Main points

Escherichia. coli (E. coli) bacteraemia

During the latest quarter, July to September 2024:

• the all-reported incidence rate of E. coli bacteraemia was 79.1 per 100,000 population
• this was a 2.6% increase compared with the same quarter last year and a 5.3% decrease when compared with the corresponding pre-COVID-19 pandemic quarter (July to September 2019), indicating a return to pre-pandemic levels
• E. coli cases remain predominantly (81.4%) community-onset, however, hospital-onset incidence rates have also continued on a steady upward trend since the start of surveillance

Klebsiella species (Klebsiella spp.) bacteraemia

During the latest quarter, July to September 2024:

• the all-reported incidence rate of Klebsiella spp. bacteraemia was 24.9 per 100,000 population
• this was a 4.6% increase compared with the same quarter last year and a 18.2% increase since the corresponding 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
• Klebsiella pneumoniae is the most common cause of Klebsiella spp. bacteraemia, accounting for 74.9% of cases and has been the primary contributor to the recent increases, which have been predominately caused by community cases

Pseudomonas aeruginosa (P. aeruginosa) bacteraemia

During the latest quarter, July to September 2024:

• the all-reported incidence rate of P. aeruginosa bacteraemia was 8.5 per 100,000 population
• this was a 4.8% increase compared with the same quarter last year and remained the same as 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, July to September 2024:

• the all-reported incidence rate of meticillin-resistant Staphylococcus aureus (MRSA) bacteraemia was 1.8 per 100,000 population
• this was a 30.7% increase compared with the same quarter last year
• rates of both hospital-onset and community-onset MRSA bacteraemia have remained elevated since October to December 2023, rising above rates not seen since 2013

MSSA bacteraemia

During the latest quarter, July to September 2024:

• the all-reported incidence rate of meticillin-susceptible Staphylococcus aureus (MSSA) bacteraemia was 23.6 per 100,000 population during the latest quarter, July to September 2024
• this was a 4.7% increase compared with the same quarter last year
• when compared with the previous quarter, hospital-onset counts and rates have increased by 0.3% and 11.8 %, respectively; overall, increases have been predominately attributed by community cases

Clostridioides difficile infection (CDI)

During the latest quarter, July to September 2024:

• the all-reported incidence rate of CDI was 36.9 per 100,000 population
• this was a 22.6% increase compared with the same quarter last year
• both community and hospital-onset rates have seen marked rises since July to September 2023, with community-onset rates increasing by 24.3% (from 17.1 to 21.2 per 100,000 population) and hospital-onset rates rising by 18.5% (from 21.6 to 25.6 per 100,000 bed days)
• these figures represent the highest rates recorded since 2011, this surge in rates is currently under further enhanced investigation

Overview of long-term trends

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

All collections returned to pre-pandemic levels relatively soon after, with the exception of E. coli, only returning to pre-pandemic levels in 2024.

We observe differing changes in trends to all collections during and post COVID-19, notably, sustained lower E. coli BSIs until 2024, sharper increases in Klebsiella spp. BSIs, and changes from relatively low and stable incidence to an increasing trend in MRSA BSIs and CDI, surpassing levels not seen for almost 12 years (Figure 1 and Table S7 in the accompanying data tables.).

In recent months:

• MRSA cases have been increasing in the latest quarter (July to September 2024), the number of cases were 29% higher than the same period in the previous year
• E. coli cases have been rising, though they remained below those observed before the pandemic until more recently; however, since December 2023, the numbers of E. coli bacteraemia cases have been comparable to the corresponding pre-pandemic month in 2019
• P. aeruginosa bacteraemia initially showed an increase in 2020, but declined between October 2021 and April 2022; this then reversed and is now beyond March 2018 levels, although, a decline has been observed in recent months
• CDI followed a general decline from the beginning of surveillance until the start of the COVID-19 pandemic, but since February 2021, CDI cases have shown a consistent upward trajectory, surpassing the levels seen in 2012
• Klebsiella spp. bacteraemia cases decreased from early 2020 to October 2020, followed by a period of increase until to November 2021; after a brief decline until April 2022, cases have been rising consistently since. (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 financial year 2017 for Klebsiella spp. and P. aeruginosa bacteraemia, December 2012 to September 2024

Epidemiological analyses of Gram-negative bacteraemia data

E. coli bacteraemia

Main findings

The total reported cases of E. coli bacteraemia in July to September 2024 increased by 38.6% from 8,275 to 11,469 cases when compared with July to September 2011, with an increase of 27.9% in the incidence rate from 61.8 to 79.1 cases per 100,000 population. This increase was primarily caused by an increase in community-onset cases, the count of which increased by 48.7% from 6,279 to 9,339, with a 37.3% increase in incidence rate from 46.9 to 64.4 cases per 100,000 population. The count of hospital-onset cases increased by 6.7% from 1,996 to 2,130 cases, and the incidence rate increased by 1.4% from 23.6 to 23.9 per 100,000 bed-days.

When comparing the most recent quarter to last year’s corresponding quarter, counts and incidence rates of total reported cases increased by 2.3% and 2.6%, respectively, from 11,212 to 11,469 cases and 77.1 to 79.1 per 100,000 population (Figure 2). The recent increase was attributed by an increase in hospital-onset cases, which increased by 3.9% from 2,050 to 2,130, compared with July to September 2023 (Figure 2), corresponding to an increase of 2.5% in incidence rate, from 23.3 to 23.9 per 100,000 bed-days. Over the same time period, the count and incidence rate of community-onset E. coli bacteraemia cases increased by 1.9% and 2.2%, respectively, from 9,162 to 9,339 and from 63.0 to 64.4 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 September 2024

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 caused by community-onset cases (Table S1 in the accompanying data tables). A sharp drop in the count and incidence rate 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 rate of hospital-onset cases remained relatively stable during the same period (20.7 cases per 100,000 bed-days), except for a sharp reduction observed in April to June 2021 (Figure 2). This was followed by a steady return to pre-pandemic levels in early 2024, with incidence rate of hospital-onset E. coli bacteraemia increased more slowly than its count. This may be due to changes in bed occupancy in England; in April to June 2020, there was a 34% drop in occupied overnight beds compared with the previous quarter. Over the following 12 months, bed occupancy slowly returned to pre-pandemic levels and has increased by 3.4% when compared with July to September 2019.

When comparing July to September 2024 with the equivalent pre-COVID-19 pandemic period (July to September 2019), there was a 3.1% decrease in total cases from 11,831 to 11,469, and a decrease of 5.3% in the incidence rate from 83.5 to 79.1 cases per 100,000 population (Figure 2). Community-onset cases decreased by 4.7% from 9,804 to 9,339, and incidence rate decreased by 6.9% from 69.2 to 64.4 cases per 100,000 population. However, the total numbers of hospital-onset cases increased by 5.1% compared with the same period, from 2,027 to 2,130 and rate increased by 1.7% from 23.5 to 23.9 cases per 100,000 bed-days (Figure 2). The steady increase in cases following the initial drop observed at the beginning of the COVID-19 pandemic highlights the slower return to pre-pandemic levels. There was a prolonged period of lower levels of E. coli bacteraemia counts and rates observed after the emergency stage of the 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 variation 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.

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 the Definitions section).

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 2021. In the current quarter, 67.5% of cases were community-onset community-associated (COCA), 13.9% were community-onset healthcare-associated (COHA), and 18.6% were hospital-onset healthcare-associated (HOHA) (Figure 3 and Table 1a in the accompanying data tables).

Figure 3. Percentage of E. coli bacteraemia cases by prior trust exposure, April 2020 to September 2024

Klebsiella spp. bacteraemia

Main findings

The total reported cases of Klebsiella spp. bacteraemia in July to September 2024 increased by 35.2% from 2,676 to 3,617 cases when compared with July to September 2017; this corresponded with an increase of 30.7% in the incidence rate from 19.1 to 24.9 cases per 100,000 population. The count of hospital-onset cases increased by 41.3% from 794 to 1,122 cases, and the incidence rate increased by 36.2% from 9.2 to 12.6 per 100,000 bed-days. The count of community-onset cases increased by 32.6% from 1,882 to 2,495, with a 28.2% increase in incidence rate from 13.4 to 17.2 cases per 100,000 population.

Comparing the most recent quarter to the same quarter in the previous year, counts and incidence rates of total reported cases increased by 4.4% and 4.6%, respectively, from 3,466 to 3,617 cases and from 23.8 to 24.9 per 100,000 population (Figure 4). The recent increase was caused by a surge in community-onset cases, which increased by 17.7% from July to September 2022. The upward trend continued with the count in July to September 2024 increasing by 2.8%, and rate, by 3.1%, respectively, from 2,426 to 2,495 and from 16.7 to 17.2 per 100,000 population. Hospital-onset cases increased by 7.9% from 1,040 to 1,122, compared with July to September 2023 (Figure 4), which corresponded to an increase of 6.4% in incidence rate, from 11.8 to 12.6 per 100,000 bed-days (Table S2 in the accompanying data tables).

Figure 4. Quarterly rates of Klebsiella spp. bacteraemia, total reported, hospital-onset and community-onset cases, by species, April 2017 to September 2024

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). Since the observed peak in hospital-onset rates, the rate has fluctuated between 12.6 and 9.6 cases per 100,000 bed-days. Community-onset cases peaked during the July to September 2021 quarter reaching 14.7 cases per 100,000 population fluctuating between 12.6 and 15 cases per 100,000 population, up until July to September 2023 where the community-onset rate peaked at 16.7; a 13.8% increase since July to September 2022. Since then, a steeper increase in rate has been observed in the community-onset case trend when compared to the hospital-onset rate trend.

When comparing the most recent quarter (July to September 2024) with the equivalent pre-COVID-19 pandemic period (July to September 2019), there was a 20.9% increase in total cases from 2,991 to 3,617, and a corresponding increase of 18.2% in the incidence rate from 21.1 to 24.9 cases per 100,000 population (Figure 4, Table S2 in the accompanying data tables). Community-onset cases increased by 19.4% from 2,090 to 2,495. Similarly, the incidence rate of community-onset cases also increased by 16.7% from 14.7 to 17.2 cases per 100,000 population. Finally, the count of hospital-onset cases increased by 24.5% from 901 to 1,122, and rate increased by 20.5% from 10.4 to 12.6 cases per 100,000 bed-days, respectively (Figure 4, Table S2 in the accompanying data tables).

During July to September 2024, 74.9% of the total reported Klebsiella spp. bacteraemia were caused by K. pneumoniae, 16.2% were caused by K. oxytoca and 3.8% were by Klebsiella aerogenes (Figure 4, Table S2 in the accompanying data tables). Since the previous quarter April to June 2024, hospital-onset Klebsiella genus cases have seen a 15.5% increase from 971 to 1,122 with a corresponding increase in rate from 10.7 to 12.6 100,000 bed days, predominantly driven by increases observed in K. pneumoniae, which increased 20.1% from 701 to 842 cases, and a 21.8% increase in incident rate, which rose from 7.8 to 9.4 100,000 bed days. During the COVID-19 pandemic, K. pneumoniae and K. aerogenes saw peaks at 10.8 and 1.8 per 100,00 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 cases were observed in the hospital setting (Sloot and colleagues, 2022). This proportion has since decreased and was 31.0% in the latest quarter. In the same period, the proportion of COHA cases was 15.4% (Figure 5 and accompanying data tables).

Figure 5: Percentage of Klebsiella spp. bacteraemia cases by prior trust exposure, April 2020 to September 2024

Pseudomonas aeruginosa bacteraemia

Main findings

Total reported cases of P. aeruginosa bacteraemia in July to September 2024 increased by 4.5% from 1,186 to 1,239 cases when compared with July to September 2017; and no substantial change in the incidence rate, which remained at 8.5 cases per 100,000 population. The count of hospital-onset cases increased by 8.3% from 423 to 458 cases, and the incidence rate increased by 4.3% from 4.9 to 5.1 per 100,000 bed-days. Over the same period, the count of community-onset cases increased by 2.4% from 763 to 781 and the incidence rate remained 5.4 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 increased by 4.6% and 4.8%, from 1,185 to 1,239 cases and from 8.1 to 8.5 per 100,000 population, respectively (Figure 6). Hospital-onset cases decreased by 2.1% from 468 to 458, compared with July to September 2023 (Figure 6). This corresponded to a decrease of 3.5% in incidence rate, from 5.3 to 5.1 per 100,000 bed-days. Over the same period, the count and incidence rate of community-onset P. aeruginosa bacteraemia cases increased by 8.9% and 9.2%, respectively, from 717 to 781 and from 4.9 to 5.4 per 100,000 population (Table S3 in the accompanying data tables).

Figure 6. Quarterly rates of P. aeruginosa bacteraemia, total reported, hospital-onset and community-onset cases April 2017 to September 2024

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 the July to September quarters in both 2020 and 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 July to September 2024 with the equivalent pre-COVID-19 pandemic period (July to September 2019), there was a 3.4% increase in total cases from 1,198 to 1,239, with no substantial change in the incidence rate, which remained 8.5 cases per 100,000 population (Figure 6). Community-onset cases decreased by 1.8% from 795 to 781. Similarly, the CO incidence rates also decreased by 4.0% from 5.6 to 5.4 cases per 100,000 population. Hospital-onset cases increased by 13.6% compared with the same period, from 403 to 458, and incidence rate increased by 10.0% from 4.7 to 5.1 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 seen at the start of the COVID-19 pandemic, the hospital-onset counts have returned to expected pre-pandemic levels.

There is evidence of seasonality in the trend of total reported P. aeruginosa bacteraemia cases, with higher rates normally observed in July to September and lower rates observed from January to March of each year (Figure 6).

Similarly to E. coli and Klebsiella spp., COCA cases make up the highest proportion of P. aeruginosa bacteraemia cases; however, they do not constitute the majority of cases. In the latest quarter, COCA’s accounted for 45.4% of the total, while 17.5% were COHA and 37.0% were HOHA. This contrasts with January to March 2021, when HOHA cases made up 48% of the total (Figure 7 and Table 3a in the accompanying data tables).

Figure 7. Percentage of P. aeruginosa bacteraemia cases by prior trust exposure, April 2020 to September 2024

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

Main findings

When comparing the most recent quarter to last year’s corresponding quarter, counts and incidence rates of total reported cases increased by 30.4% and 30.7%, respectively. This was from 204 to 266 cases and from 1.4 to 1.8 per 100,000 population, though cases remained at a relatively low level, compared with historical MRSA incidence (Figure 8).

Recent increases were more pronounced in community-onset cases. The count and incidence rate of community-onset MRSA bacteraemia cases increased by 40.8% and 41.2%, respectively, from 125 to 176 and from 0.9 to 1.2 per 100,000 population. Over the same period, hospital-onset cases increased by 13.9% from 79 to 90, when compared with July to September 2023 (Figure 8). This corresponded to an increase of 12.4% in incidence rate, from 0.9 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.

Comparing the most recent quarter with the previous quarter we note an 8.6% and 7.5% increase in community-onset counts and incidence rate, respectively. Rising from 162 to 176 community cases and 1.1 to 1.2 cases per 100,000 population. While hospital-onset cases decreased 7.2% from 97 to 90, with a corresponding decrease in incidence rate from 1.1 to 1.0. Indicating the increase in total cases is primarily community driven.

Figure 8. Quarterly rates of MRSA bacteraemia, total reported and community onset cases (April 2007 to September 2024) and hospital-onset cases (April 2008 to September 2024)

Detailed findings

There has been a considerable decrease in the incidence rate 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 rate of total reported cases fell by 85% 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, it increased to 1.8 cases per 100,000 population.

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 case per 100,000 bed-days in January to March 2014. Since then, the rate has showed no substantial change.

When comparing July to September 2024 with the equivalent pre-COVID-19 pandemic period (July to September 2019), there has been a 33.0% increase in total cases from 200 to 266, with an increase of 30.0% in the incidence rate from 1.4 to 1.8 cases per 100,000 population (Figure 8). Community-onset MRSA bacteraemia counts increased by 31.3% from 134 to 176, and incidence rate increased by 28.4% from 0.9 to 1.2 cases per 100,000 population (Figure 8). Hospital-onset cases saw the greatest increase in counts and incidence rate of 36.4% and 32.0%, respectively. Counts increasing from 66 to 90 and the incidence rate from 0.8 to 1.0 cases per 100,000 population.

In the current quarter, 52.3% of cases COCA, 13.9% COHA, and 33.8% were reported as HOHA (Figure 9 and Table S4a in the accompanying data tables). This is the highest percentage of COCA cases seen since October to December 2022.

Figure 9. Percentage of MRSA bacteraemia cases by prior trust exposure, April 2020 to September 2024

MSSA bacteraemia

Main findings

Counts and rates of MSSA bacteraemia remain higher than those seen at the beginning of surveillance in 2011. The count of total reported cases increased by 54.0% from 2,226 in July to September 2011 to 3,427 in July to September 2024. This corresponded to an increase of 42.1% in incidence rate, from 16.6 to 23.6 per 100,000 population (Figure 10, Table S5 in the accompanying data tables).

These increases are primarily attributed to the increase in community-onset cases, however, hospital onset cases have also seen large increases.  Between these two quarters, the count and incidence rate of community-onset cases increased by 59.7% and 47.4% respectively, from 1,501 to 2,397 cases and from 11.2 to 16.5 cases per 100,000 population. Over the same period, the count of hospital-onset cases increased by 42.1% from 725 to 1,030 cases, while the incidence rate increased by 35.0% from 8.6 to 11.6 cases per 100,000 bed-days.

Comparing the most recent quarter (July to September 2024) to the same period in the previous year, there was a 4.4% increase in the count of total reported cases from 3,283 to 3,427, while the incidence rate increased by 4.7% from 22.6 to 23.6 per 100,000 bed-days. Hospital-onset MSSA bacteraemia cases increased by 5.3% from 978 to 1,030, which corresponds to an increase of 3.9% in incidence rate from 11.1 to 11.6 per 100,000 bed-days. Community-onset MSSA bacteraemia cases increased by 4.0% from 2,305 to 2,397, while the community-onset incidence rate increased by 4.3% from 15.9 to 16.5 cases per 100,000 population.

Comparing the most recent quarter with the previous quarter we note a 10.3% and 11.8% increase in hospital-onset counts and incidence rate respectively. Rising from 934 to 1,030 cases and 10.3 to 11.6 cases per 100,000 bed-days. While community onset cases remained stable with a slight drop-in incidence rate.

Figure 10. Quarterly rates of MSSA bacteraemia total reported, hospital-onset and community-onset cases, January 2011 to September 2024

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. After a temporary reduction during the initial stages of the COVID-19 pandemic, the increasing trend has resumed. Comparing the latest quarter with the corresponding quarter in 2019, the count and incidence rate of MSSA bacteraemia have increased by 8.2% and 5.8% respectively, from 3,167 to 3,427 cases and from 22.3 to 23.6 cases per 100,000 population. The reasons behind these observed increases are under investigation.                                                                         

The incidence rate of hospital-onset MSSA bacteraemia cases peaked during the early stages of the COVID-19 pandemic, to 13.4 cases per 100,000 bed-days in January to March 2021. This was in part caused by reduced hospital activity, resulting in reduced occupied overnight bed-days (the denominator used to calculate hospital-onset rates). 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 July to September 2019, counts of community-onset MSSA bacteraemia cases increased by 3.4% from 2,319 to 2,397, and there was a 1.0% increase in incidence rate from 16.4 to 16.5 per 100,000 population, over the same period. Hospital-onset cases increased by 21.5% from 848 to 1,030 with a corresponding 17.5% increase in incidence rate from 9.8 to 11.6. Unlike MRSA bacteraemia, the increase in total cases for this latest quarter appears to be attributed by hospital-onset cases.

In the current quarter, 57.2% of cases were COCA, 12.6% were COHA and 30.1% were HOHA (Figure 11) and Table S5a in the accompanying data tables).

Figure 11. Percentage of MSSA bacteraemia cases by prior trust exposure, April 2020 to September 2024

Epidemiological analyses of Clostridioides difficile infection (CDI) data

Main findings

Comparing the most recent quarter (July to September 2024) to the same period in the previous year, there was a 22.3% increase in the count of total reported cases, from 4,381 to 5,358. Similarly, the incidence rate increased by 22.6%, from 30.1 to 36.9 cases per 100,000 population (Figure 12, Table S6 in the accompanying data tables).

Hospital-onset CDI cases increased by 20.1% from 1,898 to 2,280; this corresponded to an increase of 18.5% in incidence rate from 21.6 to 25.6. Community-onset CDI cases increased by 24.0% from 2,483 to 3,078, while the community-onset incidence rate increased by 24.3% from 17.1 to 21.1 (Figure 12), Table S6 in the accompanying data tables).

Comparing the most recent quarter with the previous quarter we note increases across both hospital and community onset cases. Hospital-onset counts increased by 13.9%, rising from 2,001 to 2,280 with subsequent increases in incidence rate by 15.5%, from 22.1 to 25.6 cases per 100,000 bed-days. Community-onset CDI cases increased 12.1% from 2,746 to 3,078 cases, with a corresponding 10.9% increase in incidence rate from 19.1 to 21.2 cases per 100,000 population.

Figure 12. Quarterly rates of CDI, total reported, hospital-onset and community-onset cases, April 2017 to September 2024

Detailed findings

Since the initiation of 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 of CDI.

Most of the decrease in the incidence rate occurred between April to June 2007 and January to March 2012, with a 78.0% decrease in all-reported cases of CDI from 16,864 to 3,711 cases and a similar 78.8% reduction in incidence rate from 131.6 cases per 100,000 population to 27.9. Subsequently, between January to March 2012 and July to September 2024, the count of all-reported cases increased by 44.4% from 3,711 to 5,358 cases and the incidence rate increased by 32.5% from 27.9 to 36.9 cases per 100,000 population. Most of this rise was observed following the COVID-19 pandemic, whereas prior to this, rates were generally declining with some fluctuations. This change in trend to a steady increasing trajectory in CDI counts and rates is of major concern and is the only data collection where we have seen this major shift post pandemic, along with MRSA showing a similar shift. The reasons for which are being investigated and CDI stood up as a national incident late 2024.

Hospital-onset CDI cases saw similar large reductions between April to June 2007 and January to March 2012, with an 83.5% decrease in count of cases, 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 12, Table S6 in the accompanying data tables).

This was followed by a 26.1% increase in the count of cases from 1,808 to 2,280 cases and an increase of 26.2% in the incidence rate from 20.3 to 25.6 cases per 100,000 bed-days between January to March 2012 and July to September 2024. Most of the rise in hospital-onset cases were seen following the COVID-19 pandemic, whereas prior to this, rates were generally declining with some fluctuations.

When comparing the latest quarter to the pre-pandemic period of July to September 2019, counts of hospital-onset cases increased by 64.9% from 1,383 to 2,280 with a corresponding 59.5% increase in incidence rate from 16.0 to 25.6. Community-onset CDI cases increased by 36.4% from 2,256 to 3,078, and there was a 33.3% increase in incidence rate from 15.9 to 21.2 per 100,000 population, over the same period. Increase in total cases appears to be equal across both hospital- and community-onset cases.

The largest proportion of cases are HOHA; in the last quarter, these accounted for 42.6% of the total. COHA and COCA cases constituted 18.3% and 29.1% of the total, respectively. Community-onset indeterminate-association (COIA) cases accounted for 10.0%. These percentages have been relatively stable since April 2018, when the data quality had substantially improved compared with the previous year (Figure 13 and Table S6a in the accompanying data tables).

Figure 13. Percentage of CDI cases by prior trust exposure, April 2020 to September 2024

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 4 November 2024.

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 quarter 1 (Q1) of the financial year (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 21 November 2024. 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 (RWD) for financial year 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) 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

Definitions

CDI onset categories

The division of cases into hospital-onset and community-onset cases ignores the effect of any prior admissions to hospital which could increase the risk of CDI. For this reason, and to better align surveillance in England with that performed by the European Centre for Disease Prevention and Control (ECDC) and the Centres for Disease Control and Prevention (CDC), information on prior trust exposure was introduced in April 2017.To align with ECDC and CDC definitions, Hospital-onset  infections are now defined as those occurring on or after the third day of an acute NHS trust admission, differing from the historical hospital-onset CDI classification of four days after admission.  

A case of CDI is classified as hospital-onset if it meets all of the following criteria:

1. the patient is an in-patient, day-patient, emergency assessment patient or ‘location not known’, and
2. the specimen was taken at an acute trust or at an unknown location, and
3. the specimen was taken on or after day 3 of the admission (admission date is considered day ‘one’).

Cases that do not meet all these criteria are categorised as community-onset.

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 (FY) 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

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 (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 the spread of the virus. We note that post pandemic, many of these collections have now returned to normal pre-pandemic levels, with a slower return noted for E. coli, and the exception of CDI rising to levels not seen for almost 12 years.

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. Revisions to data included 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 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 total reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MRSA bacteraemia by organisation.
• MSSA bacteraemia – counts of total reported, hospital-onset cases, community-onset cases, healthcare associated and community associated MSSA bacteraemia by organisation.
• E. coli bacteraemia – counts of total reported, hospital-onset cases, community-onset cases, healthcare associated and community associated E. coli bacteraemia by organisation.
• Klebsiella spp. bacteraemia – counts of total reported, hospital-onset cases, community-onset cases, healthcare associated and community associated Klebsiella spp. bacteraemia by organisation.
• P. aeruginosa bacteraemia – counts of total reported, hospital-onset cases, community-onset cases, healthcare associated and community associated P. aeruginosa bacteraemia by organisation.
• CDI – counts of total reported, hospital-onset cases, community-onset cases, healthcare associated and 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.

Citation

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

Reference

Sloot, Rosa, O Nsonwu, D Chudasama, G Rooney, C Pearson, H Choi, E Mason and others. ‘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 2022: volume 119, pages 175 to 181 https://doi.org/10.1016/j.jhin.2021.08.027.

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.