UNASSIGNED: Persisting HIV reservoir viruses in resting CD4 T cells and other cellular subsets are the main barrier to cure efforts. Antiretroviral therapy (ART) intensification by early initiation has been shown to enable post-treatment viral control in some cases but the underlying mechanisms are not fully understood. We hypothesized that ART initiated during the hyperacute phase of infection before peak will affect the size, decay dynamics and landscape characteristics of HIV-1 subtype C viral reservoirs.
UNASSIGNED: We studied 35 women at high risk of infection from Durban, South Africa identified with hyperacute HIV infection by twice weekly testing for plasma HIV-1 RNA. Study participants included 11 who started ART at a median of 456 (297-1203) days post onset of viremia (DPOV), and 24 who started ART at a median of 1 (1-3) DPOV. We used peripheral blood mononuclear cells (PBMC) to measure total HIV-1 DNA by ddPCR and to sequence reservoir viral genomes by full length individual proviral sequencing (FLIP-seq) from onset of detection of HIV up to 1 year post treatment initiation.
UNASSIGNED: Whereas ART in hyperacute infection blunted peak viremia compared to untreated individuals (p<0.0001), there was no difference in total HIV-1 DNA measured contemporaneously (p=0.104). There was a steady decline of total HIV DNA in early treated persons over 1 year of ART (p=0.0004), with no significant change observed in the late treated group. Total HIV-1 DNA after one year of treatment was lower in the early treated compared to the late treated group (p=0.02). Generation of 697 single viral genome sequences revealed a difference in the longitudinal proviral genetic landscape over one year between untreated, late treated, and early treated infection: the relative contribution of intact genomes to the total pool of HIV-1 DNA after 1 year was higher in untreated infection (31%) compared to late treated (14%) and early treated infection (0%). Treatment initiated in both late and early infection resulted in a more rapid decay of intact (13% and 51% per month) versus defective (2% and 35% per month) viral genomes. However, intact genomes were still observed one year post chronic treatment initiation in contrast to early treatment where intact genomes were no longer detectable. Moreover, early ART reduced phylogenetic diversity of intact genomes and limited the seeding and persistence of cytotoxic T lymphocyte immune escape variants in the reservoir.
UNASSIGNED: Overall, our results show that whereas ART initiated in hyperacute HIV-1 subtype C infection did not impact reservoir seeding, it was nevertheless associated with more rapid decay of intact viral genomes, decreased genetic complexity and immune escape in reservoirs, which could accelerate reservoir clearance when combined with other interventional strategies.

In the European Union, salmonellosis is one of the most important zoonoses reported. Poultry meat and egg products are the most common food matrices associated with Salmonella presence. Moreover, wild and domestic animals could represent an important reservoir that could favour the direct and indirect transmission of pathogens to humans. Salmonella spp. can infect carnivorous or omnivorous wild birds that regularly ingest food and water exposed to faecal contamination. Birds kept in captivity can act as reservoirs of Salmonella spp. following ingestion of infected prey or feed. In this paper, we describe the isolation of different Salmonella serovars in several species of raptors hosted in aviaries in an Italian wildlife centre and in the raw chicken necks used as their feed but intended for human consumption. Characterisations of strains were carried out by integrating classical methods and whole genome sequencing analysis. The strains of S. bredeney isolated in poultry meat and birds belonged to the same cluster, with some of them being multidrug-resistant (MDR) and carrying the Col(pHAD28) plasmid-borne qnrB19 (fluoro)quinolone resistance gene, thus confirming the source of infection. Differently, the S. infantis found in feed and raptors were all MDR, carried a plasmid of emerging S. infantis (pESI)-like plasmid and belonged to different clusters, possibly suggesting a long-lasting infection or the presence of additional undetected sources. Due to the high risk of fuelling a reservoir of human pathogens, the control and treatment of feed for captive species are crucial.

Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.

Plastic debris both affects and is affected by the beaches it accumulates on. Most studies of microplastics (MPs) in beach sand are focused on coastal beaches or beaches of large lakes near population centers. Here, we assessed MP pollution at a sandy beach near the outlet of a major flood control reservoir (Sardis Lake) in a relatively unpopulated area in north Mississippi, USA, focusing on two prominent wrack zones and areas in-between. Putative MPs were isolated by density separation and matrix digestion, and then examined using stereomicroscopy, with a subset of samples additionally analyzed by μ-FTIR. MP abundance (particles/kg ± 1 standard error (SE), n = 15) averaged of 590 ± 360, with 950 ± 100 in the lower wrack zone, 540 ± 40 in the upper wrack zone, and 270 ± 30 in areas between; these differences were statistically significant (p < 0.01). The MPs generally had similar size and shape characteristics across sites. The majority were fibers (64%), followed by fragments (23%), beads (7%) and films (6%), with a slightly greater proportion of fibers in the wrack zones compared to areas in-between. The number of MPs rose dramatically with decreasing size. Beads were only found in the < 500 μm size fraction. Clear and blue were the predominant colors for all MPs. A total of 29 different types of polymers were detected, with more than half of the particles being composed of polyethylene and polyamide, followed by poly(methyl methacrylate), polyethylene terephthalate, polycarbonate, polypropylene, and others; although this distribution varied some depending on size fraction and location. Because there are no major wastewater discharges into Sardis Lake, the source of the MPs is likely degradation of carelessly discarded plastic, as well as atmospheric fallout. Overall, we found that MP concentrations were highest in the wrack zones and influenced by rates and duration of discharge from the reservoir. Thus, like coastal beaches, wrack zones on freshwater beaches along or downstream of reservoirs accumulate both macro- and micro-plastics and are prime locations for plastic cleanup. Finally, we show that MPs made from naturally weathered LDPE plastic film are prone to fragmentation during pretreatment procedures, which may result in its overestimation.

Infectious keratoconjunctivitis (IKC) is an eye disease caused by Mycoplasma conjunctivae that affects domestic and wild caprines, including Iberian ibex (Capra pyrenaica), a medium-sized mountain ungulate. However, its role in IKC dynamics in multi-host communities has been poorly studied. This study assessed M. conjunctivae in Iberian ibex and seasonally sympatric domestic small ruminants in the Natural Space of Sierra Nevada (NSSN), a mountain habitat in southern Spain. From 2015 to 2017, eye swabs were collected from 147 ibexes (46 subadults, 101 adults) and 169 adult domestic small ruminants (101 sheep, 68 goats). Mycoplasma conjunctivae was investigated through real-time qPCR and statistically assessed according to species, sex, age category, year, period, and area. The lppS gene of M. conjunctivae was sequenced and phylogenetically analysed. Mycoplasma conjunctivae was endemic and asymptomatic in the host community of the NSSN. Three genetic clusters were shared by ibex and livestock, and one was identified only in sheep, although each host species could maintain the infection independently. Naïve subadults maintained endemic infection in Iberian ibex, with an epizootic outbreak in 2017 when the infection spread to adults. Wild ungulates are epidemiologically key in maintaining and spreading IKC and other shared diseases among spatially segregated livestock flocks.

Tick-borne flaviviruses and Borrelia spp. are globally spread pathogens of zoonotic potential that are maintained by a transmission cycle at the interface between ticks and vertebrate hosts, mainly wild animals. Aside data on pathogen burden in ticks, information on the status of various hosts relative to infection is important to acquire. We reviewed how those infections have been studied in wildlife host species in the field to discuss how collected data provided relevant epidemiological information and to identify needs for further studies. The literature was screened for observational studies on pathogen or antibody detection for tick-borne Borrelia spp. and flaviviruses in wildlife host animals. Overall, Borrelia spp. were more studied (73% of case studies, representing 297 host species) than flaviviruses (27% of case studies, representing 114 host species). Studies on both Borrelia spp. and flaviviruses focused mainly on the same species, namely bank vole and yellow-necked mouse. Most studies were order-specific and cross-sectional, reporting prevalence at various locations, but with little insight into the underlying epidemiological dynamics. Host species with potential to act as reservoir hosts of these pathogens were neglected, notably birds. We highlight the necessity of collecting both demographics and infection data in wildlife studies, and to consider communities of species, to better estimate zoonotic risk potential in the One Health context.

The role of the oral microbiota in the overall health and in systemic diseases has gained more importance in the recent years, mainly due to the systemic effects that are mediated by the chronic inflammation caused by oral diseases, such as periodontitis, through the microbial communities of the mouth. The chronic infection by the human immunodeficiency virus (HIV) interacts at the tissue level (e.g. gut, genital tract, brain) to create reservoirs; the modulation of the gut microbiota by HIV infection is a good example of these interactions. The purpose of the present review is to assess the state of knowledge on the oral microbiota (microbiome, mycobiome and virome) of HIV-infected patients in comparison to that of HIV-negative individuals and to discuss the reciprocal influence of HIV infection and oral microbiota in patients with periodontitis on the potential establishment of a viral gingival reservoir. The influence of different clinical and biological parameters are reviewed including age, immune and viral status, potent antiretroviral therapies, smoking, infection of the airway and viral coinfections, all factors that can modulate the oral microbiota during HIV infection. The analysis of the literature proposed in this review indicates that the comparisons of the available studies are difficult due to their great heterogeneity. However, some important findings emerge: (i) the oral microbiota is less influenced than that of the gut during HIV infection, although some recurrent changes in the microbiome are identified in many studies; (ii) severe immunosuppression is correlated with altered microbiota and potent antiretroviral therapies correct partially these modifications; (iii) periodontitis constitutes a major factor of dysbiosis, which is exacerbated in HIV-infected patients; its pathogenesis can be described as a reciprocal reinforcement of the two conditions, where the local dysbiosis present in the periodontal pocket leads to inflammation, bacterial translocation and destruction of the supporting tissues, which in turn enhances an inflammatory environment that perpetuates the periodontitis cycle. With the objective of curing viral reservoirs of HIV-infected patients in the future years, it appears important to develop further researches aimed at defining whether the inflamed gingiva can serve of viral reservoir in HIV-infected patients with periodontitis.

Chagas disease (CD) is a vector-borne Neglected Zoonotic Disease (NZD) caused by a flagellate protozoan, Trypanosoma cruzi, that affects various mammalian species across America, including humans and domestic animals. However, due to an increase in population movements and new routes of transmission, T. cruzi infection is presently considered a worldwide health concern, no longer restricted to endemic countries. Dogs play a major role in the domestic cycle by acting very efficiently as reservoirs and allowing the perpetuation of parasite transmission in endemic areas. Despite the significant progress made in recent years, still there is no vaccine against human and animal disease, there are few drugs available for the treatment of human CD, and there is no standard protocol for the treatment of canine CD. In this review, we highlight human and canine Chagas Disease in its different dimensions and interconnections. Dogs, which are considered to be the most important peridomestic reservoir and sentinel for the transmission of T. cruzi infection in a community, develop CD that is clinically similar to human CD. Therefore, an integrative approach, based on the One Health concept, bringing together the advances in genomics, immunology, and epidemiology can lead to the effective development of vaccines, new treatments, and innovative control strategies to tackle CD.

Chiari III malformation, a rare and severe subtype of Chiari malformations, is frequently associated with hydrocephalus. The conventional treatment approaches for hydrocephalus in Chiari III malformations have mainly focused on ventriculoperitoneal (VP) shunting, but optimal methods and timing remain uncertain. We report a case of a newborn girl with Chiari III malformation who underwent surgical closure of an occipitocervical encephalocele and ventricular reservoir implantation on her third day of life. This procedure successfully managed her hydrocephalus without significant short-term complications. Three months post-surgery, she developed secondary external hydrocephalus, which was managed through subdural-peritoneal shunting, allowing her to thrive until at least five years of age. This case demonstrates the potential of ventricular reservoir implantation in treating hydrocephalus associated with Chiari III malformation and brings to light secondary external hydrocephalus, subsequently managed by VP shunting.

Orthohantaviruses cause hantavirus cardiopulmonary syndrome; most cases occur in the southwest region of the United States. We discuss a clinical case of orthohantavirus infection in a 65-year-old woman in Michigan and the phylogeographic link of partial viral fragments from the patient and rodents captured near the presumed site of infection.