A Novel Marine Mammal Coxiella burnetii-Genome Sequencing Identifies a New Genotype with Potential Virulence.

The obligate intracellular bacterial pathogen Coxiella burnetii has been identified in a few species of marine mammals, some of which are showing population declines. It has been hypothesized that C. burnetii in marine mammals is a distinct genotype that varies significantly from the typical terrestrial genotypes. It appears to lack an IS1111. Isolates originating from Australian marine animals have a distinctly non-Australian profile of multiple-locus variable-number tandem-repeat analysis (MLVA). Extracted Coxiella DNA of Australian fur seal placental origin was sequenced using the Novaseq platform. Illumina 150 bp paired-end reads were filtered and trimmed with Trimgalore. The microbial community present in the sequenced genome was evaluated with Kraken and Bracken software using the NCBI database. A phylogenetic analysis was performed using 1131 core genes. Core genes were identified using Panaroo and inputted into Iqtree to determine the maximum-likelihood tree. A second phylogenetic tree was created using Rickettsiella grylii and using seven housekeeping genes. Results were compared with the C. burnetii Nine Mile RSA439 virulent genome. This new Australian marine mammal isolate of Coxiella (PG457) appears to be a novel genotype that lacks IS1111 and has a distinct MLVA signature (ms26, ms27, ms28, ms30, and ms31). The presence of genes for multiple virulence factors appears to give this genotype sufficient pathogenicity for it to be considered a possible causative agent of abortion in Australian fur seals as well as a potential zoonotic risk.

Psittacosis contagion in 1930: an old story in a new era of zoonotic disease.

The SARS-CoV-2 pandemic has highlighted the importance of zoonotic diseases. Psittacosis, a human disease resulting from infection spill-over from Chlamydia psittaci-infected birds, is a lesser-known example of a zoonosis. Psittacosis was responsible for numerous outbreaks in the 1930s, characterised by significant human mortality and disruption to the global trade in parrots. This paper describes the epidemiological and clinical details of one family group impacted by the purchase of an infected, imported parrot. Findings are discussed in the context of a growing awareness of the health risks of global disease outbreaks, as well as social and economic impacts. Health information recorded for cases of psittacosis associated with the 1930 cluster was reviewed using contemporary knowledge of disease symptoms and epidemiology. Case details and autopsy reports were examined. Public health investigation deduced that the cluster of infections was chronologically and physically connected to the purchase and subsequent death of an imported parrot. Disease symptoms were consistent with C. psittaci infection. Epidemiological data supported the diagnoses and causes of death, despite the presenting symptoms sharing significant overlap with other common respiratory diseases. There is growing awareness of the risks of epidemiological bridges in transmitting animal diseases to humans. Historical cases are a strong reminder of the fundamental role of scientific and public health responses in the face of such contagion.

Detection and characterisation of Bordetella hinzii in line-related bacteraemia and respiratory tract infection in Australia.

Bordetella hinzii has emerged as an unusual cause of infection in immunocompromised patients, previously linked to zoonotic transmission. Antimicrobial susceptibility and genetic diversity of B. hinzii are poorly understood. This study reports phenotypic and genomic characteristics of the first four Australian isolates of B. hinzii obtained from elderly immunocompromised patients. Bordetella hinzii isolates were identified by MALDI-TOF and whole genome sequencing (WGS). Antibiotic susceptibility testing was performed using disk diffusion or E-test. Genomes of B. hinzii were analysed in global context. A phylogenetic tree was constructed of all isolates using Roary and a maximum-likelihood tree was generated from the core-snp alignment. Bordetella hinzii minimum inhibitory concentrations (MICs) were largely uniform with high MICs to ampicillin, ceftriaxone and ciprofloxacin and low MICs to meropenem and piperacillin-tazobactam. Genomic analysis of isolate sequences divided strains analysed into two phylogenetically distinct groups, with one Australian B. hinzii isolate (AUS-4) assigned to Group 1, and the remaining isolates (AUS1-AUS3 and AUS-5) to Group 2. Single nucleotide polymorphism (SNP) analysis revealed two isolates, AUS-1 and AUS-2, were closely related with 14 SNP differences between them. All other Australian isolates were unrelated to each and all other isolates from the international dataset. Bordetella hinzii appears to pose a risk to immunocompromised individuals but remains susceptible to extended spectrum ß-lactam and carbapenem antibiotics. Genomic analysis suggested a dissemination of genetically distinct strains.

Medications for early treatment of COVID-19 in Australia.

Early treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can prevent hospitalisation and death in patients with coronavirus disease 2019 (COVID-19) who have one or more risk factors for serious COVID-19 progression. While early treatment presents a range of logistical challenges, clinicians are nevertheless aided by a growing number of approved medications for early treatment of COVID-19. Medications include drugs that inhibit SARS-CoV-2 viral replication, anti-SARS-CoV-2 monoclonal antibody formulations that provide passive immunisation, and immunomodulatory drugs that suppress the body's inflammatory response. Several drugs with different modes of action are approved in Australia for early treatment of COVID-19, including nirmatrelvir plus ritonavir, molnupiravir, and monoclonal antibody formulations. Although these drugs are recommended, clinicians are encouraged to remain up to date on current indications, contraindications and the clinical efficacy of these drugs against SARS-CoV-2 variants currently circulating in communities. Other treatments, including hydroxychloroquine, ivermectin and dietary supplements, have been popularised but are not recommended for early treatment of COVID-19. As new drugs and new data on use of existing approved drugs become available, clinicians face a growing challenge in determining the optimal treatments from the array of options. As it stands, early treatment of COVID-19 needs to be individualised depending on age, pregnancy status, existing medications, and renal and liver disease status. Future treatments in development might have roles in patients with lower risk profiles and in reducing transmission as we learn to live with SARS-CoV-2.

The first Australian experience with ward-based continuous positive airway pressure for COVID-19 respiratory failure: a retrospective cohort study.

We present the first Australian cohort of patients with COVID-19 respiratory failure managed with escalating respiratory support including continuous positive airway pressure (CPAP) on a standard medical ward at a tertiary Sydney hospital during the 2021 COVID-19 Delta variant outbreak. We demonstrate an equivalent mortality to CPAP delivered in intensive care unit and outline our ward structure and management during the pandemic.

Efficacy of Intra-Operative Topical Wound Anaesthesia to Mitigate Piglet Castration Pain-A Large, Multi-Centred Field Trial.

Piglet castration results in acute pain and stress to the animal. There is a critical need for effective on-farm methods of pain mitigation. Local anaesthesia using Tri-Solfen® (Animal Ethics Pty Ltd., Melbourne, Australia), a topical local anaesthetic and antiseptic formulation instilled to the wound during surgery, is a newly evolving on-farm method to mitigate castration pain. To investigate the efficacy of Tri-Solfen®, instilled to the wound during the procedure, to alleviate subsequent castration-related pain in neonatal piglets, we performed a large, negatively controlled, randomised field trial in two commercial pig farms in Europe. Piglets (173) were enrolled and randomised to undergo castration with or without Tri-Solfen®, instilled to the wound immediately following skin incision. A 30 s wait period was then observed prior to completing castration. Efficacy was investigated by measuring pain-induced motor and vocal responses during the subsequent procedure and post-operative pain-related behaviour in treated versus untreated piglets. There was a significant reduction in nociceptive motor and vocal response during castration and in the post-operative pain-related behaviour response in Tri-Solfen®-treated compared to untreated piglets, in the first 30 min following castration. Although not addressing pain of skin incision, Tri-Solfen® is effective to mitigate subsequent acute castration-related pain in piglets under commercial production conditions.

Dirofilaria repens microfilaremia in humans: Case description and literature review.

INTRODUCTION: Dirofilaria repens is a vector-borne filaroid helminth of carnivorous animals, primarily domesticated dogs. Humans are considered to be accidental hosts in which D. repens rarely reach sexual maturity but induce local inflammation, mainly in subcutaneous and ocular tissues. METHODS: In the current study, we present the detection of multiple adults of D. repens, endosymbiont Wolbachia sp. and microfilariae by molecular analysis in peripheral tissues and bloodstream of a human host. A subsequent meta-analysis of published literature identified 21 cases of human infection with adult D. repens producing microfilariae. RESULTS: Within the study population, there were 13 (59.09%) males, eight (36.36%) females and, in one (4.55%) case, sex was not reported. A total of 11 (50.00%) cases had subcutaneous dirofilariasis, six (27.27%) had ocular dirofiliariasis, with single cases (4.55% each) of genital, mammary, lymphatic and a combination of subcutaneous and pulmonary dirofilariasis described. In one (4.55%) case, the primary anatomical site of adult D. repens could not be found. D. repens microfilariae were detected in the local tissue (local microfilariasis) in 11 (50.00%) cases and the peripheral blood (microfilaremia) in 11 (50.50%) cases. Final identification of D. repens microfilariae was based on morphological detection in 14 (63.64%) cases, and molecular detection in eight (36.36%) cases. CONCLUSION: The results of this study suggest that humans may act as a final host for D. repens, however its role as a source of D. repens infection is less clear.

Evaluation of the BioFire Blood Culture Identification 2 panel and impact on patient management and antimicrobial stewardship.

Bloodstream infection survival is linked to timely administration of optimal antimicrobial therapy. Commercial multiplex polymerase chain reaction (PCR) assays, such as the BioFire Blood Culture Identification Panel (BCID) used for the rapid diagnosis of bloodstream infections, have significantly improved the turnaround time for optimisation of antimicrobial therapy. Reported concordance with culture-based methods and multiplex PCR analysis is high and only limited by (1) the range of targets available on the multiplex panel; and (2) the complexity of microorganisms present in the blood culture specimen. In this study, we evaluated the use of the BioFire Blood Culture Identification 2 panel (BCID2), including an expanded repertoire of targets for Gram-positive and Gram-negative bacteria, yeast and antimicrobial resistance genes compared to the BCID panel. The BCID2 panel identified microorganisms in 39/42 (92.9%) blood cultures where monomicrobial growth was detected; the three unidentified blood cultures contained organisms not included in the BCID2 panel. Polymicrobial blood culture analysis revealed a lower degree of concordance (28.6%); however, most disagreement was due to the culture-based identification of off-panel microorganisms of low clinical significance. Turnaround time, from blood culture collection to organism identification on the blood cultures correctly identified by BCID2, was 24.6 (±16.8) hours for the BCID2 panel versus 38.2 (±21.9) hours for conventional methods. Analysis of the theoretical impact of the BCID2 identification on clinical management found therapy would be altered in 45.1% (23/51) of patients. The BCID2 panel is anticipated to improve the diagnosis and antimicrobial management of patients with serious bloodstream infections.

Topical Application of Lidocaine and Bupivacaine to Disbudding Wounds in Dairy Calves: Safety, Toxicology and Wound Healing.

Tri-Solfen® is a combination topical anaesthetic and antiseptic solution containing lidocaine, bupivacaine, adrenaline and cetrimide. Applied to wounds, it is reported to reduce the pain experienced by calves following thermocautery disbudding. While lidocaine and bupivacaine are widely used in medicine, conflicting data exist on the impact of these compounds when applied directly to the surgical wound. To investigate the safety of Tri-Solfen® applied to thermocautery disbudding wounds of calves, experiments were performed to measure (i) the safety of Tri-Solfen® (including in overdose situations); and (ii) the impact of Tri-Solfen® application at recommended doses on disbudding wound healing under field conditions. Haematological, biochemical and urinalysis parameters did not show clinically significant differences between placebo and Tri-Solfen® groups (1×, 3× and 5× dose). No adverse health impacts were reported. Histopathological analysis of wounds noted a reduction in bacterial colonies in Tri-Solfen®-treated wounds. Under field conditions, no negative impacts on wound healing were noted. Conversely, there was reduced incidence of abnormal wounds, with an associated trend toward improved average daily gain at days 11-12 in Tri-Solfen®-treated animals. These data are considered to support the safety of topical anaesthesia, as formulated in Tri-Solfen®, to the thermocautery disbudding wound in calves.

An Australian diagnostic microbiology surge response to the COVID-19 pandemic.

Diagnostic microbiology services form a critical component of the response to infectious disease outbreaks. Like previous respiratory virus pandemics, the COVID-19 pandemic has placed significant strains on the standing capacity of laboratories around the world. In this case study, we describe the surge response required by our laboratory to meet the fluctuating demand for SARS-CoV-2 in our regional pathology service in Western Sydney, Australia between March and May 2020. While the overall number of SARS-CoV-2 PCR positive cases was relatively low compared to other Australian local health districts, testing numbers were highly unpredictable and changed on a weekly basis as local outbreaks were detected. As with other laboratories, numerous other challenges were also faced during this period, including the requirement to introduce a new and unaccredited diagnostic PCR assay for SARS-CoV-2, local and global shortages of reagents for sampling and sample processing, and a significant institutional SARS-CoV-2 outbreak in our laboratory catchment area. A successful service delivery during this period could only be maintained by a dynamic whole-of-laboratory and organizational response including (1) operational changes to the hours of service and the expansion of diagnostic testing at our laboratory site and other sites within our organization (2) careful management of specialist staff and re-training and recruitment of additional staff (3) changes to laboratory workflows to improve SARS-CoV-2 PCR test turnaround time and to accommodate limits to precious laboratory reagents; (4) clear communication within our laboratory and the NSW Health Pathology organization; and (5) collaborative co-ordination and support by NSW Health Pathology.

Chlamydia pecorum-Induced Arthritis in Experimentally and Naturally Infected Sheep.

Chlamydia pecorum is an obligate intracellular pathogen with a wide host range including livestock such as sheep, cattle, goats, and pigs as well as wildlife species such as koalas. Chlamydial polyarthritis is an economically important disease resulting in swollen joints, lameness, stiffness, and weight loss in young sheep. In the present study, tissues from sheep experimentally or naturally infected with Chlamydia pecorum were assessed by histopathology and immunohistochemistry. Carpal, hock, and stifle joints as well as spleen, liver, kidney, lymph nodes, lung, and brain of 35 sheep from different inoculation groups were available. Two different C. pecorum strains (IPA and E58), different routes of administration (intraarticular or intravenous), UVA-irradiated IPA strain, and corresponding noninfected control groups were investigated. Similar investigations on tissues from 5 naturally infected sheep were performed. The most obvious inflammatory lesions were observed in synovial tissues and, notably, in the renal pelvis from the experimentally infected group and naturally infected animals. This resulted in chronic or chronic-active arthritis and pyelitis. Intralesional chlamydial inclusions could be demonstrated by immunohistochemistry in both tissues. Immunohistochemical evaluation of the presence and distribution of macrophages, T and B cells in synovial tissues revealed macrophages as the most prevalent inflammatory cell population. Previous observations indicated that C. pecorum isolates can infect circulating monocytes. Together with the finding of the histological lesions in synovial tissues and internal organs alongside the presence of C. pecorum DNA, these observations suggest chlamydial arthritis in lambs is the result of hematogeneous spread of C. pecorum.

The trends of human dirofilariasis in Croatia: Yesterday - Today - Tomorrow.

INTRODUCTION: Human dirofilariasis is a disease historically linked to the Mediterranean area. For the last few decades, however, Dirofilaria nematodes have been spreading, both in terms of prevalence and the geographical expansion in non-endemic areas. Currently, cases of human dirofilariasis are recorded in more than 40 countries worldwide. Croatia is considered an endemic area of the Adriatic basin. METHODS: In a nationwide investigation, new and previously published cases of human dirofilariasis in Croatia were analyzed. RESULTS: Since 1996, 30 cases of human dirofilariosis were reported in Croatia. A total of 14 (46,67%) cases were from the coastal and 16 (53,33%) from continental regions of the country. Based on anatomical location, 13 (43,33%) cases were subcutaneous, 12 (40%) were ocular and five (16,67%) occurred in the reproductive organs. In all 30 cases, Dirofilaria repens was identified as the causative agent. CONCLUSIONS: An increase in air temperature as climate change, changes in mosquito fauna, high prevalence of D. repens in dogs and limited use of chemoprophylaxis are possible risk factors for Dirofilaria infection in the Croatian population. Since reporting to epidemiological services is not mandatory in this country, the real number of human dirofilariasis cases is probably significantly higher than published. This emphasizes the need for mandatory reporting of human cases and surveillance of Dirofilaria infection in dogs and mosquitoes in Croatia, following the "One Health" concept.

Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia.

BACKGROUND: Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites. METHODS: We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences. RESULTS: We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians. CONCLUSIONS: To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.

Optimal Methods of Documenting Analgesic Efficacy in Neonatal Piglets Undergoing Castration.

Analgesic products for piglet castration are critically needed. This requires extensive animal experimentation such as to meet regulatory-required proof of efficacy. At present, there are no validated methods of assessing pain in neonatal piglets. This poses challenges for investigators to optimize trial design and to meet ethical obligations to minimize the number of animals needed. Pain in neonatal piglets may be subtle, transient, and/or variably expressed and, in the absence of validated methods, investigators must rely on using a range of biochemical, physiological and behavioural variables, many of which appear to have very low (or unknown) sensitivity or specificity for documenting pain, or pain-relieving effects. A previous systematic review of this subject was hampered by the high degree of variability in the literature base both in terms of methods used to assess pain and pain mitigation, as well as in outcomes reported. In this setting we provide a narrative review to assist in determining the optimal methods currently available to detect piglet pain during castration and methods to mitigate castration-induced pain. In overview, the optimal outcome variables identified are nociceptive motor and vocal response scores during castration and quantitative sensory-threshold response testing and pain-associated behaviour scores following castration.