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BackgroundUrinary tract infections are one of the most common infections in primary and secondary care, with the majority of antimicrobial therapy initiated empirically before culture results are available. In some cases, however, over 40% of the bacteria that cause UTIs are resistant to some of the antimicrobials used, yet we do not know how the patient outcome is affected in terms of relapse, treatment failure, progression to more serious illness (bacteraemia) requiring hospitalization, and ultimately death. This study analyzed the current patterns of antimicrobial use for UTI in the community in Scotland, and factors for poor outcomes.ObjectivesTo explore antimicrobial use for UTI in the community in Scotland, and the relationship with patient characteristics and antimicrobial resistance inE. colibloodstream infections and subsequent mortality.MethodsWe included all adult patients in Scotland with a positive blood culture withE. coligrowth, receiving at least one UTI-related antimicrobial (amoxicillin, amoxicillin/clavulanic acid, ciprofloxacin, trimethoprim, and nitrofurantoin) between 1st January 2009 and 31st December 2012. Univariate and multivariate logistic regression analysis was performed to understand the impact of age, gender, socioeconomic status, previous community antimicrobial exposure (including long-term use), prior treatment failure, and multi-morbidity, on the occurrence ofE. colibacteraemia, trimethoprim and nitrofurantoin resistance, and mortality.ResultsThere were 1,093,227 patients aged 16 to 100 years old identified as receiving at least one prescription for the 5 UTI-related antimicrobials during the study period. Antimicrobial use was particularly prevalent in the female elderly population, and 10% study population was on long-term antimicrobials. The greatest predictor for trimethoprim resistance inE. colibacteraemia was increasing age (OR 7.18, 95% CI 5.70 to 9.04 for the 65 years old and over group), followed by multi-morbidity (OR 5.42, 95% CI 4.82 to 6.09 for Charlson Index 3+). Prior antimicrobial use, along with prior treatment failure, male gender, and higher deprivation were also associated with a greater likelihood of a resistantE. colibacteraemia. Mortality was significantly associated with both having anE. colibloodstream infection, and those with resistant growth.ConclusionIncreasing age, increasing co-morbidity, lower socioeconomic status, and prior community antibiotic exposure were significantly associated with a resistantE. colibacteraemia, which leads to increased mortality.

SynopsisBackgroundWhole genome sequencing (WGS) is increasingly applied to healthcare-associated vancomycin-resistantEnterococcus faecium(VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases.ObjectivesDetermine the impact of within-patient diversity on transmission resolution of VREfmMethodsFourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples, and Illumina WGS performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner.ResultsIn total, 229 isolates from 11 patients were sequenced. Carriage of 2-3 sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies.ConclusionsPatients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity should be considered to ensure accurate resolution of transmission networks.

Funding: Astellas Pharma, Inc. Background Clostridioides difficile infection (CDI) is associated with high healthcare demands and related costs. Aim To evaluate the healthcare and economic burden of CDI in hospitalised patients with community- (HOCA-CDI) or hospital-associated CDI (HOHA-CDI) in the National Health Service in Scotland. Methods A retrospective cohort study was conducted, examining data between August 2010 and July 2013 from four patient-level Scottish datasets, linked to death data. Data examined included prior antimicrobial prescriptions in the community, hospitalisations, length of stay and mortality. Each CDI case was matched to three hospital-based controls on the basis of age, gender, hospital and date of admission. Descriptive economic evaluations were based on bed-day costs for different types of wards. Findings Overall, 3304 CDI cases were included in the study. CDI was associated with additional median lengths of stay of 7.2 days for HOCA-CDI and 12.0 days for HOHA-CDI compared with their respective, matched controls. The 30-day mortality rate was 6.8% for HOCA-CDI and 12.4% for HOHA-CDI. Overall, recurrence within 90 days of the first CDI episode occurred in 373/2740 (13.6%) survivors. The median additional expenditure for each initial CDI case compared with matched controls was £1713. In the 6 months after the index hospitalisation, the cost associated with a CDI case was £5126 higher than for controls. Conclusion Using routinely collected national data, we demonstrate the substantial burden of CDI on healthcare services, including lengthy hospital stays and readmissions, which increase the costs of managing patients with CDI compared with matched controls. Postprint

The work was funded by the Scottish Executive via the Chief Scientists Office through the provision of a grant to establish the Scottish Healthcare Associated Infection Prevention Institute (SHAIPI). Blood stream invasion by Escherichia coli is the commonest cause of bacteremia in the UK and elsewhere with an attributable mortality of about 15–20 %; antibiotic resistance to multiple agents is common in this microbe and is associated with worse outcomes. Genes conferring antimicrobial resistance, and their frequent location on horizontally transferred genetic elements is well-recognised, but the origin of these determinants, and their ability to be maintained and spread within clinically-relevant bacterial populations is unclear. Here, we set out to examine the distribution of antimicrobial resistance genes in chromosomes and plasmids of 16 bloodstream isolates of E. coli from patients within Scotland, and how these genes are maintained and spread. Using a combination of short and long-read whole genome sequencing methods, we were able to assemble complete sequences of 44 plasmids, with 16 Inc group F and 20 col plasmids; antibiotic resistance genes located almost exclusively within the F group. blaCTX-M15 genes had re-arranged in some strains into the chromosome alone (five strains), while others contained plasmid copies alone (two strains). Integrons containing multiple antibiotic genes were widespread in plasmids, notably many with a dfrA7 gene encoding resistance to trimethoprim, thus linking trimethoprim resistance to the other antibiotic resistance genes within the plasmids. This will allow even narrow spectrum antibiotics such as trimethoprim to act as a selective agent for plasmids containing antibiotic resistance genes mediating much broader resistance, including blaCTX-M15. To our knowledge, this is the first analysis to provide complete sequence data of chromosomes and plasmids in a collection of pathogenic human bloodstream isolates of E. coli. Our findings reveal the interplay between plasmids and integrative and conjugative elements in the maintenance and spread of antibiotic resistance genes within pathogenic E. coli. Publisher PDF

The work was funded by the Scottish Executive via the Chief Scientists Office through the provision of a grant to establish the Scottish Healthcare Associated Infection Prevention Institute (SHAIPI). The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication. Bacterial type III secretion systems (T3SSs) play an important role in pathogenesis of Gram-negative infections. Enteropathogenic and enterohemorrhagic Escherichia coli contain a well-defined T3SS but in addition a second T3SS termed E. coli T3SS 2 (ETT2) has been described in a number of strains of E. coli. The majority of pathogenic E. coli contain elements of a genetic locus encoding ETT2, but which has undergone significant mutational attrition rendering it without predicted function. Only a very few strains have been reported to contain an intact ETT2 locus. To investigate the occurrence of the ETT2 locus in strains of human pathogenic E. coli, we carried out genomic sequencing of 162 isolates obtained from patient blood cultures in Scotland. We found that 22 of 26 sequence type (ST) 69 isolates from this collection contained an intact ETT2 together with an associated eip locus which encodes putative secreted ETT2 effectors as well as eilA, a gene encoding a putative transcriptional regulator of ETT2 associated genes. Using a reporter gene for eilA activation, we defined conditions under which this gene was differentially activated. Analysis of published E. coli genomes with worldwide representation showed that ST69 contained an intact ETT2 in these strains as well. The conservation of the genes encoding ETT2 in human pathogenic ST69 strains strongly suggests it has importance in infection, although its exact functional role remains obscure. Publisher PDF

Background Uropathogenic Eschericha coli are the leading cause of urinary tract infections (UTIs). The microbe can spread from bladder to kidney and finally to blood. We wished to determine whether genetic changes accompany the passage of these infections from urine to blood. Material/methods 12 paired urine and blood samples were collected from patients in Greater Glasgow and Clyde; the interval between sample collection time between pairs was less than 48 h. Whole genomic sequencing of these paired samples was performed using the Illumina MiSeq platform. De novoassembly of reads was carried out using Shovill assembler; whereas SNPs were identified using SMALT, VarScan and Gubbins tools. Results Urine and blood samples in each pair had the same MLST type. Surprisingly, however, there were multiple differences in the presence of plasmid genes, phage elements and insertion sequences within pairs, as well as numerous SNPs. For example, the mercury reductase merAgene and mercuric transport protein merPhave been acquired in a plasmid of a blood isolate compared to the contemporaneous urine sample. We also identified missense mutations in genes involved in several metabolic pathways in bloodstream isolates. Several of the observed gene deletions/insertions and SNPs were found in more than one of the paired blood and urine isolates. Conclusions The observed sequence differences between contemporaneous blood and urine isolates suggests that genomic differences accumulate within the urinary bladder prior to blood stream invasion. The observed blood stream variants may thus possess a selective advantage in invasion and/or survival within blood.

Bacterial type III secretion systems (T3SS) play an important role in pathogenesis of Gram-negative infections. Enteropathogenic and enterohemorrhagicEscherichia colicontain a well-defined T3SS but in addition a second T3SS termedE. coliT3SS 2 (ETT2) has been described in a number of strains ofE. coli.The majority ofE. colicontain elements of a genetic locus encoding ETT2, but which has undergone significant mutational attrition rendering it without predicted function. Only a very few strains have been reported to contain an intact ETT2 locus. To investigate the occurrence of the ETT2 locus in strains of human pathogenicE. coli, we carried out genomic sequencing of 162 isolates obtained from patient blood cultures in Scotland. We found that all 26 ST69 isolates from this collection contained an intact ETT2 together with an associatedeiplocus which encodes putative secreted ETT2 effectors as well aseilA, a gene encoding a putative transcriptional regulator of ETT2 associated genes. Using a reporter gene foreilAactivation, we defined conditions under which this gene was differentially activated. However, comparison of secreted proteins from ST69 strains under high and loweilAactivation failed to identify any ETT2 secreted substrates. The conservation of the genes encoding ETT2 in human pathogenic ST69 strains strongly suggests it has functional importance in infection, although its exact functional role remains obscure.ImportanceOne of the commonest bacteria causing bloodstream infections in humans isEscherichia coli, which has a significant morbidity and mortality. Better understating of the mechanisms by which this microbe can invade blood could lead to more effective prevention and treatment. One mechanism by which some strains cause disease is by elaboration of a specialized secretion system, the type III secretion system (T3SS), encoded by the locus of enterocyte effacement (LEE). In addition to this well-defined T3SS, a second T3SS has been found in someE. colistrains termedE. colitype III secretion system 2 (ETT2). Most strains carry elements of the ETT2 locus, but with significant mutational attrition rendering it functionless. The significance of our work is that we have discovered that human bloodstream isolates ofE. coliof sequence type 69 contain a fully intact ETT2 and associated genes, strongly suggesting its functional importance in human infection.

The work was funded by the Scottish Executive via the Chief Scientist Office through the provision of a grant to establish the Scottish Healthcare Associated Infection Prevention Institute (SHAIPI). Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013-2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95. Nearly 50% of the bacteraemic isolates had a urinary origin. ST69 was genetically distinct from the other STs, with significantly less sharing of accessory genes and with a distinct plasmid population. Virulence genes were widespread and diversely distributed between the dominant STs. ST131 was significantly associated with hospital-associated infections (HAIs), and ST69 with those from the community. However, there was no association of ST with outcome, although patients with HAI had a higher immediate mortality compared to those with community-associated infections (CAIs). Genome-wide association studies revealed genes involved in antibiotic persistence as significantly associated with HAIs and those encoding elements of a type VI secretion system with CAIs. Antibiotic resistance was common, and there were networks of correlated resistance genes and phenotypic antibiotic resistance. This study has revealed the complex interactions between the genotype of E. coli and its ability to cause bacteraemia, and some of the determinants influencing hospital or community acquisition. In part, these are shaped by antibiotic usage, but strain-specific factors are also important. Publisher PDF

Background: Currently a lack of consensus exists on the optimum solution and preparation methods needed to decrease bacteria present during forefoot surgery. We therefore compared the effect of povidine-iodine and chlorhexidine gluconate on lowering bacterial load and to study any additional benefits gained by pre-treatment with the use of a bristled brush. Materials and Methods: Fifty consecutive patients undergoing forefoot surgery were recruited into the study and randomized to receive one of two surgical skin preparations (Povidine-iodine 1% with isopropyl alcohol 23% or Chlorhexidine gluconate 0.5% with isopropyl alcohol 70%). In addition to the skin preparation of the foot with the randomized solution, the subjects other foot was also scrubbed with a sterile surgical bristled brush for three minutes and then painted with the same solution. Swabs were taken from three sites and analyzed via qualitative and quantitative analysis before and after prepping. Results: All four preparation methods significantly decreased ( p < 0.001), in all three sites, the number of colony forming units. Using two-way analysis of variance, no significant interaction was observed between preparation method and number of colony-forming units, suggesting that no difference in bacterial inhibition between preparation methods. Conclusion: We suggest that either povidone - iodine with no more that 23% isopropyl alcohol or chlorhexidine gluconate with 70% isopropyl alcohol be used for surgical preparation in forefoot surgery. No additional benefit in reduction in bacterial load was gained by scrubbing the foot with bristles prior to painting.

Background: Norovirus outbreaks have a significant impact on all care settings; little is known about the index cases from whom these outbreaks initiate. Aim: To identify and categorise norovirus outbreak index cases in care settings. Methods: A mixed-methods, multi-centre, prospective, enhanced surveillance study identified and categorised index cases in acute and non-acute care settings. Results: From 54 participating centres, 537 outbreaks were reported (November 2013 to April 2014): 383 (71.3%) in acute care facilities (ACF); 115 (21.4%) in residential or care homes (RCH) and 39 (7.3%) in other care settings (OCS). Index cases were identified in 424 (79%) outbreaks. Of the 245 index cases who were asymptomatic on admission and not transferred within/into the care setting, 123 (50%) had been an inpatient/resident for 4 days. Four themes emerged: missing the diagnosis, care service under pressure, delay in outbreak control measures and patient/resident location and proximity. Conclusion: The true index case is commonly not identified as the cause of a norovirus outbreak with at least 50% of index cases being misclassified. Unrecognised norovirus cross-transmission occurs frequently suggesting that either Standard Infection Control Precautions (SICPs) are being insufficiently well applied, and or SICPs are themselves are insufficient to prevent outbreaks.

Multi-drug-resistant (MDR) Gram-negative bacterial infections have become prevalent in some European countries. Moreover, increased use of broad-spectrum antimicrobial agents selects organisms with resistance and, by increasing their numbers, increases their chance of spread. This report describes measures that are clinically effective for preventing transmission when used by healthcare workers in acute and primary healthcare premises. Methods for systematic review 1946–2014 were in accordance with SIGN 501 and the Cochrane Collaboration;2 critical appraisal was applied using AGREEII.3 Accepted guidelines were used as part of the evidence base and to support expert consensus. Questions for review were derived from the Working Party Group, which included patient representatives in accordance with the Patient Intervention Comparison Outcome (PICO) process. Recommendations are made in the following areas: screening, diagnosis and infection control precautions including hand hygiene, single-room accommodation, and environmental screening and cleaning. Recommendations for specific organisms are given where there are species differences. Antibiotic stewardship is covered in a separate publication.

The Working Party recommends (section 9.5) that clear information on the standards of infection prevention and control should be available to promote confidence in the quality of care provided.1 To assist, the following four information leaflets have been created. The purpose of these leaflets is to explain the meaning of multidrug-resistant Gram-negative organisms and, more specifically, carbapenem-resistant organisms; to assist healthcare workers, patients, relatives, and visitors in understanding why these bacteria are a problem; and to explain what precautions can be taken to help prevent the spread of these bacteria.

The primary treatment of deep neck spaces odontogenic infection (DNSOI) with suppuration is surgery. Systemic antimicrobial therapy is an important adjunct. The initial prescription of antimicrobial therapy is empirical. Over the last decade we have observed a change in practice with the use of second-generation cephalosporins, in conjunction with metronidazole, replacing benzylpencillin and metronidazole. More recently evidence has emerged suggesting that antimicrobial resistance in nosocomial infections could be related to the widespread use of second and third-generation cephalosporins. This study was therefore initiated to determine whether this change in prescribing was justified. A total of 75 cases were retrospectively identified by scrutiny of the operating theatre data. These patients presented with significant DNSOI that required surgical drainage. Streptococcus milleri and mixed anaerobes were predominant. Only in three cases (4%) there were penicillin-resistant microorganisms. The substitution of benzylpenicillin for cefuroxime as an initial empiric therapy for DNSOI seems likely to have been equally efficacious in the large majority of cases. On the other hand, studies in preference of cephalosporins are based on in vitro trials. A multi-centre randomized controlled clinical trial directly comparing initial empiric second-generation cephalosporin therapy with benzylpenicillin in non-allergic patients is justified.

We assessed the ability of three commercial systems to infer carbapenem resistance mechanisms in 39 carbapenemase-producing and 16 other carbapenem-resistant Enterobacteriaceae . The sensitivity/specificity values for “flagging” a likely carbapenemase were 100%/0% (BD Phoenix), 82 to 85%/6 to 19% (MicroScan), and 74%/38% (Vitek 2), respectively. OXA-48 producers were poorly detected, but all systems reliably detected isolates with KPC and most with metallo-carbapenemases.

Chronic obstructive pulmonary disease (COPD) is a common progressive respiratory disease that is associated with infective exacerbations that lead to worsening of symptoms. Many organisms are thought to trigger infective exacerbations, but Haemophilus influenzae is the most commonly isolated bacterium. The role of H. influenzae in infective exacerbations remains uncertain, mainly because the organism chronically colonises patients whose clinical condition is stable. H. influenzae may also comprise part of the normal nasopharyngeal flora in man, making the interpretation of positive cultures difficult in some cases.