The Role of the st313-td Gene in Virulence of Salmonella Typhimurium ST313

Multidrug-resistant Salmonella enterica serovar Typhimurium ST313 has emerged in sub-Saharan Africa causing severe infections in humans. Therefore, it has been speculated that this specific sequence type, ST313, carries factors associated with increased pathogenicity. We assessed the role in virulence of a gene with a yet unknown function, st313-td, detected in ST313 through comparative genomics. Additionally, the structure of the genomic island ST313-GI, harbouring the gene was determined. The gene st313-td was cloned into wild type S. Typhimurium 4/74 (4/74-C) as well as knocked out in S. Typhimurium ST313 02-03/002 (Δst313-td) followed by complementation (02-03/002-C). Δst313-td was less virulent in mice following i.p. challenge than the wild type and this phenotype could be partly complemented in trans, indicating that st313-td plays a role during systemic infection. The gene st313-td was shown not to affect invasion of cultured epithelial cells, while the absence of the gene significantly affects uptake and intracellular survival within macrophages. The gene st313-td was proven to be strongly associated to invasiveness, harboured by 92.5% of S. Typhimurium blood isolates (n = 82) and 100% of S. Dublin strains (n = 50) analysed. On the contrary, S. Typhimurium isolates of animal and food origin (n = 82) did not carry st313-td. Six human, non-blood isolates of S. Typhimurium from Belarus, China and Nepal harboured the gene and belonged to sequence types ST398 and ST19. Our data showed a global presence of the st313-td gene and in other sequence types than ST313. The gene st313-td was shown to be expressed during logarithmic phase of growth in 14 selected Salmonella strains carrying the gene. This study reveals that st313-td plays a role in S. Typhimurium ST313 pathogenesis and adds another chapter to understanding of the virulence of S. Typhimurium and in particular of the emerging sequence type ST313

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Prevalence, antimicrobial susceptibility and risk factors associated with non-typhoidal Salmonella on Ugandan layer hen farms

Abstract Background Non-typhoidal Salmonella (NTS) are among the leading global foodborne pathogens and a significant public health threat. Their occurrence in animal reservoirs and their susceptibilities to commonly used antimicrobials are poorly understood in developing countries. The aim of this study was to estimate the prevalence, determine antimicrobial susceptibility and identify risk factors associated with NTS presence in laying hen farms in Uganda through a cross-sectional study. Results Pooled faecal samples were collected from 237 laying hen farms and these were analysed for NTS following standard laboratory procedures. In total, 49 farms (20.7%; 95% Confidence interval (CI): 15.6–25.6%) were positive for NTS presence. Altogether, ten Salmonella serotypes were identified among the confirmed 78 isolates, and the predominant serotypes were Salmonella Newport (30.8%), S. Hadar (14.1%), S. Aberdeen (12.8%), S. Heidelberg (12.8%), and S. Bolton (12.8%). Phenotypic antimicrobial resistance was detected in 45(57.7%) of the isolates and the highest resistance was against ciprofloxacin (50.0%) followed by sulphonamides (26.9%) and sulphamethoxazole/trimethoprim (7.7%). Resistance was significantly associated with sampled districts (p = 0.034). Resistance to three or more drugs, multi-drug resistance (MDR) was detected in 12 (15.4%) of the isolates, 9 (75%) of these were from Wakiso district. A multivariable logistic model identified large farm size (OR = 7.0; 95% CI: 2.5–19.8) and the presence of other animal species on the farm (OR = 5.9; 95% CI: 2.1–16.1) as risk factors for NTS prevalence on farms. Having a separate house for birds newly brought to the farms was found to be protective (OR = 0,4; 95% CI: 0.2–0.8). Conclusion This study has highlighted a high prevalence and diversity of NTS species in laying hen farms in Uganda and identified associated risk factors. In addition, it has demonstrated high levels of antimicrobial resistance in isolates of NTS. This could be because of overuse or misuse of antimicrobials in poultry production. Also importantly, the insights provided in this study justifies a strong case for strengthening One Health practices and this will contribute to the development of NTS control strategies at local, national and international levels

Characterization of ionospheric irregularities at different longitudes during quiet and disturbed geomagnetic conditions

This paper investigates the plasma irregularities at different longitudes in the month of March 2015; a 11 period that consists of both quiet and disturbed geomagnetic conditions. The average rate of change of12 TEC index (ROTIave), derived from Global Positioning System (GPS) measurements obtained at South 13 America, Africa, Asia and Oceania equatorial regions, was used as indicator. The observations 14 revealed significant longitudinal differences for both quiet and disturbed conditions. The quiet-time 15 observations indicate that irregularities were most frequent in the American and African sectors, it is 16 rarely observed in the Asian sector and mostly absent in the Oceania longitudes. The strength is 17 however observed to decrease eastward i.e. it is most prominent in the American sector (up to ~1.6 18 TECU/min.) and absent in the Oceania longitudes. The results of the investigation of the 17 March, 19 2015 storm event revealed that the storm appeared not to hinder the development of irregularities in all 20 the stations in the America sector during the night following the main phase. However, significant 21 longitudinal variation is observed within the sector on the first night following the storm’s recovery. In 22 the African sector, the storm inhibits the development of irregularities in all the stations during the 23 storm days considered: a development that is fundamentally different from the America sector. 24 Generally, no significant storm effect is observed in the Asian and Oceania stations considered. The 25 storm-time longitudinal variations of irregularities have been partly attributed to the storm timing and 26 significant longitudinal difference in the action of storm-induced related drivers. 27 28 Keywords: Irregularities; ROTI; Scintillation; Geomagnetic storm

Equatorial F-region irregularities at different seasons in Africa

Trans-ionospheric signals such as the Global Positioning System (GPS) signals propagating through irregular ionospheric plasma structures may experience phase variation and amplitude fades causing degradation in system performance. This paper investigates the latitudinal structure of equatorial F-region irregularities (EFI) in the African region at different seasons using a GPS-based proxy index (rate of change of TEC index (ROTI)). The results obtained indicate the dependence of EFI on local time, season and latitude. Its occurrence time ranges between 19:00 and 0:00LT depending on the season. Its appearance is earlier in equinoxes, particularly in March equinox, and late in June solstice. Further, its occurrence lies generally within �22� magnetic latitudes for all seasons. The probability of occurrence, which is observed to be generally higher in equinoxes than solstices, is almost comparable across the entire latitudes where it was observed in equinoxes while the observations in solstices indicate a dip around the magnetic equator. Furthermore, the average seasonal value of ROTI indicates a clear latitudinal dependence; with appearance within �(0�-12�) magnetic latitude in solstices while it extends up to 18� in equinoxes, particularly in the south. While the hemispheric asymmetry in the average seasonal values is favored by the hemispheric asymmetry of latitudinal TEC profile, the TEC gradient could help delineate the latitude of its peak occurrence. In addition, severe irregularities are mostly observed in equinoxes than in solstices across all latitudes of occurrence and are most pronounced around the crest region mainly in the south. Conversely, moderate irregularities are typically observed in solstices and are most frequent around the magnetic equator and the poleward edge of equatorial ionization anomaly (EIA) region in the northern hemisphere

International Spread of an Epidemic Population of Salmonella enterica Serotype Kentucky ST198 Resistant to Ciprofloxacin

National Salmonella surveillance systems from France, England and Wales, Denmark, and the United States identified the recent emergence of multidrug-resistant isolates of Salmonella enterica serotype Kentucky displaying high-level resistance to ciprofloxacin. A total of 489 human cases were identified during the period from 2002 (3 cases) to 2008 (174 cases). These isolates belonged to a single clone defined by the multilocus sequence type ST198, the XbaI-pulsed-field gel electrophoresis cluster X1, and the presence of the Salmonella genomic island 1 variant SGI1-K. This clone was probably selected in 3 steps in Egypt during the 1990s and the early 2000s and has now spread to several countries in Africa and, more recently, in the Middle East. Poultry has been identified as a potential major vehicle for infection by this clone. Continued surveillance and appropriate control measures should be implemented by national and international authorities to limit the spread of this strain