A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.

Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.

A cross-sectional investigation of the factors associated with awareness of PEP and PrEP among Queensland university students.

OBJECTIVE: University creates unique social environments for many young people that can result in behaviour changes that can impact sexual health-related risks and facilitate transmission of HIV. Little is known about HIV knowledge, risk, and awareness of pre-exposure prophylaxis/post-exposure prophylaxis (PrEP/PEP) among Australian university students. METHODS: A 2019 online survey distributed through Queensland universities, using active recruitment/snowball sampling. Descriptive and logistical regression analysis investigated HIV knowledge/risk and PrEP/PEP awareness. RESULTS: Of the 4,291 responses, 60.4% were 20-29 years old, 57.0% identified as heterosexual, and 31.8% were born-overseas. Mean HIV knowledge score was 9.8/12. HIV risk scores were higher among men-who-have-sex-with-men (MSM) (mean=5.2/40) compared to all other sexual behaviours (mean=3.1/40). Logistic regression indicated PrEP and PEP awareness was associated with older age (p<0.05), being non-binary/gender-diverse (p<0.05), and MSM (p<0.05). Lower odds of PrEP awareness were associated with international student status (p<0.05). CONCLUSION: This study highlights the need for future health promotion targeting younger Australians at risk of HIV to increase uptake of PrEP/PEP, particularly among overseas-born young people and those ineligible for appropriate health care in Australia. IMPLICATIONS FOR PUBLIC HEALTH: Addressing these gaps will improve sexual health outcomes for young Australians at risk of HIV and work towards virtual elimination of HIV transmission in Australia.

Linking differences in microbial network structure with changes in coral larval settlement.

Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

Validation of key sponge symbiont pathways using genome-centric metatranscriptomics.

The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.

Antimicrobial susceptibility assays for Neisseria gonorrhoeae: a proof-of-principle population-based retrospective analysis.

BACKGROUND: Neisseria gonorrhoeae treatment guided by molecular antimicrobial susceptibility assays could improve treatment options and antimicrobial stewardship; however, few commercial assays are available. We aimed to investigate antimicrobial susceptibility of N gonorrhoeae isolates in New South Wales, Australia, and estimate the potential usefulness of hypothetical combinations of rapid molecular antimicrobial susceptibility assays. METHODS: In this proof-of-principle, population-based, retrospective analysis, we assessed N gonorrhoeae susceptibility data for ceftriaxone, azithromycin, ciprofloxacin, and penicillin. Isolates were previously collected as part of the Australian Gonococcal Surveillance Programme between Jan 1, 2008, and Dec 31, 2019. All cultured N gonorrhoeae isolates with susceptibility data to all four antimicrobials were included. However, only one isolate was included if several isolates originated from the same individual within 13 days of the previous isolate originating from that individual, and there were less than two standard double-dilution minimum inhibitory concentrations between the isolates. We assessed the use of different combinations of hypothetical antimicrobial susceptibility assays and treatment combinations in terms of their ability to minimise overall ceftriaxone use, and use specifically in isolates with decreased susceptibility to ceftriaxone, compared with standard non-assay-guided empirical ceftriaxone treatment. FINDINGS: We included 23 089 N gonorrhoeae isolates. The prevalence of antimicrobial sensitivity fluctuated significantly during the study. Isolates with decreased susceptibility to ceftriaxone were more likely to be resistant to one or more antimicrobials than isolates without decreased susceptibility (782 [98·6%] of 793 vs 10 661 [47·8%] of 22 296), particularly ciprofloxacin (p<0·0001) and penicillin (p<0·0001). Compared with empirical ceftriaxone treatment, we estimated that strategies based on the use of hypothetical antimicrobial susceptibility would reduce ceftriaxone use (p<0·0001). However, because of co-resistance, most assay-directed treatment strategies, including those involving use of assays for two antibiotics, would result in only moderate reductions in ceftriaxone use among isolates with decreased susceptibility to ceftriaxone. INTERPRETATION: Individualised treatment guided by molecular antimicrobial susceptibility diagnostics could help to reduce overall ceftriaxone use in gonorrhoea. However, the use of these assays needs to be informed by the non-random nature of co-resistance among circulating N gonorrhoeae strains. FUNDING: Australian Government and Queensland Government.

STI and HIV testing: examining factors that influence uptake among domestic Australian-born, domestic overseas-born and international tertiary students studying in Australia.

OBJECTIVES: Sexual health knowledge among international students in Australia is lower than domestic students, however, little is known about what factors affect the uptake of STI testing, nor if there are differences for overseas-born domestic students. METHODS: We included sexually active respondents from a survey of university students in Australia (N = 3,075). Multivariate regression and mediation analyses investigated associations of STI and HIV testing with STI and HIV knowledge respectively, sexual risk behaviour and demographics, including comparisons among: domestic Australian-born, domestic overseas-born, and international students. RESULTS: STI and HIV knowledge was positively associated with STI and HIV testing respectively (STI OR = 1.13, 95% CI: 1.09, 1.16; HIV OR = 1.37, 95% CI: 1.27, 1.48). STI knowledge was significantly lower for international than domestic Australian-born students (10.8 vs. 12.2 out of 16), as was STI testing (32% vs. 38%); the difference in knowledge accounted for half the difference in STI testing rates between these two groups. International students from Southern Asia, and Eastern Asia reported the lowest STI testing rates. HIV testing was highest amongst international students from Africa and North America. Higher sexual risk behaviour, younger age, and identifying as gay or bisexual were positively associated with higher STI and HIV testing rates. CONCLUSIONS: Our study supports greater investment and commitment by universities for the provision of sexual health education that can promote access to testing to improve the health of their students.

Characterization of Influenza-Like Illness Burden Using Commercial Wearable Sensor Data and Patient-Reported Outcomes: Mixed Methods Cohort Study.

BACKGROUND: The burden of influenza-like illness (ILI) is typically estimated via hospitalizations and deaths. However, ILI-associated morbidity that does not require hospitalization remains poorly characterized. OBJECTIVE: The main objective of this study was to characterize ILI burden using commercial wearable sensor data and investigate the extent to which these data correlate with self-reported illness severity and duration. Furthermore, we aimed to determine whether ILI-associated changes in wearable sensor data differed between care-seeking and non-care-seeking populations as well as between those with confirmed influenza infection and those with ILI symptoms only. METHODS: This study comprised participants enrolled in either the FluStudy2020 or the Home Testing of Respiratory Illness (HTRI) study; both studies were similar in design and conducted between December 2019 and October 2020 in the United States. The participants self-reported ILI-related symptoms and health care-seeking behaviors via daily, biweekly, and monthly surveys. Wearable sensor data were recorded for 120 and 150 days for FluStudy2020 and HTRI, respectively. The following features were assessed: total daily steps, active time (time spent with >50 steps per minute), sleep duration, sleep efficiency, and resting heart rate. ILI-related changes in wearable sensor data were compared between the participants who sought health care and those who did not and between the participants who tested positive for influenza and those with symptoms only. Correlative analyses were performed between wearable sensor data and patient-reported outcomes. RESULTS: After combining the FluStudy2020 and HTRI data sets, the final ILI population comprised 2435 participants. Compared with healthy days (baseline), the participants with ILI exhibited significantly reduced total daily steps, active time, and sleep efficiency as well as increased sleep duration and resting heart rate. Deviations from baseline typically began before symptom onset and were greater in the participants who sought health care than in those who did not and greater in the participants who tested positive for influenza than in those with symptoms only. During an ILI event, changes in wearable sensor data consistently varied with those in patient-reported outcomes. CONCLUSIONS: Our results underscore the potential of wearable sensors to discriminate not only between individuals with and without influenza infections but also between care-seeking and non-care-seeking populations, which may have future application in health care resource planning. TRIAL REGISTRATION: Clinicaltrials.gov NCT04245800; https://clinicaltrials.gov/ct2/show/NCT04245800.

Predictors of Seeking Care for Influenza-Like Illness in a Novel Digital Study.

Background: Previous research has estimated that >50% of individuals experiencing influenza-like illness (ILI) do not seek health care. Understanding factors influencing care-seeking behavior for viral respiratory infections may help inform policies to improve access to care and protect public health. We used person-generated health data (PGHD) to identify factors associated with seeking care for ILI. Methods: Two observational studies (FluStudy2020, ISP) were conducted during the United States 2019-2020 influenza season. Participants self-reported ILI symptoms using the online Evidation platform. A log-binomial regression model was used to identify factors associated with seeking care. Results: Of 1667 participants in FluStudy2020 and 47 480 participants in ISP eligible for analysis, 518 (31.1%) and 11 426 (24.1%), respectively, sought health care. Participants were mostly female (92.2% FluStudy2020, 80.6% ISP) and aged 18-49 years (89.6% FluStudy2020, 89.8% ISP). In FluStudy2020, factors associated with seeking care included having health insurance (risk ratio [RR], 2.14; 95% CI, 1.30-3.54), more severe respiratory symptoms (RR, 1.53; 95% CI, 1.37-1.71), and comorbidities (RR, 1.37; 95% CI, 1.20-1.58). In ISP, the strongest predictor of seeking care was high symptom number (RR for 6/7 symptoms, 2.14; 95% CI, 1.93-2.38). Conclusions: Using PGHD, we confirmed low rates of health care-seeking behavior for ILI and show that having health insurance, comorbidities, and a high symptom burden were associated with seeking health care. Reducing barriers in access to care for viral respiratory infections may lead to better disease management and contribute to protecting public health.

Integrated silicon microfluidic chip for picoliter-scale analyte segmentation and microscale printing for mass spectrometry imaging.

A silicon single-chip microfluidics system that integrates microscale fluidic channels, an analyte segmentation device, and a nozzle for electrohydrodynamic-assisted printing is designed for hyphenation with MALDI mass spectrometry (MS) imaging. A miniaturized T-junction segments analytes into monodisperse picoliter oil-isolated compartments. The printing nozzle deposits generated droplets one-by-one into an array on a conductive substrate without splitting or coalescing. Virtually single-shot MS analysis is enabled due to the ultrasmall droplet volumes and highly localized printing. The signal-to-noise ratio indicates that detection limits at the attomole level are achieved for γ-aminobutyric acid.

Rethinking referral pathways: qualitative evaluation of general practice networks to increase access to intrauterine contraception.

BACKGROUND: Long-acting reversible contraceptives are recommended first-line contraception; however, intrauterine device (IUD) uptake remains low in Australia. OBJECTIVES: To describe the outcomes of an independent evaluation of the General Practitioner IUD Insertion Network (GPIIN), a project designed to address access barriers through formalized referral pathways between general practitioners (GPs) inserting IUDs and noninserters. METHODS: An independent qualitative pragmatic inductive evaluation, involving 14 in-depth interviews with GPIIN members, was conducted 18 months post-GPIIN implementation in 2 Australian jurisdictions to identify and explore critical success factors and limitations of the model. RESULTS: Local GP-to-GP IUD referral networks were considered a useful model to assist affordable and timely IUD access, improve noninserters' IUD knowledge and inserters' reflection on best practice. However, pathway simplification is needed to determine optimal integration of the concept into pragmatic GP-to-GP referral arrangements. CONCLUSIONS: GPIIN provides an opportunity to improve IUD access in Primary Health Care. Further consideration of organizations best positioned and resourced to facilitate sustainable delivery and coordination is necessary.

Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation.

Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.

Droplet Microfluidics with MALDI-MS Detection: The Effects of Oil Phases in GABA Analysis.

Microfluidic and mass spectrometry (MS) methods are widely used to sample and probe the chemical composition of biological systems to elucidate chemical correlates of their healthy and disease states. Though matrix-assisted laser desorption/ionization-mass spectrometry (MALDI)-MS has been hyphenated to droplet microfluidics for offline analyses, the effects of parameters related to droplet generation, such as the type of oil phase used, have been understudied. To characterize these effects, five different oil phases were tested in droplet microfluidics for producing samples for MALDI-MS analysis. Picoliter to nanoliter aqueous droplets containing 0.1 to 100 mM γ-aminobutyric acid (GABA) and inorganic salts were generated inside a polydimethylsiloxane microfluidic chip and deposited onto a conductive glass slide. Optical microscopy, Raman spectroscopy, and MALDI-mass spectrometry imaging (MSI) of the droplet samples and surrounding areas revealed patterns of solvent and oil evaporation and analyte deposition. Optical microscopy detected the presence of salt crystals in 50-100 µm diameter dried droplets, and Raman and MSI were used to correlate GABA signals to the visible droplet footprints. MALDI-MS analyses revealed that droplets prepared in the presence of octanol oil led to the poorest detectability of GABA, whereas the oil phases containing FC-40 provided the best detectability; GABA signal was localized to the footprint of 65 pL droplets with a limit of detection of 23 amol. The effect of the surfactant perfluorooctanol on analyte detection was also investigated.

Online HIV Self-Testing (HIVST) Dissemination by an Australian Community Peer HIV Organisation: A Scalable Way to Increase Access to Testing, Particularly for Suboptimal Testers.

HIV self-testing (HIVST) introduces opportunities for screening in non-conventional settings, and addresses known testing barriers. This study involved the development and evaluation of a free online HIVST dissemination service hosted by a peer-led, community-based organisation with on-site, peer-facilitated HIV testing, and established referral and support programs for people newly diagnosed with HIV to determine whether this model was feasible and acceptable for engaging MSM, particularly among infrequent and naive HIV-testers, or those living in remote and rural areas. Between December 2016 and April 2018, 927 kits were ordered by 794 individuals, the majority of whom were men who have sex with men (MSM) (62%; 494), having condomless sex (50%; 392), or living outside a major city (38%; 305). Very few (5%; 39) sought the available pre-test peer contact, despite 45% (353) being naive HIV-testers. This study demonstrates that online HIVST dissemination is acceptable and feasible for engaging at-risk suboptimal testers, including those unwilling to test elsewhere (19%; 47/225). With half (50%; 403) unwilling to buy a kit, our study suggests that HIVST will need to be subsidized (cost-neutral to users) to enhance population coverage and access.

STI and HIV knowledge and testing: a comparison of domestic Australian-born, domestic overseas-born and international university students in Australia.

University students usually consist of young people from culturally and linguistically diverse backgrounds, and a group recognised as being at increased risk of STI. This study found lower levels of STI knowledge and STI testing among international students and to a lesser extent, domestic overseas-born students, compared with domestic Australian-born students. International students exhibited lower risk sexual behaviour but were more likely to have had a HIV test than domestic students. This diversity in sexual health knowledge, sexual health services utilisation and sexual experience indicates the need for a variety of public health approaches to improve sexual health.

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.

Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.

An Assessment of the Stability of the Canine Oral Microbiota After Probiotic Administration in Healthy Dogs Over Time.

The administration of an oral probiotic has been demonstrated to impact oral microbial diversity in humans but has not been examined in canines. The objective of this study was to test the hypothesis that oral probiotic administration would impact the oral microbiota of canines compared to control. Working canines in training (n = 13) were assigned to Test or Control groups and acclimated to one of three commercially available study diets utilizing common protein sources (Purina Pro Plan Savor lamb, Purina Pro Plan Sport chicken, Purina Pro Plan Focus salmon) for a minimum of 30 days prior to initiation of the study. Following acclimation, dogs in the Test group began a daily regimen of oral probiotic (Fortiflora® Purina, St. Louis, MO) top-dressed on their midday feeding. Control dogs received their midday feeding with no probiotic. All dogs were sampled once weekly via oral pediatric swabs across the 7-week study. Next generation sequencing (Illumina, MiSeq) was utilized to develop microbial profiles specific to treatment, diet, and time. Bacterial composition was dominated by eight phyla (Proteobacteria 43.8%, Bacteroidetes 22.5%, Firmicutes 18.9%, Actinobacteria 6.1%, Fusobacteria 3.6%, Gracilibacteria 2.1%, SR1 Absconditabacteria 1.5%, and Saccharibacteria 1.3%) representing more than 99% of the relative abundance of the microbial composition. Probiotic administration failed to impact relative abundance at any taxonomic level (P > 0.05). Similarly, no effect on the oral microbiota was measured for diet (P > 0.05). Comparison using a Jaccard Index demonstrate a consistent microbial profile over the 7-week study with no impact evidenced by study week (P = 0.19). The data also revealed a profile of ubiquitous taxa that were present across all dogs and all samples regardless of breed, sex, diet, treatment or other factors. These genera include Actinomyces, Corynebacterium, Capnocytophaga, Flavobacterium, Gemella, Abiotrophia, Streptococcus, and Frederiksenia. These data demonstrate the stability of canine oral microbiota over time.

Peer-delivered point-of-care testing for Chlamydia trachomatis and Neisseria gonorrhoeae within an urban community setting: a cross-sectional analysis.

Background The advent of fully automated nucleic acid amplification test (NAAT) technology brings new public health opportunities to provide Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) point-of-care testing (POCT) in non-traditional settings. METHODS: This pilot study evaluated the integration of the CT/NG Xpert diagnostic assay into an urban peer-led community setting providing HIV and syphilis POCT. A comprehensive protocol of testing, result notification, referral and follow up, managed by peer test facilitators, was undertaken. RESULTS: Over 67 weeks, there were 4523 occasions of CT/NG testing using urine, oropharyngeal and anorectal samples with 25.7% (803) of the 3123 unique participants returning for repeat testing. The prevalence of CT and NG was 9.5% and 5.4% respectively. Where CT and or NG infection was detected, 98.4% (604/614) of participants were successfully notified of detected infection and referred for treatment. Evaluation Survey responses (11.4%, 516/4523) indicated a substantial proportion of respondents (27.1%, 140/516) 'would not have tested anywhere else'. Of note, 17.8% (92/516) of participants reported no previous CT/NG test and an additional 17.8% (92/516) reported testing more than 12 months ago. A total of 95.9% (495/516) of participants 'Strongly agreed' or 'Agreed' to being satisfied with the service. CONCLUSION: The project successfully demonstrated an acceptable and feasible model for a peer-delivered community-led service to provide targeted molecular CT/NG POCT. This model offers capacity to move beyond the traditional pathology and STI testing services and establish community-led models that build trust and increase testing rates for key populations of epidemiological significance.