Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials.

BACKGROUND: Typhoid 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 FINDINGS: Bioinformatic 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 minimal 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. SIGNIFICANCE: Antimicrobials 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.

Antibiotic resistant Shigella is a major cause of diarrhoea in the Highlands of Papua New Guinea.

INTRODUCTION: Diarrhoea remains a major cause of illness in Papua New Guinea (PNG); however, little is known about its aetiology. As a result of the cholera outbreak that spread throughout PNG in 2009-2011, we conducted diarrhoeal surveillance in Eastern Highlands Province. METHODOLOGY: Following informed consent and a brief questionnaire, participants provided a stool sample or duplicate rectal swabs. Samples were tested for common bacterial pathogens Salmonella spp., Shigella spp., Vibrio spp., Campylobacter spp. and Yersinia enterocolitica using established culture methods. Enteric parasites were detected using microscopy. RESULTS: A total of 216 participants were enrolled; where age was recorded, 42% were under 5 years of age, 6.7% were 5 to 17 years of age and 51.3% ≥18 years of age. One or more pathogens were detected in 68 (31.5%) participants, with Shigella (primarily S. flexneri) being the most commonly isolated (47 of 216 participants). Enteric parasites were detected in 23 of the 216 participants, occurring as a co-infection with another pathogen in 12 of 23 cases. No Vibrio cholerae was detected. Shigella isolates were commonly resistant to ampicillin, tetracycline, co-trimoxazole and chloramphenicol. CONCLUSIONS: Shigellae, specifically S. flexneri, are important pathogens in the highlands of PNG. While most studies in low-income settings focus on childhood aetiology, we have demonstrated the importance of Shigella in both children and adults. Enteric parasites remain present and presumably contribute to the burden of gastrointestinal illness. While improvements in sanitation and hygiene would help lower the burden of all aetiologies of infectious diarrhoea, additional control strategies targeting Shigella may also be warranted.

Evaluation of serological diagnostic tests for typhoid fever in Papua New Guinea using a composite reference standard.

Typhoid fever remains a major global health problem. A major impediment to improving outcomes is the lack of appropriate diagnostic tools, which have not significantly improved in low-income settings for 100 years. We evaluated two commercially available rapid diagnostic tests (Tubex and TyphiDot), a prototype (TyphiRapid TR-02), and the commonly used single-serum Widal test in a previously reported high-burden area of Papua New Guinea. Samples were collected from 530 outpatients with axillary temperatures of ≥37.5°C, and analysis was conducted on all malaria-negative samples (n = 500). A composite reference standard of blood culture and PCR was used, by which 47 participants (9.4%) were considered typhoid fever positive. The sensitivity and specificity of the Tubex (51.1% and 88.3%, respectively) and TyphiDot (70.0% and 80.1%, respectively) tests were not high enough to warrant their ongoing use in this setting; however, the sensitivity and specificity for the TR-02 prototype were promising (89.4% and 85.0%, respectively). An axillary temperature of ≥38.5°C correlated with typhoid fever (P = 0.014). With an appropriate diagnostic test, conducting typhoid fever diagnosis only on patients with high-grade fever could dramatically decrease the costs associated with diagnosis while having no detrimental impact on the ability to accurately diagnose the illness.