Search

BackgroundTyphoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low- and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years.Principle findingsBioinformatic analysis of 86 S. Typhi isolates collected between 1980-2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with very limited evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically conserved, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons.SignificanceAntimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting.Author SummaryTyphoid fever, caused by Salmonella enterica serovar Typhi, is a systemic infection common to many low- to middle-income settings. While the population structure of S. Typhi has been genetically characterised using whole genome sequencing in many endemic countries throughout Sub-Saharan Africa and South Asia, we are still lacking a detailed understanding for many regions including those among the Asia-Pacific islands. Genomic surveillance of isolates spanning 30 years demonstrated a population structure of S. Typhi in Papua New Guinea (PNG) dominated by a single genotype (2.1.7) that emerged in the mid-twentieth century, is genetically homogeneous, and sensitive to a wide range of antibiotics commonly used in the treatment of typhoid. There was little evidence of inter-country transmission and the setting appeared free of S. Typhi genotypes commonly associated with AMR e.g. H58 (genotype 4.3.1). These data suggest that former first line drugs (chloramphenicol, ampicillin and co-trimoxazole), fluoroquinolones, third generation cephalosporins and macrolides all remain viable options for controlling typhoid in addition to the introduction of Vi-conjugate vaccines and improvements to water, sanitation and hygiene (WaSH) related infrastructure. Routine molecular surveillance is necessary to monitor for introduced or emerging AMR to inform treatment guidelines and intervention strategies.

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.

Community-associated, methicillin-resistantStaphylococcus aureus(MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 years. 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) 93-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 (Re) and sustained transmission (Re> 1) coincided with spread of progenitor methicillin-susceptibleS. aureus(MSSA) in remote northern Australia, dissemination of the ST93-MRSA-IV geno-type into population centers on the Australian East Coast, and sub-sequent importation into the highlands of Papua New Guinea and Far North Queensland. Analysis of a ST772-MRSA-V cluster in Pakistan suggests that sustained transmission in the community following importation of resistant genotypes may be more common than previously thought. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associatedS. aureuslineages from America, Asia, Australasia and Europe. Surges in Rewere observed at the divergence of antibiotic resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed amongst drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA and MSSA lineages 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.