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Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354–1363) to estimate divergence and effective reproduction numbers (Re) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n  = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (>90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth–death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (Re > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and PNG. [ABSTRACT FROM AUTHOR]

Background Papua New Guinea (PNG) is estimated to have among the highest prevalences of HIV and sexually transmissible infections (STIs) of any Asia-Pacific country, and one of the highest burdens of maternal syphilis globally. The prevalence of curable STIs, such as Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV), among pregnant women in PNG is relatively unknown.Methods: A cross-sectional bio-behavioural survey to investigate the epidemiology of CT, NG, TV and other STIs among pregnant women in three provinces of PNG was undertaken. Women aged 18-35 years attending their first antenatal clinic visit were invited to participate. Participants completed a short interview and provided self-collected vaginal specimens for CT, NG and TV laboratory-based nucleic acid amplification tests and a venepuncture specimen for laboratory testing for syphilis and Herpes simplex virus type-2 (HSV-2) serology. Routine antenatal assessment was conducted according to national guidelines, including HIV counselling and testing and point-of-care syphilis screening.Results: A total of 765 women were enrolled. Overall, 43% (95% confidence interval (CI): 39.2-46.4) had one or more of CT, NG or TV infection. CT was the most prevalent STI (22.9%, 175/765; 95% CI: 19.9-25.9), followed by TV (22.4%, 171/765; 95% CI: 19.4-25.4), and NG (14.2%, 109/765; 95% CI: 11.7-16.7). The prevalence of active syphilis was 2.2% (17/765; 95% CI: 1.2-3.3), HSV-2 was 28.0% (214/765; 95% CI: 24.8-31.2) and HIV, 0.8% (6/765; 95% CI: 0.2-1.4). Prevalences were highest among primigravid women, women aged <25 years, and among those in Central Province.Conclusion: High prevalences of curable genital STIs were observed among women attending routine antenatal clinic services in PNG. These infections have been associated with adverse pregnancy outcomes and could be important contributors to poor maternal and neonatal health in this setting. [ABSTRACT FROM AUTHOR]

Background: Sexually transmitted and genital infections in pregnancy are associated with an increased risk of adverse maternal and neonatal health outcomes. High prevalences of sexually transmitted infections have been identified among antenatal attenders in Papua New Guinea. Papua New Guinea has amongst the highest neonatal mortality rates worldwide, with preterm birth and low birth weight major contributors to neonatal mortality. The overall aim of our study was to determine if a novel point-of-care testing and treatment strategy for the sexually transmitted and genital infections Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV) and Bacterial vaginosis (BV) in pregnancy is feasible in the high-burden, low-income setting of Papua New Guinea.Methods: Women attending their first antenatal clinic visit were invited to participate. CT/NG and TV were tested using the GeneXpert platform (Cepheid, USA), and BV tested using BVBlue (Gryphus Diagnostics, USA). Participants received same-day test results and antibiotic treatment as indicated. Routine antenatal care including HIV and syphilis screening were provided.Results: Point-of-care testing was provided to 125/222 (56 %) of women attending routine antenatal care during the three-month study period. Among the 125 women enrolled, the prevalence of CT was 20.0 %; NG, 11.2 %; TV, 37.6 %; and BV, 17.6 %. Over half (67/125, 53.6 %) of women had one or more of these infections. Most women were asymptomatic (71.6 %; 47/67). Women aged 24 years and under were more likely to have one or more STI compared with older women (odds ratio 2.38; 95 % CI: 1.09, 5.21). Most women with an STI received treatment on the same day (83.6 %; 56/67). HIV prevalence was 1.6 % and active syphilis 4.0 %.Conclusion: Point-of-care STI testing and treatment using a combination of novel, newly-available assays was feasible during routine antenatal care in this setting. This strategy has not previously been evaluated in any setting and offers the potential to transform STI management in pregnancy and to prevent their associated adverse health outcomes. [ABSTRACT FROM AUTHOR]

Much about the range of pathogens, frequency of coinfection, and clinical effects of reproductive tract infections (RTIs) among pregnant women remains unknown. We report on RTIs (Mycoplasma genitalium, Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Treponema pallidum subspecies pallidum, bacterial vaginosis, and vulvovaginal candidiasis) and other reproductive health indicators in 699 pregnant women in Papua New Guinea during 2015-2017. We found M. genitalium, an emerging pathogen in Papua New Guinea, in 12.5% of participants. These infections showed no evidence of macrolide resistance. In total, 74.1% of pregnant women had >1 RTI; most of these infections were treatable. We detected sexually transmitted infections (excluding syphilis) in 37.7% of women. Our findings showed that syndromic management of infections is greatly inadequate. In total, 98.4% of women had never used barrier contraception. These findings will inform efforts to improve reproductive healthcare in Papua New Guinea.

A retrospective study of gonorrhoea and syphilis from Health Department records was carried out in Papua New Guinea. During the ten-year period (1974-1983) 101,636 new cases of gonorrhoea and 34,422 of syphilis were reported among the general population of Papua New Guinea. The incidence of both sexually transmitted disease have significantly (P less than 0.005) increased over the decade despite the introduction and implementation of the National Sexually Transmitted Disease (STD) Control Programme. Some which contribute to the present increase in sexually transmitted diseases are segregation of health and non-health services, insufficient staff training and increased immigration to urban centres.