A tryptophan metabolite made by a gut microbiome eukaryote induces pro-inflammatory T cells.

The large intestine harbors microorganisms playing unique roles in host physiology. The beneficial or detrimental outcome of host-microbiome coexistence depends largely on the balance between regulators and responder intestinal CD4+ T cells. We found that ulcerative colitis-like changes in the large intestine after infection with the protist Blastocystis ST7 in a mouse model are associated with reduction of anti-inflammatory Treg cells and simultaneous expansion of pro-inflammatory Th17 responders. These alterations in CD4+ T cells depended on the tryptophan metabolite indole-3-acetaldehyde (I3AA) produced by this single-cell eukaryote. I3AA reduced the Treg subset in vivo and iTreg development in vitro by modifying their sensing of TGFß, concomitantly affecting recognition of self-flora antigens by conventional CD4+ T cells. Parasite-derived I3AA also induces over-exuberant TCR signaling, manifested by increased CD69 expression and downregulation of co-inhibitor PD-1. We have thus identified a new mechanism dictating CD4+ fate decisions. The findings thus shine a new light on the ability of the protist microbiome and tryptophan metabolites, derived from them or other sources, to modulate the adaptive immune compartment, particularly in the context of gut inflammatory disorders.

Detection of African Swine Fever Virus from Wild Boar, Singapore, 2023.

We detected African swine fever virus (ASFV) from a wild boar in Singapore. In <72 hours, we confirmed and reported ASFV p72 genotype II, CD2v serogroup 8, and IGR-II variant by using a combination of real-time PCR and whole-genome sequencing. Continued biosurveillance will be needed to monitor ASFV in Singapore.

Rabbit haemorrhagic disease virus 2 from Singapore 2020 outbreak revealed an Australian recombinant variant.

Rabbit haemorrhagic disease (RHD) is a significant and debilitating viral disease affecting lagomorphs. In September 2020, Singapore reported its first cases of RHD virus (RHDV) infection in domesticated rabbits. The initial findings reported that the outbreak strain belonged to genotype GI.2 (RHDV2/RHDVb), and epidemiological investigations could not identify the definitive source of the virus origin. Further recombination detection and phylogenetic analyses of the Singapore outbreak strain revealed that the RHDV was a GI.2 structural (S)/GI.4 non-structural (NS) recombinant variant. Sequence analyses on the National Centre for Biotechnology Information (NCBI) database showed high homology to recently emerged Australian variants, which were prevalent in local Australian lagomorph populations since 2017. Time-structured and phylogeographic analyses for the S and NS genes revealed a close genetic relationship between the Singapore RHDV strain and the Australian RHDV variants. More thorough epidemiological inquiries are necessary to ascertain how an Australian RHDV was introduced into the Singapore rabbit population, and opportune development of RHDV diagnostics and vaccines will be important to safeguard lagomorphs from future RHDV infection and disease management.

Development of Differentiating Infected from Vaccinated Animals (DIVA) Real-Time PCR for African Horse Sickness Virus Serotype 1.

African horse sickness (AHS) is a highly infectious and often fatal disease caused by 9 serotypes of the orbivirus African horse sickness virus (AHSV). In March 2020, an AHS outbreak was reported in Thailand in which AHSV serotype 1 was identified as the causative agent. Trivalent live attenuated vaccines serotype 1, 3, and 4 were used in a targeted vaccination campaign within a 50-km radius surrounding the infected cases, which promptly controlled the spread of the disease. However, AHS-like symptoms in vaccinated horses required laboratory diagnostic methods to differentiate infected horses from vaccinated horses, especially for postvaccination surveillance. We describe a real-time reverse transcription PCR-based assay for rapid characterization of the affecting field strain. The development and validation of this assay should imbue confidence in differentiating AHS-vaccinated horses from nonvaccinated horses. This method should be applied to determining the epidemiology of AHSV in future outbreaks.

The roles of parasite-derived extracellular vesicles in disease and host-parasite communication.

In recent years, several parasites have been shown to interact with their hosts through intra- and inter-community communication mechanisms, which were identified to be mediated by extracellular vesicles (EVs) through various uptake mechanisms. EVs are a heterogenous group of nanoparticles (~30-5000 nm) classified into three main types according to their size and biogenesis. EVs contain proteins, lipids, nucleic acids and metabolites from the cell of origin which are essential for genetic exchange, biomarker identification and diagnosis of pathological diseases. As important "forward lines of parasite infectivity", the parasite-secreted EVs function as information transmitters in the early-stage of host-parasite interaction and subsequent host-cell colonization. For this review, we summarize from the literature the relevance of EVs to the pathogenesis and development of human parasitic protistan diseases such as giardiasis, leishmaniasis, amoebiasis, malaria and Blastocystis-mediated gut pathology. Specific in vitro and in vivo interactions of the parasite-EVs and the host, with the reported cellular and immunological outcomes are discussed in this review. EVs have great potential to be further developed as diagnostic, immunomodulation and therapeutic alternatives to fill the knowledge gaps in the current parasitic diseases discussed in this review. Nanomedicine and vaccine development could be explored, with the utilization and/or modification of the parasitic EVs as novel treatment and prevention strategies.

Interaction between Antibiotic Resistance, Resistance Genes, and Treatment Response for Urinary Tract Infections in Primary Care.

Given increasing antimicrobial resistance, we aimed to determine antibiotic susceptibility and presence of resistance genes in uropathogens in primary care, factors associated with resistance to commonly prescribed antibiotics, and effect of treatment on early symptom resolution. We conducted a prospective study of primary care patients with urinary tract infection (UTI) symptoms and culture-confirmed UTI in Singapore from 2015 to 2016. Cohort characteristics and antimicrobial susceptibility of cultured isolates were analyzed. Among Enterobacteriaceae isolates, early symptom resolution (within 3 days) according to antibiotic prescribed and isolate susceptibility and factors associated with antibiotic resistance were evaluated. Of 695 symptomatic patients, 299 were urine culture positive; of these 299 patients, 259 (87%) were female. Escherichia coli was the most common uropathogen (76%). Enterobacteriaceae isolates (n = 283) were highly susceptible to amoxicillin-clavulanate (86%), nitrofurantoin (87%), and fosfomycin (98%), but >20% were resistant to ciprofloxacin and co-trimoxazole. Isolates resistant to appropriate indicator antibiotics were further tested to determine proportions positive for blaCTX-M (14/26, 54%), plasmid-mediated ampC (12/24, 50%), qnr (7/69, 10%), and fos (1/6, 17%) resistance genes. A total of 67% of patients given antibiotics with susceptible isolates reported early resolution versus 45% given antibiotics with nonsusceptible isolates (P = 0.001) and 27% not treated (P = 0.018). On multivariable analysis, Indian ethnicity and diabetes mellitus were associated with amoxicillin-clavulanate resistance. Genitourinary abnormalities, UTI in the past 12 months, and hospitalization in the past 6 months were associated with ciprofloxacin and co-trimoxazole resistance. Patients given active empirical antibiotics were most likely to report early symptom resolution, but correlation with in vitro susceptibility was imperfect. Factors associated with resistance may guide the decision to obtain initial urine culture.

Mongolians core gut microbiota and its correlation with seasonal dietary changes.

Historically, the Mongol Empire ranks among the world's largest contiguous empires, and the Mongolians developed their unique lifestyle and diet over thousands of years. In this study, the intestinal microbiota of Mongolians residing in Ulan Bator, TUW province and the Khentii pasturing area were studied using 454 pyrosequencing and q-PCR technology. We explored the impacts of lifestyle and seasonal dietary changes on the Mongolians' gut microbes. At the phylum level, the Mongolians's gut populations were marked by a dominance of Bacteroidetes (55.56%) and a low Firmicutes to Bacteroidetes ratio (0.71). Analysis based on the operational taxonomic unit (OTU) level revealed that the Mongolian core intestinal microbiota comprised the genera Prevotella, Bacteroides, Faecalibacterium, Ruminococcus, Subdoligranulum and Coprococcus. Urbanisation and life-style may have modified the compositions of the gut microbiota of Mongolians from Ulan Bator, TUW and Khentii. Based on a food frequency questionnaire, we found that the dietary structure was diverse and stable throughout the year in Ulan Bator and TUW, but was simple and varied during the year in Khentii. Accordingly, seasonal effects on intestinal microbiota were more distinct in Khentii residents than in TUW or Ulan Bator residents.

Recent advances and future perspectives in microbial phototrophy in antarctic sea ice.

Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown. In this minireview, we discuss recent advances in our understanding of phototrophic bacteria and highlight the need for future research.

The origin of cyanobacteria in Antarctic sea ice: marine or freshwater?

Cyanobacteria play an important role in the primary productivity of many ecosystems and are dominant in non-marine polar environments. Apart from detecting low levels of cyanobacteria-like pigments in the Southern Ocean, little effort has been spent in trying to elucidate Cyanobacteria in Antarctic sea ice. Here, we report the first use of culture, microscope, microarray and molecular techniques to show that marine Cyanobacteria are rare or absent in sea ice. Our infrequent positive signals were most closely related to freshwater Cyanobacteria from neighbouring terrestrial sources, which illustrates our techniques were sensitive enough to find sea-ice cyanobacteria if they were present. It is still possible that minute quantity of marine cyanobacteria may exist in sea ice and do not contribute significantly to the polar marine ecosystems.

Aerobic anoxygenic phototrophic bacteria in Antarctic sea ice and seawater.

Aerobic anoxygenic phototrophs are obligate aerobes with unusually high concentrations of carotenoids, low cellular contents of bacteriochlorophyll-a and they lack light-harvesting complex II. In this study, sea ice and seawater samples were collected from six different sites in the Ross Sea, Antarctica. Using a combination of primers for pufM (which encodes a pigment-binding protein subunit of the reaction centre complex), clone libraries of DNA and cDNA were created and a total of 63 positive clones were obtained from three sites, all clustering within the α-Proteobacteria. Fifty-three of these clones were from seawater. The remaining clones were from sea ice and all were found in the middle and bottom sections of the ice. These sea ice bacteria may favour the lower part of the ice matrix where irradiance is low. This report highlights the first findings of AAnPs in antarctic sea ice and seawater within the Ross Sea Region.

Proteorhodopsin-bearing bacteria in Antarctic sea ice.

Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.