Accredited official statistics

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

Updated 6 November 2024

Applies to England

UK Health Security Agency and this report

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

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

Data included in this quarterly epidemiological commentary

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

If 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.

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

COVID-19 and this data

Marked differences in general trends of all the data collections were observed over the course of the SARS-CoV-2 (COVID-19) pandemic. In general, we observed a reduction in the number of counts, compared to what would have been expected, across all 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 as move 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.

Epidemiological analyses of gram‑negative bacteraemia data

E. coli bacteraemia

Main findings

All reported cases of E. coli bacteraemia in April to June 2023 increased by 24.3% from 8,275 cases to 10,284 when compared to July to September 2011, with a corresponding increase in the incidence rate of 18.0% from 61.8 to 73.0 cases per 100,000 population. This increase was primarily driven by an increase in community-onset cases, the count of which increased by 31.5% from 6,279 to 8,259, with a 24.9% increase in incidence rate from 46.9 to 58.6 cases per 100,000 population. The count of hospital-onset cases also increased slightly by 1.5% from 1,996 to 2,025 cases, and the incidence rate of decreased by 2.8% from 23.6 to 22.9 per 100,000 bed-days; despite an increase in counts, the overall rate is lower as the bed-days denominator was higher, compared to previous years.

When comparing the most recent quarter to the same quarter in the previous year (2022), counts and incidence rates of all reported cases increased by 14.1% and 7.1%, respectively, from 9,011 to 10,284 cases and from 68.1 to 73.0 per 100,000 population (Figure 1a). The recent increase was driven by an increase in hospital-onset cases; these increased by 7.5% from 1,884 to 2,025, compared to April to June 2022 (Figure 1b), which corresponded to an incidence rate increase of 5.8% from 21.7 to 22.9 per 100,000 bed-days. Over the same time period, the count and incidence rate of community-onset E. coli bacteraemia cases increased by 7.0% and 7.1%, respectively, from 7,716 to 8,259 and from 54.7 to 58.6 per 100,000 population (Table S1 in the accompanying data tables).

Detailed findings

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

The incidence rate of hospital-onset E. coli bacteraemia increased more slowly than its count did. This may be due to the steady return to the typical number of overnight bed-days which were 1.6% higher in current quarter (April to June 2023) compared to the same quarter in 2019, returning from unusually low levels in April to June 2020, when occupied bed-days were 58.6% lower than current levels (April to June 2023).

When comparing April to June 2023 with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was a 6.2% decrease in total cases from 10,966 to 10,284, with a corresponding decrease of 6.6% in the incidence rate from 78.1 to 73.0 cases per 100,000 population (Figure 1a). Community-onset cases decreased by 8.7% from 9,044 to 8,259. Similarly, the incidence rate of community-onset cases also declined by 9.1% from 64.4 to 58.6 cases per 100,000 population. However, the total numbers of hospital-onset cases increased by 5.4% compared to the same period, from 1,922 to 2,025. The hospital-onset incidence rate increased marginally by 3.1% from 22.2 to 22.9 cases per 100,000 bed-days (Figure 1b). 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 not yet returning to levels seen prior to the COVID-19 pandemic. There are uncertainties in why we still see lower levels of community-onset E. coli BSI after the emergency stage of the pandemic, with further investigative work ongoing.

A strong seasonality trend is visible with all reported E. coli bacteraemia, whereby the highest rates are observed between July to September of each year, although there 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.

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

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

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

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, 66.0% of cases were community-onset community-associated (COCA), 13.7% were community-onset healthcare-associated (COHA), and 19.7% were hospital-onset healthcare-associated (HOHA) (Figure 1c and Table 1a in the accompanying data tables).

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

Klebsiella spp. bacteraemia

Main findings

All reported cases of Klebsiella species bacteraemia increased by 28.3% from 2,352 cases to 3,018 in April to June 2023 when compared to the same quarter in 2017, at the start of surveillance. The incidence rate of all reported cases also increased by 26.2% from 17.0 to 21.4 cases per 100,000 population. Hospital-onset cases increased by 28.5% from 671 to 862 cases and by 25.7% from 7.8 to 9.8 cases per 100,000 bed-days, respectively (Figure 2b). Similarly, the count of community-onset cases increased by 28.3% from 1,681 to 2,156, with a corresponding 26.2% increase in incidence rate from 12.1 to 15.3 cases per 100,000 population.

Comparing the most recent quarter to the same quarter in the previous year (2022), both counts and incidence rates of all reported cases increased by 11.4% from 2,710 cases to 3,018 and 19.2 to 21.4 per 100,000 population, respectively (Figure 2a). This was driven by an increase in community-onset cases. Over this period, community-onset Klebsiella species bacteraemia cases and rates increased by 16.6% from 1,849 to 2,156 cases and 13.1 to 15.3 per 100,000 population (Table S1 in the accompanying data tables). In April to June 2023, hospital-onset Klebsiella species bacteraemia cases remained stable, when compared to April to June 2022 (861 and 862 cases, respectively, Figure 2b). This corresponded with an incidence rate decrease of 1.4% from 9.9 to 9.8 per 100,000 bed-days over the same period (despite cases remaining the same, the rate decreased as the bed-days denominator was greater to previous years) (Table S2 in accompanying data tables).

Detailed findings

Counts and rates of hospital-onset Klebsiella spp. had a sustained peak between the July to September 2020 and January to March 2021 quarters, during the acute stage of the COVID-19 pandemic. Both counts and rates of hospital-onset cases reached their highest levels observed since the inception of mandatory Klebsiella spp. surveillance. The incidence rate of hospital-onset cases peaked at 15.6 cases per 100,000 bed-days in January to March 2021 (the highest levels seen throughout the surveillance for this bacteraemia). The specific causes of this increase are not well understood; however, it coincided with a high incidence of COVID-19, with many cases identified as COVID-19 co-infections (1).

When comparing the most recent quarter (April to June 2023) with the equivalent pre-COVID-19 pandemic period (April to June 2019), there was a 18.0% increase in total cases from 2,557 to 3,018, with a corresponding increase of 17.5% in the incidence rate from 18.2 to 21.4 cases per 100,000 population (Figure 2a, Table S2 in the accompanying data tables). Community-onset cases increased by 19.7% from 1,801 to 2,156. Similarly, the incidence rate of community-onset cases also increased by 19.2 % from 12.8 to 15.3 cases per 100,000 population. Finally, when comparing the most recent quarter (April to June 2023) with the equivalent pre-pandemic quarter (April to June 2019) the count of hospital-onset cases increased by 14.0% from 756 to 862. The rate increased by 11.5% from 8.7 to 9.8 cases per 100,000 bed-days (Figure 2b, Table S2 in the accompanying data tables), respectively. Trends have returned to pre COVID-19 levels, continuing on an upward trajectory.

During April to June 2023, 73.4% (2,216 out of 3,018) of all reported Klebsiella spp. bacteraemia were caused by K. pneumoniae, a slight increase from 71.8% in the same quarter in the previous year (April to June 2022). Over the same period, 16.2% (488 out of 3,018) were caused by K. oxytoca, a slight decrease from 17.5% in the same quarter in the previous year (April to June 2022). Over the same period, the proportion of Klebsiella spp. bacteraemia caused by Klebsiella aerogenes remained the same at 3.8% (116 out of 3,018).

The incidence rate of the majority of Klebsiella species increased at approximately the same pace (Figure 2a, Table S2 in the accompanying data tables). The exception to this was the incidence rate of K. oxytoca, which increased within hospital-onset cases around the start of the pandemic, peaking at 2.2 per 100,00 bed days and subsequently declining to 1.6 per 100,000 bed days in April to June 2023.

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

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

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

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

Since the inception of prior trust exposure classifications in April to June 2021, COCA cases have made up roughly half of all Klebsiella spp. bacteraemia, fluctuating between 51.2% and 56.3%. However, the most recent quarter (April to June 2023) has seen a peak of 57.1% - the greatest proportion of COCA cases observed since the prior exposure classifications were adopted in April to June 2020 (Figure 2c).

Since the start of surveillance, the proportion of HOHA cases peaked at 39.6% in January to March 2021, reflected by a reduction in the proportion of in COCA cases in the same quarter at 46.4% of all Klebsiella spp. bacteraemia. The increase in HOHA cases coincided with the increase in COVID-19 cases and associated hospitalisations observed in January 2021, where an increase in Klebsiella spp. BSI cases were observed in the hospital setting (1).

Comparing April to June 2023 to the same quarter in 2022, the proportion of HOHA cases of all Klebsiella spp. bacteraemia decreased slightly (from 31.8% to 28.6%), while COHA cases remained broadly the same (from 14.2% to 13.9%). Notably, the proportion of COCA cases increased from 53.9% to 57.1% of all Klebsiella spp. bacteraemia (Figure 2c, Table S2a in the accompanying data tables).

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

Pseudomonas aeruginosa bacteraemia

Main findings

In April to June 2023, there was a 6.5% and 4.8% increase in the count and incidence rate of all reported P. aeruginosa bacteraemia cases from 1,016 to 1,082 and from 7.3 to 7.7 cases per 100,000 population, respectively, compared to the corresponding quarter at the start of surveillance in 2017 (Figure 3a). The count and the incidence rate of hospital-onset cases increased by 6.6% from 376 to 401 cases and by 4.3% from 4.3 to 4.5 cases per 100,000 bed-days, respectively (Figure 3b). Over the same period, the count and the incidence rate of community-onset cases also increased by 6.4% from 640 to 681 cases and by 4.7% from 4.6 to 4.8 cases per 100,000 population, respectively (Figure 3b, Table S3 in the accompanying data tables).

Comparing the most recent quarter (April to June 2023) to the same period in the previous year (April to June 2,022) shows a 6.3% increase in the count and incidence rate of all reported cases, respectively, from 1,018 to 1,082 cases and from 7.2 to 7.7 cases per 100,000 population. Hospital-onset P. aeruginosa cases increased by 4.4% from 384 to 401 which corresponds to an increase in the incidence rate of 2.8% from 4.4 to 4.5 per 100,000 bed-days. Community-onset P. aeruginosa cases increased by 7.4% from 634 to 681 per 100,000 population, while the community-onset incidence rate increased by 7.4% from 4.5 to 4.8 per 100,000 population (Table S3 in the accompanying data tables).

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 (1).

Compared to the same pre-pandemic period in 2019 (April to June 2019), the most recent quarter saw similar levels of counts and rates of P. aeruginosa bacteraemia. There was only a marginal 1.2% increase in the count of all reported cases from 1,069 to 1,082 and a 0.8% increase in the incidence rate from 7.6 to 7.7 per 100,000 population. (Figure 3a, Table S3 in the accompanying data tables).

During the same period, counts of community-onset P. aeruginosa cases saw an increase of 1.5% from 671 to 681. The community-onset incidence rate saw no change, remaining at 4.8 per 100,000 population (Table S3 in the accompanying data tables). Hospital-onset counts and rates remained similarly unchanged, with counts increasing by 0.8%, from 398 cases to 401 and incidence rates decreasing by 1.4%, from 4.6 to 4.5 per 100,000 bed-days (despite increase in counts, rates appear reduced due to an increase in bed-days denominator compared to the previous financial year) (Figure 3b, Table S3 in the accompanying data tables).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, and that, following the initial peak in hospital-onset cases seen at the start of the COVID-19 pandemic (Figure 3b), the hospital-onset counts have returned to expected pre-pandemic levels.

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

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

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

Similarly to E. coli and Klebsiella spp., COCA cases tend to make up the highest proportion of P. aeruginosa bacteraemia cases, however, to a slightly lesser extent at around 45% of all cases between the April to June 2020 and April to June 2022 quarters. However, in January to March 2021, HOHA cases (48.2% of total) surpassed COCA cases (36.8%) for the first time since April 2020, coinciding with the peak of the second wave of the COVID-19 pandemic.

Comparing April to June 2023 to the same quarter in 2022, COHA cases increased from 17.8% to 20.6% of all P. aeruginosa bacteraemia cases, whilst COCA cases decreased from 44.1% to 42.3%. (Figure 3c, Table S3a in the accompanying data tables). HOHA cases decreased from 37.7% to 37.1% of all P. aeruginosa bacteraemia cases in the same period.

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

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

Main findings

Comparing the most recent quarter (April to June 2023) to the same period in the previous year (April to June 2022) shows a 14.7% increase in the count of all reported MRSA bacteraemia from 177 cases to 203, while the incidence rate increased by 14.7% from 1.3 to 1.4 cases per 100,000 population, albeit remaining at a low level (Figure 4a, Table S4 in the accompanying data tables).

The rise was slightly more pronounced in the community-onset cases, which increased by 17.3% from 110 to 129; the incidence rate similarly increased from 0.8 to 0.9 cases per 100,000 population (Table S4 in the accompanying data tables). The count of hospital-onset MRSA bacteraemia cases increased by 10.4% from 67 to 74, which corresponds with a 12.5% increase in the incidence rate from 0.8 to 0.9 per 100,000 bed-days.

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

Detailed findings

There has been a considerable decrease in the incidence rate of all reported MRSA bacteraemia since the enhanced mandatory surveillance of MRSA bacteraemia began in April 2007 (Figure 4a, Table S4 in the accompanying data tables). The incidence rate of all reported cases fell by 85% from 10.2 cases per 100,000 population April to June 2007 to 1.5 cases per 100,000 in January to March 2014. The rate has subsequently slowly decreased to 1.4 cases per 100,000 population between January to March 2014 and April to June 2023.

A similar trend was observed with the incidence rate of hospital-onset cases (Figure 4b, Table S4 in the accompanying data tables). There was a steep decrease of 79% from 4.9 cases per 100,000 bed-days in April to June 2008 to 1.0 January to March 2014. Subsequently, between January to March 2014 and April to June 2023, the rate has further decreased to 0.8 cases per 100,000 bed-days.

Comparing April to June 2023 with the same pre-pandemic period in 2019 (April to June 2019), an 11.5% increase was observed in the total counts from 182 to 203 cases, with a corresponding 11.0% increase in rate from 1.3 to 1.4 per 100,000 population (Figure 4a, Table S4 in the accompanying data tables). Community-onset MRSA bacteraemia counts remained the same, decreasing 0.8% from 130 to 129 and the rate remained the same at 0.9 cases per 100,000 population (Table S4 in the accompanying data tables). The count of hospital-onset MRSA bacteraemia cases also increased by 42.3% from 52 to 74, with a 39.2% increase in incidence rate from 0.6 to 0.8 per 100,000 bed-days (Figure 4b, Table S4 in the accompanying data tables).

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

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

MSSA bacteraemia

Main findings

The count of all reported cases of MSSA bacteraemia increased by 51.5% from 2,199 to 3,331 between January to March 2011 and April to June 2023. This was accompanied by a 40.7% increase in incidence rate from 16.8 to 23.6 per 100,000 population (Figure 5a, Table S5 in the accompanying data tables).

These increases are primarily driven by the increase in community-onset cases. Between January 2011 and April to June 2023, the count and the incidence rate of community-onset cases increased by 64.7% and 53.0%, respectively, from 1,464 to 2,411 cases and from 11.2 to 17.1 cases per 100,000 population (Table S5 in the accompanying data tables). Over the same period, the count of hospital-onset cases increased by 25.2% from 735 to 920 cases, while the incidence rate increased by 24.9% from 8.4 to 10.4 cases per 100,000 bed-days (Figure 5a and Figure 5b, Table S5a in the accompanying data tables). Counts and rates of MSSA bacteraemia remain higher than those seen at the beginning of the surveillance programme in 2011.

Comparing the most recent quarter (April to June 2023) to the same period in the previous year (April to June 2022), there was a 4.8% increase in the count of all reported cases from 3,177 to 3,331, while the incidence rate increased 4.8% from 22.5 to 23.6 per 100,000 bed-days. Hospital-onset MSSA bacteraemia cases decreased by 1.5% from 934 to 920, which corresponds to an incidence rate decrease of 3.0% from 10.7 to 10.4 per 100,000 bed-days. Community-onset MSSA bacteraemia cases increased by 7.5% from 2,243 to 2,411, while the community-onset incidence rate increased by 7.5% from 15.9 to 17.1 per 100,000 population.

Detailed findings

There has been a general trend of increasing count and incidence rate of cases since the mandatory reporting of MSSA bacteraemia began in January 2011. This trend has continued despite a temporary reduction (2,753 and 19.6 cases per 100,000 population, respectively) during the COVID-19 pandemic. The latest quarterly MSSA count and rate are still higher than at the beginning of the MSSA surveillance.

Since April to June 2021, all reported cases and rates have returned to a more steadily increasing trend. Between April to June 2021 and the April to June 2023, an 11.1% increase was observed in both counts and incidence rate of MSSA bacteraemia, with counts increasing from 2,998 to 3,331 cases and incidence rate increasing from 21.3 to 23.6 per 100,000 population.

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

When comparing the current quarter to the pre-pandemic period of April to June 2019, an 8.5% increase in the counts of all reported cases was observed, rising from 3,070 to 3,331 cases, along with an 8.0% increase in the rate from 21.9 to 23.6 cases per 100,000 population. Over this same period, hospital-onset MSSA bacteraemia cases have increased by 8.0% from 852 to 920; this corresponds to an 5.6% increase in the incidence rate from 9.9 to 10.4 per 100,000 bed-days. Counts of community-onset MSSA bacteraemia cases increased by of 8.7% from 2,218 to 2,441, and there was an 8.2% increase in incidence rate from 15.8 to 17.1 per 100,000 population, over the same period. Although there was an initial drop in all reported cases at the start of the COVID-19 pandemic, the total count and incidence rate have generally remained high since the inception of the MSSA surveillance (Figure 5a), and resumed the pre-pandemic year-on-year increasing trajectory. The reasons behind these observed increases are still under investigation.

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

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

Epidemiological analyses of Clostridioides difficile infection data

Main findings

Comparing the most recent quarter (April to June 2023) to the same period in the previous year (April to June 2022), there was a 7.3% increase in the count of all reported cases from 3,760 to 4,035. Similarly, the incidence rate increased by 7.3 % from 26.7 to 28.6 cases per 100,000 population (Figure 6a, Table S6 in the accompanying data tables).

Hospital-onset CDI cases increased by 6.6% from 1,560 to 1,663; this corresponds to an increase in incidence rate of 5.0% from 17.9 to 18.8 cases per 100,000 bed-days. Community-onset CDI cases increased by 7.8% from 2,200 to 2,372, while the community-onset incidence rate increased by 7.8% from 15.6 to 16.8 per 100,000 population (Figure 6b, Table S6 in the accompanying data tables).

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 6a, Figure 6b and Table S6 in the accompanying data tables).

Most of the decrease in the incidence rate occurred between April to June 2007 and January to March 2012 with a 78% decrease in all-reported cases of CDI from 16,864 to 3,711 cases and an associated 79% reduction in incidence rate from 131.6 cases per 100,000 population to 27.9. Subsequently, between January to March 2012 and April to June 2023, the count of all-reported cases increased 8.7% from 3,711 to 4,035 cases and the incidence rate increased by 2.6% from 27.9 to 28.6 cases per 100,000 population (Figure 6a, Figure 6b and Table S6 in the accompanying data tables). 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 seen this major shift post pandemic. The reasons for which are being investigated.

There were similar, but greater, reductions among hospital-onset CDI cases, with an 84.5% reduction 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 112.5 to 18.2 per 100,000 bed-days. This was followed by a 3.1% increase in the count of cases from 1,613 to 1,663 cases and an increase of 4.1% in the incidence rate from 18.1 cases per 100,000 bed-days to 18.8 between January to March 2012 and April to June 2023. 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 April to June 2023 with the corresponding pre-pandemic quarter (April to June 2019), there has been a 30.5% increase in the count of all reported cases from 3,093 to 4,035, corresponding to an 29.9% increase in the incidence rate, from 22.0 to 28.6 cases per 100,000 population (Figure 6a, Table S6 in the accompanying data tables). Community-onset CDI cases increased by 17.6% from 2,017 to 2,372 while the rate increased by 17.1% from 14.4 to 16.8 per 100,000 population (Table S6 in the accompanying data tables). The greatest rise can be seen in the hospital-onset CDI cases, which increased by 54.6% from 1,076 to 1,663; this corresponds to an incidence rate increase of 51.2% from 12.4 to 18.8 cases per 100,000 bed-days (Figure 6b, Table S6 in the accompanying data tables).

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

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

Between January to March 2018 and April to June 2023, the largest proportion of cases were HOHA, increasing from approximately 43.9% of all cases to 45.8%. Over the same period, the proportion of COCA cases also increased from 26.9% to 27.2%. While COHA cases decreased from 18.0% to 17.6% of all CDI over the same period. Community-onset indeterminate association (COIA) cases increased from 8.8% to 9.1% of all CDI. Much of the increase observed is likely due to improved data quality as shown by the sharp decline of cases with missing or not reported data (Figure 6c, Table S6c in the accompanying data tables).

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

Appendix

Bed-day data

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

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

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

KH03 data can be found on the NHS England website.

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

• Moorfields Eye Hospital NHS Foundation Trust (RP6) 2007 to 2008, and 2008 to 2009 KH03 figures: replaced with 2006 to 2007 KH03 figure
• Rotherham NHS Foundation Trust (RFR): 2009 to 2010 and from April to June 2010, to April to June 2011 KH03 figures: replaced with 2008 to 2009 KH03 figure
• Sheffield Teaching Hospitals NHS Foundation Trust (RHQ) from April to June 2010, to April to June 2011 KH03 figures: replaced with 2009 to 2010 KH03 data
• Princess Alexandra Hospital NHS Trust (RQW) April to June 2014, and October to December 2014 KH03 figures: replaced with April to June 2013, to October to December 2013 KH03 figures, respectively
• Ipswich Hospital NHS Trust (RGQ) January to March 2016 KH03 figure: replaced with January to March 2015 figures
• West Suffolk NHS Foundation Trust (RGR) April to June 2016, to October to December 2016 and April to June 2017 KH03 figures: replaced with April to June 2015, to October to December 2015 KH03 figures
• Gloucestershire Hospitals NHS Foundation Trust (RTE) October to December 2016, to January to March 2017 KH03 figures: replaced with October to December 2015, to January to March 2016 KH03 figures

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

Population data

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

Definitions

Bacteraemia hospital-onset (trust-apportioned) cases

Include patients who are:

• in-patients, day-patients, emergency assessment patients or not known, and
• have had their specimen taken at an acute trust or not known, and
• specimen was taken on or after day 3 of the admission (admission date is considered day ‘one’)

Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

CDI hospital-onset (trust-apportioned) cases

Include patients who are:

• in-patients, day-patients, emergency assessment patients or not known, and
• have had their specimen taken at an acute trust or not known, and
• specimen was taken on or after day 4 of the admission (admission date is considered day ‘one’)

Cases that do not meet these criteria are categorised as community-onset (not-trust apportioned).

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

Prior trust exposure

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

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

CDI prior trust exposure categories:

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

Bacteraemia prior trust exposure categories:

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

Cases since April 2020 have also been categorised as:

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

Total reported cases

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

Episode duration

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

Incidence rate calculations

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa bacteraemia, and CDI population incidence rate (episodes per 100,000) is calculated using the number of episodes and the mid-year population for England:

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

MRSA, MSSA and E. coli, Klebsiella spp., P. aeruginosa and CDI hospital-onset incidence rate is calculated using the number of episodes and the KH03 average bed-day activity (see bed-day data above) and is calculated as follows:

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

Graphs and percentage change calculation

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

Quarters

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

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

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

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

References

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

Data for this report was extracted from UKHSA’s HCAI data capture system (DCS) on 9 May 2023.