Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1

In the past 30 years,Salmonella bloodstream infections have become a significant health problem in sub-Saharan Africa and are responsible for the deaths of anestimated 390,000 people each year. The disease is predominantly caused by a recently described sequence type of SalmonellaTyphimurium: ST313, which has a distinctive set of prophage sequences. We have thoroughly characterized the ST313-associated prophages both genetically and experimentally. ST313 representative strain D23580 contains five full-length prophages: BTP1, Gifsy-2D23580, ST64BD23580, Gifsy-1D23580,and BTP5. We show that commonS.Typhimurium prophages Gifsy-2, Gifsy-1, andST64B are inactivated in ST313 by mutations. Prophage BTP1 was found to be a functional novel phage, and the first isolate of the proposed new species “Salmonellavirus BTP1”, belonging to the P22virusgenus. Surprisingly,∼109BTP1 virus particlesperml were detected in the supernatant of non-induced, stationary-phase culturesof strain D23580, representing the highest spontaneously induced phage titer so farreported for a bacterial prophage. High spontaneous induction is shown to be anintrinsic property of prophage BTP1, and indicates the phage-mediated lysis of around0.2% of the lysogenic population. The fact that BTP1 is highly conserved in ST313 poses interesting questions about the potential fitness costs and benefits of novel prophagesin epidemicS.Typhimurium ST313

Individual, unit and vocal clan level identity cues in sperm whale codas

Fieldwork was supported by Discovery and Equipment grants to H.W. from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Whale and Dolphin Conservation Society. S.G. and L.R. were supported by the Marine Alliance for Science and Technology for Scotland (MASTs) pooling initiative and their support is gratefully acknowledged. MASTs is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. S.G. was also supported by an NSERC Postgraduate Scholarship (PGS-M), an NSERC Canadian Graduate Scholarship (CGS-D), the Izaak Killam Memorial Scholarship, the Patrick F. Lett Fund, the Dalhousie’s Presidents Award, and an FNU fellowship for the Danish Council for Independent Research from the Ministry of Higher Education and Science supplemented by a Sapere Aude Research Talent Award.The ‘social complexity hypothesis’ suggests that complex social structure is a driver of diversity in animal communication systems. Sperm whales have a hierarchically structured society in which the largest affiliative structures, the vocal clans, are marked on ocean-basin scales by culturally transmitted dialects of acoustic signals known as ‘codas’. We examined variation in coda repertoires among both individual whales and social units—the basic element of sperm whale society—using data from nine Caribbean social units across six years. Codas were assigned to individuals using photo-identification and acoustic size measurement, and we calculated similarity between repertoires using both continuous and categorical methods. We identified 21 coda types. Two of those (‘1+1+3’ and ‘5R1’) made up 65% of the codas recorded, were shared across all units and have dominated repertoires in this population for at least 30 years. Individuals appear to differ in the way they produce ‘5R1’ but not ‘1+1+3’ coda. Units use distinct 4-click coda types which contribute to making unit repertoires distinctive. Our results support the social complexity hypothesis in a marine species as different patterns of variation between coda types suggest divergent functions, perhaps representing selection for identity signals at several levels of social structure.Publisher PDFPeer reviewe

Increased intracellular survival of Salmonella Typhimurium ST313 in HIV-1-infected primary human macrophages is not associated with Salmonella hijacking the HIV compartment.

BACKGROUND: Non-Typhoidal Salmonella (NTS) causes a severe invasive syndrome (iNTS disease) described in HIV-positive adults. The impact of HIV-1 on Salmonella pathogenesis and the molecular basis for the differences between these bacteria and classical diarrhoeal S. Typhimurium remains unclear. RESULTS: Here we show that iNTS-associated S. Typhimurium Sequence Type 313 (ST313) bacteria show greater intracellular survival in primary human macrophages, compared with a 'classical' diarrhoeal S. Typhimurium ST19 isolate. The increased intracellular survival phenotype of ST313 is more pronounced in HIV-infected macrophages. We explored the possibility that the bacteria take advantage of the HIV-associated viral-containing compartments created in human macrophages that have low pH. Confocal fluorescence microscopy and Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) tomography showed that Salmonella did not co-localise extensively with HIV-positive compartments. CONCLUSION: The capacity of ST313 bacteria to survive better than ST19 bacteria within primary human macrophages is enhanced in cells pre-infected with HIV-1. Our results indicate that the ST313 bacteria do not directly benefit from the niche created by the virus in HIV-1 infected macrophages, and that they might take advantage from a more globally modified host cell. SIGNIFICANCE: A better understanding of the interplay between HIV-1 and Salmonella is important not only for these bacteria but also for other opportunistic pathogens. This article is protected by copyright. All rights reserved

A novel method for identifying coded tags recorded on aquatic acoustic monitoring systems.

Aquatic biotelemetry increasingly relies on using acoustic transmitters ('tags') that enable passive detection of tagged animals using fixed or mobile receivers. Both tracking methods are resource-limited, restricting the spatial area in which movements of highly mobile animals can be measured using proprietary detection systems. Transmissions from tags are recorded by underwater noise monitoring systems designed for other purposes, such as cetacean monitoring devices, which have been widely deployed in the marine environment; however, no tools currently exist to decode these detections, and thus valuable additional information on animal movements may be missed. Here, we describe simple hybrid methods, with potentially wide application, for obtaining information from otherwise unused data sources. The methods were developed using data from moored, acoustic cetacean detectors (C-PODs) and towed passive receiver arrays, often deployed to monitor the vocalisations of cetaceans, but any similarly formatted data source could be used. The method was applied to decode tag detections that were found to have come from two highly mobile fish species, bass (Dicentrarchus labrax) and Twaite shad (Alosa fallax), that had been tagged in other studies. Decoding results were validated using test tags; range testing data were used to demonstrate the relative efficiency of these receiver methods in detecting tags. This approach broadens the range of equipment from which acoustic tag detections can be decoded. Novel detections derived from the method could add significant value to past and present tracking studies at little additional cost, by providing new insights into the movement of mobile animals at sea

Case-control investigation of invasive Salmonella disease in Africa - comparison of human, animal and household environmental isolates find no evidence of environmental or animal reservoirs of invasive clades/strains

Background Invasive Salmonella infections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, sampling Salmonella isolates from index cases, healthy people, animals, and the household environment. Methodology Sixty index cases of human invasive Salmonella infection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-Typhoidal Salmonella (iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment. Findings 1203 samples from 120 households, yielded 43 non-Typhoidal Salmonella (NTS) isolates from 25 households (overall sample positivity 3.6%). In the 28 iNTS patients, disease was caused by 3 STs of Salmonella Typhimurium, mainly ST313. In contrast, the isolates from households spanned 15 sequence types (STs). Two S . Typhimurium isolates from index cases closely matched isolates from their respective asymptomatic household members (2 and 3 SNP differences respectively). Despite the recovery of a diverse range of NTS, there was no overlap between the STs causing iNTS disease with any environmental or animal isolates. Conclusions The finding of NTS strains from index cases that matched household members, coupled with lack of related animal or environmental isolates, supports a hypothesis of human to human transmission of iNTS infections in the household. The breadth of NTS strains found in animals and the household environment demonstrated the robustness of NTS sampling and culture methodology, and suggests a diverse ecology of Salmonella in this setting. Healthy typhoid ( S . Typhi) carrier state was not detected. The lack of S . Typhi isolates from the household environment suggests that further methodological development is needed to culture S . Typhi from the environment. Author summary Invasive Salmonella infections cause the loss of millions of disability adjusted life years (DALYs) every year globally. The two main types of invasive Salmonella infections in Africa are i) typhoid fever, caused by Salmonella Typhi, and ii) invasive Non-Typhoidal Salmonella (iNTS) disease, primarily caused in our setting by Salmonella Typhimurium. Despite the high disease burden, and the observed differences between the epidemiology of typhoid and iNTS disease, we lack an understanding of the reservoirs and transmission routes of iNTS. Therefore, we carried out extensive microbiological sampling of the household members, domestic animals, and living environments of patients with invasive Salmonella infections, and of geographically-matched control households, and investigated the genetic relationships between household Salmonella and index-case blood-stream isolates by whole genome sequencing (WGS). We identified a wide range of NTS serovars / sequence types across all households and sample-types, but only identified Salmonella that matched iNTS that matched invasive cases strains in the stool of healthy people from the same households. Our findings support, but cannot prove, the hypothesis that iNTS-associated strains are transmitted from person-to-person. Boot-sock sampling of the household environment gave the highest yield of Salmonella of any of our sampling strategies. None of the 41 environmental Salmonella isolates from non-human sources, including 4 domestic animal-associated isolates, matched the disease-causing sequence types. Our findings are consistent with a hypothesis that the reservoir of Typhimurium iNTS infections is the human gastrointestinal tract, and transmission occurs within households. Longitudinal studies are required, however, to confirm this hypothesis