National statistics

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

Updated 11 April 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 quarterly 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 total reported, hospital-onset (previously referred to as trust-apportioned) and community-onset (CO) - 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 MRSA, MSSA and Gram-negative bacteraemia and C. difficile infection in England (up to July to September 2023) London: UK Health Security Agency, January 2024.

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 restrictions on movement and mixing were introduced nationally to limit the spread of the virus. In the post-pandemic period, we observed that the levels of most collections have returned to the baseline indicative of the pre-pandemic period. However, E. coli and CDI remain exceptions to this trend.

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

The total reported cases of E. coli bacteraemia in financial quarter (FQ) July to September 2023 increased by 34.6% from 8,275 to 11,138 cases when compared to July to September 2011, with an increase of 25.2% in the incidence rate from 61.8 to 77.4 cases per 100,000 population. This increase was primarily driven by an increase in community-onset cases, the count of which increased by 45.0% from 6,279 to 9,105, with a 34.9% increase in incidence rate from 46.9 to 63.3 cases per 100,000 population. The count of hospital-onset cases increased by 1.9% from 1,996 to 2,033 cases. However, incidence rates decreased by 1.9% from 23.6 to 23.1 per 100,000 bed-days, due to increased hospital activity.

When comparing the most recent quarter to last year’s corresponding quarter, both counts and incidence rates of total reported cases increased by 6.3%, from 10,478 to 11,138 cases and from 72.8 to 77.4 per 100,000 population (Figure 1). These increases are primarily due to increases in community-onset cases, which increased by 8.4% in both count and incidence rate, from 8,403 to 9,105 and from 58.4 to 63.3 per 100,000 population, respectively, compared to July to September 2022 (Table S1 in the accompanying data tables). Over the same time period, hospital-onset cases decreased by 2.0% from 2,075 to 2,033, which corresponded to a decrease of 2.2% in incidence rate, from 23.7 to 23.1 per 100,000 bed-days (Figure 1).

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 reduction in the count and incidence rates of total reported and community-onset cases was observed after the start of the pandemic, but these have subsequently increased. However, they remain below pre-pandemic levels (Figure 1).

In contrast, the incidence rate of hospital-onset cases remained relatively stable during the same period, except for a slight reduction (20.7 cases per 100,000 bed-days) observed in April to June 2021 (Figure 1). 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. This may be due to changes in bed occupancy in England: in April to June 2020 there was a 34.3% drop in occupied overnight beds compared to the previous quarter. Over the following 12 months, bed occupancy slowly returned to pre-pandemic levels, with more recent data showing activity levels matching that of pre-pandemic levels.

When comparing July to September 2023 with the corresponding pre-COVID-19 pandemic period (July to September 2019), there was a 5.8% decrease in total cases from 11,830 to 11,138, with a decrease of 7.3% in the incidence rate from 83.5 to 77.4 cases per 100,000 population (Figure 1). Community-onset cases decreased by 7.1% from 9,803 to 9,105. Similarly, the incidence rate of community-onset cases also decreased by 8.5% from 69.2 to 63.3 cases per 100,000 population. However, the total numbers of hospital-onset cases showed no substantial change with a 0.3% increase compared to the same period, from 2,027 to 2,033. The hospital-onset incidence rate decreased by 1.6% from 23.5 to 23.1 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 not yet returning to levels seen prior to the pandemic. The reasons behind the continuing lower levels of community-onset E. coli BSI following the emergency stage of the pandemic remain uncertain, 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 was observed between April 2015 and March 2019.

Figure 1: Quarterly rates of E. coli bacteraemia, total reported and hospital-onset cases, July 2011 to September 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, 67.1% of cases were community-onset community-associated (COCA), 14.4% were community-onset healthcare-associated (COHA), and 18.3% were hospital-onset healthcare-associated (HOHA) (Figure 2 and Table S1a in the accompanying data tables).

Figure 2: Percentage of E. coli bacteraemia cases by prior trust exposure, April 2020 to September 2023

Klebsiella spp. bacteraemia

Main findings

The total reported cases of Klebsiella spp. bacteraemia in July to September 2023 increased by 28.9% from 2,675 to 3,447 cases when compared to July to September 2017. This corresponded to an increase of 25.5% in the incidence rate from 19.1 to 23.9 cases per 100,000 population. The count of hospital-onset cases increased by 29.7% from 794 to 1,030 cases, and the incidence rate increased by 26.7% from 9.2 to 11.7 per 100,000 bed-days. Similarly, the count of community-onset cases increased by 28.5% from 1,881 to 2,417, with a 25.1% increase in the incidence rate from 13.4 to 16.8 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 both increased by 8.5% from 3,177 to 3,447 cases and from 22.1 to 23.9 per 100,000 population (Figure 3). The recent increase was driven by an increase in community-onset cases, with counts and rate increased by 14.1% from 2,118 to 2,417 and from 14.7 to 16.8 per 100,000 population. Hospital-onset cases decreased by 2.7% from 1,059 to 1,030, compared to July to September 2022 (Figure 3), which corresponded to a decrease of 3.0% in incidence rate, from 12.1 to 11.7 per 100,000 bed-days (Table S2 in the accompanying data tables).

Detailed findings

Counts and rates of hospital-onset Klebsiella spp. reached the 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 specific causes of this increase are not well understood. However, it coincided with a high incidence of COVID-19, with many cases identified as COVID-19 co-infections (Sloot and colleagues, 2022).

When comparing the most recent quarter (July to September 2023) with the equivalent pre-COVID-19 pandemic quarter (July to September 2019), there was a 15.2% increase in total cases from 2,991 to 3,447, with a corresponding increase of 13.5% in the incidence rate from 21.1 to 23.9 cases per 100,000 population (Figure 3, Table S2 in the accompanying data tables). Community-onset cases increased by 15.6% from 2,090 to 2,417. Similarly, the incidence rate of community-onset cases also increased by 13.9% from 14.7 to 16.8 cases per 100,000 population. Finally, the count of hospital-onset cases increased by 14.3% from 901 to 1,030. The rate increased by 12.1% from 10.4 to 11.7 cases per 100,000 bed-days, respectively (Figure 3, Table S2 in the accompanying data tables). Trends have returned to pre-pandemic levels, continuing on an upward trajectory.

During July to September 2023, 73.6% (2,537 out of 3,447) of the total reported Klebsiella spp. bacteraemia were caused by K. pneumoniae, 15.8% were caused by K. oxytoca, 3.7% were caused by Klebsiella aerogenes. The incidence rate of the majority of Klebsiella species increased at approximately the same pace (Figure 3, 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.

There is evidence of seasonality in the trend of total reported Klebsiella spp. bacteraemia cases, with the highest incidence rates normally observed in July to September of each year (Figure 3).

Figure 3: Quarterly rates of Klebsiella spp. bacteraemia, total reported and hospital-onset cases, by species, April 2017 to September 2023

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. BSI cases were observed in the hospital setting (Sloot and colleagues, 2022). This proportion has since decreased, and was 29.9% in the latest quarter. In the same period, the proportion of COHA cases was 15.3% (Figure 4 and accompanying data tables).

Figure 4: Percentage of Klebsiella spp. bacteraemia cases by prior trust exposure, April 2020 to September 2023

Pseudomonas aeruginosa bacteraemia

Main findings

Total reported cases of P. aeruginosa bacteraemia in July to September 2023 showed no substantial change with a 0.5% decrease from 1,182 to 1,176 cases when compared to July to September 2017. This corresponded to a decrease of 3.1% in the incidence rate from 8.4 to 8.2 cases per 100,000 population. The count of hospital-onset cases increased by 9.2% from 422 to 461 cases, and the incidence rate increased by 6.7% from 4.9 to 5.2 per 100,000 bed-days. Over the same period, the count of community-onset cases decreased by 5.9% from 760 to 715, with an 8.4% decrease in incidence rate from 5.4 to 5.0 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 both decreased by 1.7%, from 1,196 to 1,176 cases and from 8.3 to 8.2 per 100,000 population (Figure 5). Hospital-onset cases increased by 2.0% from 452 to 461, compared to July to September 2022 (Figure 5). The incidence rate remained unchanged at 5.2 per 100,000 bed-days. In some instances throughout this report, we observe marginal increases the incidence rate. However, when the rate is rounded to one decimal place, there appears to be no change. For more precise rate change calculations, please consult the accompanying data tables. Over the same time period, both the count and incidence rate of community-onset P. aeruginosa bacteraemia cases decreased by 3.9%, from 744 to 715 and from 5.2 to 5.0 per 100,000 population (Table S3 in the from (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  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 2023 with the equivalent pre-COVID-19 pandemic period (July to September 2019), there was 1.8% decrease in total cases from 1,198 to 1,176, with a decrease of 3.3% in the incidence rate from 8.5 to 8.2 cases per 100,000 population (Figure 5). Community-onset cases decreased by 10.1% from 795 to 715. Similarly, the CO incidence rates also decreased by 11.4% from 5.6 to 5.0 cases per 100,000 population. Hospital-onset cases increased by 14.4% compared to the same period, from 403 to 461. The hospital-onset incidence rate increased by 12.2% from 4.7 to 5.2 cases per 100,000 bed-days (Figure 5). Despite increase in counts, rates appear reduced due to an increase in bed-days denominator compared to the previous financial year. 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, the hospital-onset counts have returned to expected pre-pandemic levels.

Figure 5: Quarterly rates of P. aeruginosa bacteraemia, total reported and hospital-onset cases, April 2017 to September 2023

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 constituted 42.9% of the total, whilst 17.4% were COHA and 39.2% were HOHA. This contrasts with January to March 2021, when HOHA cases made up 48.2% of the total (Figure 6 and Table S3a in the accompanying data tables).

Figure 6: Percentage of P. aeruginosa bacteraemia cases by prior trust exposure, April 2020 to September 2023

Epidemiological analyses of Staphylococcus aureus bacteraemia data

MRSA bacteraemia

Main findings

When comparing the most recent quarter to last year’s corresponding quarter, counts of total reported cases increased by 2.5% from 199 to 204 cases and the incidence rate remained unchanged at 1.4 per 100,000 population (Figure 7).

Both the count and incidence rate of community-onset MRSA bacteraemia cases increased by 3.3%, from 121 to 125 and from 0.8 to 0.9 per 100,000 population. Over the same period, hospital-onset cases  marginally increased from 78 to 79, compared to July to September 2022 (Figure 7), with the incidence rate remaining at 0.9 per 100,000 bed-days (Table S4 in the accompanying data tables).

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 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 85.3% 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, subsequently falling further to 1.4 cases per 100,000 population.

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 79.6% from 4.9 cases per 100,000 bed-days in April to June 2008 to 1.0 January to March 2014. Since then, the rate has decreased to 0.9 cases per 100,000 bed-days.

When comparing July to September 2023 with the equivalent pre-COVID-19 pandemic period (July to September 2019), there was a 2.0% increase in total cases from 200 to 204, with the incidence rate remaining at 1.4 cases per 100,000 population (Figure 7). Community-onset MRSA bacteraemia counts decreased by 6.7% from 134 to 125. The incidence rate of community-onset cases remained the same at 0.9 cases per 100,000 population (Figure 7).

Figure 7: Quarterly rates of MRSA bacteraemia, total reported cases (April 2007 to September 2023) and hospital-onset cases (April 2008 to September 2023)

In the current quarter, 50.0% of cases were community-onset community-associated (COCA), 10.8% were community-onset healthcare-associated (COHA), and 38.7% were hospital-onset healthcare-associated (HOHA), which is generally in keeping with previous quarters, with some exceptions during the COVID-19 pandemic period (Figure 8 and Table S4a in the accompanying data tables).

Figure 8: Percentage of MRSA bacteraemia cases by prior trust exposure, April 2020 to September 2023

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 46.9% from 2,226 in July to September 2011 to 3,269 in July to September 2023. This corresponded to an increase of 36.6% in incidence rate, from 16.6 to 22.7 per 100,000 population (Figure 9, Table S5 in the accompanying data tables).

These increases are primarily driven by the increase in community-onset cases. Between these 2 quarters, the both the count and incidence rate of community-onset cases increased by 52.9%, from 1,501 to 2,295 cases and from 11.2 to 15.9 cases per 100,000 population. Over the same period, the count of hospital-onset cases increased by 34.3% from 725 to 974 cases, while the incidence rate increased by 29.4% from 8.6 to 11.1 cases per 100,000 bed-days.

Comparing the most recent quarter (July to September 2023) to the same period in the previous year (July to September 2022), there was a marginal decrease of 0.5% in the counts and incidence rate of total reported cases from 3,286 to 3,269 and from 22.8 to 22.7 per 100,000 bed-days. Hospital-onset MSSA bacteraemia cases decreased by 2.0% from 994 to 974, which corresponds to a decrease of 2.2% in incidence rate from 11.3 to 11.1 per 100,000 bed-days. Community-onset MSSA bacteraemia cases and incidence rate showed little change, with cases increasing by 0.1% from 2,292 to 2,295, and the incidence rate remaining at 15.9 cases 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. 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 3.2% and 1.6%, respectively, from 3,167 to 3,269 cases and from 22.3 to 22.7 cases per 100,000 population. The reasons behind these observed increases are under investigation.

On the other hand, the incidence rate of hospital-onset MSSA bacteraemia cases peaked during the early stages of the COVID-19 pandemic. This was in part caused by reduced hospital activity, resulting in reduced occupied overnight bed-days, the denominator used to calculate hospital-onset rates. HO rates peaked in January to March 2021, where we observed 13.4 cases per 100,000 bed-days, for 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 latest quarter to the pre-pandemic period of July to September 2019, counts of community-onset MSSA bacteraemia cases decreased by 1.0% from 2,319 to 2,295, and there was a 2.6% decrease in incidence rate from 16.4 to 15.9 per 100,000 population, over the same period.

Figure 9: Quarterly rates of MSSA bacteraemia, total reported and hospital-onset cases, January 2011 to September 2023

MSSA infection is predominantly driven by community onset cases. In the current quarter, 57.6% of cases were community-onset community-associated (COCA), 12.4% were community-onset healthcare-associated (COHA), and 29.8% were hospital-onset healthcare-associated (HOHA) (Figure 10 and Table S5a in the accompanying data tables).

Figure 10: Percentage of MSSA bacteraemia cases by prior trust exposure, April 2020 to September 2023

Epidemiological analyses of Clostridioides difficile infection data

Main findings

Comparing the most recent quarter (July to September 2023) to the same period in the previous year (July to September 2022), there was a 2.1% decrease in the count and rate of CDI cases, from 4,453 to 4,359, and from 30.9 to 30.3 cases per 100,000 population (Figure 11, Table S6 in the accompanying data tables).

For the same period, hospital-onset CDI cases decreased by 2.8% from 1,738 to 1,689 – this corresponds to a 3.0% decrease in incidence rate from 19.8 to 19.2 cases per 100,000 bed-days. Community-onset CDI cases and incidence rate both decreased by 1.7% from 2,715 to 2,670 cases, and from 18.9 to 18.5 per 100,000 population (Figure 11, Table S6a 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 11 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 77.9% decrease in all-reported cases of CDI from 16,864 to 3,711 cases and an associated 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 2023, the count of all-reported cases increased by 17.5% from 3,711 to 4,359 cases and the incidence rate increased by 8.6% from 27.9 to 30.3 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. Counts and rates have now returned to 2012 levels. 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. The reasons for which are being investigated.

There were similar, but greater, reductions among hospital-onset CDI cases, with 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 18.0 per 100,000 bed-days (Figure 11).

This was followed by a 4.7% increase in the count of cases from 1,613 to 1,689 cases and an increase of 6.3% in the incidence rate from 18.1 to 19.2 cases per 100,000 bed-days between January to March 2012 and July to September 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.

Figure 11: Quarterly rates of C. difficile infection, total reported and hospital-onset cases, April 2017 to September 2023

The largest proportion of cases are HOHA – in the last quarter, these accounted for 43.2% of the total. COHA and COCA cases constituted 16.7% and 28.6% of the total respectively. Community-onset indeterminate-association (COIA) cases were 11.1%. These percentages have been relatively stable since April 2018, when the data quality had substantially improved compared to the previous year (Figure 12 and Table S6a in the accompanying data tables).

Figure 12: Percentage of C. difficile infection cases by prior trust exposure, April 2020 to September 2023

Appendix

Data sources

Numerator data

Infection episode data used in this report was extracted from UKHSA’s HCAI data capture system (DCS) on 27th November 2023.

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 was published by NHS England on 23 November 2023 and may include revisions of previously published KH03 data used in earlier reports.

On 1 December 2015, UKHSA 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

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’.
2. The specimen was taken at an acute trust or at an unknown location.
3. The specimen was taken on or after day 3 of the admission (admission date is considered day 1).

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’.
2. The specimen was taken at an acute trust or at an unknown location.
3. The specimen was taken on or after day 4 of the admission (admission date is considered day 1).

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 split into 6 categories 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. Not reported: the reporting trust did not provide any answer for questions on prior admission.

Bacteraemia 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 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. 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

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.