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Microbiology Spectrum Jun 2024, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and...
, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of , while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings. A range of virulence factors and antibiotic resistances were also detected, suggesting may operate as an undescribed opportunistic pathogen.
PubMed: 38934605
DOI: 10.1128/spectrum.04157-23 -
MSystems Jun 2024The application of fecal metaproteomics to large-scale studies of the gut microbiota requires high-throughput analysis and standardized experimental protocols. Although...
The application of fecal metaproteomics to large-scale studies of the gut microbiota requires high-throughput analysis and standardized experimental protocols. Although high-throughput protein cleanup and digestion methods are increasingly used in shotgun proteomics, no studies have yet critically compared such protocols using human fecal samples. In this study, human fecal protein extracts were processed using several different protocols based on three main approaches: filter-aided sample preparation (FASP), solid-phase-enhanced sample preparation (SP3), and suspension trapping (S-Trap). These protocols were applied in both low-throughput (i.e., microtube-based) and high-throughput (i.e., microplate-based) formats, and the final peptide mixtures were analyzed by liquid chromatography coupled to high-resolution tandem mass spectrometry. The FASP-based methods and the combination of SP3 with in-StageTips (iST) yielded the best results in terms of the number of peptides identified through a database search against gut microbiome and human sequences. The efficiency of protein digestion, the ability to preserve hydrophobic peptides and high molecular weight proteins, and the reproducibility of the methods were also evaluated for the different protocols. Other relevant variables, including interindividual variability of stool, duration of protocols, and total costs, were considered and discussed. In conclusion, the data presented here can significantly contribute to the optimization and standardization of sample preparation protocols in human fecal metaproteomics. Furthermore, the promising results obtained with the high-throughput methods are expected to encourage the development of automated workflows and their application to large-scale gut microbiome studies.IMPORTANCEFecal metaproteomics is an experimental approach that allows the investigation of gut microbial functions, which are involved in many different physiological and pathological processes. Standardization and automation of sample preparation protocols in fecal metaproteomics are essential for its application in large-scale studies. Here, we comparatively evaluated different methods, available also in a high-throughput format, enabling two key steps of the metaproteomics analytical workflow (namely, protein cleanup and digestion). The results of our study provide critical information that may be useful for the optimization of metaproteomics experimental pipelines and their implementation in laboratory automation systems.
PubMed: 38934547
DOI: 10.1128/msystems.00661-24 -
Emerging Microbes & Infections Jun 2024Chikungunya virus has caused millions of cases worldwide over the last twenty years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa....
Chikungunya virus has caused millions of cases worldwide over the last twenty years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the re-emergence of an endemic strain evolving linearly in a sylvatic context.
PubMed: 38934257
DOI: 10.1080/22221751.2024.2373308 -
Emerging Microbes & Infections Jun 2024, a group of multi-drug resistant, Gram-positive, aerobic and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the...
, a group of multi-drug resistant, Gram-positive, aerobic and partially acid-fast bacteria, are emerging causes of bacterial conjunctivitis and keratitis. However, the pathogenesis of keratitis is largely unknown. To address this, we used New Zealand White rabbits to develop the first eye infection model and conducted tests to study the pathogenesis mechanisms of . There is increasing evidence that biofilms play a significant role in ocular infections, leading us to hypothesize that biofilm formation is crucial for effective infection. In order to look for potential candidate genes which are important in biofilm formation and keratitis. We performed genome sequencing of two ocular isolates, -PW1004 and -PW899, to identify potential virulence factors. Through and studies, we characterized their biological roles in mediating keratitis. Our findings confirmed that is an ocular pathogen by fulfilling the Koch's postulates, and using genome sequence data, we identified encoding a mycolyltransferase, as a crucial gene in biofilm formation and causing keratitis in the rabbit model. This is the first report demonstrating the novel role of mycolyltransferase in causing ocular infections. Overall, our findings contribute to a better understanding of pathogenesis and provide a potential target for treatment. Specific inhibitors targeting TmytC could serve as an effective treatment option for infections.
PubMed: 38934251
DOI: 10.1080/22221751.2024.2373317 -
Intervirology Jun 2024This study aimed to investigate the differences between pregnant women with chronic hepatitis B virus (HBV) infection and intrafamilial infection and those without...
INTRODUCTION
This study aimed to investigate the differences between pregnant women with chronic hepatitis B virus (HBV) infection and intrafamilial infection and those without intrafamilial infection.
METHODS
HBV DNA was extracted from the sera of 16 pregnant women with chronic hepatitis B (CHB) and their family members for gene sequencing and phylogenetic analyses. A total of 74 pregnant women with CHB were followed up from the second trimester to three months postpartum. Viral markers and other laboratory indicators were compared between pregnant women with CHB with and without intrafamilial infection.
RESULTS
The phylogenetic tree showed that HBV lines in the mother-spread pedigree shared a node, whereas there was an unrelated genetic background for HBV lines in individuals without intrafamilial infection. From delivery to three months postpartum, compared with those without intrafamilial infection, pregnant women with intrafamilial infection were related negatively to HBV DNA (β=-0.43, 95% Confidence Interval [CI]: -0.76 to -0.12, p=0.009), HBeAg (β=-195.15, 95% CI: -366.35 to -23.96, p=0.027), and hemoglobin changes (β=-8.09, 95%CI: -15.54 to -0.64, p=0.035) and positively to changes in the levels of alanine aminotransferase (β=73.9, 95%CI:38.92-108.95, p<0.001) and albumin (β=2.73, 95% CI:0.23-5.23, p=0.033).
CONCLUSION
The mother-spread pedigree spread model differs from that of non-intrafamilial infections. Pregnant women with intra-familial HBV infection have less hepatitis flares and liver damage, but their HBV DNA and HBeAg levels rebound faster after delivery, than those without intra-familial infection by the virus.
PubMed: 38934174
DOI: 10.1159/000539994 -
Kidney Research and Clinical Practice May 2024Patients with end-stage kidney disease (ESKD) are more susceptible to viral epidemics and are known to have higher incidence and death rates of coronavirus disease 2019...
BACKGROUND
Patients with end-stage kidney disease (ESKD) are more susceptible to viral epidemics and are known to have higher incidence and death rates of coronavirus disease 2019 (COVID-19) compared to the general population. We determined COVID-19 incidence and mortality among chronic hemodialysis (HD), peritoneal dialysis (PD), and kidney transplantation (KT) patients in Korea.
METHODS
We conducted a retrospective cohort study and data regarding Korean ESKD adults (aged ≥18 years) were obtained from the National Health Insurance Service of Korea from October 2020 to December 2021. We examined and compared the incidence of COVID-19-related infections and deaths among the patients receiving HD, PD, and KT.
RESULTS
Of all ESKD patients, 85,018 (68.1%) were on HD, 8,399 (6.7%) on PD, and 31,343 (25.1%) on KT. The COVID-19 incidence was 1.3% for HD, 1.2% for PD, and 1.5% for KT. COVID-19 mortality was 16.3% for HD, 12.2% for PD, and 4.7% for KT. PD patients had a lower incidence of infection compared to HD patients (odds ratio [OR], 0.76; 95% confidence interval [CI], 0.607-0.93), but KT patients had a significantly higher risk of infection (OR, 1.28; 95% CI, 1.13-1.44). Compared with HD, the risk of COVID-19-related death was not different for PD patients but was significantly lower for KT patients (hazard ratio, 0.55; 95% CI, 0.35-0.88).
CONCLUSION
COVID-19 incidence was lower in PD patients than in HD patients, but mortality was not different between them. KT was associated with a higher risk of COVID-19 infection but lower mortality compared to HD.
PubMed: 38934044
DOI: 10.23876/j.krcp.23.287 -
Frontiers in Veterinary Science 2024Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that targets pig intestines to cause disease. It is globally widespread and causes huge economic...
Nucleotide metabolism-related host proteins RNA polymerase II subunit and uridine phosphorylase 1 interacting with porcine epidemic diarrhea virus N proteins affect viral replication.
Porcine epidemic diarrhea virus (PEDV) is a highly infectious pathogen that targets pig intestines to cause disease. It is globally widespread and causes huge economic losses to the pig industry. PEDV N protein is the protein that constitutes the core of PEDV virus particles, and most of it is expressed in the cytoplasm, and a small part can also be expressed in the nucleus. However, the role of related proteins in host nucleotide metabolic pathways in regulating PEDV replication have not been fully elucidated. In this study, PEDV-N-labeled antibodies were co-immunoprecipitated and combined with LC-MS to screen for host proteins that interact with N proteins. Bioinformatics analyses showed that the selected host proteins were mainly enriched in metabolic pathways. Moreover, co-immunoprecipitation and confocal microscopy confirmed that the second-largest subunit of RNA polymerase II (RPB2) and uridine phosphorylase 1 (UPP1) interacted with the N protein. RPB2 is the main subunit of RNA polymerase II and plays an important role in eukaryotic transcription. UPP1 is an enzyme that catalyzes reversible phosphorylation of uridine to uracil and ribo-1-phosphate to promote catabolism and bio anabolism. RPB2 overexpression significantly promoted viral replication, whereas UPP1 overexpression significantly inhibited viral replication. Studies on interactions between the PEDV N and host proteins are helpful in elucidating the pathogenesis and immune escape mechanism of PEDV.
PubMed: 38933700
DOI: 10.3389/fvets.2024.1417348 -
Frontiers in Veterinary Science 2024There are no microbiological regulatory limits for viruses in animal feed and feed ingredients.
INTRODUCTION
There are no microbiological regulatory limits for viruses in animal feed and feed ingredients.
METHODS
A performance objective (PO) was proposed in this study to manufacture a spray-dried porcine plasma (SDPP) batch absent of any infectious viral particles. The PO levels of -7.0, -7.2, and -7.3 log TCID/g in SDPP were estimated for three batch sizes (10, 15, and 20 tons).
RESULTS AND DISCUSSION
A baseline survey on the presence of porcine epidemic diarrhea virus (PEDV) in raw porcine plasma revealed a concentration of -1.0 ± 0.6 log TCID/mL as calculated using a TCID-qPCR derived standard curve. The mean African swine fever virus (ASFV) concentration in raw plasma was estimated to be 0.6 log HAD/mL (0.1-1.4, 95% CI) during a pre-clinical scenario (collected from asymptomatic and undetected viremic pigs). Different processing scenarios (baseline: spray-drying + extended storage) and baseline + ultraviolet (UV) radiation were evaluated to meet the PO levels proposed in this study. The baseline and baseline + UV processing scenarios were >95 and 100% effective in achieving the PO for PEDV by using different batch sizes. For the ASFV in SDPP during a pre-clinical scenario, the PO compliance was 100% for all processing scenarios evaluated. Further research is needed to determine the underlying mechanisms of virus inactivation in feed storage to further advance the implementation of feed safety risk management efforts globally.
PubMed: 38933699
DOI: 10.3389/fvets.2024.1371774 -
Frontiers in Cellular and Infection... 2024
Topics: Inflammasomes; Humans; Virus Diseases; Animals; Host-Pathogen Interactions
PubMed: 38933692
DOI: 10.3389/fcimb.2024.1438310 -
The Pan African Medical Journal 2024tuberculosis (TB) and Human Immunodeficiency Virus (HIV) remain major public health threats globally and worse when they co-exist in susceptible individuals. The study...
INTRODUCTION
tuberculosis (TB) and Human Immunodeficiency Virus (HIV) remain major public health threats globally and worse when they co-exist in susceptible individuals. The study examined TB treatment outcomes and their predictive factors among people living with HIV (PLHIVs).
METHODS
a review of TB/HIV co-infected patients who had TB treatments across comprehensive antiretroviral therapy (ART) sites with ≥500 patients was conducted in seven United States of America President's Emergency Plan for AIDS Relief (PEPFAR)-supported States in Nigeria. Data on patient background, HIV and TB care, and TB treatment outcomes were collected using an Excel abstraction template. The data was analyzed using SPSS and an association was examined using a chi-square test while binary logistic regression was used to determine predictors of TB treatment outcomes (P< 0.05).
RESULTS
two thousand six hundred and fifty-two co-infected patients participated in the study. The mean age of participants was 37 ± 14 years. A majority had TB treatment success (cured = 1059 (39.9%), completed = 1186 (44.7%)). Participants who had pulmonary TB, virally suppressed and commenced isoniazid (INH) before TB diagnosis were more likely to have a favorable TB treatment outcome compared to those who had extrapulmonary TB (AOR = 7.110, 95% CI = 1.506 - 33.565), virally unsuppressed (AOR = 1.677, 95% CI = 1.036 - 2.716) or did not commence INH before TB diagnosis (AOR = 1.486, 95% CI = 1.047 - 2.109).
CONCLUSION
site of infection, immune status, exposure to ART, and INH prophylaxis were found to predict TB treatment outcomes among PLHIVs. Stakeholders should ensure early commencement of ART and INH prophylaxis for PLHIVs.
Topics: Humans; Nigeria; HIV Infections; Adult; Female; Antitubercular Agents; Male; Tuberculosis; Middle Aged; Coinfection; Treatment Outcome; Young Adult; Anti-HIV Agents; Isoniazid; Retrospective Studies; Tuberculosis, Pulmonary
PubMed: 38933432
DOI: 10.11604/pamj.2024.47.149.35719