Data from a previous survey 
, a national trachoma risk map 
and TRA 
had indicated trachoma to be endemic throughout Unity State, but provided an insufficient baseline to initiate interventions. The present study therefore set out to generate the required data. The results established that trachoma prevalence in Unity State far exceeds the WHO recommended threshold of 10% TF prevalence in children aged 1–9 years for initiation of antibiotic MDA 
and of 1% for TT in adults for surgery provision. Alongside the obvious need for MDA and surgery, both the ‘F’ and ‘E’ components of the SAFE strategy 
will need to be scaled up to address key trachoma risk factors, hence maximising the impact of intervention and contributing towards sustaining trachoma control once it has been achieved.
The very high prevalence of trachoma found in the eight surveyed counties is consistent with results from previous work in Mayom county of Unity State 
, predictions generated by a national trachoma risk map 
and findings from most other trachoma surveys in South Sudan [see map in 
The uniformly high prevalence of trachoma found across Unity State is also reflected in the results from the sampling simulation. These provide evidence that more economical survey designs, sampling fewer clusters, can be used for decision making in areas where trachoma is likely to be hyperendemic. This may support a move towards regional level surveys in areas where there is evidence that the prevalence of trachoma is high. Hyperendemic areas, such as Unity State, will have more uniform treatment requirements than areas of lower prevalence, in which individual foci may be above treatment thresholds but overall, the health district does not qualify for MDA. In meso- and hypo-endemic areas, higher resolution surveys will therefore be required to capture high prevalence foci and sufficiently understand spatial variation in disease and treatment needs. Lot Quality Assurance Sampling, which allows decisions on control to be made using small sample sizes, has previously been explored in Malawi 
and Vietnam 
and may offer a potential solution. Further exploration of this principle would be possible using data from states to the west of Unity State, where trachoma prevalence is predicted to be much lower 
Compared to data from other trachoma endemic areas of Sub-Saharan Africa, the levels of TF and TT found in Unity State were considerably higher. For example, in Kenya's Samburu district, prevalences of 35% TF were reported in children below 10 years and 6% TT in adults above 14 years of age. The same survey covered five other districts and found prevalence of both signs to be lower in all of them 
. A regional survey in Chad found that TF was present in 31.5% of children under 10 years and that 1.5% of women over 14 years had signs of TT 
. In Ethiopia, the national prevalence of TF in children below 10 years has been reported as 26.2%, while 3.1% of women above the age of 14 years showed signs of TT 
. These proportions obviously vary considerably throughout the country; an overall prevalence of 32.7% TF and 6.2% TT has been reported from Amhara regional state 
, Ethiopia's worst affected region 
. Unity State, like other parts of South Sudan 
, is therefore among the most severely affected by trachoma in Africa.
The present study identified a number of risk factors for trachoma in Unity State. For TF, ocular and/or nasal discharge and the presence of flies in and around the living areas or on children's faces were associated with an increased risk of trachoma infection, and children between 3–5 years of age were at highest risk. Risk factors for TT in those aged 15 years and above were age, sex, ocular discharge, number of children residing in the household and time (as a proxy for distance) to the nearest water collection site. These observations are consistent with our general understanding of trachoma epidemiology 
and findings of other studies in South Sudan 
and in the region 
While eye discharge was identified as a TT risk factor in adults we think that it is likely to be a consequence of TT rather than a cause and may also be indicative of being generally unwell, which could be due to having eye health problems. Latrine provision and close access to water were both limited throughout the study villages, but the strong associations with increased risk of TT is suggestive of poorer hygiene in those with more pronounced eye problems, as were poor waste disposal practices. MDA of antibiotics is unlikely to have an effect on these risk factors, highlighting the importance of health education and environmental improvements as part of a comprehensive control programme 
Adult females, rather than males, were at much higher risk of having TT, which is generally thought to be due to the close contact of women with children, children being the main reservoir of infection 
. Fewer adult males were examined from the enumerated population and if these unexamined males were unaffected by the later stages of disease, the sex effect seen would be greater. We found that TT increased with decreased household size and distance to waste disposal. Increased TT in adults in smaller households, after adjustment for other factors, may also be indicative of adults with TT living in isolation and poverty rather than a smaller household being a risk factor for TT.
The present study has a number of limitations. Unlike other PBPS conducted in South Sudan and elsewhere, relatively few villages were sampled in each county, which may have affected the precision of the prevalence estimates for the State, particularly if there was much variation in prevalence within the survey area. Sampling of a total of 40 sites over a large geographical area was, however, considered justified because GIS-based risk-mapping and TRA data had provided a reasonable indication that Unity State was trachoma endemic throughout 
. As indicated by the summary measures of household attributes there was some variability between counties and this will not have been captured in as much detail as sampling of 20 sites per county would have allowed. It is nevertheless thought that the overall results generated by the study are reflective of the population in the study area and suitable for decision-making on intervention, particularly as WHO thresholds are very clearly exceeded at all population levels. In the course of scaling up the SAFE strategy it may, however, be found that TT surgery requirements need to be adjusted up- or downwards. This is because we were unable to examine 55% of the enumerated adult males, meaning that the prevalence of TT, CO and visual impairment in the study area could differ somewhat from the estimates provided here.
It was not possible to collect DNA samples from children in order to conduct laboratory testing to detect Chlamydia trachomatis
. It has been suggested that in a high prevalence setting, prior to availability of mass antibiotic treatment, a diagnosis of TF may not reflect infection with C. trachomatis
in 30% of children aged 1–10 
. In Unity State, a reduction of 30% in overall prevalence would still imply that the area is hyper-endemic and in desperate need of MDA. Data used to generate simulated realisations were also based on estimates of TF and/or TI in children aged 1–9 years. The inherent measurement error in using clinical signs as opposed to infection prevalence is also a limitation of the realisations, which were based on real survey data. Additionally, generation of the gold standard database is necessary to evaluate alternative sampling designs, but involves a number of assumptions. Included surveys span nearly a decade and it is possible that the spatial characteristics of infection may have changed over time. However, the lack of MDA in many suspected trachoma endemic areas and the general absence of health infrastructure and services in South Sudan makes it unlikely that the spatial distribution of infection will have changed significantly. Even if there had been changes in the rest of South Sudan over time, sampling simulations were conducted within Unity State and this area will have been most strongly influenced by the recent survey reported here.
Much remains to be done if South Sudan is to eliminate blinding trachoma by 2020. As a first step, a comprehensive intervention program needs to be scaled up across Unity state, now that the baseline data are available. Secondly, there is a need for further large-scale surveys, such as the one reported here, in other states. As much as half of the country may need to be targeted with SAFE interventions 
, but for many areas this still needs to be confirmed. For large suspected endemic areas with little to no available data, such as Upper Nile State and parts of Warrap, Lakes and Central Equatoria States, a two-step procedure such as that used in Unity State would seem the most effective way to get control activities quickly under way. TRAs should be conducted to determine whether there is evidence of transmission in suspected endemic areas. Where the proportion of children with signs of TF is found to be very high, counties could then be combined under one survey area to more quickly identify SAFE intervention needs.