Understanding adherence to self-isolation in the first phase of the COVID-19 pandemic in England: a cross-sectional mixed-methods study.

BACKGROUND: During the early "containment" phase of the COVID-19 response in England (January-March 2020), contact tracing was managed by Public Health England (PHE). Adherence to self-isolation during this phase and how people were making those decisions has not previously been determined. The aim of this study was to gain a better understanding of decisions around adherence to self-isolation during the first phase of the COVID-19 response in England. METHODS: A mixed-methods cross sectional study was conducted, including an online survey and qualitative interviews. The overall pattern of adherence was described as never leaving home, leaving home for lower-contact reasons and leaving home for higher-contact reasons. Fisher's exact test was used to test associations between adherence and potentially predictive binary factors. Factors showing evidence of association overall were then considered in relation to the three aspects of adherence individually. Qualitative data were analysed using inductive thematic analysis. RESULTS: Of 250 respondents who were advised to self-isolate, 63% reported not leaving home at all during their isolation period, 20% reported leaving only for lower-contact activities (dog walking or exercise) and 16% reported leaving for higher-contact, and therefore higher-risk, reasons. Factors associated with adherence to never going out included: the belief that following isolation advice would save lives, experiencing COVID-19 symptoms, being advised to stay in their room, having help from outside and having regular contact by text message from PHE. Factors associated with non-adherence included being angry about the advice to isolate, being unable to get groceries delivered and concerns about losing touch with friends and family. Interviews highlighted that a sense of duty motivated people to adhere to isolation guidance and where people did leave their homes, these decisions were based on rational calculations of the risk of transmission - people would only leave their homes when they thought they were unlikely to come into contact with others. CONCLUSIONS: Understanding adherence to isolation and associated reasoning during the early stages of the pandemic is essential to pandemic preparedness for future emerging infectious disease outbreaks. Individuals make complex decisions around adherence by calibrating transmission risks, therefore treating adherence as binary should be avoided.

Exploring the impact of shielding advice on the wellbeing of individuals identified as clinically extremely vulnerable amid the COVID-19 pandemic: a mixed-methods evaluation.

BACKGROUND: The national shielding programme was introduced by UK Government at the beginning of the COVID-19 pandemic, with individuals identified as clinically extremely vulnerable (CEV) offered advice and support to stay at home and avoid all non-essential contact. This study aimed to explore the impact and responses of "shielding" on the health and wellbeing of CEV individuals in Southwest England during the first COVID-19 lockdown. METHODS: A two-stage mixed methods study, including a structured survey (7 August-23 October 2020) and semi-structured telephone interviews (26 August-30 September 2020) with a sample of individuals who had been identified as CEV and advised to "shield" by Bristol, North Somerset & South Gloucestershire (BNSSG) Clinical Commissioning Group (CCG). RESULTS: The survey was completed by 203 people (57% female, 54% > 69 years, 94% White British, 64% retired) in Southwest England identified as CEV by BNSSG CCG. Thirteen survey respondents participated in follow-up interviews (53% female, 40% > 69 years, 100% White British, 61% retired). Receipt of 'official' communication from NHS England or General Practitioner (GP) was considered by participants as the legitimate start of shielding. 80% of survey responders felt they received all relevant advice needed to shield, yet interviewees criticised the timing of advice and often sought supplementary information. Shielding behaviours were nuanced, adapted to suit personal circumstances, and waned over time. Few interviewees received community support, although food boxes and informal social support were obtained by some. Worrying about COVID-19 was common for survey responders (90%). Since shielding had begun, physical and mental health reportedly worsened for 35% and 42% of survey responders respectively. 21% of survey responders scored ≥ 10 on the PHQ-9 questionnaire indicating possible depression and 15% scored ≥ 10 on the GAD-7 questionnaire indicating possible anxiety. CONCLUSIONS: This research highlights the difficulties in providing generic messaging that is applicable and appropriate given the diversity of individuals identified as CEV and the importance of sharing tailored and timely advice to inform shielding decisions. Providing messages that reinforce self-determined action and assistance from support services could reduce the negative impact of shielding on mental health and feelings of social isolation.

Impact of new consent procedures on uptake of the schools-based human papillomavirus (HPV) vaccination programme.

BACKGROUND: Local policy change initiating new consent procedures was introduced during 2017-2018 for the human papillomavirus (HPV) vaccination programme year in two local authorities in the south-west of England. This study aims to assess impact on uptake and inequalities. METHODS: Publicly available aggregate and individual-level routine data were retrieved for the programme years 2015-2016 to 2018-2019. Statistical analyses were undertaken to show: (i) change in uptake in intervention local authorities in comparison to matched local authorities and (ii) change in uptake overall, and by local authority, school type, ethnicity and deprivation. RESULTS: Aggregate data showed uptake in Local Authority One increased from 76.3% to 82.5% in the post-intervention period (risk difference: 6.2% P = 0.17), with a difference-in-differences effect of 11.5% (P = 0.03). There was no evidence for a difference-in-differences effect in Local Authority Two (P = 0.76). Individual-level data showed overall uptake increased post-intervention (risk difference: +1.1%, P = 0.05), and for young women attending school in Local Authority One (risk difference: 2.3%, P < 0.01). No strong evidence for change by school category, ethnic group and deprivation was found. CONCLUSION: Implementation of new consent procedures can improve and overcome trends for decreasing uptake among matched local authorities. However, no evidence for reduction in inequalities was found. IMPLICATIONS AND DISCUSSION: The new consent procedures increased uptake in one of the intervention sites and appeared to overcome trends for decreasing uptake in matched sites. There are issues in relation to the quality of data which require addressing.

Replacement of Enterococcus faecalis by Enterococcus faecium as the predominant enterococcus in UK bacteraemias.

OBJECTIVES: To review temporal changes in the proportions of different Enterococcus species recorded in two UK bacteraemia surveillance systems. Antibiotic resistance trends were also considered. METHODS: We reviewed data for enterococci from 2001 to 2019 in: (a) the BSAC Resistance Surveillance Programme, which collected up to 7-10 bloodstream enterococci every year from each of 23-39 hospitals in the UK and Ireland and tested these centrally; and (b) PHE bacteraemia surveillance, using routine results from NHS microbiology laboratories in England. RESULTS: BSAC surveillance, based upon 206-255 enterococci each year (4486 in total), indicated that the proportion of Enterococcus faecium rose from 31% (212/692) in the period 2001-3 to 51% (354/696) in the period 2017-19, balanced by corresponding falls in the proportion of Enterococcus faecalis. PHE surveillance provided a larger dataset, with >5000 enterococcus reports per year; although its identifications are less precise, it too indicated a rise in the proportion of E. faecium. BSAC surveillance for E. faecium indicated no consistent trends in resistance to ampicillin (≥86% in all years), vancomycin (annual rates 19%-40%) or high-level resistance to gentamicin (31%-59%). Resistance to vancomycin remained <4% in E. faecalis in all years, whilst high-level resistance to gentamicin fell, perhaps partly reflecting the decline of two initially prevalent gentamicin- and ciprofloxacin-resistant clones. CONCLUSIONS: Both surveillance systems indicate a growing proportion of E. faecium in enterococcal bloodstream infections. This is important because fewer therapeutic options remain against this frequently multiresistant species than against E. faecalis.

Cost-effectiveness of rapid laboratory-based mass-spectrometry diagnosis of bloodstream infection: evidence from the RAPIDO randomised controlled trial.

OBJECTIVES AND INTERVENTION: Bloodstream infection, the presence of viable micro-organisms in the blood, is a prevalent clinical event associated with substantial mortality. Patient outcomes may be improved when the causative micro-organism is identified quickly. We assessed the cost-effectiveness of rapid microbial identification by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry. DESIGN: Economic evaluation alongside a randomised multicentre trial (RAPIDO: RAPId Diagnosis on Outcome) assessing the impact of rapid identification by MALDI-TOF spectrometry. SETTING: Adult inpatients with bloodstream infections at seven National Health Service hospital trusts in England and Wales. PRIMARY OUTCOME: Net monetary benefit, estimated as incremental costs compared with incremental 28-day survival, of rapid identification by MALDI-TOF spectrometry compared with conventional identification. METHODS: Patients were randomised (1:1) to receive diagnosis by conventional methods of microbial identification (conventional arm) only or by MALDI-TOF spectrometry in addition to conventional identification (RAPIDO arm). RESULTS: Data from 5550 patients were included in primary analysis. Mean imputed costs in 2018/2019 prices per patient were lower by £126 in the RAPIDO arm (95% CI -£784 to £532) but the proportion of patients alive at day 28 was lower (81.4% vs 82.3%). The probability of cost-effectiveness of MALDI-TOF was <0.5 at cost-effectiveness thresholds between £20 000 and £50 000. CONCLUSIONS: Adjunctive MALDI-TOF diagnosis was unlikely to be cost-effective when measured as cost per death avoided at 28 days. However, the differences between arms in cost and effect were modest, associated with uncertainty and may not accurately reflect 'real-world' routine use of MALDI-TOF technology in this patient group. TRIAL REGISTRATION NUMBERS: ISRCTN97107018/UKCRN 11978.

Elucidating Drivers for Variations in the Explosive Human Immunodeficiency Virus Epidemic Among People Who Inject Drugs in Pakistan.

BACKGROUND: Pakistan's explosive human immunodeficiency virus (HIV) epidemic among people who inject drugs (PWID) varies widely across cities. We evaluated possible drivers for these variations. METHODS: Multivariable regression analyses were undertaken using data from 5 national surveys among PWID (n = 18 467; 2005-2017) to determine risk factors associated with variations in city-level HIV prevalence. A dynamic HIV model was used to estimate the population-attributable fraction (PAF; proportion of HIV infections prevented over 10 years when that risk factor is removed) of these risk factors to HIV transmission and impact on HIV incidence of reducing their prevalence. RESULTS: Regression analyses suggested that city-level HIV prevalence is strongly associated with the prevalence of using professional injectors at last injection, heroin use in last month, and injecting ≥4 times per day. Through calibrating a model to these associations, we estimate that the 10-year PAFs of using professional injectors, heroin use, and frequent injecting are 45.3% (95% uncertainty interval [UI], 4.3%-79.7%), 45.9% (95% UI, 8.1%-78.4%), and 22.2% (95% UI, 2.0%-58.4%), respectively. Reducing to lowest city-level prevalences of using professional injectors (2.8%; median 89.9% reduction), heroin use (0.9%; median 91.2% reduction), and frequent injecting (0.1%; median 91.8% reduction) in 2020 reduces overall HIV incidence by 52.7% (95% UI, 6.1%-82.0%), 53.0% (95% UI, 11.3%-80.2%), and 28.1% (95% UI, 2.7%-66.6%), respectively, over 10 years. CONCLUSIONS: Interventions should focus on these risk factors to control Pakistan's explosive HIV epidemic among PWID, including a concomitant expansion of high-coverage needle/syringe provision, opioid substitution therapy, and antiretroviral therapy.

Secondary analyses to test the impact on inequalities and uptake of the schools-based human papillomavirus (HPV) vaccination programme by stage of implementation of a new consent policy in the south-west of England.

OBJECTIVES: To test the impact on inequalities and uptake of the schools-based human papillomavirus (HPV) vaccination programme by stage of implementation of a new policy providing additional opportunities to consent. SETTING: Two local authorities in the south-west of England. PARTICIPANTS: Young women (n=7129) routinely eligible for HPV vaccination aged 12-13 years during the intervention period (2017/2018 to 2018/2019 programme years). INTERVENTIONS: Local policy change that included additional opportunities to provide consent (parental verbal consent and adolescent self-consent). OUTCOMES: Secondary analyses of cross-sectional intervention data were undertaken to examine uptake by: (1) receipt of parental written consent forms and; (2) percentage of unvaccinated young women by stage of implementation. RESULTS: During the intervention period, 6341 (89.0%) eligible young women initiated the HPV vaccination series. Parental written consent forms were less likely to be returned where young women attended alternative education provider settings (p<0.001), belonged to non-white British ethnic groups (p<0.01) or more deprived quintiles (p<0.001). Implementation of parental verbal consent and adolescent self-consent reduced the percentage of unvaccinated young women from 21.3% to 16.5% (risk difference: 4.8%). The effect was greater for young women belonging to the most deprived compared with the least deprived quintile (risk difference: 7.4% vs 2.3%, p<0.001), and for young women classified as Unknown ethnic category compared with white British young women (6.7% vs 4.2%, p<0.001). No difference was found for non-white British young women (5.4%, p<0.21). CONCLUSIONS: Local policy change to consent procedures that allowed parents to consent verbally and adolescents to self-consent overcame some of the barriers to vaccination of young women belonging to families less likely to respond to paper-based methods of gaining consent and at greater risk of developing cervical cancer. TRIAL REGISTRATION NUMBER: 49 086 105.

Incidence of Clostridioides difficile infection (CDI) related to antibiotic prescribing by GP surgeries in Wales.

BACKGROUND: Clostridioides difficile infection (CDI) is a healthcare-acquired infection (HAI) causing significant morbidity and mortality. Welsh CDI rates are high in comparison with those in England and Scotland. OBJECTIVES: This retrospective ecological study used aggregated disease surveillance data to understand the impact of total and high-risk Welsh GP antibiotic prescribing on total and stratified inpatient/non-inpatient CDI incidence. METHODS: All cases of confirmed CDI, during the financial years 2014-15 to 2017-18, were linked to aggregated rates of antibiotic prescribing in their GP surgery and classified as 'inpatient', 'non-inpatient' or 'unknown' by Public Health Wales. Multivariable negative-binomial regression models, comparing CDI incidence with antibiotic prescribing rates, were adjusted for potential confounders: location; age; social deprivation; comorbidities (estimated from prevalence of key health indicators) and proton pump inhibitor (PPI) prescription rates. RESULTS: There were 4613 confirmed CDI cases, with an incidence (95% CI) of 1.44 (1.40-1.48) per 1000 registered patients. Unadjusted analysis showed that an increased risk of total CDI incidence was associated with higher total antibiotic prescribing [relative risk (RR) (95% CI) = 1.338 (1.170-1.529) per 1000 items per 1000 specific therapeutic group age-sex related GP prescribing units (STAR-PU)] and that high-risk antibiotic classes were positively associated with total CDI incidence. Location, age ≥65 years and diabetes were associated with increased risk of CDI. After adjusting for confounders, prescribing of clindamycin showed a positive association with total CDI incidence [RR (95% CI) = 1.079 (1.001-1.162) log items per 1000 registered patients]. CONCLUSIONS: An increased risk of CDI is demonstrated at a primary care practice population level, reflecting their antibiotic prescribing rates, particularly clindamycin, and population demographics.

Are resistance rates among bloodstream isolates a good proxy for other infections? Analysis from the BSAC Resistance Surveillance Programme.

BACKGROUND: Bacteraemia data are often used as a general measure of resistance prevalence but may poorly represent other infection types. We compared resistance prevalence between bloodstream infection (BSI) and lower respiratory tract infection (LRTI) isolates collected by the BSAC Resistance Surveillance Programme. METHODS: BSI isolates (n = 8912) were collected during 2014-18 inclusive and LRTI isolates (n = 6280) between October 2013 to September 2018 from participating laboratories in the UK and Ireland, to a fixed annual quota per species group. LRTI isolates, but not BSI, were selected by onset: community for Streptococcus pneumoniae; hospital for Staphylococcus aureus, Pseudomonas aeruginosa and Enterobacterales. MICs were determined centrally by agar dilution; statistical modelling adjusted for ICU location and possible clustering by collection centre. RESULTS: Resistance was more prevalent among the LRTI isolates, even after adjusting for a larger proportion of ICU patients. LRTI P. aeruginosa and S. pneumoniae were more often resistant than BSI isolates for most antibiotics, and the proportion of MRSA was higher in LRTI. For S. pneumoniae, the observation reflected different serotype distributions in LRTI and BSI. Relationships between LRTI and resistance were less marked for Enterobacterales, but LRTI E. coli were more often resistant to ß-lactams, particularly penicillin/ß-lactamase inhibitor combinations, and LRTI K. pneumoniae to piperacillin/tazobactam. For E. cloacae there was a weak association between LRTI, production of AmpC enzymes and cephalosporin resistance. CONCLUSIONS: Estimates of resistance prevalence based upon bloodstream isolates underestimate the extent of the problem in respiratory isolates, particularly for P. aeruginosa, S. pneumoniae, S. aureus and, less so, for Enterobacterales.

Modifiable healthcare factors affecting 28-day survival in bloodstream infection: a prospective cohort study.

BACKGROUND: Bloodstream infection is common in the UK and has significant mortality depending on the pathogen involved, site of infection and other patient factors. Healthcare staffing and ward activity may also impact on outcomes in a range of conditions, however there is little specific National Health Service (NHS) data on the impact for patients with bloodstream infection. Bloodstream Infections - Focus on Outcomes is a multicentre cohort study with the primary aim of identifying modifiable risk factors for 28-day mortality in patients with bloodstream infection due to one of six key pathogens. METHODS: Adults under the care of five NHS Trusts in England and Wales between November 2010 and May 2012 were included. Multivariable Cox regression was used to quantify the association between modifiable risk factors, including staffing levels and timing of appropriate therapy, and 28-day mortality, after adjusting for non-modifiable risk factors such as patient demographics and long-term comorbidities. RESULTS: A total of 1676 patients were included in the analysis population. Overall, 348/1676 (20.8%) died within 28 days. Modifiable factors associated with 28-day mortality were ward speciality, ward activity (admissions and discharges), movement within ward speciality, movement from critical care, and time to receipt of appropriate antimicrobial therapy in the first 7 days. For each additional admission or discharge per 10 beds, the hazard increased by 4% (95% CI 1 to 6%) in medical wards and 11% (95% CI 4 to 19%) in critical care. Patients who had moved wards within speciality or who had moved out of a critical care ward had a reduction in hazard of mortality. In the first 7 days, hazard of death increased with increasing time to receipt of appropriate antimicrobial therapy. CONCLUSION: This study underlines the importance of appropriate antimicrobials within the first 7 days, and the potential for ward activity and ward movements to impact on survival in bloodstream infection.

Inherent colistin resistance in genogroups of the Enterobacter cloacae complex: epidemiological, genetic and biochemical analysis from the BSAC Resistance Surveillance Programme.

BACKGROUND: Polymyxins have re-entered use against problem Gram-negative bacteria. Resistance rates are uncertain, with estimates confounded by selective testing. METHODS: The BSAC Resistance Surveillance Programme has routinely tested colistin since 2010; we reviewed data up to 2017 for relevant Enterobacterales (n = 10 914). Unexpectedly frequent resistance was seen among the Enterobacter cloacae complex isolates (n = 1749); for these, we investigated relationships to species, genome, carbon source utilization and LPS structure. RESULTS: Annual colistin resistance rates among E. cloacae complex isolates were 4.4%-20%, with a rising trend among bloodstream organisms; in contrast, annual rates for Escherichia coli and Klebsiella spp. (including K. aerogenes) generally remained <2%. WGS split the E. cloacae complex isolates into seven genogroup clusters, designated A-G. Among isolates assigned to genogroups A-D, 47/50 sequenced were colistin resistant, and many of those belonging to genogroups A-C identified as E. asburiae. Isolates belonging to genogroups E-G consistently identified as E. cloacae and were rarely (only 3/45 representatives sequenced) colistin resistant. Genogroups F and G, the predominant colistin-susceptible clusters, were metabolically distinct from other clusters, notably regarding utilization or not of l-fucose, formic acid, d-serine, adonitol, myo-inositol, l-lyxose and polysorbates. LPS from resistant organisms grown without colistin pressure lacked substitutions with 4-amino-arabinose or ethanolamine but was more structurally complex, with more molecular species present. CONCLUSIONS: Colistin resistance is frequent in the E. cloacae complex and increasing among bloodstream isolates. It is associated with: (i) particular genomic and metabolic clusters; (ii) identification as E. asburiae; and (iii) with more complex LPS architectures.

Influence of commissioned provider type and deprivation score on uptake of the childhood flu immunization.

BACKGROUND: Since 2015/16 the UK seasonal influenza immunization programme has included children aged 5 and 6 years. In the South West of England school-based providers, GPs or community pharmacies were commissioned to deliver the vaccine depending on the locality. We aimed to assess variation in vaccine uptake in relation to the type of commissioned provider, and levels of socioeconomic deprivation. METHODS: Data from the South West of England (2015-16 season) were analysed using multilevel logistic regression to assess variation in vaccine uptake by type of commissioned provider, allowing for clustering of children within delivery sites. RESULTS: Overall uptake in 5 and 6 year olds was 34.3% (37 555/109 404). Vaccine uptake was highest when commissioned through school-based programmes 50.2% (9983/19 867) and lowest when commissioned through pharmacies, 23.1% (4269/18 479). Delivery through schools resulted in less variation by site and equal uptake across age groups, in contrast to GP and pharmacy delivery for which uptake was lower among 6 year olds. Vaccine uptake decreased with increasing levels of deprivation across all types of commissioned provider. CONCLUSION: School-based programmes achieve the highest and most consistent rates of childhood influenza vaccination. Interventions are still needed to promote more equitable uptake of the childhood influenza vaccine.

The Hepatitis C Awareness Through to Treatment (HepCATT) study: improving the cascade of care for hepatitis C virus-infected people who inject drugs in England.

BACKGROUND AND AIMS: Previous studies have shown low rates of diagnosis and treatment of hepatitis C virus (HCV) infection in people who inject drugs (PWID). Our aims were to test the effect of a complex intervention [Hepatitis C Awareness Through to Treatment (HepCATT)] in drug and alcohol clinics-primarily, on engagement of HCV-positive PWID with therapy and, secondarily, on testing for HCV, referral to hepatology services and start of HCV treatment. DESIGN AND SETTING: A non-randomized pilot study in three specialist addiction clinics in England comparing an intervention year (starting between September 2015 and February 2016) with a baseline year (2014), together with three control clinics. PARTICIPANTS: Analysis included all attendees at the intervention and control specialist addiction clinics identified as PWID. INTERVENTION: The intervention comprised the placement of a half-time facilitator in each clinic for 12 months with the brief to increase diagnosis of HCV infection within clients at those services and the engagement of diagnosed individuals with an appropriate care pathway. The facilitator undertook various activities, which could include training of key workers, direct interaction with clients, streamlining and support for hepatology appointments and introduction of dried blood-spot testing. MEASUREMENTS: For each clinic and period, we obtained the total number of clients and, as relevant, their status as PWID, tested for HCV, known HCV-positive, engaged with HCV therapy or treated. FINDINGS: Compared with baseline, there was strong evidence that engagement with HCV therapy in the intervention year increased (P < 0.001) more in the HepCATT centres than controls, up + 31 percentage points [95% confidence interval (CI) = 19-43] versus -12 (CI = -31 to + 6) and odds ratio (OR) = 9.99 (CI = 4.42-22.6) versus 0.35 (CI = 0.08-1.56). HepCATT centres also had greater increases in HCV testing (OR = 3.06 versus 0.78, P < 0.001), referral to hepatology (OR = 9.60 versus 0.56, P < 0.001) and treatment initiation (OR = 9.5 versus 0.74, P < 0.001). CONCLUSIONS: Introducing a half-time facilitator into drug and alcohol clinics in England increased engagement of HCV-positive people who inject drugs with hepatitis C virus care pathways, with increased uptake also of testing, referral to hepatology and initiation of treatment.

Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns.

Antibiotic resistance forms a serious threat to the health of hospitalised patients, rendering otherwise treatable bacterial infections potentially life-threatening. A thorough understanding of the mechanisms by which resistance spreads between patients in different hospitals is required in order to design effective control strategies. We measured the differences between bacterial populations of 52 hospitals in the United Kingdom and Ireland, using whole-genome sequences from 1085 MRSA clonal complex 22 isolates collected between 1998 and 2012. The genetic differences between bacterial populations were compared with the number of patients transferred between hospitals and their regional structure. The MRSA populations within single hospitals, regions and countries were genetically distinct from the rest of the bacterial population at each of these levels. Hospitals from the same patient referral regions showed more similar MRSA populations, as did hospitals sharing many patients. Furthermore, the bacterial populations from different time-periods within the same hospital were generally more similar to each other than contemporaneous bacterial populations from different hospitals. We conclude that, while a large part of the dispersal and expansion of MRSA takes place among patients seeking care in single hospitals, inter-hospital spread of resistant bacteria is by no means a rare occurrence. Hospitals are exposed to constant introductions of MRSA on a number of levels: (1) most MRSA is received from hospitals that directly transfer large numbers of patients, while (2) fewer introductions happen between regions or (3) across national borders, reflecting lower numbers of transferred patients. A joint coordinated control effort between hospitals, is therefore paramount for the national control of MRSA, antibiotic-resistant bacteria and other hospital-associated pathogens.

Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing.

BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility of whole-genome sequencing in defining nosocomial VREfm transmission. METHODS: A retrospective study at a single hospital in the United Kingdom identified 342 patients with E. faecium bloodstream infection over 7 years. Of these, 293 patients had a stored isolate and formed the basis for the study. The first stored isolate from each case was sequenced (200 VREfm [197 vanA, 2 vanB, and 1 isolate containing both vanA and vanB], 93 vancomycin-susceptible E. faecium) and epidemiological data were collected. Genomes were also available for E. faecium associated with bloodstream infections in 15 patients in neighboring hospitals, and 456 patients across the United Kingdom and Ireland. RESULTS: The majority of infections in the 293 patients were hospital-acquired (n = 249) or healthcare-associated (n = 42). Phylogenetic analysis showed that 291 of 293 isolates resided in a hospital-associated clade that contained numerous discrete clusters of closely related isolates, indicative of multiple introductions into the hospital followed by clonal expansion associated with transmission. Fine-scale analysis of 6 exemplar phylogenetic clusters containing isolates from 93 patients (32%) identified complex transmission routes that spanned numerous wards and years, extending beyond the detection of conventional infection control. These contained both vancomycin-resistant and -susceptible isolates. We also identified closely related isolates from patients at Cambridge University Hospitals NHS Foundation Trust and regional and national hospitals, suggesting interhospital transmission. CONCLUSIONS: These findings provide important insights for infection control practice and signpost areas for interventions. We conclude that sequencing represents a powerful tool for the enhanced surveillance and control of nosocomial E. faecium transmission and infection.

Rise of multidrug-resistant non-vaccine serotype 15A Streptococcus pneumoniae in the United Kingdom, 2001 to 2014.

Conjugate vaccines have reduced pneumococcal disease in vaccinated children and unvaccinated adults, but non-vaccine serotypes are of concern, particularly if antibiotic resistant. We reviewed Streptococcus pneumoniae collected via: (i) the British Society for Antimicrobial Chemotherapy (BSAC) surveillances from 2001-2014; (ii) Public Health England's (PHE) invasive isolate surveillance from 2005-2014 and (iii) referral to PHE for resistance investigation from 2005-2014. Serotype 15A increased in all series, with many representatives showing triple resistance to macrolides, tetracyclines and penicillin. 15A was consistently among the 10 most prevalent serotypes from 2011 in PHE and BSAC invasive isolate/bacteraemia surveillance but never previously; 26-33% of these invasive 15A isolates had triple resistance. BSAC respiratory isolates were only serotyped in 2013/14 and 2014/15 (October to September); 15A was most prevalent serotype in both periods, comprising 9-11% of isolates, 38-48% of them with triple resistance. Serotype 15A represented 0-4% of S. pneumoniae referred to PHE for reference investigation annually until 2008 but rose to 29% (2013) and 32% (2014). Almost all multidrug-resistant 15A isolates were sequence type (ST) 63 variants, whereas susceptible 15A isolates were clonally diverse. The rise of serotype 15A suggests that pneumococcal conjugate vaccines will need ongoing adaptation.

Genome-based characterization of hospital-adapted Enterococcus faecalis lineages.

Vancomycin-resistant Enterococcus faecalis (VREfs) is an important nosocomial pathogen(1,2). We undertook whole genome sequencing of E. faecalis associated with bloodstream infection in the UK and Ireland over more than a decade to determine the population structure and genetic associations with hospital adaptation. Three lineages predominated in the population, two of which (L1 and L2) were nationally distributed, and one (L3) geographically restricted. Genome comparison with a global collection identified that L1 and L3 were also present in the USA, but were genetically distinct. Over 90% of VREfs belonged to L1-L3, with resistance acquired and lost multiple times in L1 and L2, but only once followed by clonal expansion in L3. Putative virulence and antibiotic resistance genes were over-represented in L1, L2 and L3 isolates combined, versus the remainder. Each of the three main lineages contained a mixture of vancomycin-resistant and -susceptible E. faecalis (VSEfs), which has important implications for infection control and antibiotic stewardship.

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland.

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001-2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.