-onset incidence has remained predominantly stable with some fluctuations during the surveillance period

Klebsiella species (spp.) bacteraemia

During the latest quarter, April to June 2025: 

• the total-reported incidence of Klebsiella spp. bacteraemia was 22.5 per 100,000 population
• this was a 1.6% increase compared with the same quarter last year and a 23.1% increase compared with the equivalent quarter in 2019
• hospital-onset Klebsiella spp. rates peaked during the acute stages of the COVID-19 pandemic before declining soon after but have continued to remain higher than pre-pandemic levels, with counts and rates rising more sharply
• K. pneumoniae is the most common cause of Klebsiella spp. bacteraemia, accounting for 73.8% 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, April to June 2025: 

• the total reported incidence of P. aeruginosa bacteraemia was 7.4 per 100,000 population
• this was a 2.5% decrease compared with the same quarter last year. The total reported incidence initially increased before returning to a level comparable to that observed in the equivalent quarter of 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

Meticillin-resistant Staphylococcus aureus (MRSA) bacteraemia

During the latest quarter, April to June 2025: 

• the total reported incidence of MRSA bacteraemia was 1.9 per 100,000 population
• this was a 6.7% increase compared with the same quarter last year and a 48.3% increase compared with the equivalent quarter in 2019
• the total reported rate has been steadily increasing since the COVID-19 pandemic in community-onset cases and to a lesser degree for hospital-onset
• in the past year, there was a notable increase in the proportion of community-onset community-associated cases

Meticillin-sensitive Staphylococcus aureus (MSSA) bacteraemia

During the latest quarter, April to June 2025: 

• the total reported incidence of MSSA bacteraemia was 24.2 per 100,000 population during the latest quarter April to June 2025
• this was a 4.3% increase compared with the same quarter last year and a 10.6% increase compared with the equivalent quarter in 2019
• overall, cases remain at their highest since April to June 2023 with increases predominately attributed to community cases
• when compared with the same quarter last year, the hospital-onset counts increased by 5.9% and the rates increased by 6.7%

Clostridioides difficile (C. difficile) infection (CDI)

During the latest quarter, April to June 2025: 

• the total reported incidence of C. difficile infection was 29.9 per 100,000 population
• this was a 9.7% decrease compared with the same quarter last year and a 35.3% increase compared with the equivalent quarter in 2019
• both community-onset and hospital-onset rates have declined since July to September 2023, with community-onset rates decreasing by 1.9% (from 17.1 to 16.8 per 100,000 population) and hospital-onset rates decreasing by 2.6% (from 21.6 to 21.0 per 100,000 bed-days)

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. Case numbers from all data collections declined to varying degrees in 2020, coinciding with the beginning of the COVID-19 pandemic.

Total reported cases for all collections returned to pre-pandemic levels relatively soon after, apart from E. coli which returned to pre-pandemic levels in July 2024.

From 2021 until the latest quarter (April to June 2025), the highest percentage increases in 12-month rolling case counts were observed in MRSA bacteraemia (especially in community-onset cases) and CDI, followed by MSSA, Klebsiella spp. and E. coli bacteraemia and lastly P. aeruginosa bacteraemia. All six organisms surpassed records of counts since their respective data collection began. There were lower sustained increases in Klebsiella spp. and E. coli bacteraemia over this period, with a sharp increase since 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 June 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) April to June 2025 increased by 39.6% from 8,074 to 11,268 cases when compared with April to June 2012 (the corresponding quarter in the starting year of surveillance). There was an increase of 29.1% in the incidence from 60.7 to 78.3 cases per 100,000 population. This increase was primarily due to an increase in community-onset cases, which increased by 49.9% from 6,154 to 9,225 cases, with a 38.7% increase in incidence from 46.3 to 64.1 cases per 100,000 population. The count of hospital-onset cases increased by 6.4% from 1,920 to 2,043 cases, and the incidence rate increased by 2.4% from 22.3 to 22.8 per 100,000 bed-days.

When comparing the most recent quarter to last year’s corresponding quarter, the counts and incidence of total reported cases of E. coli bacteraemia increased by 2.5% and 2.2%, respectively, from 10,994 to 11,268 cases and from 76.6 to 78.3 per 100,000 population (Figure 2). Hospital-onset count and incidence remained similar to the corresponding quarter in the previous year. Over the same period, the count and incidence of community-onset E. coli bacteraemia cases increased by 3.3% and 3.0%, respectively. This was from 8,933 to 9,225 and from 62.3 to 64.1 per 100,000 population (Table S1 in the accompanying data tables).

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

Detailed findings

The incidence of total reported E. coli bacteraemia increased each financial year between the start of 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 due to community-onset cases (Table S1 in the accompanying data tables). A sharp drop in the count and incidence of total reported and community-onset cases was observed after the start of the pandemic but remained higher than they were at the start of surveillance (Figure 2). In contrast, the incidence 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 2). This was followed by a steady return to pre-pandemic rates. The incidence of hospital-onset E. coli bacteraemia has remained stable since the start of the surveillance (see the sub-section COVID-19 and this data).

When comparing April to June 2025 with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was a 2.7% increase in total cases from 10,969 to 11,268. There was no substantial change in the incidence (78.2 to 78.3 cases per 100,000 population) (Figure 2). Community-onset cases increased by 2.0% from 9,047 to 9,225. Similarly, the incidence of community-onset cases also showed no substantial change (64.5 to 64.1 cases per 100,000 population). Both hospital-onset cases and incidence saw increases. Cases increased by 6.3%, from 1,922 to 2,043. Incidence increased by 2.5%, from 22.2 to 22.8 cases per 100,000 bed-days, compared with the same period (Figure 2). In the latest quarter, the number of E. coli bacteraemia cases returned to 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 each year. However, 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. This was 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 since April 2020. While there have been some fluctuations, the proportion of COCA cases has remained similar at around two-thirds of all cases since January 2020.

The distribution of cases by these categories has remained broadly stable since 2021. In the current quarter, 67.4% of cases were community-onset community-associated (COCA). 14.5% were community-onset healthcare-associated (COHA), and 18.1% 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 June 2025

Klebsiella spp. bacteraemia

Main findings

The total reported cases of Klebsiella spp. bacteraemia in April to June 2025 increased by 37.5% from 2,359 to 3,243 cases when compared with April to June 2017. This corresponded with an increase of 32.5% in the incidence, from 17.0 to 22.5 cases per 100,000 population. The count of hospital-onset cases increased by 40.8% from 676 to 952 cases. The incidence increased by 35.7%, from 7.8 to 10.6 per 100,000 bed-days. The count of community-onset cases increased by 36.1% from 1,683 to 2,291, with a 31.2% increase in incidence, from 12.1 to 15.9 cases per 100,000 population.

Comparing the most recent quarter to the same quarter in the previous year, counts and incidence of total reported cases increased by 1.9% and 1.6%, respectively. This was from 3,183 to 3,243 cases and from 22.2 to 22.5 per 100,000 population (Figure 4). The recent increase was due to an increase in community-onset cases. Their count increased by 3.6% and their rate by 3.3%, respectively. This was from 2,212 to 2,291 cases and from 15.4 to 15.9 per 100,000 population. Hospital-onset cases decreased by 2.0% from 971 to 952, when compared with April to June 2024 (Figure 4). This corresponded to a decrease of 1.2% in incidence, from 10.7 to 10.6 per 100,000 bed-days (Table S2 in the accompanying data tables).

Figure 4. Quarterly rates of Klebsiella spp. bacteraemia, total-reported and hospital-onset cases, by species, April 2017 to June 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 (see the sub-section COVID-19 and this data). The incidence rate of hospital-onset cases peaked at 15.6 cases per 100,000 bed-days in January to March 2021. This coincided with a high incidence of COVID-19, with many cases identified as COVID-19 co-infections.

When comparing the most recent quarter (April to June 2025) with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was a 26.3% increase in total cases. Cases went from 2,567 to 3,243, and there was a corresponding an increase of 23.1% in the incidence rate from 18.3 to 22.5 cases per 100,000 population (Figure 4, Table S2 in the accompanying data tables). Community-onset cases increased by 26.7% from 1,808 to 2,291. Similarly, the incidence rate of community-onset cases also increased by 23.5% from 12.9 to 15.9 cases per 100,000 population. Finally, the count of hospital-onset cases increased by 25.4% from 759 to 952. The rate increased by 20.9% from 8.8 to 10.6 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 April to June 2025, 73.9% of the total reported Klebsiella spp. bacteraemia were due to K. pneumoniae, 15.8% by K. oxytoca, and 3.8% by K. aerogenes (Figure 4, Table S2 in the accompanying data tables). Since the previous quarter (January to March 2025), hospital-onset Klebsiella genus rates have seen 4.76% reduction from 11.1 to 10.6 cases per 100,000 bed-days. This decrease was predominantly due to an increase of 7.03% in K. oxytoca, from 3.33 to 3.56 cases per 100,000 bed-days. During the COVID-19 pandemic, K. pneumoniae and K. aerogenes saw peaks at 12.1 and 0.95 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. This proportion has since decreased and was 29.4% in the latest quarter. In the same period, the proportion of COHA cases was 13.8% (Figure 5, Table S2a in the accompanying data tables).

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

Pseudomonas aeruginosa bacteraemia

Main findings

Total reported cases of P. aeruginosa bacteraemia in April to June 2025 increased by 5.3% from 1,016 to 1,070 cases when compared with April to June 2017. This corresponded with an increase of 1.5% in the incidence from 7.3 to 7.4 cases per 100,000 population. The count of hospital-onset cases increased by 2.7% from 376 to 386 cases, and the incidence remained stable at 4.3 per 100,000 bed-days. Over the same period, the count of community-onset cases increased by 6.9% from 640 to 684, with a 3.0% increase in incidence rate from 4.6 to 4.8 cases per 100,000 population.

When comparing the most recent quarter to last year’s corresponding quarter, counts and incidence of total reported cases decreased by 2.2% and decreased by 2.5%, respectively. This was from 1,094 to 1,070 cases and from 7.6 to 7.4 per 100,000 population (Figure 6). Hospital-onset cases decreased by 11.3% from 435 to 386, compared with April to June 2024 (Figure 6), which corresponded to a decrease of 10.6% in incidence, from 4.8 to 4.3 per 100,000 bed-days. Over the same period, the count and incidence of community-onset P. aeruginosa bacteraemia cases increased by 3.8% and 3.5%, respectively, from 659 to 684 and from 4.6 to 4.8 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 June 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 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.

When comparing April to June 2025 with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was no substantial change in total cases. This remained at 1,070 in both periods, while the incidence decreased by 2.5% from 7.6 to 7.4 cases per 100,000 population (Figure 6). Community-onset cases increased by 1.8% from 672 to 684. Similarly, the community-onset incidence also showed no substantial change remaining at 4.8 cases per 100,000 population. Hospital-onset cases decreased by 3.0% compared with the same period, from 398 to 386. The hospital-onset incidence decreased by 6.5% from 4.6 to 4.3 cases per 100,000 bed-days (Figure 6) (see the sub-section COVID-19 and this data). 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, 20.5% were COHA and 36.1% 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 June 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 of total reported cases increased by 6.9% and increased by 6.7%, respectively, from 259 to 277 cases and from 1.8 to 1.9 per 100,000 population, reaching levels not seen since FY (financial year) 2011 to 2012 (Figure 8). The rise was more pronounced in the community-onset cases. The count and incidence of community-onset MRSA bacteraemia cases increased by 13.6% and 13.3%, respectively, from 162 to 184 and from 1.1 to 1.3 per 100,000 population. Over the same period, hospital-onset cases decreased by 4.1% from 97 to 93, compared with April to June 2024 (Figure 8), which corresponded to a decrease of 3.4% in incidence, from 1.1 to 1.0 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 June 2025), hospital-onset cases (April 2008 to June 2025) and community-onset cases (April 2008 to June 2025)

Detailed findings

There has been a considerable decrease in the incidence of total reported MRSA bacteraemia since the enhanced mandatory surveillance of MRSA bacteraemia began in April 2007 (Figure 8), Table S4 in the accompanying data tables). The incidence of total reported cases fell by 85.0% 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, until the latest quarter, it has increased to 1.9 cases per 100,000 population, with increases seen following the beginning of the COVID-19 pandemic.

A similar trend was observed with the incidence 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 January to March 2014. Since then, until the latest quarter, the rate has increased to 1.0 cases per 100,000 bed-days.

When comparing April to June 2025 with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was a 52.2% increase in total cases from 182 to 277, with an increase of 48.3% in the incidence from 1.3 to 1.9 cases per 100,000 population (Figure 8). Community-onset MRSA bacteraemia counts increased by 41.5% from 130 to 184 and incidence increased by 38.0% from 0.9 to 1.3 cases per 100,000 population (Figure 8).

In the current quarter, 49.5% of cases were community-onset community-associated (COCA), 17.0% were community-onset healthcare-associated (COHA), and 33.6% were hospital-onset healthcare-associated (HOHA) (Figure 9), Table S4a in the accompanying data tables).

Figure 9. Percentage of MRSA bacteraemia cases by prior trust exposure, April 2020 to June 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 59.0% from 2,191 in April to June 2011 to 3,484 in April to June 2025. This corresponded to an increase of 46.4% in incidence, from 16.5 to 24.2 per 100,000 population (Figure 10, Table S5 in the accompanying data tables).

These increases were primarily due to the increase in community-onset cases. Between these two quarters, the count and incidence of community-onset cases increased by 67.1% and 53.8% respectively. This was from 1,493 to 2,495 cases and from 11.3 to 17.3 cases per 100,000 population. Over the same period, the count of hospital-onset cases increased by 41.7% from 698 to 989 cases, while the incidence increased by 36.3% from 8.1 to 11.0 cases per 100,000 bed-days.

Comparing the most recent quarter (April to June 2025) to the same period in the previous year (April to June 2024), there was a 4.6% increase in the count of total reported cases, from 3,330 to 3,484, while the incidence increased by 4.3% from 23.2 to 24.2 per 100,000 population. Hospital-onset MSSA bacteraemia cases increased by 5.9% from 934 to 989, which corresponds to an increase of 6.7% in incidence from 10.3 to 11.0 per 100,000 bed-days. Community-onset MSSA bacteraemia cases increased by 4.1% from 2,396 to 2,495, while the community-onset incidence increased by 3.8% from 16.7 to 17.3 cases per 100,000 population.

Figure 10. Quarterly rates of MSSA bacteraemia, total reported, hospital-onset and community-onset cases, January 2011 to June 2025

Detailed findings

There has been a general trend of increasing count and incidence 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 of MSSA bacteraemia have increased by 13.4% and 10.6%, respectively, from 3,071 to 3,484 cases and from 21.9 to 24.2 cases per 100,000 population. The reasons behind these observed increases are under investigation.

The incidence of hospital-onset MSSA bacteraemia cases peaked during the early stages of the COVID-19 pandemic. This was 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 13.5 cases per 100,000 bed-days. This was the highest MSSA hospital-onset rate and count observed since the inception 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 April to June 2019, counts of community-onset MSSA bacteraemia cases increased by 12.5% from 2,218 to 2,495. There was a 9.6% increase in incidence from 15.8 to 17.3 per 100,000 population, over the same period.

In the current quarter, 59.5% of cases were community-onset community-associated (COCA), 12.0% community-onset healthcare-associated (COHA), and 28.4% hospital-onset healthcare-associated (HOHA) (Figure 11, Table S5a in the accompanying data tables).

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

Laboratory blood cultures

On a quarterly basis, NHS acute trusts are mandated to report the total number of blood culture sets tested. 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 3.0% in the latest quarter of April to June 2025, with some minor fluctuations in the intervening quarters (Figure 12), Table S9 in the accompanying data tables).

The rate of blood culture sets tested gradually increased from April to June 2010, rising by 18.1% 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 tested 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 44.1 tests per 1,000 population in April to June 2025, which is 45.4% 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, 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 April to June 2025

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

Epidemiological analyses of Clostridioides difficile infection (CDI) data

Main findings

Comparing the most recent quarter (April to June 2025) to the same period in the previous year (April to June 2024), there was a 9.4% decrease in the count of total reported cases, from 4,742 to 4,295. Similarly, the incidence decreased by 9.7%, from 33.1 to 29.9 cases per 100,000 population (Figure 14, Table S6 in the accompanying data tables).

Over the same period, hospital-onset CDI cases decreased by 5.7% from 1,999 to 1,885; this corresponded to a decrease of 5.0% in incidence from 22.1 to 21.0. Community-onset CDI cases decreased by 12.1% from 2,743 to 2,410, while the community-onset incidence decreased by 12.4% from 19.1 to 16.8 (Figure 14, Table S6 in the accompanying data tables).

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

Detailed findings

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

Most of the decrease in counts and incidence of cases occurred between April to June 2007 and April to June 2012, with a 78.3% decrease in total-reported cases of CDI from 16,864 to 3,656 cases and an associated 79.1% reduction in incidence from 131.6 cases per 100,000 population to 27.5. Cases and rates were then stable until between January to March 2021 and April to June 2025.

This is when the count of total-reported cases increased by 43.6% from 2,911 to 4,295 cases and the incidence increased by 39.2% from 21.4 to 29.9 cases per 100,000 population.

This change in trend to a steadily increasing trajectory in CDI counts and rates is of major concern and is the only organism among the six showing this major shift post pandemic. The reasons for this are being investigated.

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).

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 in the past four quarters have ranged from 15.2 to 21.3 cases per 100,000 population in April to June 2025.

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

The largest proportion of cases in the latest quarter were HOHA, accounting for 43.9% of the total (Figure 1 5, Table S6a in the accompanying data tables), have steadily risen from 36.6% in July to September 2020. COCA cases in the latest quarter are 27.8% of the total which has gradually reduced from 31.9% over the same period. COHA and community-onset indeterminate-association (COIA) cases constituted 17.8% and 10.5% 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 tested and the total number of stool specimens tested 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 12.6 to 26.2 in the corresponding quarter in 2019. This was followed by a sharper 48.0% 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 33.4 tests per 1,000 population in April to June 2025 (Figure 16, Table S8 in the accompanying data tables).

At the start of surveillance, in April to June 2010, the sampling rate of stool specimens tested for C. difficile diagnosis was 12.9 per 1,000 population. By the same quarter in 2019, the rate saw a similar decline by 22.1 to 10.0. This downward trend continued into the start of the pandemic, with a further 28.5 decline to 6.9. Since then, the sampling rate has returned to an upward trend, increasing to 11.8 per 1,000 population in April to June 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 2.4% in the latest quarter of April to June 2025 (Figure 17, Table S9 in the accompanying data tables). While the sampling rate has increased concurrently with the increase in CDI incidence, 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 tested for CDI diagnosis and overall stool specimens examined, England, by financial year: April to June 2010 to April to June 2025

Figure 17. Trends in percentage positivity of stool specimens tested for CDI diagnosis, England, by financial year: April to June 2010 to April to June 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 18 August 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 and the community-onset incidence.

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. 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 was published by NHS England on 3 September 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 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 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 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 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.  Changes in bed occupancy in England saw a 33.3% drop in occupied overnight beds in April to June 2020 compared with the previous quarter. Over the following 12 months, bed occupancy slowly returned to pre-pandemic levels and has increased by 3.7% when compared with April to June 2019. Various other general restrictions on movement and mixing were introduced nationally to limit the spread of the virus. We note that post-pandemic, many of these collections have now returned to normal pre-pandemic levels, with some collections observing an increase following the pandemic, such as CDI and MRSA.

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 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 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:

• 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.

Accredited official statistics

Our statistical practice is regulated by the Office for Statistics Regulation (OSR). OSR sets the standards of trustworthiness, quality and value in the Code of Practice for Statistics that all producers of Official Statistics should adhere to. You are welcome to contact us directly by emailing mandatory.surveillance@ukhsa.gov.uk with any comments about how we meet these standards. Alternatively, you can contact OSR by emailing regulation@statistics.gov.uk or via the OSR website.

UKHSA is committed to ensuring that these statistics comply with the Code of Practice for Statistics. This means users can have confidence in the people who produce UKHSA statistics because our statistics are robust, reliable and accurate. Our statistics are regularly reviewed to ensure they support the needs of society for information.

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 April to June 2025). London: UK Health Security Agency, October 2025.