Background Tuberculous meningitis is the most severe form of extrapulmonary TB and accounted for 5% of 10 million global TB cases in the WHO 2018 report, with mortality as high as 19% in children and 30% in adults. Clinicians in resource-poor settings are often challenged by limited diagnostic and therapeutic options for optimal patient care, and often rely on clinical parameters for diagnosis, treatment, monitoring and outcome. Aim This study was done to identify potential clinical predictors of i) 28-day mortality and ii) length of hospitalization, amongst Melanesian adults with TB meningitis at a provincial hospital in Papua New Guinea. Method A retrospective observational study was conducted on 65 Melanesian adults with TB meningitis at a provincial hospital in Papua New Guinea between 2015 and 2019. Result High case fatality (49%) and mortality rates (2.22 per 100 000 per year) for TB Meningitis were observed in this study. Even higher case fatality of 93% observed for HIV-TBM co-infection. 28-day mortality associated with HIV-TBM co-infection (p-value=0.007, 95% CI 2.49-289.19), positive fluid balance 24-hours after admission (p-value=0.019, 95% CI 1.23-10.19) and admission GCS ≤10 (p-value=0.049, 95% CI 1.01-16.58). Conclusion Study showed high case fatality (49%) and mortality rates (2.22 per 100,000 per year) for TB Meningitis in Melanesian adults, with significantly high case fatality (93%) for HIV-TBM co-infection. HIV-TBM co-infection was strongly associated with 28-day mortality whilst a positive fluid balance 24-hours after admission and admission-GCS ≤10 were weakly associated with 28-day mortality.

Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole-genome sequencing data for the Australian sequence type (ST) ST93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (R-e) and sustained transmission (R-e > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australian populations, dissemination of the ST93-MRSA-IV genotype into population centers on the Australian East Coast, and subsequent importation into the highlands of Papua New Guinea and Far North Queensland. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia, and Europe. Surges in R-e were observed at the divergence of antibiotic-resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed among drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA in the late 20th century was driven by a combination of antibiotic-resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.

Genomic neighbor typing enables heuristic inference of bacterial lineages and phenotypes from nanopore sequencing data. However, small reference databases may not be sufficiently representative of the diversity of lineages and genotypes present in a collection of isolates. In this study, we explore the use of genomic neighbor typing for surveillance of community-associated Staphylococcus aureus outbreaks in Papua New Guinea (PNG) and Far North Queensland, Australia (FNQ). We developed Sketchy , an implementation of genomic neighbor typing that queries exhaustive whole genome reference databases using MinHash. Evaluations were conducted using nanopore read simulations and six species-wide reference sketches (4832 - 47616 genomes), as well as two S. aureus outbreak data sets sequenced at low depth using a sequential multiplex library protocol on the MinION (n = 160, with matching Illumina data). Heuristic inference of lineages and antimicrobial resistance profiles allowed us to conduct multiplex genotyping in situ at the Papua New Guinea Institute of Medical Research in Goroka, on low-throughput Flongle adapters and using multiple successive libraries on the same MinION flow cell (n = 24 - 48). Comparison to phylogenetically informed genomic neighbor typing with RASE on the dominant outbreak sequence type suggests slightly better performance at predicting lineage-scale genotypes using large sketch sizes, but inferior performance in resolving clade-specific genotypes (methicillin resistance). Sketchy can be used for large-scale bacterial outbreak surveillance and in challenging sequencing scenarios, but improvements to clade-specific genotype inference are needed for diagnostic applications. Sketchy is available open-source at: https://github.com/esteinig/sketchy

Nanopore sequencing and phylodynamic modelling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Here, we implement Random Forest models for single nucleotide polymorphism (SNP) polishing to estimate divergence and effective reproduction numbers (Re) of two community-associated, methicillin-resistant Staphylococcus aureus (MRSA) outbreaks in remote Far North Queensland and Papua New Guinea (n = 159). Successive bar-coded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low-coverage (> 5x - 10x) provided sufficient data to accurately infer assembly genotypes with high recall when compared with Illumina references. De novo SNP calling with Clair was followed by SNP polishing using intra- and inter-species models trained on Snippy reference calls. Models achieved sufficient resolution on ST93 outbreak sequence types (> 70 - 90% accuracy and precision) for phylodynamic modelling from lineage-wide hybrid alignments and birth-death skyline models in BEAST2. Our method reproduced phylogenetic topology, geographical source of the outbreaks, and indications of sustained transmission (Re > 1). We provide Nextflow pipelines that implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks using nanopore sequencing.

Association of Microalbuminuria with High HbA1C levels in Melanesian Adults with Diabetes of at-least 1 Year Duration. Ian Billy1, Izzard Aglua2. 1. Specialist Physician (MMed, MBBS), Nonga General Hospital. Papua New Guinea. 2. Clinical Research Fellow & Internal Medicine Registrar (MPH, MBBS). Sir Joseph Nombri Memorial-Kundiawa General Hospital. Papua New Guinea. Abstract Background Evidence suggest a potential relationship between high or variable HbA1C levels and presence or rate of change of microalbuminuria. Disruption of the vascular endothelial glycocalyx has been linked to chronic hyperglycemia and microalbuminuria, suggesting a possible shared pathophysiological mechanism. Aim To 1) explore potential association between microalbuminuria and high HbA1C levels in Melanesian adults with diabetes mellitus, and 2) asses predictive value of a high HbA1C reading as an indicator of the presence or progression of microalbuminuria. Method A cross-sectional study on 190 patients with either type 1 or 2 diabetes of at least 1-year duration done at a provincial hospital in Papua New Guinea in 2017. Result A significant [P=0.0221], though weak [R2=0.028 <0.70], correlation between UACR and HbA1C [95% statistical confidence] was observed in univariate regression, which was marginally significant [P=0.056] after controlling for weight, systolic hypertension, duration of diabetes, gender and age in multivariate regression. Conclusion A significant [p=0.022], though weak, correlation between UACR and HbA1C levels was observed, which may support usefulness of HbA1C as a predictor for microalbuminuria and diabetic kidney disease. In settings without microalbuminuria testing, high HbA1c levels can be used as a proxy to indicate presence or progression of microalbuminuria, thus prompting timely interventions to prevent further progression of diabetic nephropathy.

Background: Methicillin-Resistant Staphylococcus aureus (MRSA) has been an important cause of bone infection since the 1940s. Current guidelines recommend targeted antibiotic use for osteomyelitis treatment informed by microbial sensitivity patterns. However, in settings without microbiology facilities, empirical antibiotic use is common. Unrecognized antibiotic resistance potentiates persistence of MRSA with osteomyelitis progression to chronic forms with complications despite antibiotic treatment. Materials and Methods: A prospective observational study was done to identify common etiological agent (s) in bone infection in Melanesian children (that were admitted to the two surgical and one pediatric wards of the SJNM-KUGH in the Simbu province of Papua New Guinea in 2012 and 2017), observe for presence of antimicrobial resistance, and determine effective antibiotic regimes for treatment of bone pediatric osteomyelitis. Seventy pediatric patients presenting from the community with osteomyelitis were recruited, with bone and non-bone specimens sampled, cultured and isolates tested for resistance to common antibiotics. Results: Staphylococcus aureus (S. aureus) was isolated in 67% (47/70) of collected specimens. Of the 47 isolates, there was 91.5% resistance to penicillin, 85.1% resistance to methicillin, 89.4% resistance to oxacillin, 93.6% resistance to ampicillin and 80.9% resistance to ceftriaxone. S. aureus showed 91.5% sensitivity to gentamycin, 93.6% sensitivity to erythromycin, tetracycline and clindamycin, and 95.7% sensitivity to Co-trimoxazole. Conclusion: MRSA was the leading cause of haematogenous osteomyelitis in Melanesian children. S.aureus was isolated mainly from infected long bones of the lower limbs (79%) of children presenting from the community, suggesting a predominantly community-associated MRSA.