The Strain Australia

[Ling Baus]

Withgeneral use, muscles gently contract to resist overstretching. However, sudden twists or jolts can apply greater force than the tissue can tolerate, resulting in a tear or rupture of the fibres. The damage to these fibres triggers an immune reaction called inflammation.

Inflammation is a complex cascade of biological processes that results in the classic swelling, redness and tenderness associated with sprains and strains. In higher-grade injuries, bleeding from broken blood vessels increases the degree of swelling.

Muscles contract (or shorten) and pull on their tendon insertion into the bone and thus produce movement of a joint. Multi-joint muscles (like the hamstrings, quadriceps and our main calf muscle called the gastrocnemius) are injured at much higher rates than single joint muscles.

Most soft tissue injuries take a few weeks to heal, depending on the severity of the sprain or strain, any subsequent injuries or issues such as weakness, stiffness, poor balance or function, and the general health of the person.

Lateral ankle sprains (one of the most common ligament sprains) have an average return to play time of 2.5 weeks. However, the variation can be large with some studies citing return to play times of over 100 days for some hamstring strains and ankle sprains.

Severe injuries, where the tissue has completely ruptured, may need surgery to put the torn pieces back together. Surgically repaired grade III injuries will require significant treatment to regain strength and function.

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Now genomic research by our team of scientists has identified this new strain in the Australian community for the first time. In parallel, we have seen an increase in invasive strep A cases across New South Wales, Queensland, Western Australia and Victoria.

Our researchers will have access to a repository of national strep A strains. We will be piloting a national strep A genomic surveillance program within the AusPathoGen program, which will speed up our ability to identify and track emerging strep A variants.

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Scarlet fever isolates circulating in Asia are associated with a repertoire of toxin genes, which encode superantigens ssa and speC, and the DNase spd1 toxin6,8,9,10,24. In Australia, 26% of circulating M1UK sub-lineages also contain this novel toxin gene repertoire, suggesting independent acquisition of mobile genetic elements into distinct M1UK sub-lineages, likely as a result of strong positive selection pressure. The contribution of SSA, SpeC, and Spd1 to intranasal colonization of HLA-B6 mice has been explored in an emm12 scarlet fever isolate10, and future studies to determine the contribution of SSA, SpeC, and Spd1 to M1UK virulence are warranted.

The emergence of the M1UK lineage in the UK has been epidemiologically linked to increases in invasive disease and seasonal surges of scarlet fever19,20. Over the course of this study, neither scarlet fever nor S. pyogenes invasive infections were nationally notifiable in Australia. While we have not seen an increase in Queensland notifiable invasive S. pyogenes51 and Queensland Emergency Department Information System scarlet fever numbers in 2020 and 2021, any potential increase may have been mitigated by the public health interventions in response to COVID-19. Comparatively, social distancing measures introduced to combat the COVID-19 pandemic more effectively suppressed other respiratory infections such as pertussis and influenza51 (Supplementary Table 2). The ongoing replacement of the S. pyogenes M1global clone with M1UK in Australia and elsewhere demands heightened vigilance to determine the future clinical impact of this new variant.

All 318 Australian S. pyogenes isolates were obtained from the Queensland Health Department (Human Research Ethics Committee Reference numbers: HREC/10/QRCH/113 and HEC20-01) or from the Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria (Human Research Ethics Committee Reference number: 1954615) under the Victorian Public Health and Wellbeing Act 2008. These came predominantly from state-based public health reference laboratories in Queensland and Victoria, which together provided 310 invasive isolates from sterile body sites collected between 2005 and 2020. In Queensland, invasive S. pyogenes infections are notifiable and 238 invasive isolates originated from this state, while another 72 were from Victoria where such infections became notifiable only in 2022 prior to which, referral to the state public health microbiology laboratory was not a routine requirement. The remaining eight isolates were from the throats of Queensland children with scarlet fever.

Reference genomes were aligned using MAUVE v2.4.0 genome aligner. Smaller genomic differences were assessed using a custom pipeline based on the tool ekidna v0.3.0 ( ). In brief, reference genomes were mapped and variants called using paftools as part of minimap2 v2.2454. Conserved indels present in all 4 M1UK reference genomes and absent in the 2 M1global reference strains (HKU488, SP1426) were obtained using vcf-isec from VCFtools v0.1.16.

A database of 736 M1 S. pyogenes genomes (317 from this study) and 419 high-quality sequences from publicly available genome sequences across 5 continents was generated (BioProject PRJNA872282, Supplementary Data 1). Illumina paired-end short reads were mapped to the reference sequence (MGAS5005) using BWA-MEM2 as part of snippy v4.6.0 (github/tseemann/snippy) and the core genome alignment determined using snippy-core with default settings. Functional annotations of SNPs and small indels were performed using SnpEff v4.3t55 as part of snippy and multi-VCF file collated with VCFtools.

Virulence factors and genes of interest identified in the mobile genetic elements contained in genome sequences were screened using screen_assembly v1.2.764. Initial screens to detect gene presence were undertaken with 80% identity and 80% length. emm-typer commit: 500d048 on branch: master ( -PHL/emmtyper) was used to define S. pyogenes emm type.

Raw RNA-seq reads were quality assured using FastQC v0.11.068 and MultiQC v1.969. TrimGalore v0.6.5 was used to trim Illumina primers ( ). Reads of ribosomal RNA were filtered using SortMeRNA v4.2.070 and rRNA extracted from S. pyogenes stain SF370, 5448, and HKU488. Reads were aligned to respective reference genomes using BWA-MEM v0.7.17. Reads within features were counted using featureCounts from Subreads v2.0.071. Reads were counted with strand specificity and multi-mapped reads were counted at largest overlapping feature. Differential expression analysis was done using DEseq2 v1.32.072 and edgeR v2.23.173 in R 4.1.1.

The work was supported by the National Health and Medical Research Council of Australia. We acknowledge the support of staff at Queensland Health Forensic and Scientific Services (funded by the Queensland Government) and the Microbiological Diagnostic Unit Public Health Laboratory (funded by the Victorian Government). We acknowledge Prof. Kwok-Yung Yuen (Hong Kong University) for providing S. pyogenes isolate HKU488.

The first detection of an H7N3 HPAI strain was confirmed on 22 May 2024 at a poultry farm near Meredith, in the Golden Plains Shire, Victoria. Six other poultry farms in the shire are now infected, with the most recent confirmed on 24 June.

The NSW Department of Primary Industries is currently responding to 6 outbreaks of H7N8 in poultry in the Hawkesbury district. The first was an egg farm confirmed on 19 June, and then on 22 June a broiler (chicken meat) farm located within the existing Restricted Area, was confirmed with the same strain.

A nationally agreed response plan to control and eradicate HPAI in Victoria is being implemented and regularly reviewed as the response progresses. A response plan has been prepared for implementation in NSW.

Testing at the CSIRO's Australian Centre for Disease Preparedness laboratory confirmed that these strains are genetically related to viruses previously detected in Australian wild birds. The viruses are not the H5 strain currently causing concern globally.

Restricted Areas have been established around all infected premises in Victoria, NSW, and the ACT. A broader Control Area buffers the restricted areas. Within Restricted and Control areas, there are restrictions on the movement of poultry and birds, poultry products, equipment and certain vehicles.

Housing requirements have been issued by Agriculture Victoria for poultry and birds on properties within the Restricted and Control Areas. This requirement to house or keep poultry enclosed in cages or sheds helps to minimise contact with wild birds and reduces but does not eliminate the risk of spreading the disease.

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