Australian forensic textile damage examinations - Finding a way forward since PCAST

Textile damage examinations are requested in a range of crime types such as assault, sexual assault and homicide. They typically involve the examination of clothing for damage such as cut, tear or thermal damage, often then followed by experimental scenario testing to help ascertain the cause of the damage. Understanding the underpinning science is central to the accurate interpretation of the complex mechanism of damage formation. In a stabbing incident for example, an understanding of the dynamic relationship between the knife blade, fabric and skin (or skin simulant) is critical. Recent reports, including the President's Council of Advisors on Science and Technology (PCAST) report, have scrutinised forensic feature-based comparison techniques. Whilst textile damage was not a focus area, it can be considered a feature-based evidence class, and one which is currently largely reliant upon a practitioner's opinion, experience and professional judgement. This paper will review the current state of textile damage examinations in Australia and survey research being conducted to address the issues raised in the context of the PCAST report. The central contribution of observational data to the evidence class of textile damage will also be explored, as well as some practical measures to counter the effects of cognitive bias.

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Large-scale bacterial population genetics studies are now routine due to cost-effective Illumina short-read sequencing. However, analysing plasmid content remains difficult due to incomplete assembly of plasmids. Bacterial isolates can contain any number of plasmids and assembly remains complicated due to the presence of repetitive elements. Numerous tools have been developed to analyse plasmids but the performance and functionality of the tools are variable. The MOB-suite was developed as a set of modular tools for reconstruction and typing of plasmids from draft assembly data to facilitate characterization of plasmids. Using a set of closed genomes with publicly available Illumina data, the MOB-suite identified contigs of plasmid origin with both high sensitivity and specificity (95 and 88 %, respectively). In comparison, plasmidfinder demonstrated high specificity (99 %) but limited sensitivity (50 %). Using the same dataset of 377 known plasmids, MOB-recon accurately reconstructed 207 plasmids so that they were assigned to a single grouping without other plasmid or chromosomal sequences, whereas plasmidSPAdes was only able to accurately reconstruct 102 plasmids. In general, plasmidSPAdes has a tendency to merge different plasmids together, with 208 plasmids undergoing merge events. The MOB-suite reduces the number of errors but produces more hybrid plasmids, with 84 plasmids undergoing both splits and merges. The MOB-suite also provides replicon typing similar to plasmidfinder but with the inclusion of relaxase typing and prediction of conjugation potential. The MOB-suite is written in Python 3 and is available from https://github.com/phac-nml/mob-suite.

Responding to Mycobacterium chimaera heater-cooler unit contamination: international and national intersectoral collaboration coordinated in the state of Queensland, Australia

BACKGROUND

The index case of Mycobacterium chimaera infection in a patient following open cardiac surgery in the state of Queensland, Australia prompted a centralized coordinated response to mitigate the risk.

AIM

To describe the public health response to M. chimaera contamination of heater-cooler units (HCUs) and patient infection.

METHODS

A public health sector strategy was developed with national and international consultation to respond to the threat of HCUs contaminated with M. chimaera. Data linkage of non-tuberculous mycobacterium notifications and selected procedures was undertaken where potential use of HCUs was identified through hospitalization records. Water sampling and testing protocols were standardized. Public disclosure and patient notification were undertaken.

FINDINGS

A single case of disseminated M. chimaera infection in a patient has been diagnosed to date in Queensland, Australia. Ten of 12 (83%) LivaNova Stockert 3T HCUs from five hospitals tested positive for M. chimaera. In total, 5650 patients were notified by post of their potential risk of exposure. Use of the telehealth call centre was modest. M. chimaera was also found in extracorporeal membrane oxygenation heater units produced by two other device manufacturers, four of which tested positive prior to commissioning for use.

CONCLUSIONS

Rapid international collaboration optimized the Queensland Health response to potential M. chimaera exposure during cardiac surgery. State-wide collaboration ensured a transparent, consistent approach to contacting patients and informing the public of the potential risk. A framework for ongoing risk management, clinical awareness and laboratory diagnosis was established. No further cases of M. chimaera infection have been identified in Queensland.

A Systems Approach to Biometrics in the Military Domain

Forensic biometrics is the application of forensic science principles to physical and behavioral characteristics. Forensic biometrics is a secondary sub-system in the forensic science "system of systems," which describes forensic science as a sub-system in the larger criminal justice, law enforcement, intelligence, and military system. The purpose of this paper is to discuss biometrics in the military domain and integration into the wider forensic science system of systems. The holistic system thinking methodology was applied to the U.S. biometric system to map it to the system of systems framework. The U.S. biometric system is used as a case study to help guide other countries to develop military biometric systems that are integrated and interoperable at the whole-of-government level. The aim is to provide the system of systems framework for agencies to consider for proactive design of biometric systems.

Abstract PD5-05: Genomic instability and poor antiproliferative response to aromatase inhibitor treatment: A POETIC study

Background:

More than 20% of early-stage patients with estrogen positive (ER+) disease relapse. Higher levels of the proliferation marker Ki67, and lack of reduction of Ki67 in response to AI indicate poorer prognosis. Somatic mutations have been the focus of research in treatment resistance. However, recurrent somatic copy number alterations (SCNAs) are more common and affect more genes in primary breast cancer (BC) than somatic mutations. Previous studies have suggested an increased risk of recurrence for patients with high genomic instability and for patients with loss of heterozygosity (LOH) at the TP53 locus, but it is unknown if these SCNA events impact response to AI treatment. In addition, LOH and mutations at the TP53 locus had a higher risk of recurrence than LOH or mutations at TP53 alone. We hypothesised that genomic instability and SCNAs at particular loci would be increased in early BC patients with high baseline Ki67, and particularly in patients with high Ki67 despite pre-operative AI therapy.

Methods:

In a substudy of POETIC (UK-wide, phase III, randomised trial with 4483 women testing perioperative AI in postmenopausal women with early BC), SNParray technology was used to determine SCNAs in baseline and surgical tumour core-cuts and blood from 76 patients (59 AI-treated, 17 controls). Proliferation rate was estimated as percentage (%) of cancer cells staining for Ki67 by IHC. Poor AI responders (PR, <60% reduction in Ki67 between baseline and surgery, n=31) and good AI responders (GR, > 75% reduction in Ki67, n=28) were selected from POETIC samples. Mutation data from exome sequencing was available for tumours from 75 of the patients.

Results:

The fraction of the genome with SCNAs correlated with Ki67 expression in both baseline and surgical samples (baseline Spearman rho=0.5, p < 10-5; surgical Spearman rho=0.44, p < 10-3). In paired baseline vs surgical samples, 24% of samples showed discordance in SCNAs that covered > 10% of the genome. The samples showing the highest discordance were from PRs.

The fraction of the genome with LOH was greater in PR (median PR 20%, GR 10%, p = .065), and the best SCNA to predict the fraction of the genome altered in a sample were segments with LOH at Chr17p13.3 (adjusted p < .001, logistic regression). There was a higher percentage of patients with LOH at Chr17p13.3 that contains the TP53 gene in the PR compared to GR group (PR 71%, GR 39%, p = .029), and integration of previously generated mutation data with SCNA showed that 9 out of 31 PRs have mutations and LOH at the TP53 locus compared to 3 out of 28 GRs (p = 0.16).

Conclusions:

There is discordance between the observed SCNAs in paired samples with high genomic instability and multiple biopsies may be needed to confidently assess all SCNAs. However, LOH at Chr17p13.3 is a biomarker for genomic instability and frequency of LOH is significantly greater in patients that show a poor response to AI treatment. Finally, high genomic instability is associated with high proliferation rates at baseline and surgery after 2 weeks of AI treatment suggesting de novo resistance in tumours with high instability that may lead to a higher rate of recurrence seen in these patients.

Citation Format: Schuster EF, Gellert P, Segal CV, López-Knowles E, Buus R, Morden J, Robertson J, Bliss J, Smith I, Dowsett M, POETIC Trial Management Group and Trialists P. Genomic instability and poor antiproliferative response to aromatase inhibitor treatment: A POETIC study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD5-05.

Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR)

Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conventional methods for characterizing Salmonella for use in surveillance and outbreak response. Falling costs and increased throughput of WGS have resulted in an explosion of data, but questions remain as to the reliability and robustness of the data. Due to the critical importance of serovar information to public health, it is essential to have reliable serovar assignments available for all of the Salmonella records. The current study used a systematic assessment and curation of all Salmonella in the sequence read archive (SRA) to assess the state of the data and their utility. A total of 67 758 genomes were assembled de novo and quality-assessed for their assembly metrics as well as species and serovar assignments. A total of 42 400 genomes passed all of the quality criteria but 30.16 % of genomes were deposited without serotype information. These data were used to compare the concordance of reported and predicted serovars for two in silico prediction tools, multi-locus sequence typing (MLST) and the Salmonella in silico Typing Resource (SISTR), which produced predictions that were fully concordant with 87.51 and 91.91 % of the tested isolates, respectively. Concordance of in silico predictions increased when serovar variants were grouped together, 89.25 % for MLST and 94.98 % for SISTR. This study represents the first large-scale validation of serovar information in public genomes and provides a large validated set of genomes, which can be used to benchmark new bioinformatics tools.