Whole genomes from bacteria collected at diagnostic units around the world 2020

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Restricting access to antibiotics: The effectiveness of a 'no repeats' government policy intervention

BACKGROUND

Australia has a high rate of antibiotic use. Government policy interventions are one strategy to optimise the use of antibiotics. On 1 April 2020, the Australian Government Department of Health introduced a policy intervention to increase the quality use of four antibiotics.

OBJECTIVES

To assess if the government policy intervention improved the appropriate supply of the four antibiotics amoxicillin, amoxicillin-clavulanic acid, cefalexin and roxithromycin.

METHOD

This study employed a retrospective cohort study design comparing a 10% sample (n = 345,018) of four antibiotics prescribed and dispensed in Australia during a three-month period (May, June, July) in 2019, and again in 2020 (after the policy intervention). The 10% sample of PBS data was obtained from the Australian Government Department of Health. Descriptive statistics, bivariate and multivariable logistic regression analysis were carried out.

RESULTS

The results suggest the policy change improved the appropriate supply of original prescriptions in 2020 compared to 2019 OR = 1.75 (95% CI = 1.68-1.82, p < 0.001), and appropriate supply of repeat prescriptions OR = 1.56 (95% CI = 1.25-1.96, p < 0.001). In 2020, the proportion of appropriate supply of original prescriptions increased by an absolute difference of 1.8% (95% CI = 1.6-1.9%; P < 0.001), and appropriate supply of repeat prescriptions increased by 3.9% (95% CI = 2.2-5.5%; P < 0.001). The total number of antibiotic prescriptions prescribed and dispensed in 2019 (N = 219,960) reduced in 2020 (N = 125,058) after the policy intervention.

CONCLUSION

The study provides evidence for the impact of a government policy intervention to improve the appropriate supply of antibiotics, although some of the reduction in antibiotic use was likely due to the concomitant COVID-19 pandemic. Further research is required to assess the impact of the intervention outside a pandemic.

Key lessons from the COVID-19 public health response in Australia

Australia avoided the worst effects of the COVID-19 pandemic, but still experienced many negative impacts. Reflecting on lessons from Australia's public health response, an Australian expert panel composed of relevant discipline experts identified the following key lessons: 1) movement restrictions were effective, but their implementation requires careful consideration of adverse impacts, 2) disease modelling was valuable, but its limitations should be acknowledged, 3) the absence of timely national data requires re-assessment of national surveillance structures, 4) the utility of advanced pathogen genomics and novel vaccine technology was clearly demonstrated, 5) decision-making that is evidence informed and consultative is essential to maintain trust, 6) major system weaknesses in the residential aged-care sector require fixing, 7) adequate infection prevention and control frameworks are critically important, 8) the interests and needs of young people should not be compromised, 9) epidemics should be recognised as a 'standing threat', 10) regional and global solidarity is important. It should be acknowledged that we were unable to capture all relevant nuances and context specific differences. However, the intent of this review of Australia's public health response is to critically reflect on key lessons learnt and to encourage constructive national discussion in countries across the Western Pacific Region.

An Old Defence Against New Infections: The Open-Air Factor and COVID-19

Outdoors, the risks of transmission of COVID-19 and many other respiratory infections are low. Several environmental factors are known to reduce the viability of viruses and other infectious pathogens in the air. They include variations in temperature, relative humidity, solar ultraviolet radiation, and dilution effects. But one agent that reduces the viability of both viruses and bacteria outdoors, the germicidal open-air factor (OAF), has not been properly recognized for decades. This is despite robust evidence that the OAF can influence both the survival of airborne pathogens and the course of infections.

The germicidal effects of outdoor air were widely exploited during the late 19th and early 20th centuries. Firstly, in the treatment of tuberculosis patients who underwent 'open-air therapy' in sanatoria; and secondly by military surgeons during the First World War. They used the same open-air regimen in specially designed hospital wards to disinfect and heal severe wounds among injured soldiers. It was also used on influenza patients during the 1918-19 pandemic. Later, in the 1950s, open-air disinfection and treatment of burns were proposed in the event of nuclear warfare. During the 1960s, the OAF briefly returned to prominence when biodefence scientists conducted experiments proving that open air has a potent germicidal effect. When this work ended in the 1970s, interest in the OAF again fell away, and it remains largely ignored.

The COVID-19 pandemic has revived interest in understanding the transmission dynamics and survival of viruses in the air. The pandemic has also stimulated research in the science and practice of improved ventilation to control respiratory infections. Such work is incomplete without an appreciation of the inactivation of viruses and other pathogens by the OAF, but this needs further investigation as a matter of urgency. Research to better understand the conditions under which the OAF can be preserved indoors is urgently needed. We need to review building design with better regard to infection control and patient recovery. But we need to act without delay, as there is already sufficient evidence to show that public health generally would improve if more emphasis was placed on increased exposure to outdoor air.

Increasing incidence and antimicrobial resistance in Escherichia coli bloodstream infections: a multinational population-based cohort study

BACKGROUND

Escherichia coli is an important pathogen in humans and is the most common cause of bacterial bloodstream infections (BSIs). The objectives of our study were to determine factors associated with E. coli BSI incidence rate and third-generation cephalosporin resistance in a multinational population-based cohort.

METHODS

We included all incident E. coli BSIs (2014-2018) from national (Finland) and regional (Australia [Canberra], Sweden [Skaraborg], and Canada [Calgary, Sherbrooke, and western interior]) surveillance. Incidence rates were directly age and sex standardized to the European Union 28-country 2018 population. Multivariable negative binomial and logistic regression models estimated factors significantly associated with E. coli BSI incidence rate and third-generation cephalosporin resistance, respectively. The explanatory variables considered for inclusion in both models were year (2014-2018), region (six areas), age (< 70-years-old and ≥ 70-years-old), and sex (female and male).

RESULTS

We identified 31,889 E. coli BSIs from 40.7 million person-years of surveillance. Overall and third-generation cephalosporin-resistant standardized rates were 87.1 and 6.6 cases/100,000 person-years, respectively, and increased 14.0% and 40.1% over the five-year study. Overall, 7.8% (2483/31889) of E. coli BSIs were third-generation cephalosporin-resistant. Calgary, Canberra, Sherbrooke, and western interior had significantly lower E. coli BSI rates compared to Finland. The significant association between age and E. coli BSI rate varied with sex. Calgary, Canberra, and western interior had significantly greater odds of third-generation cephalosporin-resistant E. coli BSIs compared to Finland. Compared to 2014, the odds of third-generation cephalosporin-resistant E. coli BSIs were significantly increased in 2016, 2017, and 2018. The significant association between age and the odds of having a third-generation cephalosporin-resistant E. coli BSI varied with sex.

CONCLUSIONS

Increases in overall and third-generation cephalosporin-resistant standardized E. coli BSI rates were clinically important. Overall, E. coli BSI incidence rates were 40-104% greater than previous investigations from the same study areas. Region, sex, and age are important variables when analyzing E. coli BSI rates and third-generation cephalosporin resistance in E. coli BSIs. Considering E. coli is the most common cause of BSIs, this increasing burden and evolving third-generation cephalosporin resistance will have an important impact on human health, especially in aging populations.

Mortality in Escherichia coli bloodstream infections: a multinational population-based cohort study

Background

Escherichia coli is the most common cause of bloodstream infections (BSIs) and mortality is an important aspect of burden of disease. Using a multinational population-based cohort of E. coli BSIs, our objectives were to evaluate 30-day case fatality risk and mortality rate, and determine factors associated with each.

Methods

During 2014–2018, we identified 30-day deaths from all incident E. coli BSIs from surveillance nationally in Finland, and regionally in Sweden (Skaraborg) and Canada (Calgary, Sherbrooke, western interior). We used a multivariable logistic regression model to estimate factors associated with 30-day case fatality risk. The explanatory variables considered for inclusion were year (2014–2018), region (five areas), age (< 70-years-old, ≥70-years-old), sex (female, male), third-generation cephalosporin (3GC) resistance (susceptible, resistant), and location of onset (community-onset, hospital-onset). The European Union 28-country 2018 population was used to directly age and sex standardize mortality rates. We used a multivariable Poisson model to estimate factors associated with mortality rate, and year, region, age and sex were considered for inclusion.

Results

From 38.7 million person-years of surveillance, we identified 2961 30-day deaths in 30,923 incident E. coli BSIs. The overall 30-day case fatality risk was 9.6% (2961/30923). Calgary, Skaraborg, and western interior had significantly increased odds of 30-day mortality compared to Finland. Hospital-onset and 3GC-resistant E. coli BSIs had significantly increased odds of mortality compared to community-onset and 3GC-susceptible. The significant association between age and odds of mortality varied with sex, and contrasts were used to interpret this interaction relationship. The overall standardized 30-day mortality rate was 8.5 deaths/100,000 person-years. Sherbrooke had a significantly lower 30-day mortality rate compared to Finland. Patients that were either ≥70-years-old or male both experienced significantly higher mortality rates than those < 70-years-old or female.

Conclusions

In our study populations, region, age, and sex were significantly associated with both 30-day case fatality risk and mortality rate. Additionally, 3GC resistance and location of onset were significantly associated with 30-day case fatality risk. Escherichia coli BSIs caused a considerable burden of disease from 30-day mortality. When analyzing population-based mortality data, it is important to explore mortality through two lenses, mortality rate and case fatality risk.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06326-x.

COVID-19 and future pandemics: is isolation and social distancing the new norm?

The coronavirus, named SARS‐CoV‐2, is the cause of COVID‐19. This virus spreads readily from person to person and predominantly to and from the respiratory route and through droplets. There are many different interventions that can be and are used to decrease successfully the risk and spread of COVID‐19. Most of the principles underpinning these interventions relate to isolation and social distancing. These will need to be continued, at least in part, until safe and very effective vaccines become widely available and are delivered extensively and successfully globally. This new norm is isolation, plus social and physical distancing, and this new norm will likely be with us for some time to come. It will also be with us in any future pandemics, whether caused by bacteria or viruses, but especially when the causative pathogen spreads predominantly through the respiratory route. However, lockdowns and restrictions also cause many adverse but unintended economic, social and health consequences. Therefore, what is put into place needs to be proportionate to levels of risk of disease as well as spread, and which will vary in different localities and with time.

Identification and characterisation of fosfomycin resistance in Escherichia coli urinary tract infection isolates from Australia

Of 1033 Escherichia coli urinary tract infection isolates collected from females >12 years of age in Australia in 2019, only 2 isolates were resistant to fosfomycin with a minimum inhibitory concentration (MIC) of >256 mg/L. Despite having different multilocus sequence types, the two isolates harboured an identical plasmid-encoded fosA4 gene. The fosA4 gene has previously been identified in a single clinical E. coli isolate cultured in Japan in 2014. Each fosfomycin-resistant isolate harboured two conjugative plasmids that possessed an array of genes conferring resistance to aminoglycosides, β-lactams, macrolides, quinolones, sulfonamides and/or trimethoprim.

CON: COVID-19 will not result in increased antimicrobial resistance prevalence

Antimicrobial resistance (AMR) is affected by many factors, but too much of our focus has been on antimicrobial usage. The major factor that drives resistance rates globally is spread. The COVID-19 pandemic should lead to improved infection prevention and control practices, both in healthcare facilities and the community. COVID-19 will also have ongoing and profound effects on local, national and international travel. All these factors should lead to a decrease in the spread of resistant bacteria. So overall, COVID-19 should lead to a fall in resistance rates seen in many countries. For this debate we show why, overall, COVID-19 will not result in increased AMR prevalence. But globally, changes in AMR rates will not be uniform. In wealthier and developed countries, resistance rates will likely decrease, but in many other countries there are already too many factors associated with poor controls on the spread of bacteria and viruses (e.g. poor water and sanitation, poor public health, corrupt government, inadequate housing, etc.). In these countries, if economies and governance deteriorate further, we might see even more transmission of resistant bacteria.

Not sick enough to worry? "Influenza-like" symptoms and work-related behavior among healthcare workers and other professionals: Results of a global survey

BACKGROUND

Healthcare workers (HCWs) and non-HCWs may contribute to the transmission of influenza-like illness (ILI) to colleagues and susceptible patients by working while sick (presenteeism). The present study aimed to explore the views and behavior of HCWs and non-HCWs towards the phenomenon of working while experiencing ILI.

METHODS

The study was a cross-sectional online survey conducted between October 2018 and January 2019 to explore sickness presenteeism and the behaviour of HCWs and non-HCWs when experiencing ILI. The survey questionnaire was distributed to the members and international networks of the International Society of Antimicrobial Chemotherapy (ISAC) Infection Prevention and Control (IPC) Working Group, as well as via social media platforms, including LinkedIn, Twitter and IPC Blog.

RESULTS

In total, 533 respondents from 49 countries participated (Europe 69.2%, Asia-Pacific 19.1%, the Americas 10.9%, and Africa 0.8%) representing 249 HCWs (46.7%) and 284 non-HCWs (53.2%). Overall, 312 (58.5%; 95% confidence interval [CI], 56.2-64.6) would continue to work when sick with ILI, with no variation between the two categories. Sixty-seven (26.9%) HCWs and forty-six (16.2%) non-HCWs would work with fever alone (p<0 .01) Most HCWs (89.2-99.2%) and non-HCWs (80%-96.5%) would work with "minor" ILI symptoms, such as sore throat, sinus cold, fatigue, sneezing, runny nose, mild cough and reduced appetite.

CONCLUSION

A future strategy to successfully prevent the transmission of ILI in healthcare settings should address sick-leave policy management, in addition to encouraging the uptake of influenza vaccine.

Risk factors for acquisition of multidrug-resistant Enterobacterales among international travellers: a synthesis of cumulative evidence

BACKGROUND

Recent studies have shown that over 50% of people travelling to Southeast Asia return colonized with multidrug-resistant Enterobacterales (MRE) including carbapenemase-producing Enterobacterales. Importation of MRE by travellers and subsequent spread to family members, communities and healthcare facilities poses real risks that have not yet been adequately assessed. This systematic review and meta-analysis aims to quantify the risk factors and interventions for reducing the risk of MRE acquisition among international travellers.

METHODS

A systematic search was conducted in PubMed, Web of Science and Scopus for analytical epidemiological studies containing data post-2000 that assessed the risk factors to acquire and/or interventions to reduce the risk of MRE acquisition in travellers. Two researchers independently screened all the studies and extracted the information, and disagreements were resolved through consensus. The proportions of MRE acquisition by the region of destination and the odds ratio (OR) for the different risk factors and/or interventions were pooled using the inverse variance heterogeneity model.

RESULTS

A total of 20 studies (5253 travellers from high-income countries) were included in the meta-analysis. South Asia [58.7%; 95% confidence interval (CI), 44.5-72.5%] and Northern Africa (43.9%; 95% CI 37.6-50.3%) were the travel destinations with the highest proportion of MRE acquisition. Inflammatory bowel disease (OR 2.1; 95% CI 1.2-3.8), use of antibiotics (OR 2.4; 95% CI 1.9-3.0), traveller's diarrhoea (OR 1.7; 95% CI 1.3-2.3) and contact with the healthcare system overseas (OR 1.5; 95% CI 1.1-2.2) were associated with MRE colonization. Vegetarians (OR 1.4; 95% CI 1.0-2.0) and backpackers (OR 1.5; 95% CI 1.2-1.8) were also at increased odds of MRE colonization. Few studies (n = 6) investigated preventive measures and found that consuming only bottled water/beverages, meticulous hand hygiene and probiotics had no protective effect on MRE colonization.

CONCLUSIONS

International travel is an important driver for MRE spread worldwide. Future research needs to identify effective interventions to reduce the risk of MRE acquisition as well as design strategies to reduce local transmission on return.

'Antibiotic footprint' as a communication tool to aid reduction of antibiotic consumption

'Superbugs', bacteria that have become resistant to antibiotics, have been in numerous media headlines, raising awareness of antibiotic resistance and leading to multiple action plans from policymakers worldwide. However, many commonly used terms, such as 'the war against superbugs', risk misleading people to request 'new' or 'stronger' antibiotics from their doctors, veterinary surgeons or pharmacists, rather than addressing a fundamental issue: the misuse and overuse of antibiotics in humans and animals. Simple measures of antibiotic consumption are needed for mass communication. In this article, we describe the concept of the 'antibiotic footprint' as a tool to communicate to the public the magnitude of antibiotic use in humans, animals and industry, and how it could support the reduction of overuse and misuse of antibiotics worldwide. We propose that people need to make appropriate changes in behaviour that reduce their direct and indirect consumption of antibiotics.

Socioeconomic Enablers for Contagion: Factors Impelling the Antimicrobial Resistance Epidemic

Antimicrobial resistance is a growing global problem that causes increased deaths as well as increased suffering for people. Overall, there are two main factors that drive antimicrobial resistance: the volumes of antimicrobials used and the spread of resistant micro-organisms along with the genes encoding for resistance. Importantly, a growing body of evidence points to contagion (i.e., spread) being the major, but frequently under-appreciated and neglected, factor driving the increased prevalence of antimicrobial resistance. When we aggregate countries into regional groupings, it shows a pattern where there is an inverse aggregate relationship between AMR and usage. Poor infrastructure and corruption levels, however, are highly and positively correlated with antimicrobial resistance levels. Contagion, antibiotic volumes, governance, and the way antibiotics are used are profoundly affected by a host of social and economic factors. Only after we identify and adequately address these factors can antimicrobial resistance be better controlled.

Chlorhexidine versus saline in reducing the risk of catheter associated urinary tract infection: A cost-effectiveness analysis

BACKGROUND

Catheter associated urinary tract infections are one of the most common infections acquired in hospital. A recent randomised control study demonstrated the benefit of using chlorhexidine (0.1%) for meatal cleaning prior to urinary catheter insertion, by reducing both catheter associated asymptomatic bacteriuria and infection. These findings raise the important question of whether a decision to switch from saline to chlorhexidine was likely to be cost-effective. The aim of this paper was to evaluate the cost-effectiveness of adopting routine use of chlorhexidine for meatal cleaning prior to urinary catheter insertion METHODS: The outcomes of this cost-effectiveness study are changes to health service costs in $AUD and changes to quality adjusted life years from a decision to adopt 0.1% chlorhexidine for meatal cleaning prior to urinary catheter insertion as compared to saline. Effectiveness outcomes for this study were taken from a 32 week stepped wedge randomised controlled study conducted in three Australian hospitals.

RESULTS

The changes in health costs from switching from saline to 0.1% chlorhexidine per 100,000 catheterisations would save hospitals AUD$387,909 per 100,000 catherisations, prevent 70 cases of catheter associated urinary tract infections, release 282 bed days and provide a small improvement in health benefits of 1.43 quality adjusted life years. Using a maximum willingness to pay for a marginal quality adjusted life year threshold of AUD$28,000 per 100,000 catherisations, suggests that adopting chlorhexidine would be cost effective and potentially cost-saving.

CONCLUSION

The findings from our work provide evidence to health system administrators and those responsible for drafting catheter associated urinary tract infections prevention guidelines that investing in switching from saline to chlorhexidine is not only clinically effective but also a sensible decision in the context of allocating finite healthcare resources.

Incidence of single-drug resistant, multidrug-resistant and extensively drug-resistant Escherichia coli urinary tract infections: An Australian laboratory-based retrospective study

OBJECTIVES

The aim of this study was to evaluate the incidence of single-drug resistant, multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) Escherichia coli urinary tract infections (UTIs) in a sample of Australian Capital Territory (ACT) residents.

METHODS

Laboratory-based retrospective data from all ACT residents whose urine samples were processed from January 2009 to December 2013 at ACT Pathology were utilised. Multivariate logistic regression models were constructed to determine the associations of age, sex, urine sample source and socioeconomic status with risk of resistant infections.

RESULTS

A total of 146 915 urine samples from 57 837 ACT residents were identified over 5 years. The mean±standard deviation age of residents at first sample submitted was 48±26years, and 64.4% were female. The 5-year incidence of single-drug resistant E. coli UTI was high for ampicillin, trimethoprim and cefazolin (6.8%, 3.5% and 1.9%, respectively). No PDR E. coli UTI was detected. Five-year incidences of MDR and XDR E. coli UTIs were 1.9% and 0.2%, respectively, which is low in comparison with international rates. Female sex and age ≥38 years were significantly associated with single-drug and multidrug resistance. The risk of single-drug resistance was significantly higher in samples from after-hours general practice (GP) clinics compared with hospitals, office-hours GP clinics, and community and specialist health services (adjusted odds ratio=2.6, 95% confidence interval 2.2-3.1).

CONCLUSIONS

These findings have significant implications for antimicrobial prescribing given the identified risk factors for the detection of resistance, especially in patients attending after-hours GP clinics.

The new screening program to prevent cervical cancer using HPV DNA: getting the balance right in maintaining quality

Along with the reduction in human papillomavirus (HPV) infection and cervical abnormalities as a result of the successful HPV vaccination program, Australia is adopting a new screening strategy. This involves a new paradigm moving from cervical cytological screening to molecular nucleic acid technology (NAT), using HPV DNA assays as primary screening methodology for cervical cancer prevention. These assays must strike a balance between sufficient clinical sensitivity to detect or predict high-grade cervical intraepithelial lesions, the precursor to cervical cancer, without being too sensitive and detecting transient infection not destined for disease. Ensuring the highest quality HPV NAT is thus a priority in order to reduce the possibility of falsely negative screens and manage the risk associated with false positive HPV NAT test results. How to do this needs informed discussion and on-going refinement of the screening algorithm. This is of relevance as more countries move to more sensitive HPV NAT tests for secondary prevention of cervical cancer and as more HPV assays become available.

Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis

BACKGROUND

Understanding of the factors driving global antimicrobial resistance is limited. We analysed antimicrobial resistance and antibiotic consumption worldwide versus many potential contributing factors.

METHODS

Using three sources of data (ResistanceMap, the WHO 2014 report on antimicrobial resistance, and contemporary publications), we created two global indices of antimicrobial resistance for 103 countries using data from 2008 to 2014: Escherichia coli resistance-the global average prevalence of E coli bacteria that were resistant to third-generation cephalosporins and fluoroquinolones, and aggregate resistance-the combined average prevalence of E coli and Klebsiella spp resistant to third-generation cephalosporins, fluoroquinolones, and carbapenems, and meticillin-resistant Staphylococcus aureus. Antibiotic consumption data were obtained from the IQVIA MIDAS database. The World Bank DataBank was used to obtain data for governance, education, gross domestic product (GDP) per capita, health-care spending, and community infrastructure (eg, sanitation). A corruption index was derived using data from Transparency International. We examined associations between antimicrobial resistance and potential contributing factors using simple correlation for a univariate analysis and a logistic regression model for a multivariable analysis.

FINDINGS

In the univariate analysis, GDP per capita, education, infrastructure, public health-care spending, and antibiotic consumption were all inversely correlated with the two antimicrobial resistance indices, whereas higher temperatures, poorer governance, and the ratio of private to public health expenditure were positively correlated. In the multivariable regression analysis (confined to the 73 countries for which antibiotic consumption data were available) considering the effect of changes in indices on E coli resistance (R² 0·54) and aggregate resistance (R² 0·75), better infrastructure (p=0·014 and p=0·0052) and better governance (p=0·025 and p<0·0001) were associated with lower antimicrobial resistance indices. Antibiotic consumption was not significantly associated with either antimicrobial resistance index in the multivariable analysis (p=0·64 and p=0·070).

INTERPRETATION

Reduction of antibiotic consumption will not be sufficient to control antimicrobial resistance because contagion-the spread of resistant strains and resistance genes-seems to be the dominant contributing factor. Improving sanitation, increasing access to clean water, and ensuring good governance, as well as increasing public health-care expenditure and better regulating the private health sector are all necessary to reduce global antimicrobial resistance.

FUNDING

None.

Utilization of a Neural Network in the Elaboration of an Evaluation Scale for Pain in Cerebral Palsy

An interesting aspect of neural networks is shown in the elaboration of an evaluation scale for pain in cerebral palsy with severe mental retardation. Because of the diversity of cases, the number of items had to be limited in the final step of statistical validation. Classical analysis on prior data did not allow to decide whether the variability in results is more likely due to the type of disability (i. e., the possibility of pain expression) than to the actual presence of pain. A neural network was used to find implicit relations between the data, with the advantage of having total control on the variables’ status by applying variations in the network architecture. This allowed for the rapid identification more significant item combinations as a function of degree of relationship to pain in cerebral palsy.

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.

Reducing catheter-associated urinary tract infections in hospitals: study protocol for a multi-site randomised controlled study

INTRODUCTION

Despite advances in infection prevention and control, catheter-associated urinary tract infections (CAUTIs) are common and remain problematic. A number of measures can be taken to reduce the risk of CAUTI in hospitals. Appropriate urinary catheter insertion procedures are one such method. Reducing bacterial colonisation around the meatal or urethral area has the potential to reduce CAUTI risk. However, evidence about the best antiseptic solutions for meatal cleaning is mixed, resulting in conflicting recommendations in guidelines internationally. This paper presents the protocol for a study to evaluate the effectiveness (objective 1) and cost-effectiveness (objective 2) of using chlorhexidine in meatal cleaning prior to catheter insertion, in reducing catheter-associated asymptomatic bacteriuria and CAUTI.

METHODS AND ANALYSIS

A stepped wedge randomised controlled trial will be undertaken in three large Australian hospitals over a 32-week period. The intervention in this study is the use of chlorhexidine (0.1%) solution for meatal cleaning prior to catheter insertion. During the first 8 weeks of the study, no hospital will receive the intervention. After 8 weeks, one hospital will cross over to the intervention with the other two participating hospitals crossing over to the intervention at 8-week intervals respectively based on randomisation. All sites complete the trial at the same time in 2018. The primary outcomes for objective 1 (effectiveness) are the number of cases of CAUTI and catheter-associated asymptomatic bacteriuria per 100 catheter days will be analysed separately using Poisson regression. The primary outcome for objective 2 (cost-effectiveness) is the changes in costs relative to health benefits (incremental cost-effectiveness ratio) from adoption of the intervention.

DISSEMINATION

Results will be disseminated via peer-reviewed journals and presentations at relevant conferences.A dissemination plan it being developed. Results will be published in the peer review literature, presented at relevant conferences and communicated via professional networks.

ETHICS

Ethics approval has been obtained.

TRIAL REGISTRATION NUMBER

12617000373370, approved 13/03/2017. Protocol version 1.1.

[Neonatal presentation of Prader-Willi syndrome: A report of five cases]

Prader-Willi syndrome (PWS) is a fingerprint disease caused by the loss of paternally inherited chromosome 15q11.2-q13. In several populations studied, prevalence is estimated to be from 1/10,000 to 1/25,000 births. The disease initially manifests by neonatal hypotonia associated with orality disorders. Secondly, hyperphagia appears with significant obesity and hypogonadism. Motor milestones and language development are delayed, and all individuals have variable degrees of cognitive disability during childhood. Frequently, the most prominent features do not become evident until the later childhood stage, which can lead to underdiagnosis or late diagnosis in early childhood. Because of the long-term implications of this syndrome, it is important to recognize its features as soon as possible so that early counseling of parents and the affected child is possible. The diagnosis is suspected on clinical grounds and confirmed by genetic analysis. Prenatal diagnosis is possible and can be considered in polyhydramnios, decreased fetal active movements, malpresentation, oddly positioned hands and feet, and abnormal fetal heart rhythm. Since PWS can also lead to complications in both pregnancy and labor, proper prenatal diagnosis can also help optimize perinatal care for affected children. We report a series of five newborns for whom PWS was diagnosed in the neonatal period over 6 years. During this period, no prenatal signs of PWS were detected. The incidence in our population was 1/7937 births. The disease was diagnosed on clinical criteria: severe hypotonia, failure to thrive with poor sucking, and dysmorphic and abnormalities of the genitalia. Polyhydramnios was observed in only one case. The delivery was normal for only one patient. All except one were term newborns. There were three males and two females. We noted abnormal fetal heart rate for 80 % of the patients. The birth weight was close to the 10th percentile for two patients, less than the 3rd percentile for two others. All individuals had eutrophic cranial perimeter and four presented peculiar position of fingers. Genetic analyses found a deletion of the paternal chromosome 15 in three patients (60 %) and maternal uniparental disomy for the two others (40 %). The distribution by sex, weight, cranial perimeter, and mutations are those reported in the literature. PWS should be sought in cases of severe neonatal hypotonia, most particularly if it combines dysmorphism, hypogonadism, malposition of the fingers, and suggestive prenatal history. An early diagnosis provides better multidisciplinary care for the patient and family. We have no explanation for the higher incidence of the disease than in the general population. It is possible that this incidence is only fortuitous, but further studies would help to identify potential risk factors for the disease.

Outbreak of health care-associated Burkholderia cenocepacia bacteremia and infection attributed to contaminated sterile gel used for central line insertion under ultrasound guidance and other procedures

BACKGROUND

We report an outbreak of Burkholderia cenocepacia bacteremia and infection in 11 patients predominately in intensive care units caused by contaminated ultrasound gel used in central line insertion and sterile procedures within 4 hospitals across Australia.

METHODS

Burkholderia cenocepacia was first identified in the blood culture of a patient from the intensive care unit at the Gold Coast University Hospital on March 26, 2017, with 3 subsequent cases identified by April 7, 2017. The outbreak response team commenced investigative measures.

RESULTS

The outbreak investigation identified the point source as contaminated gel packaged in sachets for use within the sterile ultrasound probe cover. In total, 11 patient isolates of B cenocepacia with the same multilocus sequence type were identified within 4 hospitals across Australia. This typing was the same as identified in the contaminated gel isolate with single nucleotide polymorphism-based typing, demonstrating that all linked isolates clustered together.

CONCLUSION

Arresting the national point-source outbreak within multiple jurisdictions was critically reliant on a rapid, integrated, and coordinated response and the use of informal professional networks to first identify it. All institutions where the product is used should look back at Burkholderia sp blood culture isolates for speciation to ensure this outbreak is no larger than currently recognized given likely global distribution.

Influenza Vaccination of Healthcare Workers: Critical Analysis of the Evidence for Patient Benefit Underpinning Policies of Enforcement

BACKGROUND

Four cluster randomized controlled trials (cRCTs) conducted in long-term care facilities (LTCFs) have reported reductions in patient risk through increased healthcare worker (HCW) influenza vaccination. This evidence has led to expansive policies of enforcement that include all staff of acute care hospitals and other healthcare settings beyond LTCFs. We critique and quantify the cRCT evidence for indirect patient benefit underpinning policies of mandatory HCW influenza vaccination.

METHODS

Plausibility of the four cRCT findings attributing indirect patient benefits to HCW influenza vaccination was assessed by comparing percentage reductions in patient risk reported by the cRCTs to predicted values. Plausibly predicted values were derived according to the basic mathematical principle of dilution, taking into account HCW influenza vaccine coverage and the specificity of patient outcomes for influenza. Accordingly, predicted values were calculated as a function of relevant compound probabilities including vaccine efficacy (ranging 40-60% in HCWs and favourably assuming the same indirect protection conferred through them to patients) × change in proportionate HCW influenza vaccine coverage (as reported by each cRCT) × percentage of a given patient outcome (e.g. influenza-like illness (ILI) or all-cause mortality) plausibly due to influenza virus. The number needed to vaccinate (NNV) for HCWs to indirectly prevent patient death was recalibrated based on real patient data of hospital-acquired influenza, with adjustment for potential under-detection (5.2-fold), and using favourable assumptions of HCW-attributable risk (ranging 60-80%).

RESULTS

In attributing patient benefit to increased HCW influenza vaccine coverage, each cRCT was found to violate the basic mathematical principle of dilution by reporting greater percentage reductions with less influenza-specific patient outcomes (i.e., all-cause mortality > ILI > laboratory-confirmed influenza) and/or patient mortality reductions exceeding even favourably-derived predicted values by at least 6- to 15-fold. If extrapolated to all LTCF and hospital staff in the United States, the prior cRCT-claimed NNV of 8 would implausibly mean >200,000 and >675,000 patient deaths, respectively, could be prevented annually by HCW influenza vaccination, inconceivably exceeding total US population mortality estimates due to seasonal influenza each year, or during the 1918 pandemic, respectively. More realistic recalibration based on actual patient data instead shows that at least 6000 to 32,000 hospital workers would need to be vaccinated before a single patient death could potentially be averted.

CONCLUSIONS

The four cRCTs underpinning policies of enforced HCW influenza vaccination attribute implausibly large reductions in patient risk to HCW vaccination, casting serious doubts on their validity. The impression that unvaccinated HCWs place their patients at great influenza peril is exaggerated. Instead, the HCW-attributable risk and vaccine-preventable fraction both remain unknown and the NNV to achieve patient benefit still requires better understanding. Although current scientific data are inadequate to support the ethical implementation of enforced HCW influenza vaccination, they do not refute approaches to support voluntary vaccination or other more broadly protective practices, such as staying home or masking when acutely ill.

Five-Year Antimicrobial Resistance Patterns of Urinary Escherichia coli at an Australian Tertiary Hospital: Time Series Analyses of Prevalence Data

This study describes the antimicrobial resistance temporal trends and seasonal variation of Escherichia coli (E. coli) urinary tract infections (UTIs) over five years, from 2009 to 2013, and compares prevalence of resistance in hospital- and community-acquired E. coli UTI. A cross sectional study of E. coli UTIs from patients attending a tertiary referral hospital in Canberra, Australia was undertaken. Time series analysis was performed to illustrate resistance trends. Only the first positive E. coli UTI per patient per year was included in the analysis. A total of 15,022 positive cultures from 8724 patients were identified. Results are based on 5333 first E. coli UTIs, from 4732 patients, of which 84.2% were community-acquired. Five-year hospital and community resistance rates were highest for ampicillin (41.9%) and trimethoprim (20.7%). Resistance was lowest for meropenem (0.0%), nitrofurantoin (2.7%), piperacillin-tazobactam (2.9%) and ciprofloxacin (6.5%). Resistance to amoxycillin-clavulanate, cefazolin, gentamicin and piperacillin-tazobactam were significantly higher in hospital- compared to community-acquired UTIs (9.3% versus 6.2%; 15.4% versus 9.7%; 5.2% versus 3.7% and 5.2% versus 2.5%, respectively). Trend analysis showed significant increases in resistance over five years for amoxycillin-clavulanate, trimethoprim, ciprofloxacin, nitrofurantoin, trimethoprim-sulphamethoxazole, cefazolin, ceftriaxone and gentamicin (P<0.05, for all) with seasonal pattern observed for trimethoprim resistance (augmented Dickey-Fuller statistic = 4.136; P = 0.006). An association between ciprofloxacin resistance, cefazolin resistance and ceftriaxone resistance with older age was noted. Given the relatively high resistance rates for ampicillin and trimethoprim, these antimicrobials should be reconsidered for empirical treatment of UTIs in this patient population. Our findings have important implications for UTI treatment based on setting of acquisition.

Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia

Unlike Escherichia coli strains belonging to phylogroup B2, the clinical significance of strains belonging to phylogroup F is not well understood. Here we report on a collection of phylogroup F strains recovered in Australia from faeces and extra-intestinal sites from humans, companion animals and native animals, as well as from poultry meat and water samples. The distribution of sequence types was clearly non-random with respect to isolate source. The antimicrobial resistance and virulence trait profiles also varied with the sequence type of the isolate. Phylogroup F strains tended to lack the virulence traits typically associated with phylogroup B2 strains responsible for extra-intestinal infection in humans. Resistance to fluoroquinolones and/or expanded-spectrum cephalosporins was common within ST648, ST354 and ST3711. Although ST354 and ST3711 are part of the same clonal complex, the ST3711 isolates were only recovered from native birds being cared for in a single wildlife rehabilitation centre, whereas the ST354 isolates were from faeces and extra-intestinal sites of dogs and humans, as well as from poultry meat. Although ST354 isolates from chicken meat in Western Australia were distinct from all other ST354 isolates, those from poultry meat samples collected in eastern Australia shared many similarities with other ST354 isolates from humans and companion animals.

Phenotypic variability and diffuse arterial lesions in a family with Loeys-Dietz syndrome type 4

Syndromic thoracic aortic aneurysm and dissection (TAAD) can suggest Marfan, vascular Ehlers-Danlos or Loeys-Dietz (LDS) syndromes. Several of the TGFβ-pathway-related genes predispose to different types of LDS. Heterozygous loss-of-function variations in TGFβ2 have been shown to be responsible for a novel form of syndromic TAAD associated with an impairment of the mitral valve and cerebrovascular disease called Loeys-Dietz syndrome type 4 (LDS4). We report the clinical characterization of a LDS4 French family with sudden deaths and diffuse vascular lesions, caused by a frameshift mutation in TGFβ2 gene: c.[995del]; p.(Leu332TrpfsTer27). Clinical characteristics include aneurysm of aortic sinus, skeletal and cutaneous features compatible with a syndromic form of TAAD (joint hypermobility, scoliosis, and easy bruises), intracranial aneurysms and rare mitral valve involvement. Iliac aneurysms, systemic medium caliber arteries dissections, and mild developmental delay were present in the family, and have not been described in LDS4. Phenotypic variability was also an important finding, including absence of clinical vascular events at advanced age in one case. Our data expand the phenotype of LDS4: we confirm that TGFβ2 mutations are responsible for true LDS syndrome with non-specific features of connective tissue disorders and diffuse vascular lesions. Adapted vascular follow up and prevention has to be proposed for these patients.

World Health Organization Ranking of Antimicrobials According to Their Importance in Human Medicine: A Critical Step for Developing Risk Management Strategies to Control Antimicrobial Resistance From Food Animal Production

Antimicrobial use in food animals selects for antimicrobial resistance in bacteria, which can spread to people. Reducing use of antimicrobials-particularly those deemed to be critically important for human medicine-in food production animals continues to be an important step for preserving the benefits of these antimicrobials for people. The World Health Organization ranking of antimicrobials according to their relative importance in human medicine was recently updated. Antimicrobials considered the highest priority among the critically important antimicrobials were quinolones, third- and fourth-generation cephalosporins, macrolides and ketolides, and glycopeptides. The updated ranking allows stakeholders in the agriculture sector and regulatory agencies to focus risk management efforts on drugs used in food animals that are the most important to human medicine. In particular, the current large-scale use of fluoroquinolones, macrolides, and third-generation cephalosporins and any potential use of glycopeptides and carbapenems need to be addressed urgently.

Australian Group on Antimicrobial Resistance Australian Staphylococcus aureus Sepsis Outcome Programme annual report, 2014

From 1 January to 31 December 2014, 27 institutions around Australia participated in the Australian Staphylococcal Sepsis Outcome Programme (ASSOP). The aim of ASSOP 2014 was to determine the proportion of Staphylococcus aureus bacteraemia (SAB) isolates in Australia that are antimicrobial resistant, with particular emphasis on susceptibility to methicillin and to characterise the molecular epidemiology of the isolates. Overall, 18.8% of the 2,206 SAB episodes were methicillin resistant, which was significantly higher than that reported in most European countries. The 30-day all-cause mortality associated with methicillin-resistant SAB was 23.4%, which was significantly higher than the 14.4% mortality associated with methicillin-sensitive SAB (P <0.0001). With the exception of the beta-lactams and erythromycin, antimicrobial resistance in methicillin-sensitive S. aureus remains rare. However in addition to the beta-lactams, approximately 50‰ of methicillin-resistant S. aureus (MRSA) were resistant to erythromycin and ciprofloxacin and approximately 15% were resistant to co-trimoxazole, tetracycline and gentamicin. When applying the European Committee on Antimicrobial Susceptibility Testing breakpoints, teicoplanin resistance was detected in 2 S. aureus isolates. Resistance was not detected for vancomycin or linezolid. Resistance to non-beta-lactam antimicrobials was largely attributable to 2 healthcare-associated MRSA clones; ST22-IV [2B] (EMRSA-15) and ST239-III [3A] (Aus-2/3 EMRSA). ST22-IV [2B] (EMRSA-15) has become the predominant healthcare associated clone in Australia. Sixty per cent of methicillin-resistant SAB were due to community-associated (CA) clones. Although polyclonal, almost 44% of community-associated clones were characterised as ST93-IV [2B] (Queensland CA-MRSA) and ST1-IV [2B] (WA1). CA-MRSA, in particular the ST45-V [5C2&5] (WA84) clone, has acquired multiple antimicrobial resistance determinants including ciprofloxacin, erythromycin, clindamycin, gentamicin and tetracycline. As CA-MRSA is well established in the Australian community it is important that antimicrobial resistance patterns in community and healthcare-associated SAB is monitored as this information will guide therapeutic practices in treating S. aureus sepsis.

Preparedness of institutions around the world for managing patients with Ebola virus disease: an infection control readiness checklist

BACKGROUND

In response to global concerns about the largest Ebola virus disease (EVD), outbreak to-date in West Africa documented healthcare associated transmission and the risk of global spread, the International Society of Chemotherapy (ISC) Infection Control Working Group created an Ebola Infection Control Readiness Checklist to assess the preparedness of institutions around the globe. We report data from the electronic checklist that was disseminated to medical professionals from October to December 2014 and identify action needed towards better preparedness levels.

FINDINGS

Data from 192 medical professionals (one third from Africa) representing 125 hospitals in 45 countries around the globe were obtained through a specifically developed electronic survey. The survey contained 76 specific questions in 7 major sections: Administrative/operational support; Communications; Education and audit; Human resources, Supplies, Infection Prevention and Control practices and Clinical management of patients. The majority of respondents were infectious disease specialists/infection control consultants/clinical microbiologists (75; 39 %), followed by infection control professionals (59; 31 %) and medical doctors of other specialties (17; 9 %). Nearly all (149; 92 %) were directly involved in Ebola preparedness activities. Whilst, 54 % indicated that their hospital would need to handle suspected and proven Ebola cases, the others would subsequently transfer suspected cases to a specialized centre.

CONCLUSION

The results from our survey reveal that the general preparedness levels for management of potentially suspected cases of Ebola virus disease is only partially adequate in hospitals. Hospitals designated for admitting EVD suspected and proven patients had more frequently implemented Infection Control preparedness activities than hospitals that would subsequently transfer potential EVD cases to other centres. Results from this first international survey provide a framework for future efforts to improve hospital preparedness worldwide.

Antimicrobial resistance: the major contribution of poor governance and corruption to this growing problem

Objectives

To determine how important governmental, social, and economic factors are in driving antibiotic resistance compared to the factors usually considered the main driving factors—antibiotic usage and levels of economic development.

Design

A retrospective multivariate analysis of the variation of antibiotic resistance in Europe in terms of human antibiotic usage, private health care expenditure, tertiary education, the level of economic advancement (per capita GDP), and quality of governance (corruption). The model was estimated using a panel data set involving 7 common human bloodstream isolates and covering 28 European countries for the period 1998–2010.

Results

Only 28% of the total variation in antibiotic resistance among countries is attributable to variation in antibiotic usage. If time effects are included the explanatory power increases to 33%. However when the control of corruption indicator is included as an additional variable, 63% of the total variation in antibiotic resistance is now explained by the regression. The complete multivariate regression only accomplishes an additional 7% in terms of goodness of fit, indicating that corruption is the main socioeconomic factor that explains antibiotic resistance. The income level of a country appeared to have no effect on resistance rates in the multivariate analysis. The estimated impact of corruption was statistically significant (p< 0.01). The coefficient indicates that an improvement of one unit in the corruption indicator is associated with a reduction in antibiotic resistance by approximately 0.7 units. The estimated coefficient of private health expenditure showed that one unit reduction is associated with a 0.2 unit decrease in antibiotic resistance.

Conclusions

These findings support the hypothesis that poor governance and corruption contributes to levels of antibiotic resistance and correlate better than antibiotic usage volumes with resistance rates. We conclude that addressing corruption and improving governance will lead to a reduction in antibiotic resistance.