A systematic approach to microbial forensics

The coronavirus disease 2019 pandemic accelerated developments in biotechnology that underpin infection science. These advances present an opportunity to refresh the microbial forensic toolkit. Integration of novel analytical techniques with established forensic methods will speed up acquisition of evidence and better support lines of enquiry. A critical part of any such investigation is demonstration of a robust causal relationship and attribution of responsibility for an incident. In the wider context of a formal investigation into agency, motivation and intent, the quick and efficient assembly of microbiological evidence sets the tone and tempo of the entire investigation. Integration of established and novel analytical techniques from infection science into a systematic approach to microbial forensics will therefore ensure that major perspectives are correctly used to frame and shape the evidence into a clear narrative, while recognizing that forensic hypothesis generation, testing and refinement comprise an iterative process. Development of multidisciplinary training exercises that use this approach will enable translation into practice and efficient implementation when the need arises.

Developing machine learning systems worthy of trust for infection science: a requirement for future implementation into clinical practice

Infection science is a discipline of healthcare which includes clinical microbiology, public health microbiology, mechanisms of microbial disease, and antimicrobial countermeasures. The importance of infection science has become more apparent in recent years during the SARS-CoV-2 (COVID-19) pandemic and subsequent highlighting of critical operational domains within infection science including the hospital, clinical laboratory, and public health environments to prevent, manage, and treat infectious diseases. However, as the global community transitions beyond the pandemic, the importance of infection science remains, with emerging infectious diseases, bloodstream infections, sepsis, and antimicrobial resistance becoming increasingly significant contributions to the burden of global disease. Machine learning (ML) is frequently applied in healthcare and medical domains, with growing interest in the application of ML techniques to problems in infection science. This has the potential to address several key aspects including improving patient outcomes, optimising workflows in the clinical laboratory, and supporting the management of public health. However, despite promising results, the implementation of ML into clinical practice and workflows is limited. Enabling the migration of ML models from the research to real world environment requires the development of trustworthy ML systems that support the requirements of users, stakeholders, and regulatory agencies. This paper will provide readers with a brief introduction to infection science, outline the principles of trustworthy ML systems, provide examples of the application of these principles in infection science, and propose future directions for moving towards the development of trustworthy ML systems in infection science.

Machine learning pipeline for blood culture outcome prediction using Sysmex XN-2000 blood sample results in Western Australia

BACKGROUND

Bloodstream infections (BSIs) are a significant burden on the global population and represent a key area of focus in the hospital environment. Blood culture (BC) testing is the standard diagnostic test utilised to confirm the presence of a BSI. However, current BC testing practices result in low positive yields and overuse of the diagnostic test. Diagnostic stewardship research regarding BC testing is increasing, and becoming more important to reduce unnecessary resource expenditure and antimicrobial use, especially as antimicrobial resistance continues to rise. This study aims to establish a machine learning (ML) pipeline for BC outcome prediction using data obtained from routinely analysed blood samples, including complete blood count (CBC), white blood cell differential (DIFF), and cell population data (CPD) produced by Sysmex XN-2000 analysers.

METHODS

ML models were trained using retrospective data produced between 2018 and 2019, from patients at Sir Charles Gairdner hospital, Nedlands, Western Australia, and processed at Pathwest Laboratory Medicine, Nedlands. Trained ML models were evaluated using stratified 10-fold cross validation.

RESULTS

Two ML models, an XGBoost model using CBC/DIFF/CPD features with boruta feature selection (BFS) , and a random forest model trained using CBC/DIFF features with BFS were selected for further validation after obtaining AUC scores of [Formula: see text] and [Formula: see text] respectively using stratified 10-fold cross validation. The XGBoost model obtained an AUC score of 0.76 on a internal validation set. The random forest model obtained AUC scores of 0.82 and 0.76 on internal and external validation datasets respectively.

CONCLUSIONS

We have demonstrated the utility of using an ML pipeline combined with CBC/DIFF, and CBC/DIFF/CPD feature spaces for BC outcome prediction. This builds on the growing body of research in the area of BC outcome prediction, and provides opportunity for further research.

The foundations of aetiology: a common language for infection science

With the adoption of infection science as an umbrella term for the disciplines that inform our ideas of infection, there is a need for a common language that links infection's constituent parts. This paper develops a conceptual framework for infection science from the major themes used to understand causal relationships in infectious diseases. The paper proposes using the four main themes from the Principia Aetiologica to classify infection knowledge into four corresponding domains: Clinical microbiology, Public health microbiology, Mechanisms of microbial disease and Antimicrobial countermeasures. This epistemology of infection gives form and process to a revised infection ontology and an infectious disease heuristic. Application of the proposed epistemology has immediate practical implications for organization of journal content, promotion of inter-disciplinary collaboration, identification of emerging priority themes, and integration of cross-disciplinary areas such as One Health topics and antimicrobial resistance. Starting with these foundations, we can build a coherent narrative around the idea of infection that shapes the practice of infection science.

Plasma cfDNA predictors of established bacteraemic infection

Introduction. Increased plasma cell-free DNA (cfDNA) has been reported for various diseases in which cell death and tissue/organ damage contribute to pathogenesis, including sepsis.

Gap Statement. While several studies report a rise in plasma cfDNA in bacteraemia and sepsis, the main source of cfDNA has not been identified.

Aim. In this study, we wanted to determine which of nuclear, mitochondrial or bacterial cfDNA is the major contributor to raised plasma cfDNA in hospital subjects with bloodstream infections and could therefore serve as a predictor of bacteraemic disease severity.

Methodology. The total plasma concentration of double-stranded cfDNA was determined using a fluorometric assay. The presence of bacterial DNA was identified by PCR and DNA sequencing. The copy numbers of human genes, nuclear β globin and mitochondrial MTATP8, were determined by droplet digital PCR. The presence, size and concentration of apoptotic DNA from human cells were established using lab-on-a-chip technology.

Results. We observed a significant difference in total plasma cfDNA from a median of 75 ng ml⁻¹ in hospitalised subjects without bacteraemia to a median of 370 ng ml⁻¹ (P=0.0003) in bacteraemic subjects. The copy numbers of nuclear DNA in bacteraemic also differed between a median of 1.6 copies µl⁻¹ and 7.3 copies µl⁻¹ (P=0.0004), respectively. In contrast, increased mitochondrial cfDNA was not specific for bacteraemic subjects, as shown by median values of 58 copies µl⁻¹ in bacteraemic subjects, 55 copies µl⁻¹ in other hospitalised subjects and 5.4 copies µl⁻¹ in healthy controls. Apoptotic nucleosomal cfDNA was detected only in a subpopulation of bacteraemic subjects with documented comorbidities, consistent with elevated plasma C-reactive protein (CRP) levels in these subjects. No bacterial cfDNA was reliably detected by PCR in plasma of bacteraemic subjects over the course of infection with several bacterial pathogens.

Conclusions. Our data revealed distinctive plasma cfDNA signatures in different groups of hospital subjects. The total cfDNA was significantly increased in hospital subjects with laboratory-confirmed bloodstream infections comprising nuclear and apoptotic, but not mitochondrial or bacterial cfDNAs. The apoptotic cfDNA, potentially derived from blood cells, predicted established bacteraemia. These findings deserve further investigation in different hospital settings, where cfDNA measurement could provide simple and quantifiable parameters for monitoring a disease progression.

Estimating COVID Risk During a Period of Pandemic Decline

Background: Many parts of the world that succeeded in suppressing epidemic coronavirus spread in 2020 have been caught out by recent changes in the transmission dynamics of SARS-CoV-2. Australia's early success in suppressing COVID-19 resulted in lengthy periods without community transmission. However, a slow vaccine rollout leaves this geographically isolated population vulnerable to leakage of new variants from quarantine, which requires internal travel restrictions, disruptive lockdowns, contact tracing and testing surges.

Methods: To assist long term sustainment of limited public health resources, we sought a method of continuous, real-time COVID-19 risk monitoring that could be used to alert non-specialists to the level of epidemic risk on a sub-national scale. After an exploratory data assessment, we selected four COVID-19 metrics used by public health in their periodic threat assessments, applied a business continuity matrix and derived a numeric indicator; the COVID-19 Risk Estimate (CRE), to generate a daily spot CRE, a 3 day net rise and a seven day rolling average. We used open source data updated daily from all Australian states and territories to monitor the CRE for over a year.

Results: Upper and lower CRE thresholds were established for the CRE seven day rolling average, corresponding to risk of sustained and potential outbreak propagation, respectively. These CRE thresholds were used in a real-time map of Australian COVID-19 risk estimate distribution by state and territory.

Conclusions: The CRE toolkit we developed complements other COVID-19 risk management techniques and provides an early indication of emerging threats to business continuity.

Development, deployment and in-field demonstration of mobile coronavirus SARS-CoV-2 Nucleic acid amplification test

Introduction. The evolving SARS-CoV-2 coronavirus pandemic presents a series of challenges to clinical diagnostic services. Many proprietary PCR platforms deployed outside centralised laboratories have limited capacity to upscale when public health demands increase. We set out to develop and validate an open-platform mobile laboratory for remote area COVID-19 diagnosis, with a subsequent field trial.Gap Statement. In regional Western Australia, molecular diagnostic support is limited to near point-of-care devices. We therefore aimed to demonstrate open-platform capability in a rapidly deployable format within the context of the COVID-19 pandemic.Methodology. We compared, selected and validated components of a SARS-CoV-2 RT-PCR assay in order to establish a portable molecular diagnostics laboratory. The optimal combination of PCR assay equipment, reagents and consumables required for operation to national standards in regional laboratories was identified. This comprised RNA extraction and purification (QuickGene-480, Kurabo, Japan), a duplex RT-PCR assay (Logix Smart COVID-19, Co-Diagnostics, USA), a Myra liquid handling robot (Biomolecular Systems, Australia) and a magnetic induction thermal cycler (MIC, Biomolecular Systems).Results The 95 and 99% limits of detection were 1.01 copies μl-1 (5.05 copies per reaction) and 2.80 copies μl-1 (14.00 copies per reaction) respectively. The Co-Diagnostics assay amplified both SARS-CoV-1 and -2 RNA but showed no other cross reactivity. Qualitative results aligned with the reference laboratory SARS-CoV-2 assay (sensitivity 100% [95 % CI 96.48-100%], specificity 100% [95% CI 96.52-100%]). In field trials, the laboratory was operational within an hour of arrival on-site, can process up to 36 samples simultaneously, produces results in two and a half hours from specimen reception, and performed well during six consecutive runs during a 1 week deployment.Conclusion. Our mobile laboratory enables an adaptive response to increased test demand, and unlike many proprietary point-of-care PCR systems, rapid substitution with an alternative assay if gene targets change or reagent supply chains fail. We envisage operation of this RT-PCR assay as a standby capability to meet varying regional test demands under public health emergency operations guidance.

2020: the year of living cautiously

2020 was the year when microbiology burst onto the world stage, not just as the science of small living things, but as the prism through which we understood global events. Clinical logic suffered under pressure arising from an urgent need to confirm or exclude severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This is a generation’s Hobbesian moment in which the public concern for safety and security from infection outweighs the pursuit of personal freedom. The strangeness of a world in which a minute particle wields superhuman power has generated its list of unlikely heroes and mendacious villains. As the year comes to an end, there are glimmers of light amid the gloom: the prospect of an effective vaccine, and life after the pandemic.

A fast impedance-based antimicrobial susceptibility test

There is an urgent need to develop simple and fast antimicrobial susceptibility tests (ASTs) that allow informed prescribing of antibiotics. Here, we describe a label-free AST that can deliver results within an hour, using an actively dividing culture as starting material. The bacteria are incubated in the presence of an antibiotic for 30 min, and then approximately 105 cells are analysed one-by-one with microfluidic impedance cytometry for 2-3 min. The measured electrical characteristics reflect the phenotypic response of the bacteria to the mode of action of a particular antibiotic, in a 30-minute incubation window. The results are consistent with those obtained by classical broth microdilution assays for a range of antibiotics and bacterial species.

Pandemic planning: plotting a course through the coronawars

The biological motor behind the current coronavirus pandemic has placed microbiology on a global stage, and given its practitioners a role among the architects of recovery. Planning for a return to normality or the new normal is a complex, multi-agency task for which healthcare scientists may not be prepared. This paper introduces a widely used military planning framework known as the Joint Military Appreciation Process, and outlines how it can be applied to deal with the next phase of the COVID-19 pandemic. Recognition of SARS-CoV-2's critical attributes, targetable vulnerabilities, and its most likely and most dangerous effects is a necessary precursor to scoping, framing and mission analysis. From this flows course of action development, analysis, concept of operations development, and an eventual decision to act on the plan. The same planning technique is applicable to the larger scale task of setting a microbiology-centric plan in the broader context of social and economic recovery.

Same-day antimicrobial susceptibility test using acoustic-enhanced flow cytometry visualized with supervised machine learning

Purpose. Antimicrobial susceptibility is slow to determine, taking several days to fully impact treatment. This proof-of-concept study assessed the feasibility of using machine-learning techniques for analysis of data produced by the flow cytometer-assisted antimicrobial susceptibility test (FAST) method we developed.Methods. We used machine learning to assess the effect of antimicrobial agents on bacteria, comparing FAST results with broth microdilution (BMD) antimicrobial susceptibility tests (ASTs). We used Escherichia coli (1), Klebsiella pneumoniae (1) and Staphylococcus aureus (2) strains to develop the machine-learning algorithm, an expanded panel including these plus E. coli (2), K. pneumoniae (3), Proteus mirabilis (1), Pseudomonas aeruginosa (1), S. aureus (2) and Enterococcus faecalis (1), tested against FAST and BMD (Sensititre, Oxoid), then two representative isolates directly from blood cultures.Results. Our data machines defined an antibiotic-unexposed population (AUP) of bacteria, classified the FAST result by antimicrobial concentration range, and determined a concentration-dependent antimicrobial effect (CDE) to establish a predicted inhibitory concentration (PIC). Reference strains of E. coli, K. pneumoniae and S. aureus tested with different antimicrobial agents demonstrated concordance between BMD results and machine-learning analysis (CA, categoric agreement of 91 %; EA, essential agreement of 100 %). CA was achieved in 35 (83 %) and EA in 28 (67 %) by machine learning on first pass in a challenge panel of 27 Gram-negative and 15 Gram-positive ASTs. Same-day AST results were obtained from clinical E. coli (1) and S. aureus (1) isolates.Conclusions. The combination of machine learning with the FAST method generated same-day AST results and has the potential to aid early antimicrobial treatment decisions, stewardship and detection of resistance.

Logic in the time of coronavirus

Much has happened here since the local news media trumpeted the first Australian COVID-19 fatality, and stirred up a medieval fear of contagion. We now need to take a step back to examine the logic underlying the use of our limited COVID-19 countermeasures. Emerging infectious diseases by their nature, pose new challenges to the diagnostic-treatment-control nexus, and push our concepts of causality beyond the limits of the conventional Koch-Henle approach to aetiology. We need to use contemporary methods of assessing causality to ensure that clinical, laboratory and public health measures draw on a rational, evidence-based approach to argumentation. The purpose of any aetiological hypothesis is to derive actionable insights into this latest emerging infectious disease. This review is an introduction to a conversation with medical microbiologists, which will be supported by a moderated blog.

Rapid antimicrobial susceptibility tests for sepsis; the road ahead

Current methods for antimicrobial susceptibility testing (AST) are too slow to affect initial treatment decisions in the early stages of sepsis, when the prescriber is most concerned to select effective therapy immediately, rather than finding out what will not work 1 or 2 days later. There is a clear need for much faster differentiation between viral and bacterial infection, and AST, linked to earlier aetiological diagnosis, without sacrificing either the accuracy of quantitative AST or the low cost of qualitative AST. Truly rapid AST methods are eagerly awaited, and there are several candidate technologies that aim to improve the targeting of our limited stock of effective antimicrobial agents. However, none of these technologies are approaching the point of care and nor can they be described as truly culture-independent diagnostic tests. Rapid chemical and genomic methods of resistance detection are not yet reliable predictors of antimicrobial susceptibility and often rely on prior bacterial isolation. In order to resolve the trade-off between diagnostic confidence and therapeutic efficacy in increasingly antimicrobial-resistant sepsis, we propose a series of three linked decision milestones: initial clinical assessment (e.g. qSOFA score) within 10 min, initial laboratory tests and presumptive antimicrobial therapy within 1 h, and definitive AST with corresponding antimicrobial amendment within an 8 h window (i.e. the same working day). Truly rapid AST methods therefore must be integrated into the clinical laboratory workflow to ensure maximum impact on clinical outcomes of sepsis, and diagnostic and antimicrobial stewardship. The requisite series of development stages come with a substantial regulatory burden that hinders the translation of innovation into practice. The regulatory hurdles for the adoption of rapid AST technology emphasize technical accuracy, but progress will also rely on the effect rapid AST has on prescribing behaviour by physicians managing the care of patients with sepsis. Early adopters in well-equipped teaching centres in close proximity to large clinical laboratories are likely to be early beneficiaries of rapid AST, while simplified and lower-cost technology is needed to support poorly resourced hospitals in developing countries, with their higher burden of AMR. If we really want the clinical laboratory to deliver a specific, same-day diagnosis underpinned by definitive AST results, we are going to have to advocate more effectively for the clinical benefits of bacterial detection and susceptibility testing at critical decision points in the sepsis management pathway.

Legionnaires' Disease Outbreak on a Merchant Vessel, Indian Ocean, Australia, 2015

Two cases of Legionnaires' disease and 1 of Pontiac fever occurred among the crew of a merchant ship operating off the shores of Australia. PCR assays identified potential sources in the ship's cabins. Modification of maritime regulations for Legionnaires' disease prevention in commercial vessels is needed for nonpassenger merchant ships.

Field trials of blood culture identification FilmArray in regional Australian hospitals

Purpose. In this field trial of rapid blood culture identification (BCID), we aimed to determine whether the improved speed and accuracy of specific BCID predicted in our earlier pilot study could be obtained in regional hospitals by deploying a multiplex PCR FilmArray (Biomerieux, France) capability in their laboratories.Methods. We trained local hospital laboratory staff to operate the FilmArray equipment and act on the results. To do this, we integrated the multiplex PCR into the standard laboratory blood culture workflow and reporting procedure.Results. Of 100 positive blood culture episodes, BCID FilmArray results were correct in all 42 significant monobacterial cultures, with a fully predictive identity in 38 (90.5 %) and a partial identity in another four (9.5 %). There was one major error; a false positive Pseudomonas aeruginosa. The minor errors were the detection of one methicillin-resistant Staphylococcus aureus, which proved to be a methicillin-sensitive S. aureus mixed with a methicillin-resistant coagulase-negative staphylococcus, five false negative coagulase-negative staphylococci and one false negative streptococcus species. We found that 41/49 (84 %) clinically significant mono- and polymicrobial culture results were fully predictive of culture-based identification to bacterial species level at a mean of 1.15 days after specimen collection.Conclusions. There was a reduction of 1.21 days in the time taken to produce a definitive BCID compared to the previous year, translating into earlier communication of more specific blood culture results to the treating physician. Reduced time to definitive blood culture results has a direct benefit for isolated Australian communities at great distances from specialist hospital services.

Cutaneous Melioidosis Cluster Caused by Contaminated Wound Irrigation Fluid

Burkholderia pseudomallei can cause healthcare-associated infections outside its recognized tropical zone.

Melioidosis usually occurs after environmental exposure to Burkholderia pseudomallei in the tropics. A cluster of 5 cutaneous melioidosis cases occurred in suburban southwest Australia after an earlier case in January 2012. We collected environmental samples at the first patient’s home in January 2012 and from a nearby health center in December 2013 after 2 new cases occurred in the same postal district. We isolated genotypically identical B. pseudomallei from the first patient and 5 other patients in the district. Environmental sampling implicated an opened bottle of saline wound irrigation fluid containing >10⁶B. pseudomallei/mL. The bottle included instructions to discard within 24 hours of opening. No further cases of B. pseudomallei infection occurred after removing the contaminated bottle. This cutaneous melioidosis cluster demonstrates that B. pseudomallei can survive and disseminate in widely used medical fluids beyond its known geographic distribution, highlighting a need to use these products according to manufacturers’ instructions.

Clinical, Bacteriologic, and Geographic Stratification of Melioidosis Emerges from the Sri Lankan National Surveillance Program

Melioidosis, a potentially fatal tropical infection, is said to be underdiagnosed in low-income countries. An increase in melioidosis cases in Sri Lanka allowed us to analyze the relationship among clinical outcome, bacteriology, epidemiology, and geography in the first 108 laboratory-confirmed cases of melioidosis from a nationwide surveillance program. The additional 76 cases of laboratory-confirmed melioidosis confirmed further associations between Burkholderia pseudomallei multilocus sequence typing (MLST) and infection phenotype; ST1137/unifocal bacteremic infection (χ² = 3.86, P < 0.05), ST1136/multifocal infection without bacteremia (χ² = 15.8, P < 0.001), and ST1132/unifocal nonbacteremic infection (χ² = 6.34, P = 0.02). ST1137 infections were predominantly seen in the Western Province, whereas ST1132, 1135, and 1136 infections predominated in the Northwestern Province. Early participating centers in the surveillance program had a lower melioidosis-associated mortality than later participants (χ² = 3.99, P < 0.05). The based upon related sequence types (eBURST) algorithm, a MLST clustering method that infers founding genotypes and patterns of descent for related isolates and clonal complexes in an unrooted tree, showed uneven distribution of sequence types (STs). There was spatial clustering of the commonest STs (ST1132, 1136, and 1137) in the Western, Northwestern, and Central provinces. The recent increase in melioidosis in Sri Lanka uncovered by laboratory-enhanced surveillance is likely to be the result of a combination of improved laboratory detection, increased clinician awareness, recruitment of clinical centers, and small outbreaks. Further development of the surveillance program into a national genotyping-supported melioidosis registry will improve melioidosis diagnosis, treatment, and prevention where underdiagnosis and mortality rates remain high.

The Role of Climate in the Epidemiology of Melioidosis

PURPOSE OF REVIEW

Melioidosis epidemiology is susceptible to climate change through direct and indirect effects on human encounter with the causative agent, Burkholderia pseudomallei. This review describes the current depth of knowledge and recent advances in the understanding of this relationship and applies it to observations of melioidosis in Western Australia.

RECENT FINDINGS

High maximum rainfall and dense cloud cover have been shown to predict environmental presence of B. pseudomallei and cases of melioidosis, probably through correspondingly high moisture levels in B. pseudomallei-receptive soils. Increased melioidosis cases have been observed following storms in Taiwan and cyclones in the Australian Northern Territory and strengthen the association between melioidosis and extreme weather events. Indirect weather effects contribute to bacterial exposure through mechanisms such as increasing B. pseudomallei output from water seeps after heavy rain or localised flooding. Climate and weather have been directly implicated in dissemination of B. pseudomallei and cases of melioidosis in several notable events in Western Australia. Over a 10-year surveillance period, the cases that lay in the path of a tropical cyclone co-located with cyclone systems that repeatedly crossed the Western Australian coast. Cyclone-associated cases were caused by different B. pseudomallei MLST genotypes, arguing against airborne dissemination from a common source.

SUMMARY

Predicted increases in temperature, changes in global precipitation patterns and an increased incidence of extreme weather events are expected to change melioidosis epidemiology. Further studies of the physical geographic drivers of melioidosis will deepen understanding of the impact of climate on melioidosis.

Where Sepsis and Antimicrobial Resistance Countermeasures Converge

The United Nations General Assembly debate on antimicrobial resistance (AMR) recognizes the global significance of AMR. Much work needs to be done on technology capability and capacity to convert the strategic intent of the debate into operational plans and tangible outcomes. Enhancement of the biomedical science–clinician interface requires better exploitation of systems biology tools for in-laboratory and point of care methods that detect sepsis and characterize AMR. These need to link sepsis and AMR data with responsive, real-time surveillance. We propose an AMR sepsis register, similar in concept to a cancer registry, to aid coordination of AMR countermeasures.

Deployable Molecular Detection of Arboviruses in the Australian Outback

The most common causes of human infection from the arboviruses that are endemic in Australia are the arthritogenic alphaviruses: Ross River virus (RRV) and Barmah Forest virus (BFV). The most serious infections are caused by the neurotropic flaviviruses, Murray Valley encephalitis virus (MVEV) and the Kunjin subtype of West Nile virus. The greatest individual risk of arbovirus infection occurs in tropical/subtropical northern Australia because of the warm, wet summer conditions from December to June, where conventional arbovirus surveillance is difficult due to a combination of low population density, large distances between population centers, poor roads, and seasonal flooding. Furthermore, virus detection requires samples to be sent to Perth up to 2,000 km away for definitive analysis, causing delays of days to weeks before test results are available and public health interventions can be started. We deployed a portable molecular biology laboratory for remote field detection of endemic arboviruses in northern Queensland, then in tropical Western Australia and detected BFV, MVEV, and RRV RNA by polymerase chain reaction (PCR) assays of extracts from mosquitoes trapped in Queensland. We then used a field-portable compact real-time thermocycler for the samples collected in the Kimberley region of Western Australia. Real-time field PCR assays enabled concurrent endemic arbovirus distribution mapping in outback Queensland and Western Australia. Our deployable laboratory method provides a concept of operations for future remote area arbovirus surveillance.

Improved blood culture identification by FilmArray in cultures from regional hospitals compared with teaching hospital cultures

Rapid identification of bacteria isolated from blood cultures by direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now in wide spread use in major centres but is not yet feasible in smaller hospital laboratories. A FilmArray multiplex PCR panel for blood culture isolate identification (BCID) provides an alternative approach to near point-of-care microbial identification in regional hospitals. We assessed the accuracy and time to identification of the BCID FilmArray in a consecutive series of 149 blood cultures from 143 patients in a teaching hospital and smaller regional hospitals, currently identified by direct MALDI-TOF and proprietary molecular methods. The BCID FilmArray contained 18 of 34 species and 20 of 23 species isolated from teaching and regional hospital, respectively. Overall, 85 % of the teaching hospital and 100 % of the regional hospital monomicrobial blood cultures were identified, compared with 60 and 68 %, respectively, for direct MALDI-TOF on the same cultures. There were no incorrect results from blood cultures containing Staphylococcus aureus, streptococci, Pseudomonas aeruginosa or Enterobacteriaceae. The three discrepant results were all in mixed cultures. The mean reduction in time to identification of blood culture isolates was 53 h, which did not include the time required to transport cultures from regional centres to a central laboratory. The overall performance of the BCID FilmArray is stronger in blood cultures from smaller regional hospitals that encounter a narrower range of bacterial species dominated by the commonest species. This approach is more suited to smaller clinical laboratories than the MALDI-TOF direct method.

Temporal flux in β-lactam resistance among Klebsiella pneumoniae in Western Australia

Our aim was to identify long-term β-lactam resistance trends in local Klebsiella pneumoniae isolates, which are a common cause of sepsis in Western Australia. We studied three collections of K. pneumoniae isolates from Western Australia between 1977 and 2015 comprising contemporary blood culture (n = 98), multiresistant (n = 21) and historical (n = 50) isolates. Antimicrobial resistance was determined by Clinical and Laboratory Standards Institute agar dilution methods. PCR DNA sequencing identified β-lactamase variants and porin mutations contributing to β-lactam resistance. Isolates were genotyped by PFGE, multilocus sequence typing and a variable number tandem repeat method. From 1989 onwards, we detected the SHV-2a extended-spectrum β-lactamase (ESBL) in ceftriaxone-resistant isolates, and in ceftazidime- and aztreonam-resistant isolates from 1993. Ceftriaxone, ceftazidime and aztreonam resistance persisted, with blaCTX-M types becoming the dominant ESBLs by 2010. CTX-M-15 was encountered in both multiresistant and blood culture isolates. Meropenem resistance was detected for the first time in 2011 in a locally isolated blaIMP-4-positive K. pneumoniae. We found sequence types ST23 and ST86 that occurred in multiple isolates from invasive infections. ST86 was the most common and maintained a high degree (90 %) of similarity by PFGE since 1977. Ceftazidime-resistant K. pneumoniae sequence types have caused invasive infections in Western Australia since 1993. Invasive isolates producing CTX-M-14 and CTX-M-15 appeared in Western Australia during the last decade, before the appearance of carbapenemases. The diversity of β-lactam resistance and β-lactamase resistance mechanisms in Western Australian K. pneumoniae has increased since ESBLs were first described locally.

The implications of endemic IMP-4 carbapenemase for clinical laboratory susceptibility testing

A local predominance of carbapenemase producing Enterobacteriaceae with low minimum inhibitory concentrations (MIC) to meropenem prompted a review of methods available for carbapenemase detection. We report on results using two selective media, temocillin discs, CarbaNP test, GeneXpert Carba-R assay and an in-house PCR assay.

Sri Lankan National Melioidosis Surveillance Program Uncovers a Nationwide Distribution of Invasive Melioidosis

The epidemiologic status of melioidosis in Sri Lanka was unclear from the few previous case reports. We established laboratory support for a case definition and started a nationwide case-finding study. Suspected Burkholderia pseudomallei isolates were collated, identified by polymerase chain reaction assay, referred for Matrix Assisted Laser Desorption Ionization-Time of Flight analysis and multilocus sequence typing (MLST), and named according to the international MLST database. Between 2006 and early 2014, there were 32 patients with culture-confirmed melioidosis with an increasing annual total and a falling fatality rate. Patients were predominantly from rural communities, diabetic, and male. The major clinical presentations were sepsis, pneumonia, soft tissue and joint infections, and other focal infection. Burkholderia pseudomallei isolates came from all parts of Sri Lanka except the Sabaragamuwa Province, the south central hill country, and parts of northern Sri Lanka. Bacterial isolates belonged to 18 multilocus sequence types, one of which (ST 1137) was associated with septicemia and a single-organ focus (Fisher's exact, P = 0.004). Melioidosis is an established endemic infection throughout Sri Lanka, and is caused by multiple genotypes of B. pseudomallei, which form a distinct geographic group based upon related sequence types (BURST) cluster at the junction of the southeast Asian and Australasian clades.

First case of Francisella bacteraemia in Western Australia

Francisella species are Gram-negative, nonmotile, pleomorphic coccobacilli, facultative intracellular fastidious bacteria. We report the isolation of a Francisella-like species from a blood culture collected from a 44-year-old bacteraemic patient in Perth, Western Australia. The organism was identified to species level by 16S rRNA sequencing and by fatty acid methyl esters analysis. The strain genotypically resembled Francisella hispaniensis, a species previously isolated from human blood in Spain.

A Review of Melioidosis Cases in the Americas

Melioidosis is a bacterial infection caused by Burkholderia pseudomallei, a gram-negative saprophytic bacillus. Cases occur sporadically in the Americas with an increasing number of cases observed among people with no travel history to endemic countries. To better understand the incidence of the disease in the Americas, we reviewed the literature, including unpublished cases reported to the Centers for Disease Control and Prevention. Of 120 identified human cases, occurring between 1947 and June 2015, 95 cases (79%) were likely acquired in the Americas; the mortality rate was 39%. Burkholderia pseudomallei appears to be widespread in South, Central, and North America.

Effects of a Statewide Protocol for the Management of Peritoneal Dialysis-Related Peritonitis on Microbial Profiles and Antimicrobial Susceptibilities: A Retrospective Five-Year Review

♦

BACKGROUND

Peritonitis is a major complication of peritoneal dialysis (PD) and is associated with significant morbidity and mortality. Early empirical antibiotic therapy is recommended, with the choice of agents guided by local resistance patterns. As routine use of specific antimicrobial agents can drive resistance, regular assessment of causative organisms and their susceptibility to empirical therapy is essential. ♦

METHODS

We conducted a retrospective review of all PD peritonitis cases and positive PD fluid cultures obtained over a 5-year period in Western Australia following the introduction of a statewide protocol for the initial management of PD peritonitis with intraperitoneal vancomycin and gentamicin. ♦

RESULTS

The incidence of PD peritonitis decreased from 1 in 16 patient months (0.75/year at risk) to 1 in 29 patient months (0.41/year at risk) over the 5 years. There were 1,319 culture-positive samples and 1,069 unique isolates identified. Gram-positive bacteria accounted for 69.9% of positive cultures, with vancomycin resistance averaging 2% over the study period. Gram-negative bacteria accounted for 25.4% of positive cultures, with gentamicin resistance identified in an average of 8% of organisms. No increase in antimicrobial resistance to vancomycin or gentamicin occurred over the 5 years and there was no change in the proportion of gram-positive (69.9%), gram-negative (25.4%) or fungal (4.4%) organisms causing PD peritonitis. ♦

CONCLUSIONS

Over time, the peritonitis rates have dramatically improved although the profile of causative organisms remains similar. Empirical treatment of PD peritonitis with intraperitoneal vancomycin and gentamicin remains efficacious, with high levels of susceptibility and no evidence that the introduction of this statewide empirical PD peritonitis treatment protocol is driving resistance to these agents.

First case of Chlorella wound infection in a human in Australia

A 30-year-old man developed an infected knee wound 2 days after jumping his bicycle into a freshwater dam. He required repeated debridement and tissue grew bright green colonies typical of the alga Chlorella plus Aeromonas hydrophila. This, and one previously reported case, responded to surgical debridement and careful wound management.

Molecular mechanisms of β-lactam resistance in carbapenemase-producing Klebsiella pneumoniae from Sri Lanka

Carbapenemases are increasingly important antimicrobial resistance determinants. Little is known about the carbapenem resistance mechanisms in Sri Lanka. We examined 22 carbapenem-resistant Klebsiella pneumoniae from Sri Lanka to determine their β-lactam resistance mechanisms. The predominant resistance mechanisms we detected in this study were OXA-181, NDM-1 carbapenemases and extended-spectrum β-lactamase CTX-M-15. All isolates were then genotyped by pulsed-field gel electrophoresis, variable-number tandem repeat sequence analysis and multilocus sequence typing, and seven distinct genotypes were observed. Five OXA-181-positive Klebsiella pneumoniae isolates were genotypically related to an isolate of Indian origin. Multilocus sequence typing found that these related isolates belong to ST-14, which has been associated with dissemination of OXA-181 from the Indian subcontinent. Other genotypes we discovered were ST-147 and ST-340, also associated with intercontinental spread of carbapenemases of suspected subcontinental origin. The major porin genes ompK35 and ompK36 from these isolates had insertions, deletions and substitutions. Some of these were exclusive to strains within single pulsotypes. We detected one ompK36 variant, ins AA134-135GD, in six ST-14- and six ST-147, blaOXA-181-positive isolates. This porin mutation was an independent predictor of high-level meropenem resistance in our entire Sri Lankan isolate collection (P=0.0030). Analysis of the Sri Lankan ST-14 and ST-147 ins AA134-135GD-positive isolates found ST-14 was more resistant to meropenem than other isolates (mean MIC: 32±0 µg ml(-1) and 20±9.47 µg ml(-1), respectively, P=0.0277). The likely international transmission of these carbapenem resistance determinants highlights the need for regional collaboration and prospective surveillance of carbapenem-resistant Enterobacteriaceae.

Canibacter oris gen. nov., sp. nov., isolated from an infected human wound

A facultatively anaerobic, Gram-reaction-positive, catalase- and oxidase-negative, rod-shaped bacterium isolated from an infected human wound caused by a dog bite was characterized by phenotypic and molecular genetic methods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMMIB Q2029717T was a member of the order Micrococcales of the class Actinobacteria, displaying 91.6% to 96% sequence similarity with members of the family Microbacteriaceae. Phylogentic trees generated by different algorithms indicated that the strain forms an independent phylogenetic line of descent that consistently clustered proximal to the base of the genus Leucobacter. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type B1α), major menaquinone (MK-10) and a DNA G+C content of 56.9 mol%. The distinct phylogenetic position, ribotyping and matrix-assisted laser desorption/ionization time-of-flight MS profiles and the significant phenotypic differences clearly separate strain IMMIB Q2029717T from its nearest phylogenetic neighbour and support its classification as a representative of a novel genus and species, with the suggested name Canibacter oris gen. nov., sp. nov. The type strain is IMMIB Q2029717T (=DSM 27064T=CCUG 64069T).

Co-selection may explain high rates of ciprofloxacin non-susceptible Escherichia coli from retail poultry reared without prior fluoroquinolone exposure

Australia has never permitted fluoroquinolone use in food-producing animals. We examined local retail poultry for contamination with fluoroquinolone non-susceptible Escherichia coli, then explored the hypothesis that their presence may be due to co-selection of resistance determinants. Between August and November 2010, samples from 30 locally produced, uncooked retail poultry carcasses from four different processing centres underwent selective enrichment culture for ciprofloxacin non-susceptible E. coli. Their chromosomal- and plasmid-mediated resistance determinants were characterized, and phylogenetic analysis and transformation experiments were performed. Unexpectedly, we found nine (30 %) of our small collection of poultry samples carried fluoroquinolone non-susceptible E. coli of which nearly half possessed aac(6')-Ib-cr, a novel plasmid-mediated gene encoding an aminoglycoside acetylating enzyme that also confers fluoroquinolone resistance. All nine isolates were co-resistant to amoxicillin, gentamicin, tetracycline and trimethoprim/sulfamethoxazole--all antibiotic classes that are registered for use in poultry reared for food production within Australia. Their unique phylogenetic relatedness suggested clonal dissemination driven by non-fluoroquinolone selective pressures. aac(6')-Ib-cr was successfully transformed and selected for using non-fluoroquinolone antibiotic pressure. Vertical and perhaps horizontal co-selection may be contributing to the emergence of fluoroquinolone resistance in poultry and could play a similar role in the human setting. This suggests that preservation of the usefulness of fluoroquinolones may require more than just restriction of their use in isolation from other interventions.

Aeromonas australiensis sp. nov., isolated from irrigation water

A Gram-negative, facultatively anaerobic bacillus, designated strain 266T, was isolated from an irrigation water system in the south-west of Western Australia. Analysis of the 16S rRNA gene sequence confirmed that strain 266T belonged to the genus Aeromonas , with the nearest species being Aeromonas fluvialis (99.6 % similarity to the type strain, with 6 nucleotide differences) followed by Aeromonas veronii and Aeromonas allosaccharophila (both 99.5 %). Analysis of gyrB and rpoD sequences suggested that strain 266T formed a phylogenetic line independent of other species in the genus. This was confirmed using the concatenated sequences of six housekeeping genes (gyrB, rpoD, recA, dnaJ, gyrA and dnaX) that also indicated that A. veronii and A. allosaccharophila were the nearest relatives. DNA–DNA reassociation experiments and phenotypic analysis further supported the conclusion that strain 266T represents a novel species, for which the name Aeromonas australiensis sp. nov. is proposed, with type strain 266T ( = CECT 8023T  = LMG 2670T).

The lab without walls: a deployable approach to tropical infectious diseases

The Laboratory Without Walls is a modular field application of molecular biology that provides clinical laboratory support in resource-limited, remote locations. The current repertoire arose from early attempts to deliver clinical pathology and public health investigative services in remote parts of tropical Australia, to address the shortcomings of conventional methods when faced with emerging infectious diseases. Advances in equipment platforms and reagent chemistry have enabling rapid progress, but also ensure the Laboratory Without Walls is subject to continual improvement. Although new molecular biology methods may lead to more easily deployable clinical laboratory capability, logistic and technical governance issues continue to act as important constraints on wider implementation.