Pathwest Laboratory Medicine

Short tandem repeat expansions are associated with over 50 diseases, many with primary neurological presentations. Despite the prevalence of short tandem repeat expansion disorders, genetically diagnosing these conditions is complicated by a lack of efficient and comprehensive diagnostic screening approaches. We integrated a new short tandem repeat genotyping tool, STRipy, into the analytical workflow for short-read sequencing data generated by the comprehensive neurological disease gene panel used in the Diagnostic Genomics Department, PathWest Laboratory Medicine. We tested STRipy on Versions 6 and 7 of the panel. Version 6 already included probes covering five short tandem repeat expansion loci in the following genes: CACNA1A, PPP2R2B, TBP, NOP56 and RFC1. Additional probes targeting 13 neurological disease short tandem repeat expansion loci were designed and included in Version 7. All expansions detected by STRipy were validated and sized using PCR-based diagnostic techniques. Four hundred and eighteen patients with ataxia were tested on Version 6 of the panel, and 61 (14.6%) had reportable pathogenic variants, including 11 patients with pathogenic repeat expansions detected by STRipy. Sixty-seven ataxia patients were tested on Version 7 of the panel, and 15 (22.4%) had reportable pathogenic variants, including three repeat expansions detected by STRipy. Therefore, STRipy contributed 18.0% and 20.0% of the solved cases from Version 6 and 7 of the ataxia subpanels, respectively. STRipy accurately identified and sized loci with shorter pathogenic repeat thresholds where the expansion was smaller than the read length. In addition to increased diagnostic yield, implementation of STRipy into diagnostic analysis pipelines has streamlined clinical diagnosis of short tandem repeat expansion disorders.

Immune checkpoint inhibitor immunotherapy enhances T cell activity against cancer cells but often leads to the immune system targeting healthy cells, causing 'immune-related adverse events' (irAEs). We report the case of a man in his 70s with metastatic melanoma being treated with ipilimumab and nivolumab. He presented with febrile neutropenia after lacerating a thumb on his compost bin. The neutrophil count only recovered once oral prednisolone was commenced, indicating a haematological irAE. A restaging Positron Emission Tomography scan revealed intramuscular ring-enhancing collections throughout his body, one of which was aspirated and cultured the fungus Lomentospora prolificans He was treated with voriconazole plus terbinafine, both of which were later substituted with olorofim due to a voriconazole-induced rash. After 4 months, the collections had resolved on repeat imaging, and olorofim was ceased due to transaminitis. This case highlights neutropenia as a lesser-known adverse effect of immunotherapy and raises awareness about L. prolificans infection.

Anaplastic thyroid cancer (ATC) is a rare and aggressive malignancy with limited treatment options and a poor prognosis. This study evaluates the outcomes of patients with locally advanced or metastatic ATC treated at two tertiary centres, focusing on the efficacy of pembrolizumab and lenvatinib, and the impact of BRAF status. A retrospective review of 16 ATC patients treated between January 2018 and June 2024 at two tertiary Australian hospitals was conducted. Pathological confirmation was required for inclusion. Clinical data, including treatment regimens, response rates assessed by Response Evaluation Criteria in Solid Tumours version 1.1 (RECIST 1.1), progression-free survival (PFS), and overall survival (OS), were analysed. Fifteen out of 16 patients (94%) had metastatic disease. Five patients (31%) had a BRAFV600E mutation, with four receiving first-line (1L) dabrafenib/trametinib, achieving a 75% (3/4) objective response rate. Eleven patients (50%) were BRAF wildtype, and eight received pembrolizumab and lenvatinib as both 1L and second-line (2L) settings, with an objective response rate of 75% (6/8) in both 1L and 2L settings, including three complete responses. Programmed death-ligand 1 tumour proportional score ≥50% was found in 64% (9/14) of patients, correlating with better outcomes. Median time on treatment for the pembrolizumab and lenvatinib group was not reached, with the longest survival exceeding 12 months at the time of data cut-off. This case series highlights promising outcomes with systemic treatment options in ATC, but the analysis is limited by a small sample size, emphasising the need for further research and collaboration to improve clinical outcomes.

BAP1-inactivated melanocytic tumor (BIMT) represents a distinct subtype of melanocytoma, with characteristic morphologic features. These lesions are associated with inactivation of the BAP1 tumor suppressor gene. Although there are frequently histologic features that might otherwise cause concern for malignancy, including enlarged cells with nuclear variability, prominent nucleoli, and a lymphocytic inflammatory infiltrate, empirical data suggest that the majority behave in a clinically benign fashion. We report 2 cases of cutaneous BIMT with a distinctive morphologic pattern of clonal expansion with p16 loss. In both cases, there was liver metastasis after complete excision, in the absence of locoregional recurrence. These rare cases highlight the possibility of a distinct pathway of malignant progression in BIMT.

Neisseria meningitidis is a colonizer of the human nasopharynx which occasionally causes invasive meningococcal disease. Despite numerous reports of penicillin-resistant isolates, antimicrobial-resistant meningococcal clones have historically not persisted over long time periods or become globally distributed, presumably due to the imposed fitness cost associated with antimicrobial resistance. One exception is a penicillin-resistant clade of serogroup W clonal complex 11 (MenW:cc11) isolates identified in Western Australia in 2013, which has since caused disease globally. Here, we investigated the genomic changes associated with penicillin resistance in MenW:cc11 isolated during the 2013-2020 Western Australian meningococcal outbreak. Seventy-six MenW:cc11 disease-causing isolates underwent short-read whole genome sequencing. Reference genomes were generated for three isolates. In accordance with previous analysis, two phylogenetically distinct clusters were identified: cluster A (12 penicillin-susceptible isolates) and cluster B (63 penicillin-resistant isolates). Genomic comparison of the cluster A and cluster B isolates revealed 128 allelic differences present at the branching point between the two lineages. The differences included polymorphisms in genes associated with cell wall regulation, pilus biogenesis and the MtrR transcriptional regulator. A further 60 allelic changes were identified in the Western Australian isolates which were not identified in globally distributed cluster B isolates. In a search of the PubMLST Neisseria database, all allelic variants associated with the emergence of cluster B were found exclusively in other hypervirulent lineages. Taken together, the data suggest the global success of the penicillin-resistant N. meningitidis is due to compensatory mutations acquired through horizontal exchange from other hypervirulent lineages.

The kava plant is native to the Pacific Islands. A mildly psychoactive beverage, also referred to as kava, made from the roots and stems of this plant, is widely ingested in these regions for social, cultural, and medicinal purposes. In recent years, kava extracts in various forms have been used in conventional Western and alternative medicine. Although chronic ingestion of large amounts of kava is well known to cause an icthyosiform skin condition, acute reactions are less well described. We report 3 patients of non-Pacific Islander background who developed acute reactions, clinically resembling drug reaction with eosinophilia and systemic symptoms, after commencement of kava ingestion following recent regulatory changes, making this product more widely available. In all 3 patients, skin biopsy revealed a distinctive and unusual pattern of sebaceous adenitis with single cell apoptosis.

Short Synacthen testing (SST) is resource intensive and may be unnecessary if adrenal sufficiency (AS) can be predicted reliably using basal cortisol (BC). This work aimed to identify the BC threshold predictive of AS and evaluate the utility of 30- and 60-minute stimulated cortisol measurements in response to SST. This research took place at a public tertiary pathology service (PathWest) in Western Australia. Of 1216 SSTs performed, 704 adult results were eligible. Exclusions were based on incomplete data or protocol deviations. Intervention was intramuscular Synacthen 250 mcg with cortisol measured at baseline, 30, and 60 minutes. AS was defined as serum cortisol greater than 430 nmol/L at 30 minutes and/or greater than 500 nmol/L at 60 minutes. Receiver operating characteristic analysis identified BC thresholds predicting AS with 95% specificity. Of 704 SSTs included, 571 (81%) demonstrated AS. BC of 335 nmol/L or greater predicted AS at either 30 or 60 minutes. In a subgroup with pituitary pathology, a lower threshold of 240 nmol/L or greater maintained 95% specificity. For samples collected after 0945 hours, BC of 251 nmol/L or greater predicted AS. Applying these thresholds could have avoided 31.1% of SSTs. Nineteen patients (2.7%) passed SST solely at the 60-minute cortisol result with median cortisol of 420 nmol/L. BC reliably predicts AS, avoiding unnecessary SST in a substantial number of patients. Adjusted thresholds for pituitary pathology and by time of day can enhance accuracy. Both 30- and 60-minute poststimulation cortisol identified a small group who would have failed SST using a single poststimulation measurement.