Towards Equitable Access to Public Health Pathogen Genomics in the Western Pacific.

The COVID-19 pandemic has increased interest and understanding of the utility of pathogen genomics across the Western Pacific region. Access to genomic data enhances surveillance and response to COVID-19, and will also support surveillance of other infectious diseases and antimicrobial resistant pathogens. Models of access can be determined based on intended purpose, use and sustainability. Achieving equitable access to genomics across the Western Pacific will contribute to the development of a regional public health genomics network to respond to major disease threats in the future.

Sample pooling on the Cepheid Xpert® Xpress SARS-CoV-2 assay.

The COVID-19 pandemic has placed unprecedented global demand on laboratory supplies required for testing. Sample pooling has been investigated by laboratories as a strategy to preserve testing capacity. We evaluate the performance of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay for testing samples in pools of 4 and 6. Clinical samples containing SARS-CoV-2, and confirmed negative clinical samples were used to create sample pools. Clinical samples had 'neat' Xpert® E gene cycle threshold values ranging between 20 and 28 and all were detected qualitatively when contained in pools of 4 or 6 samples. For these samples, pooling had a median change in cycle threshold value of 2.0 in pools of 4, and of 2.9 in pools of 6. With the use of Cepheid Xpert® Xpress SARS-CoV-2 RT-PCR assay, pooling of 4 or 6 samples may be an effective strategy to increase testing capacity.

Cancer control in the Pacific: big challenges facing small island states.

This Series paper describes the current state of cancer control in Pacific island countries and territories (PICTs). PICTs are diverse but face common challenges of having small, geographically dispersed, isolated populations, with restricted resources, fragile ecological and economic systems, and overburdened health services. PICTs face a triple burden of infection-related cancers, rapid transition to lifestyle-related diseases, and ageing populations; additionally, PICTs are increasingly having to respond to natural disasters associated with climate change. In the Pacific region, cancer surveillance systems are generally weaker than those in high-income countries, and patients often present at advanced cancer stage. Many PICTs are unable to provide comprehensive cancer services, with some patients receiving cancer care in other countries where resources allow. Many PICTs do not have, or have poorly developed, cancer screening, pathology, oncology, surgical, and palliative care services, although some examples of innovative cancer planning, prevention, and treatment approaches have been developed in the region. To improve cancer outcomes, we recommend prioritising regional collaborative approaches, enhancing cervical cancer prevention, improving cancer surveillance and palliative care services, and developing targeted treatment capacity in the region.

The clinical and molecular epidemiology of Staphylococcus aureus infections in Fiji.

BACKGROUND: There are few data describing the microbiology and genetic typing of Staphylococcus aureus that cause infections in developing countries. METHODS: In this study we observed S. aureus infections in Pacific Island nation of Fiji in both the community and hospital setting with an emphasis on clonal complex (CC) genotyping and antimicrobial susceptibility. RESULTS: S. aureus was commonly found in impetigo lesions of school children and was recovered from 57% of impetigo lesions frequently in conjunction with group A streptococcal infection. Methicillin-resistant S. aureus (MRSA) comprised 7% (20/299) of isolates and were all non-multi-resistant and all genotyped as CC1. In contrast, there was a diverse selection of 17 CCs among the 105 genotyped methicillin-susceptible S.aureus (MSSA) strains. Isolates of the rare, phylogenetically divergent and non-pigmented CC75 lineage (also called S. argenteus) were found in Fiji.From hospitalized patients the available 36 MRSA isolates from a 9-month period were represented by five CCs. The most common CCs were CC1 and CC239. CC1 is likely to be a community-acquired strain, reflecting what was found in the school children, whereas the CC239 is the very successful multi-drug resistant MRSA nosocomial lineage. Of 17 MSSA isolates, 59% carried genes for Panton-Valentine leukocidin. The S. aureus bacteraemia incidence rate of 50 per 100,000 population is among the highest reported in the literature and likely reflects the high overall burden of staphylococcal infections in this population. CONCLUSIONS: S. aureus is an important cause of disease in Fiji and there is considerable genotypic diversity in community skin infections in Fijian schoolchildren. Community acquired- (CA)- MRSA is present at a relatively low prevalence (6.7%) and was solely to CC1 (CA-MRSA). The globally successful CC239 is also a significant pathogen in Fiji.

The high burden of cervical cancer in Fiji, 2004-07.

BACKGROUND: There are few population-based data on the disease burden of cervical cancer from developing countries, especially South Pacific islands. This study aimed to determine the incidence and mortality associated with cervical cancer and the coverage of Papanicolaou (Pap) cervical cytology in 20- to 69-year-old women in Fiji from 2004 to 2007. METHODS: National data on the incident cases of histologically confirmed cervical cancer and the associated deaths, and on Pap smear results were collected from all pathology laboratories, and cancer and death registries in Fiji from 2004 to 2007. RESULTS: There were 413 incident cases of cervical cancer and 215 related deaths during the study timeframe. The annualised incidence and mortality rates in 20- to 69-year-old Melanesian Fijian women, at 49.7 per 100?000 (95% confidence interval (CI): 43.7-56.4) and 32.3 per 100?000 (95% CI: 26.9-38.4) respectively, were significantly higher than among 20- to 69-year-old Indo-Fijian women at 35.2 per 100?000 (P<0.001, 95% CI: 29.5-41.7) and 19.8 per 100?000 (P=0.002, 95% CI: 15.1-25.5) respectively. Of 330 cases diagnosed between 2004 and 2006, 186 (56%) had died by 31 December 2006. Pap smear coverage for this period was 8.0% (95% CI: 7.9-8.1) of the target population. CONCLUSIONS: The incidence and mortality related to cervical cancer in Fiji is high, whereas Pap smear coverage is very low. Greater investment in alternative screening strategies and preventive measures should be integrated into a comprehensive, strategic cervical cancer control program in Fiji.

Human papillomavirus genotype prevalence in cervical biopsies from women diagnosed with cervical intraepithelial neoplasia or cervical cancer in Fiji.

BACKGROUND: There is currently limited information about human papillomavirus (HPV) genotype distribution in women in the South Pacific region. This study's objective was to determine HPV genotypes present in cervical cancer (CC) and precancers (cervical intraepithelial lesion (CIN) 3) in Fiji. METHODS: Cross-sectional analysis evaluated archival CC and CIN3 biopsy samples from 296 women of Melanesian Fijian ethnicity (n=182, 61.5%) and Indo-Fijian ethnicity (n=114, 38.5%). HPV genotypes were evaluated using the INNO-LiPA assay in archival samples from CC (n=174) and CIN3 (n=122) among women in Fiji over a 5-year period from 2003 to 2007. RESULTS: Overall, 99% of the specimens tested were HPV DNA-positive for high-risk genotypes, with detection rates of 100%, 97.4% and 100% in CIN3, squamous cell carcinoma (SCC) and adenosquamous carcinoma biopsies, respectively. Genotypes 16 and 18 were the most common (77%), followed by HPV 31 (4.3%). Genotype HPV 16 was the most common identified (59%) in CIN3 specimens, followed by HPV 31 (9%) and HPV 52 (6.6%). Multiple genotypes were detected in 12.5-33.3% of specimens, depending on the pathology. CONCLUSION: These results indicated that the two most prevalent CC-associated HPV genotypes in Fiji parallel those described in other regions worldwide, with genotype variations thereafter. These data suggest that the currently available bivalent and quadrivalent HPV vaccines could potentially reduce cervical cancers in Fiji by over 80% and reduce precancers by at least 60%.

Invasive pneumococcal disease in Fiji: clinical syndromes, epidemiology, and the potential impact of pneumococcal conjugate vaccine.

Invasive pneumococcal disease (IPD) epidemiology and the potential impact of the pneumococcal conjugate vaccine in Fiji are documented. The annual incidence was 26.5 and 10.9 in those aged <5 and > or =55 years per 100,000, respectively. The case fatality rate was 9.4% and 67% in <5 and >65 year olds, respectively. One pneumococcal death and case would be prevented in <5 years olds for every 1930 and 128 infants vaccinated with 7vPCV, respectively.

The burden of hospitalised rotavirus infections in Fiji.

Rotavirus is the most common cause of acute severe dehydrating diarrhoea in young children worldwide. We describe the burden of rotavirus disease and the rotavirus types causing it in the largest city in Fiji. During 2006 and 2007, 592 children under 5 years of age were admitted to hospital in Suva, Fiji with acute diarrhoea. Of the 454 children for whom a stool specimen was tested, 39% were positive for rotavirus and the predominant strain found was the serotype G3[P8]. There is a significant burden of disease due to rotavirus in Fiji and the introduction of rotavirus vaccines into the national immunization schedule may drastically reduce inpatient diarrhoeal disease.

The high burden of rheumatic heart disease found on autopsy in Fiji.

Rheumatic heart disease causes more than 200,000 deaths worldwide annually, with the vast majority of these deaths occurring in developing countries, yet there are few autopsy studies of rheumatic heart disease in these countries. We performed a retrospective review of 6218 autopsies performed during the period from 1990 through 2006, searching for cases of rheumatic heart disease based upon the macroscopic pathologic examination of the heart. We found 147 cases (2.4%) of rheumatic heart disease. There was an apparent increase in the number of cases in the past 5 years. There were 95 deaths that were directly attributable to rheumatic heart disease, with congestive cardiac failure being the most common cause of death in 75 cases. The mean age at death due to rheumatic heart disease was 38 years. There were more cases of rheumatic heart disease in Indigenous Fijians than Indo-Fijians, with an adjusted relative risk of 1.26 (95% confidence intervals from 0.87 to 1.86). Our findings reflect the high burden and early age of death due to rheumatic heart disease in Fiji and the Pacific region generally, and underline the need for early detection and adequate secondary penicillin prophylaxis in this region.

Laboratory-based Salmonella surveillance in Fiji, 2004-2005.

Although foodborne diseases are an important public health problem worldwide, the burden of foodborne illness is not well described in most Pacific Island Countries and Territories. Laboratory-based surveillance programs can detect trends and outbreaks, estimate burden of illness, and allow subtyping of enteric pathogens (e.g. Salmonella serotyping), which is critical for linking illness to food vehicles and animal reservoirs. To enhance public health capacity in Fiji for foodborne disease surveillance, we developed the Salmonella Surveillance Project (SSP), a collaboration to pilot laboratory-based surveillance for Salmonella. A network of national and international partners was formed including epidemiologists, microbiologists, and environmental health personnel. Ministry of Health personnel were trained in foodborne disease surveillance and outbreak investigation. Three clinical microbiology laboratories from different parts of the country functioned as sentinel sites, reporting all laboratory-confirmed Salmonella infections using a standardized case report form. Non-Typhi Salmonella isolates were collected for serotyping. In 2004-2005, 86 non-Typhi Salmonella and 275 S. Typhi laboratory-confirmed infections were reported. Salmonella enterica serotype I 3,10: r:- and Salmonella enterica serotype Weltevreden were the most commonly isolated non-Typhi serotypes. In Fiji, the SSP utilized international partnerships to facilitate training, and to enhance laboratory capacity and surveillance for salmonellosis. Incorporating laboratory-based foodborne disease reporting into national disease surveillance will enable public health officials to describe the burden of foodborne illness, identify outbreaks, conduct analytic epidemiology studies, and improve food safety.