Accredited official statistics

Quarterly epidemiological commentary: Mandatory Gram-negative bacteraemia, MRSA, MSSA and C. difficile infections (data up to January to March 2024)

Updated 6 November 2024

Applies to England

Correction notice

This is a correction notice for this statistical release, first published on 11 July 2024 and revised on 6 September 2024.

Since the initial release of these statistics, it was identified that the quarter 4 of financial year 2023 to 2024 national population estimate did not account for the leap year. As a result, minor corrections were made, leading to small decimal point differences in the overall and community-onset rates. However, these corrections did not affect the direction of trends.

All identified errors have been corrected in this revised report and accompanying tables, both superseding the initial release of these statistics in July 2024.

Main points

The main messages of this report are:

• the all-reported incidence rate of E. coli bacteraemia was 72.7 per 100,000 population during the latest quarter, January to March 2024. This was a 10.0% increase compared to the same quarter last year, with no substantial change when compared to pre-COVID19 pandemic quarter (January to March 2019), indicating a return to pre-pandemic levels. E. coli cases were caused predominantly by community-onset cases, however, hospital-onset incidence rates have also continued on an upward trend

• the all-reported incidence rate of Klebsiella spp. bacteraemia has increased by 36.9% compared with the same quarter in 2018, rising from 16.4 to 22.4 per 100,000 population. Hospital-onset Klebsiella spp. rate peaked during the acute stages of the COVID-19 pandemic, before declining soon after, but it has continued to remain higher than pre-pandemic levels. K. pneumoniae is the most common cause, accounting for 73.6% of Klebsiella spp. bacteraemias, and has been causing the recent increase

• there has been a marginal decrease in the all-reported incidence rate of Pseudomonas aeruginosa (P. aeruginosa) bacteraemia of 5.8% from 7.0 to 7.4 per 100,000 population. This was when comparing the latest quarter to the same quarter in 2018. 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

• the all-reported incidence rate of meticillin-resistant Staphylococcus aureus (MRSA) bacteremia increased by 17.6% in the most recent quarter compared with the same quarter in the previous year, rising from 1.5 to 1.8 per 100,000 population. This marks the second quarter with the highest observed rate since early 2018 and is similar to the rate observed throughout 2013

• the all-reported incidence rate of MSSA bacteraemia has increased 43.5% since the same quarter in 2011 from 16.8 to 24.3 per 100,000 population. This marks the highest community-onset and all-reported rates since the start of MSSA surveillance. A notable spike in the hospital-onset incidence rate of 13.4 per 100,000 bed-days during the alpha wave of the COVID-19 pandemic was observed

• there was a 18.0% increase in the all-reported incidence rate of Clostridioides difficile infection (CDI) in January to March 2024, rising from 25.5 to 30.1 per 100,000 population. This was when compared with the same quarter in the previous year, This rise was primarily driven by an increase in the community-onset incidence count and rate, which rose by 25.7%, from 1,993 to 2,527, and 14.2 to 17.8 per 100,000 population.

Epidemiological analyses of Gram-negative bacteraemia data

Escherichia coli bacteraemia

Main findings

The total reported cases of E. coli bacteraemia in financial quarter (FQ) January to March 2024 increased by 34.0% from 7,698 to 10,317 cases when compared with January to March 2012. There was an increase of 25.6% in the incidence rate from 57.9 to 72.7 cases per 100,000 population. This increase was primarily driven by an increase in community-onset cases, the count of which increased by 43.5% from 5,774 to 8,286, with a 34.5% increase in incidence rate from 43.4 to 58.4 cases per 100,000 population. The count of hospital-onset cases increased by 5.6% from 1,924 to 2,031 cases, and the incidence rate increased by 1.8% from 21.6 to 22.0 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 10.9%. This was from 9,302 to 10,317 cases and from 66.1 to 72.7 per 100,000 population, respectively (Figure 1). The recent increase was caused by an increase in hospital-onset cases. These increased by 7.0% from 1,899 to 2,031, compared with January to March 2023 (Figure 1), which corresponded to an increase of 3.6% in incidence rate, from 21.2 to 22.0 per 100,000 bed-days. Over the same time period, the count and incidence rate of community-onset E. coli bacteraemia cases increased by 11.9% for counts and 11.0% for rates. It went from 7,403 to 8,286 and 52.6 to 58.4 per 100,000 population (Table S1 in the accompanying data tables).

Figure 1: Quarterly rates of E. coli bacteraemia, total reported and hospital-onset cases, July 2011 to March 2024

Detailed findings

The incidence rate of total reported E. coli bacteraemias 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 1). This increase was primarily driven by community-onset cases (Table S1 in the accompanying data tables). A sharp drop in the count and incidence rates of total reported (Figure 1).and community-onset cases was observed after the start of the pandemic but remained higher than they were at the start of this surveillance

In contrast, the incidence rate of hospital-onset cases remained relatively stable during the same period, with the exception of a sharp reduction (20.7 cases per 100,000 bed-days) observed in April to June 2021 (Figure 1). The incidence rate of hospital-onset E. coli bacteraemia increased more slowly than counts. This is 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 more slowly returned to pre-pandemic levels and has increased 5.4% when compared with January to March 2019.

When comparing January to March 2024 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was no substantial change in total cases or incidence rates (from 10,250 to 10,317 and 73.9 to 72.7 cases per 100,000 population, respectively) (Figure 1). Community-onset cases decreased by 1.3% from 8,395 to 8,286. Similarly, the incidence rate of community-onset cases also decreased by 3.6% from 60.5 to 58.4 cases per 100,000 population. However, the total numbers of hospital-onset cases increased by 9.5% compared to the same period, from 1,855 to 2,031. The hospital-onset incidence rate increased by 3.9% from 21.1 to 22.0 cases per 100,000 bed-days (Figure 1). 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, particularly with community-onset counts and rates only beginning to return to levels seen prior to the pandemic. There are uncertainties in why we still see lower levels of community-onset E. coli BSI after the emergency stage of the pandemic, with further investigative work ongoing.

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. 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 Background information).

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, 65.7% of cases were community-onset community-associated (COCA), 14.6% were community-onset healthcare-associated (COHA), and 19.7% were hospital-onset healthcare-associated (HOHA) (Figure 2 and Table 1a in the accompanying data tables).

Figure 2: Percentage of E. coli bacteraemia cases by prior trust exposure, April 2020 to March 2024

Klebsiella spp. bacteraemia

Main findings

The total reported cases of Klebsiella spp. bacteraemia in January to March 2024 increased by 41.0% from 2,258 to 3,183 cases when compared with January to March 2018. This corresponded with an increase of 36.9% in the incidence rate from 16.4 to 22.4 cases per 100,000 population. The count of hospital-onset cases increased by 38.6% from 702 to 973 cases, and the incidence rate by 33.5% from 7.9 to 10.5 per 100,000 bed-days. The count of community-onset cases increased by 42.0% from 1,556 to 2,210, with a 37.9% increase in incidence rate from 11.3 to 15.6 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 11.6%, from 2,829 to 3,183 cases and from 20.1 to 22.4 per 100,000 population (Figure 3). The recent increase was caused by an increase in community-onset cases. The count and rates increased by 14.7%, from 1,911 to 2,210 and from 13.6 to 15.6 per 100,000 population, respectively. Hospital-onset cases increased by 6.0% from 918 to 973, compared with January to March 2023 (Figure 3). This corresponded to an increase of 2.6% in incidence rate, from 10.3 to 10.5 per 100,000 bed-days (Table S2 in the accompanying data tables).

Figure 3: Quarterly rates of Klebsiella spp. bacteraemia, total reported and hospital-onset cases, by species, April 2017 to March 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, but have since returned to pre-pandemic levels. 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 et al. 2022).

When comparing the most recent quarter (January to March 2024) with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was a 23.2% increase in total cases from 2,583 to 3,183. There was also a corresponding increase of 20.3% in the incidence rate, from 18.6 to 22.4 cases per 100,000 population (Figure 3, Table S2 in the accompanying data tables). Community-onset (CO) cases increased by 20.3% from 1,837 to 2,210. Similarly, the incidence rate of community-onset cases also increased by 17.5%, from 13.2 to 15.6 cases per 100,000 population. There was a sharp increase in Klebsiella spp. cases in the July to September 2023 quarter, which is still under investigation. In the same period, the count of hospital-onset cases increased by 30.4%, from 746 to 973. The rate increased by 23.8% from 8.5 to 10.5 cases per 100,000 bed-days, respectively (Figure 3, Table S2 in the accompanying data tables).

During January to March 2024, 73.6% of the total reported Klebsiella spp. bacteraemia were caused by K. pneumoniae, 16.2% were caused by K. oxytoca, and 4.1% were caused by Klebsiella aerogenes (Figure 3, Table S2 in the accompanying data tables). Since the previous quarter (October to December 2023), hospital-onset Klebsiella spp. cases have seen a 13.2% decrease, from 12.1 to 10.5 per 100,000 bed days, and are broadly in line with seasonal trends. This decrease was predominantly caused by a decrease in K. pneumoniae, which decreased 12.5% from 8.7 to 7.6 per 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 3).

Since the inception 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. bloodstream infection (BSI) cases were observed in the hospital setting (Sloot et al. 2022). This proportion has since decreased and was 30.6% in the latest quarter. In the same period, the proportion of COHA cases was 14.6% (Figure 4 and accompanying data tables).

Figure 4: Percentage of Klebsiella spp. bacteraemia cases by prior trust exposure, April 2020 to March 2024

Pseudomonas aeruginosa bacteraemia

Main findings

Total reported cases of P. aeruginosa bacteraemia in January to March 2024 increased by 8.9%, from 964 to 1,050 cases. This was when compared with January to March 2018. This corresponded to an increase of 5.8% in the incidence rate, from 7.0 to 7.4 cases per 100,000 population. The count of hospital-onset cases showed no substantial change (394 to 392 cases), however, the incidence rate decreased by 4.2% from 4.4 to 4.2 per 100,000 bed-days. Over the same period, the count of community-onset cases increased by 15.4% from 570 to 658, with a 12.1% increase in incidence rate, from 4.1 to 4.6 cases per 100,000 population.

Counts and incidence rates of total reported cases increased when comparing the most recent quarter with last year’s corresponding quarter. They increased from 1,030 to 1,050 cases and from 7.3 to 7.4 per 100,000 population, respectively (Figure 5). Hospital-onset cases decreased by 5.1% from 413 to 392, compared with January to March 2023 (Figure 5). This corresponded to a decrease of 8.1% in incidence rate, from 4.6 to 4.2 per 100,000 bed-days. Over the same time period, the count of community-onset P. aeruginosa bacteraemia cases increased by 6.6%, from 617 to 658 cases. There was a corresponding 5.8% increase in rate, from 4.4 to 4.6 per 100,000 population (Table S3 in the accompanying data tables).

Figure 5: Quarterly rates of P. aeruginosa bacteraemia, total reported and hospital-onset cases, April 2017 to March 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 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 et al. 2022).

When comparing January to March 2024 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was an 8.8% increase in total cases, from 965 to 1,050. There was an increase of 6.3% in the incidence rate, from 7.0 to 7.4 cases per 100,000 population (Figure 5). Community-onset (CO) cases increased by 8.9% from 604 to 658. Similarly, the CO incidence rates also increased by 6.4% from 4.4 to 4.6 cases per 100,000 population. Hospital-onset cases increased by 8.6% compared to the same period, from 361 to 392. The hospital-onset incidence rate increased by 3.0% from 4.1 to 4.2 cases per 100,000 bed-days (Figure 5). 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.

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, they made up 45.6% of the total, whilst 17.0% were COHA and 37.3% were HOHA. This contrasts with January to March 2021, when HOHA cases made up 48.2% of the total (Figure 6 and Table 3a in the accompanying data tables).

Figure 6: Percentage of P. aeruginosa bacteraemia cases by prior trust exposure, April 2020 to March 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 18.6% and 17.6%, from 210 to 249 cases and from 1.5 to 1.8 per 100,000 population, respectively. Although rates remain relatively low, this is the second quarter the incident rate has been the highest since January to March 2018, and it continues on an upward trajectory (Figure 7 and Table S4 in the accompanying data tables).

The rise was evenly distributed between the community-onset and hospital-onset cases. The count and incidence rate of community-onset MRSA bacteraemia cases increased by 17.7% and 16.7%, from 130 to 153 and 0.9 to 1.1 per 100,000 population. Over the same period, hospital-onset cases increased by 20.0% from 80 to 96, compared with January to March 2023 (Figure 7). This corresponded to an increase of 16.2% in the incidence rate, from 0.9 to 1.0 per 100,000 bed-days (Table S4 in the accompanying data tables).

Due to the low incidence of MRSA bacteraemia, proportions should be interpreted with caution.

Figure 7: Quarterly rates of MRSA bacteraemia, total reported cases (April 2007 to March 2024) and hospital-onset cases (April 2008 to March 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 7, Table S4 in the accompanying data tables). The incidence rate 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. Another peak was observed in January to March 2018, where the rate reached 1.8 per 100,000 population, before dropping to 1.0 per 100,000 population during the pandemic. Since then, incidence has broadly remained stable, fluctuating between 1.0 and 1.5 per 100,000 population. However, looking at the same quarter, since January to March 2022 there has been an upward trajectory. Incidence has increased by 39.1% from 1.3 to 1.8 cases per 100,000 population, surpassing 2013 levels for the second time consistently since the beginning of the surveillance programme.

A similar trend was observed with the incidence rate of hospital-onset cases (Figure 7, Table S4 in the accompanying data tables). There was a steep decrease of 79% from 4.9 cases per 100,000 bed-days in April to June 2008, to 1.0 cases per 100,000 bed-days January to March 2014. This has remained broadly stable until January to March 2021, where incidence increased to 1.4 per 100,000 population. Since then, the incidence rate has fluctuated between 0.6 and 0.9 per 100,000 population. The last two quarters show the incidence rate remaining above 1.0 per 100,000 population.

When comparing January to March 2024 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was a 39.1% increase in total cases from 179 to 249. There was an increase of 35.8% in the incidence rate, from 1.3 to 1.8 cases per 100,000 population (Figure 7). Community-onset MRSA bacteraemia counts increased by 28.6% from 119 to 153. The incidence rate of community-onset cases increased by 25.6%, from 0.9 to 1.1 cases per 100,000 population (Figure 7).

In the current quarter, 45.0% of cases were community-onset community-associated (COCA), 16.5% were community-onset healthcare-associated (COHA), and 38.6% were hospital-onset healthcare-associated (HOHA) (Figure 8 and Table 4a in the accompanying data tables).

Figure 8: Percentage of MRSA bacteraemia cases by prior trust exposure, April 2020 to March 2024

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 55.6%, from 2,199 in January to March 2011 to 3,422 in January to March 2024. This corresponded to an increase of 43.5% in incidence rate, from 16.8 to 24.1 per 100,000 population (Figure 9, Table S5 in the accompanying data tables).

These increases are primarily driven by an increase in community-onset cases. Between these two quarters, the count of community-onset cases increased by 65.8%. The incidence rate increased by 52.9% per 100,000 bed-days, from 1,464 to 2,427 cases and from 11.2 to 17.1 cases per 100,000 population, respectively. Over the same period, the count of hospital-onset cases increased by 35.4%, from 735 to 995 cases. The incidence rate increased by 29.1%, from 8.3 to 10.8 cases per 100,000 bed-days.

Comparing the most recent quarter (January to March 2024) with the same period in the previous year (January to March 2023), there was a 4.6% increase in the count of total reported cases, from 3,272 to 3,422. . The incidence rate increased by 3.7% from 23.2 to 24.1 per 100,000 bed-days. Hospital-onset MSSA bacteraemia cases increased by 6.1% from 938 to 995. This corresponds to an increase of 2.7% in incidence rate, from 10.5 to 10.8 per 100,000 bed-days. Community-onset MSSA bacteraemia cases increased by 4.0% from 2,334 to 2,427, while the community-onset incidence rate increased by 3.1% from 16.6 to 17.1 cases per 100,000 population.

Figure 9: Quarterly rates of MSSA bacteraemia, total reported and hospital-onset cases, January 2011 to March 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, trends returned to pre-pandemic levels and resumed their upward trajectory. Comparing the latest quarter with the corresponding quarter in 2019, the count and incidence rate of MSSA bacteraemia have increased by 13.0% and 10.3%, respectively. This went from 3,029 to 3,422 cases and from 21.8 to 24.1 cases per 100,000 population. The reasons behind these observed increases are under investigation.

Conversely, the incidence rate of hospital-onset MSSA bacteraemia cases peaked in January to March 2021, when it was 13.4 cases per 100,000 bed-days, coinciding with the COVID-19 pandemic. This was the highest MSSA hospital-onset rate and count observed since the start of MSSA surveillance. This pattern is similar to that observed in both Klebsiella spp. and P. aeruginosa. This was in part caused by reduced hospital activity, resulting in reduced occupied overnight bed-days (the denominator used to calculate hospital-onset rates).

When comparing the latest quarter to the pre-pandemic period of January to March 2019, counts of community-onset MSSA bacteraemia cases increased by 11.1% from 2,185 to 2,427. There was a 8.5% increase in incidence rate from 15.8 to 17.1 per 100,000 population, over the same period.

In the current quarter, 58.2% of cases were community-onset community-associated (COCA), 12.5% were community-onset healthcare-associated (COHA), and 29.1% were hospital-onset healthcare-associated (HOHA) (Figure 10 and Table 5a in the accompanying data tables).

Figure 10: Percentage of MSSA bacteraemia cases by prior trust exposure, April 2020 to March 2024

Epidemiological analyses of Clostridioides difficile infection data

Main findings

Comparing the most recent quarter (January to March 2024) to the same period in the previous year (January to March 2023), there was a 19.0% increase in the count and 18.0% increase in the incidence rate of total reported cases. Cases went from 3,596 to 4,280 and from 25.5 to 30.1 cases per 100,000 population, respectively (Figure 11, Table S6 in the accompanying data tables).

Hospital-onset CDI cases increased by 9.4% from 1,603 to 1,753. This corresponded to an increase of 5.9% in incidence rate, from 17.9 to 19.0 per 100,000 bed-days. Community-onset CDI cases increased by 26.8% from 1,993 to 2,527, while the community-onset incidence rate increased by 25.7% from 14.2 to 17.8 (Figure 11, Table S6 in the accompanying data tables).

Figure 11: Quarterly rates of C. difficile infection, total reported and hospital-onset cases, April 2017 to March 2024

Detailed findings

Since the initiation of C. difficile (CDI) surveillance in April 2007, there has been an overall decrease in the count and associated incidence rate of both all-reported and hospital-onset cases of CDI (Figure 11).

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. Cases went from 16,864 to 3,711 cases, and there was an associated 79% reduction in incidence rate, from 131.6 cases per 100,000 population to 27.9. There were similar, but greater, reductions among hospital-onset CDI cases. There was an 84.5% decrease in count of cases between April to June 2007 and January to March 2012, from 10,436 to 1,613 cases, and an 83.9% reduction in the incidence rate, from 112.1 to 18.1 per 100,000 bed-days

Subsequently, between January to March 2012 and January to March 2024, the count of all-reported cases increased by 15.3% from 3,711 to 4,280 cases. The incidence rate increased by 8.1% from 27.9 to 30.1 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 under investigation (Figure 11, Table S6 in the accompanying data tables).

This was followed by an 8.7% increase in the hospital-onset cases, from 1,613 to 1,753 cases. There was also an increase of 4.9% in the incidence rate, from 18.1 to 19.0 cases per 100,000 bed-days between January to March 2012 and January to March 2024. Most of the rise in hospital-onset cases were seen following the COVID-19 pandemic, whereas prior to this, rates were observed as generally declining with some fluctuations.

When comparing January to March 2024 with the equivalent pre-COVID-19 pandemic period (January to March 2019), there was a 64.4% increase in total cases from 2,604 to 4,280. There was a similar increase of 60.5% in the incidence rate, from 18.8 to 30.1 cases per 100,000 population (Figure 7). Hospital-onset CDI counts increased by 84.5%, from 950 to 1,753. The incidence rate also increased by 75.1% from 10.8 to 19.0 cases per 100,000 bed-days (Figure 7). Community-onset CDI cases increased by 52.8% from 1,654 to 2,527. The community-onset incidence rate increased by 49.2% from 11.9 to 17.8 cases per 100,000 population.

The largest proportion of cases are HOHA; in the last quarter, these accounted for 45.8% of the total. COHA and COCA cases constituted 16.6% and 27.2% of the total, respectively. Community-onset indeterminate-association (COIA) cases were 10.3%. These percentages have been relatively stable since April 2018, when the data quality had substantially improved compared with the previous year (Figure 12 and Table 6a in the accompanying data tables).

Figure 12: Percentage of CDI cases by prior trust exposure, April 2017 to March 2024

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.

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.

Data sources and methodology

Data sources

Numerator data

Infection episode data used in this report were extracted from UKHSA’s HCAI data capture system (DCS) on 3 June 2024.

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 28 February 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 are 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 continues to use the data as published in the KH03 data set. Incidence rate rates published before December 2015 will differ slightly as a result.

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

Episode duration

The length of an infection episode is defined as:

• 14 days from the earliest specimen date, for bacteraemia
• 28 days from the earliest specimen date, for CDI

Total reported cases

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

Onset

Cases are classified into hospital-onset and community-onset according to the definitions below. Reports published before September 2017 used the term ‘trust-apportioned’ for hospital-onset cases and ‘not trust-apportioned’ for community-onset cases. Please note that this was simply a change in terminology and does not constitute a change in the methodology for apportionment.

Bacteraemia onset categories

A case of bacteraemia 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.

CDI onset categories

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 4 of the admission (admission date is considered day ‘one’).

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

Prior trust exposure

From April 2017, reporting trusts have been asked to provide information on whether patients with CDI had been admitted to the reporting trust within the 3 months prior to the onset of the current case. In addition, in April 2020, the HCAI DCS has included questions relating to prior trust exposure to the same acute trust reporting Gram-negative bacteraemia cases. This allows a greater granulation of the healthcare association of cases.

Cases are classified into six categories for CDI and five categories for the bacteraemias.

CDI prior trust exposure categories:

• hospital-onset healthcare-associated (HOHA): date of onset is greater than 2 days after admission (where day of admission is day 1)
• community-onset healthcare-associated (COHA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the date of discharge)
• community-onset indeterminate association (COIA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust between 29 and 84 days prior to the specimen date (where day 1 is the date of discharge)
• community-onset community-associated (COCA): is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 84 days prior to the specimen date (where day 1 is the date of discharge)
• unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the 3 months prior to CDI case
• not reported: the reporting trust did not provide any answer for questions on prior admission

Bacteraemia prior trust exposure categories:

• hospital-onset healthcare-associated (HOHA): date of onset is greater than 2 days after admission (where day of admission is day 1)
• community-onset healthcare-associated (COHA): is not categorised HOHA and the patient was most recently discharged from the same reporting trust in the 28 days prior to the specimen date (where day 1 is the specimen date)
• community-Onset, Community Associated (COCA): is not categorised HOHA and the patient has not been discharged from the same reporting organisation in the 28 days prior to the specimen date (where day 1 is the specimen date)
• unknown: the reporting trust answered ‘Don’t know’ to the question regarding previous discharge in the month prior to the current episode
• not reported: the reporting trust did not provide any answer for questions on prior admission

Incidence rate of total and CO cases

The incidence rate of total reported cases is calculating using their quarterly count and the mid-year population for England. It is converted to an annualised incidence rate in order to facilitate comparisons with annual incidence. The following formula is used:

That is: the count of reported episodes in England in a given quarter is divided by the mid-year population of England in that year, multiplied by the number of days in that year, divided by the number of days in that quarter, and finally multiplied by 100,000.

An equivalent formula is used for CO cases.

Incidence rate of HO cases

The incidence rate of HO cases is calculating using their quarterly count and the KH03 average bed-day activity for England. The following formula is used:

That is: the count of reported episodes in a given quarter in England is divided by the daily average number of occupied overnight beds in that quarter in England, then divided by the number of days in the same quarter, and finally multiplied by 100,000.

Percentage change

The percent change between the values in 2 quarters is calculated as follows:

That is, by subtracting the value for the earlier quarter from the value in the later quarter, dividing this difference by the value in the earlier quarter, and multiplying the result by 100.

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

Quarters

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

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

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

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

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 (BSI) and CDI cases in the initial stages, followed by various fluctuations.

Analysis of voluntary laboratory surveillance data from April 2020 to March 2022 reflected the changes seen in the mandatory surveillance system during this time, though to varying degrees. 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 the pandemic, many of these collections have now returned to normal pre-pandemic levels, with the exception of 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.

References

1. Sloot R, Nsonwu O, Chudasama D, Rooney G, Pearson C, Choi H, Mason E, Springer A, Gerver S, Brown C, Hope R. ‘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.

Further information

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

Annual report output

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

Monthly report outputs

The following reports are produced by UKHSA monthly.

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

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

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

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

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

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

Enquiries and feedback

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

Citation

UK Health Security Agency. Quarterly epidemiology commentary: mandatory MRSA, MSSA and Gram-negative bacteraemia and C. difficile infection in England (up to October to December 2023) London: UK Health Security Agency, April 2024.