Nocardia species distribution and antimicrobial susceptibility within Australia

BACKGROUND

Nocardia is a ubiquitous saprophyte capable of causing human disease. Disease is primarily respiratory or cutaneous, usually acquired via inhalation or inoculation. Under the influence of environmental and host factors, Nocardia incidence and species distribution demonstrate geographical variation.

AIMS

To examine for differences in Nocardia incidence within Western Australia (WA) and analyse species distribution in the context of prior published studies. To analyse antibiogram data from a nationwide passive antimicrobial resistance surveillance program.

METHODS

Retrospective extraction of laboratory data for Western Australian Nocardia isolates over a 21-year period. Analysis of Nocardia antimicrobial susceptibility testing data submitted to the Australian Passive Antimicrobial Resistance Surveillance (APAS) program between 2005 and 2022.

RESULTS

Nine hundred sixty WA isolates were identified, giving an annual incidence of 3.03 per 100 000 population with apparent latitudinal variation. The four most common species identified within WA and amongst APAS isolates were N. nova, N. cyriacigeorgica, N. brasiliensis and N. farcinica. APAS data demonstrated that all species exhibited high rates of susceptibility to linezolid (100%) and trimethoprim-sulfamethoxazole (98%). Amikacin (>90% susceptibility for all species except N. transvalensis) was the next most active parenteral agent, superior to both carbapenems and third-generation cephalosporins. Susceptibility to oral antimicrobials (other than linezolid) demonstrated significant interspecies variation.

CONCLUSIONS

We demonstrate geographical variation in the distribution of Nocardia incidence. Four species predominate in the Australian setting, and nationwide data confirm a high in vitro susceptibility to trimethoprim-sulphamethoxazole and linezolid, justifying their ongoing role as part of first-line empiric therapy.

Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory

The COVID-19 pandemic has presented a unique opportunity to understand how real-time pathogen genomics can be used for large-scale outbreak investigations. On 12 August 2021, the Australian Capital Territory (ACT) detected an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant. Prior to this date, SARS-CoV-2 had been eliminated locally since 7 July 2020. Several public health interventions were rapidly implemented in response to the incursion, including a territory-wide lockdown and comprehensive contact tracing. The ACT has not previously used pathogen genomics at a population level in an outbreak response; therefore, this incursion also presented an opportunity to investigate the utility of genomic sequencing to support contact tracing efforts in the ACT. Sequencing of >75% of the 1793 laboratory-confirmed cases during the 3 months following the initial notification identified at least 13 independent incursions with onwards spread in the community. Stratification of cases by genomic cluster revealed that distinct cohorts were affected by the different incursions. Two incursions resulted in most of the community transmission during the study period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. The high rates of SARS-CoV-2 sequencing in the ACT and the relatively small population size facilitated detailed investigations of the patterns of virus transmission, revealing insights beyond those gathered from traditional contact tracing alone. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.

Preoperative Rehabilitation Is Feasible in the Weeks Prior to Surgery and Significantly Improves Functional Performance

BACKGROUND

Frailty is a multidimensional state of increased vulnerability. Frail patients are at increased risk for poor surgical outcomes. Prior research demonstrates that rehabilitation strategies deployed after surgery improve outcomes by building strength.

OBJECTIVES

Examine the feasibility and impact of a novel, multi-faceted prehabilitation intervention for frail patients before surgery.

DESIGN

Single arm clinical trial.

SETTING

Veterans Affairs hospital.

PARTICIPANTS

Patients preparing for major abdominal, urological, thoracic, or cardiac surgery with frailty identified as a Risk Analysis Index≥30.

INTERVENTION

Prehabilitation started in a supervised setting to establish safety and then transitioned to home-based exercise with weekly telephone coaching by exercise physiologists. Prehabilitation included (a)strength and coordination training; (b)respiratory muscle training (IMT); (c)aerobic conditioning; and (d)nutritional coaching and supplementation. Prehabilitation length was tailored to the 4-6 week time lag typically preceding each participant's normally scheduled surgery.

MEASUREMENTS

Functional performance and patient surveys were assessed at baseline, every other week during prehabilitation, and then 30 and 90 days after surgery. Within-person changes were estimated using linear mixed models.

RESULTS

43 patients completed baseline assessments; 36(84%) completed a median 5(range 3-10) weeks of prehabilitation before surgery; 32(74%) were retained through 90-day follow-up. Baseline function was relatively low. Exercise logs show participants completed 94% of supervised exercise, 78% of prescribed IMT and 74% of home-based exercise. Between baseline and day of surgery, timed-up-and-go decreased 2.3 seconds, gait speed increased 0.1 meters/second, six-minute walk test increased 41.7 meters, and the time to complete 5 chair rises decreased 1.6 seconds(all P≤0.007). Maximum and mean inspiratory and expiratory pressures increased 4.5, 7.3, 14.1 and 13.5 centimeters of water, respectively(all P≤0.041).

CONCLUSIONS

Prehabilitation is feasible before major surgery and achieves clinically meaningful improvements in functional performance that may impact postoperative outcomes and recovery. These data support rationale for a larger trial powered to detect differences in postoperative outcomes.

Tracking the source of contaminant lead in children's blood

Pb isotope ratios are used for apportioning the sources of Pb in the blood of children (ages 1-6) screened for high blood Pb levels (>5 μg/dL) surrounding urban areas of Kansas City, MO. We compared Pb isotope ratios measured in the child's blood with those of the most likely sources of Pb in that child's home environment. The environmental sources sampled consisted of topsoils, paints, occupational sources (e.g., oil rig workers' uniforms, mechanics' clothes), indoor air filters, dusts, and dietary sources (e.g., spices). Blood lead levels (BLL) ranged from 2.9 to 12.7 μg/dL in children from the five homes participating in this study. Measurements of ²⁰⁶Pb/²⁰⁴Pb, ²⁰⁷Pb/²⁰⁴Pb and ²⁰⁸Pb/²⁰⁴Pb isotope ratios were made by multi-collector ICP-MS. Comparison of the Pb isotope ratios in home environment samples versus those in the child's blood in each home allowed the identification of possible sources of a child's Pb exposure in three homes. In five homes investigated, children's blood Pb levels were most likely to be derived from dusts inside, and topsoil outside, the homes, or a mixture thereof. In one case, blood Pb was derived from turmeric spice and, in another, the Pb was derived from paint. It is not always possible to directly link high BLLs to the environmental sources collected when Pb isotope ratios of the environmental samples did not overlap with those of the blood.

Consensus guidelines for the diagnosis and management of invasive fungal disease due to moulds other than Aspergillus in the haematology/oncology setting, 2021

Invasive fungal disease (IFD) due to moulds other than Aspergillus is a significant cause of mortality in patients with malignancies or post haemopoietic stem cell transplantation. The current guidelines focus on the diagnosis and management of the common non-Aspergillus moulds (NAM), such as Mucorales, Scedosporium species (spp.), Lomentospora prolificans and Fusarium spp. Rare but emerging NAM including Paecilomyces variotii, Purpureocillium lilacinum and Scopulariopsis spp. are also reviewed. Culture and histological examination of tissue biopsy specimens remain the mainstay of diagnosis, but molecular methods are increasingly being used. As NAM frequently disseminate, blood cultures and skin examination with biopsy of any suspicious lesions are critically important. Treatment requires a multidisciplinary approach with surgical debridement as a central component. Other management strategies include control of the underlying disease/predisposing factors, augmentation of the host response and the reduction of immunosuppression. Carefully selected antifungal therapy, guided by susceptibility testing, is critical to cure. We also outline novel antifungal agents still in clinical trial which offer substantial potential for improved outcomes in the future. Paediatric recommendations follow those of adults. Ongoing epidemiological research, improvement in diagnostics and the development of new antifungal agents will continue to improve the poor outcomes that have been traditionally associated with IFD due to NAM.

Impact of telehealth in the outpatient management of atrial fibrillation during the COVID-19 pandemic

Background

The COVID-19 pandemic accelerated adoption of a telehealth model to replace outpatient visits. We studied quality indicators and clinical outcomes associated with virtual visits in comparison to in-person ambulatory visits for patients with atrial fibrillation (AF) seen by electrophysiology providers.

Methods

Quality indicators and outcomes for patients with primary diagnosis of AF seen by electrophysiology providers (6 physicians and 4 nurse practitioners) for the 12 week period of March 22–June 13, 2020 were compared with those from the 12 week period of March 24–June 15, 2019.

Result

We identified 2340 clinic visits for AF (1081 in 2019 and 1259 in 2020). Telehealth was not used in 2019, and was used in 90.5% of the 2020 visits. On multivariate analysis during 120 days following each encounter, there was no difference in hospital admissions between 2019 and 2020 (OR 0.89; 95% CI 0.69–1.14; p=0.3624), and there was trend towards lower emergency department visits in 2020 compared with 2019 (OR 0.77; 95% CI 0.6–1; p=0.0509). There were 36 deaths at 120 days, mortality was similar in 2020 as compared with 2019 (OR 1.5; 95% CI 0.74–3.03; p=0.2601). There was no difference in completed procedures including permanent pacemakers, cardiac resynchronization therapy devices, implantable cardioverter-defibrillators and catheter ablations. There was a significant difference in anticoagulant (OR 0.71; 95% CI 0.52–0.99; p=0.0412) and antiarrhythmic (OR 0.78; 95% CI 0.61–0.99; p=0.0384) dose adjustment or new prescriptions in 2019 compared with 2020.

Conclusion

Telehealth was associated with similar intermediate-term clinical outcomes when compared to traditional ambulatory encounters. However, adjusting or providing new prescriptions for anticoagulant or anti-arrhythmic medications was more common with in-person than with virtual visits.

Funding Acknowledgement

Type of funding sources: None.

Risk factors for candidaemia: A prospective multi-centre case-control study

OBJECTIVES

Candidaemia carries a mortality of up to 40% and may be related to increasing complexity of medical care. Here, we determined risk factors for the development of candidaemia.

METHODS

We conducted a prospective, multi-centre, case-control study over 12 months. Cases were aged ≥18 years with at least one blood culture positive for Candida spp. Each case was matched with two controls, by age within 10 years, admission within 6 months, admitting unit, and admission duration at least as long as the time between admission and onset of candidaemia.

RESULTS

A total of 118 incident cases and 236 matched controls were compared. By multivariate analysis, risk factors for candidaemia included neutropenia, solid organ transplant, significant liver, respiratory or cardiovascular disease, recent gastrointestinal, biliary or urological surgery, central venous access device, intravenous drug use, urinary catheter and carbapenem receipt.

CONCLUSIONS

Risk factors for candidaemia derive from the infection source, carbapenem use, host immune function and organ-based co-morbidities. Preventive strategies should target iatrogenic disruption of mucocutaneous barriers and intravenous drug use.

Hospital readmissions after catheter ablation for atrial fibrillation among patients with heart failure in the United States

Background

Catheter ablation for atrial fibrillation may improve quality of life and long-term mortality among patients with heart failure.

Purpose

The rates of hospital readmission after catheter ablation for atrial fibrillation among patients with an established diagnosis of heart failure are largely unknown. We aimed to assess the rates and causes of 30-day readmission among patients with heart failure undergoing catheter ablation vs. medical therapy for atrial fibrillation in the United States.

Methods

The 2016 Nationwide Readmissions Database was screened for patients with diagnosis of heart failure and atrial fibrillation using the 10th Revision of International Classification of Diseases codes. Patients undergoing catheter ablation for atrial fibrillation were grouped separately from those treated medically for atrial fibrillation. Thirty-day readmissions were assessed for both groups.

Results

The analytical cohort included 749,776 (national estimate of 1,421,673) patients with heart failure and atrial fibrillation. This included 2,204 patients that underwent catheter ablation. Patients treated with catheter ablation had lower 30-day readmissions compared to the medical therapy group (16.8% vs 20.1%, p<0.001). Fifty-five percent of all readmissions among the catheter ablation cohort were related to cardiac events. Heart failure exacerbation (40%) and arrhythmia (36%) were the most common cardiac causes for readmission after catheter ablation (Figure).

Conclusions

In a contemporary nationwide analysis of patients with heart failure and atrial fibrillation, compared to medical therapy those treated with catheter ablation for atrial fibrillation had fewer 30-day readmissions after index hospital discharge. The most common cause for readmission among patients treated with catheter ablation was heart failure exacerbation and arrhythmia.

Causes of readmission

Funding Acknowledgement

Type of funding source: None

The anti-ageing effects of a natural peptide discovered by artificial intelligence

OBJECTIVE

As skin ages, impaired extracellular matrix (ECM) protein synthesis and increased action of degradative enzymes manifest as atrophy, wrinkling and laxity. There is mounting evidence for the functional role of exogenous peptides across many areas, including in offsetting the effects of cutaneous ageing. Here, using an artificial intelligence (AI) approach, we identified peptide RTE62G (pep_RTE62G), a naturally occurring, unmodified peptide with ECM stimulatory properties. The AI-predicted anti-ageing properties of pep_RTE62G were then validated through in vitro, ex vivo and proof of concept clinical testing.

METHODS

A deep learning approach was applied to unlock pep_RTE62G from a plant source, Pisum sativum (pea). Cell culture assays of human dermal fibroblasts (HDFs) and keratinocytes (HaCaTs) were subsequently used to evaluate the in vitro effect of pep_RTE62G. Distinct activities such as cell proliferation and ECM protein production properties were determined by ELISA assays. Cell migration was assessed using a wound healing assay, while ECM protein synthesis and gene expression were analysed, respectively, by immunofluorescence microscopy and PCR. Immunohistochemistry of human skin explants was employed to further investigate the induction of ECM proteins by pep_RTE62G ex vivo. Finally, the clinical effect of pep_RTE626 was evaluated in a proof of concept 28-day pilot study.

RESULTS

In vitro testing confirmed that pep_RTE62G is an effective multi-functional anti-ageing ingredient. In HaCaTs, pep_RTE62G treatment significantly increases both cellular proliferation and migration. Similarly, in HDFs, pep_RTE62G consistently induced the neosynthesis of ECM protein elastin and collagen, effects that are upheld in human skin explants. Lastly, in our proof of concept clinical study, application of pep_RTE626 over 28 days demonstrated anti-wrinkle and collagen stimulatory potential.

CONCLUSION

pep_RTE62G represents a natural, unmodified peptide with AI-predicted and experimentally validated anti-ageing properties. Our results affirm the utility of AI in the discovery of novel, functional topical ingredients.

Gas Chromatographic Method for Putrescine and Cadaverine in Canned Tuna and Mahimahi and Fluorometric Method for Histamine (Minor Modification of AOAC Official Method 977.13): Collaborative Study

A collaborative study was conducted to test a modification to the AOAC fluorometric method for histamine (AOAC® Official Method 977.13) that substitutes 75% methanol as the extracting solvent. All other steps remain unchanged. The extracts prepared with 75% methanol were also used to collaboratively test a gas chromatographic (GC) method for determination of putrescine and cadaverine in seafood. In the GC method, the extracted diamines are converted to fluorinated derivatives, the reaction mixtures are passed through solid-phase extraction columns, and the derivatives are quantitated by electron capture GC after separation on an OV-225 column. Fourteen laboratories using the GC method for putrescine and cadaverine and 16 laboratories using the fluorometric method for histamine analyzed 14 canned tuna and raw mahimahi (including blind duplicates and a spike) containing 0.2-2.6 ppm putrescine, 0.6-9.1 ppm cadaverine, and 0.6-154 ppm histamine. At the 5 ppm level, recoveries ranged from 71 to 102% for putrescine and 77 to 112% for cadaverine; the respective repeatability relative standard deviations (RSDr) were 5.2 and 15%, and the respective reproducibility relative standard deviations (RSDR) were 8.8 and 18%. At the 50 ppm level, histamine recoveries ranged from 84 to 125%, RSDr was 3.6%, and RSDR was 9.4%. The GC method for determination of putrescine in canned tuna and cadaverine in canned tuna and mahimahi has been adopted first action by AOAC INTERNATIONAL, and the AOAC Official Method 977.13, Histamine in Seafood, Fluorometric Method, has been modified

Short-read fastA files dataset from complexity-reduced genotyping by sequencing data of bacterial isolates from a public hospital in Australia

This data article contains short-read sequences (length 30-69 bp) obtained from complexity-reduced genotyping by sequencing (GBS) of 165 samples bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015. These samples represented 14 bacterial species. Data format is shown as filtered fastA files obtained from an Illumina HiSeq2500 sequencer. The experimental factors of this research used three complexity reduction methods with three combinations of restriction enzymes: PstI with MseI, PstI with HpaII and MseI with HpaII.

Candidaemia and a risk predictive model for overall mortality: a prospective multicentre study

Background

Candidaemia is associated with high mortality. Variables associated with mortality have been published previously, but not developed into a risk predictive model for mortality. We sought to describe the current epidemiology of candidaemia in Australia, analyse predictors of 30-day all-cause mortality, and develop and validate a mortality risk predictive model.

Methods

Adults with candidaemia were studied prospectively over 12 months at eight institutions. Clinical and laboratory variables at time of blood culture-positivity were subject to multivariate analysis for association with 30-day all-cause mortality. A predictive score for mortality was examined by area under receiver operator characteristic curves and a historical data set was used for validation.

Results

The median age of 133 patients with candidaemia was 62 years; 76 (57%) were male and 57 (43%) were female. Co-morbidities included underlying haematologic malignancy (n = 20; 15%), and solid organ malignancy in (n = 25; 19%); 55 (41%) were in an intensive care unit (ICU). Non-albicans Candida spp. accounted for 61% of cases (81/133). All-cause 30-day mortality was 31%. A gastrointestinal or unknown source was associated with higher overall mortality than an intravascular or urologic source (p < 0.01). A risk predictive score based on age > 65 years, ICU admission, chronic organ dysfunction, preceding surgery within 30 days, haematological malignancy, source of candidaemia and antibiotic therapy for ≥10 days stratified patients into < 20% or ≥ 20% predicted mortality. The model retained accuracy when validated against a historical dataset (n = 741).

Conclusions

Mortality in patients with candidaemia remains high. A simple mortality risk predictive score stratifying patients with candidaemia into < 20% and ≥ 20% 30-day mortality is presented. This model uses information available at time of candidaemia diagnosis is easy to incorporate into decision support systems. Further validation of this model is warranted.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4065-5) contains supplementary material, which is available to authorized users.

Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping

Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.

Whole Genome Sequencing of Australian Candida glabrata Isolates Reveals Genetic Diversity and Novel Sequence Types

Candida glabrata is a pathogen with reduced susceptibility to azoles and echinocandins. Analysis by traditional multilocus sequence typing (MLST) has recognized an increasing number of sequence types (STs), which vary with geography. Little is known about STs of C. glabrata in Australia. Here, we utilized whole genome sequencing (WGS) to study the genetic diversity of 51 Australian C. glabrata isolates and sought associations between STs over two time periods (2002-2004, 2010-2017), and with susceptibility to fluconazole by principal component analysis (PCA). Antifungal susceptibility was determined using Sensititre YeastOne^TM Y010 methodology and WGS performed on the NextSeq 500 platform (Illumina) with in silico MLST STs inferred by WGS data. Single nucleotide polymorphisms (SNPs) in genes linked to echinocandin, azole and 5-fluorocytosine resistance were analyzed. Of 51 isolates, WGS identified 18 distinct STs including four novel STs (ST123, ST124, ST126, and ST127). Four STs accounted for 49% of isolates (ST3, 15.7%; ST83, 13.7%; ST7, 9.8%; ST26, 9.8%). Split-tree network analysis resolved isolates to terminal branches; many of these comprised multiple isolates from disparate geographic settings but four branches contained Australian isolates only. ST3 isolates were common in Europe, United States and now Australia, whilst ST8 and ST19, relatively frequent in the United States, were rare/absent amongst our isolates. There was no association between ST distribution (genomic similarity) and the two time periods or with fluconazole susceptibility. WGS identified mutations in the FKS1 (S629P) and FKS2 (S663P) genes in three, and one, echinocandin-resistant isolate(s), respectively. Both mutations confer phenotypic drug resistance. Twenty-five percent (13/51) of isolates were fluconazole-resistant (MIC ≥ 64 μg/ml) of which 9 (18%) had non wild-type MICs to voriconazole and posaconazole. Multiple SNPs were present in genes linked to azole resistance such as CgPDR1 and CgCDR1, as well as several in MSH2; however, SNPs occurred in both azole-susceptible and azole-resistant isolates. Although no particular SNP in these genes was definitively associated with resistance, azole-resistant/non-wild type isolates had a propensity to harbor SNPs resulting in amino acid substitutions in Pdr1 beyond the first 250 amino acid positions. The presence of SNPs may be markers of STs. Our study shows the value of WGS for high-resolution sequence typing of C. glabrata, discovery of novel STs and potential to monitor trends in genetic diversity. WGS assessment for echinocandin resistance augments phenotypic susceptibility testing.

Chlorhexidine washing in intensive care does not reduce bloodstream infections, blood culture contamination and drug-resistant microorganism acquisition: an interrupted time series analysis

BACKGROUND

Health care-associated infections are a major cause of morbidity and mortality in intensive care patients. The effect of daily washing with chlorhexidine on these infections is controversial.

METHODS

Single-centre, retrospective, open-label, sequential period, interrupted time series (ITS) analysis in a 31-bed tertiary referral mixed intensive care unit (ICU), comparing daily washing with water and soap (from January 2011 to August 2013) with chlorhexidine washing (from November 2013 to December 2015), after the introduction of a unit-level policy of chlorhexidine washing. All patients in the ICU were included in the study, except: if they were under 18 years of age, if their ICU stay was less than 24 hours (to ensure that all studied patients had at least one exposure to the daily wash intervention), or if patients had a known allergy to chlorhexidine. Outcome measures included: clinically significant positive blood cultures attributable to the ICU stay; contaminated blood cultures; newly acquired multidrug-resistant microorganisms (MDRO) such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococcus (VRE) or multidrug-resistant gram-negative (MRGN) isolates attributable to ICU from clinical and screening cultures; and newly acquired Clostridium difficile infections (CDIs). Incidence rates of these outcomes were calculated per 1000 patient days. MDRO acquisition rates were corrected for background hospital period prevalence rates of MDRO.

RESULTS

A total of 6634 patients were included in the study. ITS analysis showed no significant level or slope changes in any of the outcome measures after implementation of chlorhexidine washing. The incidence rate of clinically significant positive blood cultures during the chlorhexidine period compared with the water and soap period was 3.6 v 4.7 (P =0.37); blood culture contamination rates were 11.8 v 9.5 (P =0.56); incidence rates of new ICU-associated MDRO acquisitions were 3.22 v 3.69 (P =0.27); incidence rates of new CDI were 2.01 v 0.79 (P =0.16). Outcomes after adjustment for known and potential confounders were similar.

CONCLUSIONS

In this real-world, long term ICU study, implementation of a unit-level policy of daily washing with chlorhexidine impregnated cloths was not associated with a reduction in the rates of ICU-associated clinically significant positive blood cultures, blood culture contamination, newly acquired MDRO isolates, and CDIs.

Point Prevalence of Adult Intestinal Failure in Republic Of Ireland

Parenteral Nutrition (PN) is a life-saving treatment used for patients with Intestinal Failure (IF). PN is complex and demands highly specialised care to avoid serious complications in the home setting. All tertiary centres in the Republic of Ireland (ROI) were contacted to assess the prevalence of IF requiring PN and complications, over a one year period. Sixty-seven patients were treated across 15 centres: a period prevalence of 14.6 and 9.6 patients per million for long-term PN and home PN respectively. Three-quarters of patients experienced at least one major complication with 18% mortality rate over the study period. There were 2.86 admissions per HPN patient, each lasting mean 13.4 days. One-third experienced catheter-related infections. There was a reduced length of stay during emergency re-admissions in high volume centres (mean 31 v 43 days, p=0.17). The establishment of a National Centre for IF/HPN in ROI is integral to reducing PN-associated complications.

Factors affecting the presence, genetic diversity and antimicrobial sensitivity of Escherichia coli in poultry meat samples collected from Canberra, Australia

To investigate the factors determining the clonal composition of Escherichia coli in poultry meat samples, 306 samples were collected from 16 shops, representing three supermarket chains and an independent butchery located in each of the four town centers of Canberra, Australia, during the summer, autumn and winter. A total of 3415 E. coli isolates were recovered and assigned to a phylogenetic group using the Clermont quadruplex PCR method, fingerprinted using repetitive element palindromic (REP) PCR and screened for their antimicrobial susceptibility profiles. The probability of detecting E. coli and the number of fingerprint types detected per sample, as well as the phylogroup membership of the isolates and their antimicrobial sensitivity profiles varied, with one or more of retailer, store, meat type, season and husbandry. The results of this study demonstrate that poultry meat products are likely to be contaminated with a genetically diverse community of E. coli and suggest that factors relating to the nature of the meat product and distribution chain are determinants of the observed diversity.

Changing epidemiology of candidaemia in Australia

Objectives

Knowledge of contemporary epidemiology of candidaemia is essential. We aimed to identify changes since 2004 in incidence, species epidemiology and antifungal susceptibilities of Candida spp. causing candidaemia in Australia.

Methods

These data were collected from nationwide active laboratory-based surveillance for candidaemia over 1 year (within 2014-2015). Isolate identification was by MALDI-TOF MS supplemented by DNA sequencing. Antifungal susceptibility testing was performed using Sensititre YeastOne™.

Results

A total of 527 candidaemia episodes (yielding 548 isolates) were evaluable. The mean annual incidence was 2.41/105 population. The median patient age was 63 years (56% of cases occurred in males). Of 498 isolates with confirmed species identity, Candida albicans was the most common (44.4%) followed by Candida glabrata complex (26.7%) and Candida parapsilosis complex (16.5%). Uncommon Candida species comprised 25 (5%) isolates. Overall, C. albicans (>99%) and C. parapsilosis (98.8%) were fluconazole susceptible. However, 16.7% (4 of 24) of Candida tropicalis were fluconazole- and voriconazole-resistant and were non-WT to posaconazole. Of C. glabrata isolates, 6.8% were resistant/non-WT to azoles; only one isolate was classed as resistant to caspofungin (MIC of 0.5 mg/L) by CLSI criteria, but was micafungin and anidulafungin susceptible. There was no azole/echinocandin co-resistance.

Conclusions

We report an almost 1.7-fold proportional increase in C. glabrata candidaemia (26.7% versus 16% in 2004) in Australia. Antifungal resistance was generally uncommon, but azole resistance (16.7% of isolates) amongst C. tropicalis may be emerging.

A combined reed bed/freezing bed technology for septage treatment and reuse in cold climate regions

A combined reed bed-freezing bed (RB-FB) technology was effective at treating septage under Canadian climatic conditions over a 5-year period with average loading rates of 82-104 kg TS/m²/y. Varying hydraulic and solid loading rates as well as the increasing sludge cake with time had little to no effect on treatment efficiency, with almost complete removal of organic matter, solids, heavy metals and nutrients. Filtrate concentrations varied significantly between the freeze-thaw and growing seasons for many parameters, although the differences were not important from a treatment or reuse perspective with filtrate quality similar to a low to medium strength domestic wastewater. The potential to reuse the filtrate as a source of irrigation water will depend upon local regulations. The dewatered sludge cake consistently met biosolids land application standards in terms of pathogen and metals content, with Escherichia coli numbers declining with time as sludge cake depth increased. A combined RB-FB technology can provide a cost-effective solution for septage management in northern rural communities with potential for beneficial reuse of both the filtrate and dewatered sludge cake.

Identification of genetic markers of resistance to echinocandins, azoles and 5-fluorocytosine in Candida glabrata by next-generation sequencing: a feasibility study

OBJECTIVES

Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next-generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata.

METHODS

The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne^® YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs. Single nucleotide polymorphisms (SNPs) in genes known to be linked to echinocandin, azole and 5-fluorocytosine resistance were analysed in all isolates through NGS.

RESULTS

High-quality non-synonymous SNPs in antifungal resistance genes such as FKS1, FKS2, CgCDR1, CgPDR1 and FCY2 were identified. For two of three isolate pairs, there was a >60-fold rise in MICs to all echinocandins in the second isolate from each pair; one echinocandin-resistant isolate harboured a mutation in FKS1 (S629P) and the other in FKS2 (S663P). Of the third pair, both the 5-fluorocytosine-susceptible, and resistant isolates had a mutation in FCY2 (A237T). SNPs in CgPDR1 were found in pan-azole-resistant isolates. SNPs in other genes linked to azole resistance (CgCDR1, ERG9 and CgFLR1) were present in both azole-susceptible and azole-resistant isolates. SNPs were also identified in Candida adhesin genes EPA1, EPA6, PWP2 and PWP5 but their presence was not associated with higher drug MICs.

CONCLUSIONS

Genome-wide analysis of antifungal resistance markers was feasible and simultaneously revealed mutation patterns of genes implicated in resistance to different antifungal drug classes.

The impact of providing blood to the scene of an accident on transfusion laboratory practice

BACKGROUND

Haemorrhage is the leading cause of mortality during trauma. In 2012, London's Air Ambulance introduced Blood on Board (BOB), transfusing group O red cells (RBC) to trauma patients at the scene.

OBJECTIVES

This study assessed the impact of BOB on the number of mixed field samples received by the laboratory, the number of group O RBC transfused to non-group O patients and the ratio of RBC to fresh frozen plasma (FFP) transfused in the initial 24 h.

METHODS

Three major trauma centres collected data on patients for whom the major haemorrhage protocol was activated between August 2008 and February 2012 pre-BOB and March 2012 and December 2013 post-BOB.

RESULTS

A total of 233 trauma patients were identified pre-BOB and 119 post-BOB. There was no significant difference in the percentage of group O units transfused to non-group O patients (75 vs 82%, P = 0·21) or the RBC : FFP ratio (pre-BOB mean 1·6 [interquartile range (IQR) 1·0-2·0]; post-BOB mean 1·7 [IQR 1·1-2·2], P = 0·24). There was no significant difference in the percentage of mixed field samples received (23% vs 27%, P = 0·3).

CONCLUSION

The introduction of BOB did not change the proportion of group O RBC transfused or the RBC : FFP ratio; however, the proportion of acceptable samples decreased. This is largely due to an increase in blood samples not received from the post-BOB cohort, which we believe is probably due to patients who died at the scene. We have introduced robust systems to indicate reasons for not obtaining samples.