bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance
Authors: Phan Tin , Ribeiro Ruy M. , Edelstein Gregory E. , Boucau Julie , Uddin Rockib , Marino Caitlin , Liew May Y. , Barry Mamadou , Choudhary Manish C. , Tien Dessie , Su Karry , Reynolds Zahra , Li Yijia , Sagar Shruti , Vyas Tammy D. , Kawano Yumeko , Sparks Jeffrey A. , Hammond Sarah P. , Wallace Zachary , Vyas Jatin M. , Li Jonathan Z. , Siedner Mark J. , Barczak Amy K. , Lemieux Jacob E. , Perelson Alan S. 
Published: February 2025

ABSTRACT

In a subset of SARS-CoV-2-infected individuals treated with the antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of N-R near the time of symptom onset, coupled with incomplete viral clearance, appears to be the main factor leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by the time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. A comparison with an untreated cohort suggests that early treatments with nirmatrelvir-ritonavir may be associated with a delay in the onset of an adaptive immune response. Nevertheless, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment to a 10-day regimen may greatly diminish the chance of rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2.

IMPORTANCE
Nirmatrelvir-ritonavir is an effective treatment for SARS-CoV-2. In a subset of individuals treated with nirmatrelvir-ritonavir, the initial reduction in viral load is followed by viral rebound once treatment is stopped. We show that the timing of treatment initiation with nirmatrelvir-ritonavir may influence the risk of viral rebound. Nirmatrelvir-ritonavir stops viral growth and preserves target cells but may not lead to full clearance of the virus. Thus, once treatment ends, if an effective adaptive immune response has not adequately developed, the remaining virus can lead to rebound. Our results provide insights into the mechanisms of rebound and can help develop better treatment strategies to minimize this possibility.
Conventional and antibody-enhanced DENV infection of human macrophages induces differential immunotranscriptomic profiles
Authors: Hardy Céline S. C. , Wegman Adam D. , Waldran Mitchell J. , Chan Gary C. , Waickman Adam T. 
Published: February 2025

ABSTRACT

Dengue virus (DENV) is a mosquito-borne flavivirus which coexists as four genetically and immunologically distinct serotypes (DENV-1 to -4). In secondary heterologous DENV infection, pre-existing immunity is believed to contribute to severe disease through antibody-dependent enhancement (ADE). Although the elevated pathology observed in ADE conditions has been described, the cell-intrinsic mechanisms governing this process remain unclear. Using single-cell RNA sequencing (scRNAseq), we investigated the transcriptomic profiles of human monocyte-derived macrophages infected by DENV-2 in ADE compared to conventional infection conditions. Unsupervised analysis of scRNAseq data enabled the identification of two distinct cell populations in a heterogeneous cell culture, likely representing infected and bystander/uninfected cells. Differential gene expression and ingenuity pathway analyses revealed a number of significantly upregulated and downregulated genes and gene networks between cells infected by ADE compared to conventional infection. Specifically, these pathways indicated mechanisms such as suppressed interferon signaling and inflammatory chemokine transcription in cells infected via ADE. Further analysis revealed that transcriptomic changes were independent of viral RNA within infected cells, suggesting that the observed changes are reflective of cell-intrinsic responses and not simply a function of per-cell viral burden. The interpreted “bystander” cell population also demonstrated distinct profiles in ADE conditions, indicating an immunologically activated phenotype enriched for the expression of gene networks involved with protein translation, cytokine production, and antigen presentation. Together, these findings support the concept that DENV infection via ADE induces a qualitatively different transcriptomic response in infected cells, contributing to our understanding of ADE as a mechanistic driver of disease and pathogenesis.

IMPORTANCE
Dengue virus (DENV) is a mosquito-borne human pathogen with a significant and growing global health burden. Although correlates of severe dengue disease are poorly understood, pre-existing immunity to DENV has been associated with severe disease risk and known to contribute to an alternative route of viral entry termed antibody-dependent enhancement (ADE). Using single-cell RNA sequencing, we identified distinct transcriptomic processes involved in antibody-mediated DENV entry compared to conventional receptor-mediated entry. These data provide meaningful insight into the discrete processes contributing to DENV pathogenesis in ADE conditions.
Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia
Authors: Zhao Meixi , Shi Yanyan , Zhang Congcong , Lu Meiqin , Shen Meili , Xie Lijian , Wang Libo , Lu Aizhen 
Published: February 2025

ABSTRACT

Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%,
P
< 0.001), bacterial (69.29% vs 12.60%,
P
< 0.001), and fungal (11.81% vs 3.15%,
P
= 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%,
P
= 0.99) and
Mycoplasma pneumoniae
(48.03% vs 45.67%,
P
= 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for
M. pneumoniae
had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of
M. pneumoniae
and respiratory viruses. Different detection methods should be rationalized for different pathogens.

IMPORTANCE

This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of
Mycoplasma pneumoniae
and respiratory viruses and may have greater application advantages in combination with CMTs, such as
M. pneumoniae
IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.
Children who develop celiac disease are predicted to exhibit distinct metabolic pathways among their gut microbiota years before diagnosis
Authors: Kelley Kristina , Dogru Dogus , Huang Qian , Yang Yi , Palm Noah W. , Altindis Emrah , Ludvigsson Johnny 
Published: February 2025

ABSTRACT

Celiac disease (CD) is an autoimmune disease caused by a loss of gluten tolerance in genetically predisposed individuals. While 30%–40% of people possess the predisposing alleles, only 1%–2% are diagnosed with CD, suggesting that environmental factors are involved in disease pathogenesis. To determine an association between pediatric CD and the gut microbiome, we analyzed fecal samples from a prospective cohort study (ABIS). These samples were collected from children who later developed CD (CD progressors) and age-matched healthy children (at ages 1, 2.5, and 5) with similar HLA genotypes, breastfeeding durations, and gluten exposure times. We previously reported gut microbiome differences at ages 2.5 and 5 in this cohort; here, we present findings from samples collected at age 1 (
n
= 5). We identified 14 ASVs differing significantly between CD progressors and controls, including taxa linked to CD pathogenesis. CD progressors had increased Firmicutes and higher alpha diversity in IgA− bacteria. Using PICRUSt, we analyzed metabolic pathways enriched in CD progressors compared to controls at ages 1, 2.5, and 5 (
n
= 5–16), revealing enriched inflammatory and pathogenic pathways potentially contributing to CD-related immune dysregulation. While results are based on the primary EdgeR analysis, we also applied a non-parametric method of statistical analysis, reporting those results with supplementary figures. In conclusion, our findings suggest distinct metabolic pathways enriched in the gut microbiome of CD progressors years before diagnosis, which could inform targeted therapeutics for CD. As discussed in the limitations section, this small pilot study should be replicated with larger sample sizes for broader generalization.

IMPORTANCE

We analyzed gut microbiome data from children who later developed celiac disease (CD progressors) compared to healthy children in the first 5 years of life. Using fecal samples corresponding to the three phases of gut microbiome development, we uncovered enriched functional microbial pathways in CD progressors at age 1. Some of these pathways, implicated in bacterial pathogenesis, microbiota modulation, and inflammation, have been correlated with CD. We also identified taxa in CD progressors at age 1 including
Lachnospiraceae
,
Alistipes
, and
Bifidobacterium dentium
that were previously associated with CD. These findings suggest a potential role for these taxa and enriched pathways in pediatric CD onset years before diagnosis, highlighting potential for early interventions. While the findings of this exploratory study should be validated with larger sample sizes, our study suggests microbial metabolic pathways related to CD onset, enhancing our understanding of CD pathogenesis and the role of gut microbiome-mediated early alterations.
Microbial players in autoimmunity: multicentric analysis of the association between
Mycoplasma hominis
serostatus and rheumatoid arthritis
Authors: Erre G. L. , Phan Ngoc Dan Thanh , Diaz N. , Congiargiu A. , Mundula N. , Mangoni A. A. , Phan Thi Minh Phuong , Margarita V. , Fiori P. L. , Rappelli P. , Cacciotto C. , Alberti A. , Dessì D. 
Published: February 2025

ABSTRACT

Resident mucosal pathogens may induce immune tolerance breach, specific autoimmune response, and the development of rheumatoid arthritis (RA) in susceptible individuals. Despite a number of studies linking infections by
Mollicutes
bacteria to autoimmune disorders’ onset and progression, the role of
Mycoplasma hominis
, a common urogenital mucosa colonizing bacterium, in inducing a specific humoral response in RA has been seldom addressed. This study reports
M. hominis
seroprevalence in RA patients compared to healthy controls (HC) by testing two separate cohorts sampled in two distinct geographical settings (Italy and Vietnam). The amount of circulating anti-lipid-associated membrane proteins (LAMPs) antibodies was significantly higher in RA patients than HC in both cohorts. Also, a significantly higher seroprevalence of anti-
M
.
hominis
antibodies in RA patients compared to HC in both cohorts was observed. Notably, neither ELISA OD values nor positivity of anti-LAMPs were significantly associated with RA-specific variables. Further studies are essential to elucidate the underlying mechanisms by which
Mycoplasma
species may contribute to the pathogenesis of RA, thereby advancing our understanding of the potential causal links between
Mollicutes
and autoimmune disorders.

IMPORTANCE

Mycoplasmas may cause persistent asymptomatic mucosal infections and elicit chronic host immune responses. In this study, we evaluated the prevalence of serological response to the sexually transmitted bacterium
Mycoplasma hominis
in patients with rheumatoid arthritis. We show that sera of patients with rheumatoid arthritis are enriched with antibodies specifically recognizing microbial surface antigens compared with the general population. This suggests that
M. hominis
genital infection, with its peculiar host immunity subversion mechanisms, might play a role in predisposing to the development and progression of chronic arthritis in susceptible individuals. Thus, the range of microbes with a role as triggers of autoimmune disease (
P. gingivalis
, A.
actinomycetemcomitans
,
Streptococcus
spp., and
F. nucleatum
, among others) might have a new member in
M. hominis
. The potential role of the interactions taking place at the host–pathogen interface during persistent
M. hominis
infections in inducing autoimmunity should be further explored and characterized.
Development and characterization of a double-fluorescent HIV-1 reporter cellular model to tackle the Rev-dependent export pathway
Authors: Wadas Jakub , Ali Haider , Osiecka Aleksandra , Dorman Agnieszka , Pyrc Krzysztof , Kula-Pacurar Anna 
Published: February 2025

ABSTRACT

The Rev-dependent nuclear export of unspliced and singly-spliced transcripts of human immunodeficiency virus type 1 (HIV-1) constitutes a critical yet poorly characterized post-transcriptional event essential for effective viral replication. In this study, we engineered a dual-fluorescent HIV-1-based cellular reporter system to elucidate the mechanisms underpinning Rev-dependent export. By generating multiple stably integrated inducible cellular clones, we ensured the expression of two distinct fluorescent proteins, mKO2, and ECFP, from unspliced (Rev dependent) and multiply spliced (Rev independent) HIV-1 transcripts, respectively. Utilizing flow cytometry, we performed quantitative analyses of dual-fluorescent cell populations. The developed tool enables precise assessment of the Rev-dependent export, and we validated it using known inhibitors of this pathway (leptomycin D), as well as targeted depletion of MATR3, an essential cofactor of Rev, and CRNKL1, a repressor of unspliced HIV-1 RNA export.

IMPORTANCE
The developed dual-fluorescent reporter system represents a powerful and handy tool for the identification and characterization of novel molecular players involved in the Rev-dependent export pathway. This system not only holds promise for advancing our understanding of human immunodeficiency virus type 1 (HIV-1) biology but also serves as an invaluable platform for high-throughput drug screening aimed at targeting post-transcriptional HIV-1 RNA processes, particularly nuclear export. Consequently, this study offers significant implications for the development of novel therapeutic strategies to eradicate the virus.
Partially purified
Strongyloides ratti
antigen improved the diagnostic performance of strongyloidiasis by enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test (ICT)
Authors: Wongphutorn Phattharaphon , Worasith Chanika , Kopolrat Kulthida Y. , Eamudomkarn Chatanun , Pitaksakulrat Opal , Hongsrichan Nuttanan , Tippayawat Patcharaporn , Techasen Anchalee , Sithithaworn Jiraporn , Homsombut Teeranat , Odermatt Peter , Noordin Rahmah , Sithithaworn Paiboon 
Published: February 2025

ABSTRACT

Strongyloides stercoralis
infection is a neglected tropical disease with a global distribution. Serodiagnosis is a sensitive method, but improving its performance and simplifying into a point-of-care test (POCT) are needed. This study aimed to improve the diagnostic performance of serological tests using partially purified
Strongyloides ratti
antigen in an enzyme-linked immunosorbent assay (ELISA) and an immunochromatographic test (ICT). Crude
S. ratti
antigen was purified by an IgG affinity column to partition the antigen into flow-through, washing fraction (WF), and elution fractions. Optimized ELISA and ICT using crude and antigen fractions were used to analyze sera from three groups of subjects. Group 1 comprised subjects with proven strongyloidiasis, Group 2 were subjects with other parasitic infections, and Group 3 were negative parasitic infections. The diagnostic performance and Kappa agreement of the serological tests were analyzed and compared, using larvae detection as the reference test (fecal examination). The results showed that the WF was the most efficient antigen in terms of sensitivity and specificity, as determined by the ELISA and ICT. Kappa’s agreement between fecal examination and WF-ELISA was moderate (Kappa = 0.52), and WF-ICT was almost perfect (Kappa = 0.94). The WF antigen reduced cross-reactivity to other parasitic infections, that is,
Opisthorchis viverrini
,
Taenia
spp., and hookworms, compared to crude
S. ratti
antigen when assessed by ELISA and ICT. We concluded that the WF of purified
S. ratti
improved the ELISA and ICT diagnostic performance, and the latter assay format could be used as a POCT for screening and controlling strongyloidiasis.

IMPORTANCE

This study aimed to improve the serological diagnosis of strongyloidiasis, a disease caused by infection with the intestinal nematode
Strongyloides stercoralis
, by evaluating the impact of
Strongyloides ratti
antigen purification using an IgG affinity column for detecting parasite-specific IgG in serum via enzyme-linked immunosorbent assay (ELISA) and immunochromatographic test (ICT) formats. Compared to crude
S. ratti
antigen, the washing fraction (WF) of the purified antigen demonstrated significantly improved sensitivity and specificity in both ELISA and ICT, achieving strong diagnostic concordance with the gold-standard fecal examination. Furthermore, the WF antigen fraction exhibited reduced cross-reactivity with coinfections caused by the liver fluke (
Opisthorchis viverrini
), tapeworms (
Taenia
spp.), and hookworms. These findings underscore antigen purification as a promising strategy to enhance the accuracy of strongyloidiasis serodiagnosis.
Exploring the effect of sequential antibiotic exposure in resistant
Escherichia coli
causing urinary tract infections: a proof of principle study
Authors: Göpel Lisa , Kirchhoff Laura , Gopleac Olivia , Tüeffers Leif , Hauswaldt Susanne , Boutin Sébastien , Rupp Jan , Nurjadi Dennis 
Published: February 2025

ABSTRACT

Antimicrobial resistance development, particularly in infections such as urinary tract infections (UTIs), is a global clinical concern. The objective of this study was to determine if sequential antibiotic exposure with ciprofloxacin and mecillinam can reduce the growth of resistant clinical
Escherichia coli
strains, thus improving the effectiveness of antibiotic therapy. Six
E. coli
isolates with heterogeneous resistance to ciprofloxacin and/or mecillinam obtained from patients with UTIs were exposed to one of the antibiotics (0.75 × minimum inhibitory concentration, MIC) for 1 h. This was followed by treatment with the second antibiotic at different concentrations (0.0375/0.075/0.375/0.75 × MIC). Continuous growth measurements were conducted in order to assess the impact of sequential exposure. One representative strain was selected for intact cell counting. In addition, a checkerboard assay was conducted to investigate the synergistic impact of ciprofloxacin and mecillinam, and genetic analyses were performed to identify the mechanisms of resistance for all isolates. The six
E. coli
strains were phylogenetically different, and none exhibited a synergistic effect for ciprofloxacin and mecillinam. Our data suggest that sequential exposure to mecillinam and ciprofloxacin appears to reduce the growth capacity of clinical
E. coli
isolates with phenotypic resistance to either or both agents. Sequential antibiotic exposure may be an interesting strategy to improve the antibiotic efficacy of current agents to overcome phenotypic resistance in
E. coli
.

IMPORTANCE

As global rates of antibiotic resistance increase and the development of new antibiotics become more difficult and costly, it is important to explore alternative strategies to improve the effectiveness of existing antibiotics. Previous studies have shown that sequential exposure of
Pseudomonas aeruginosa
to two antibiotics can effectively kill the bacteria and reduce the likelihood of resistance developing. However, the potential of this sequential approach for the treatment of
Escherichia coli
infections has not been thoroughly investigated. In our study, we conducted a proof-of-principle study to determine whether sequential exposure to mecillinam and ciprofloxacin can overcome phenotypic resistance to one or both drugs. We found that when
E. coli
were treated with subinhibitory doses of mecillinam followed by ciprofloxacin, their growth was significantly inhibited compared to treatment with ciprofloxacin alone, suggesting that sequential antibiotic exposure may be a viable strategy for treating infections caused by resistant
E. coli
.
Human milk and bronchopulmonary dysplasia have a dose-dependent effect: a cohort study
Authors: Yang Jiaming , Li Jiaxin , Wang Huiyan , Chen Xueyu , Yang Chuanzhong , ChaoMu Liga , Cao Aifen , Xiong Xiaoyun 
Published: February 2025

BackgroundHuman milk (HM) is considered a potential protective factor against bronchopulmonary dysplasia (BPD), but the specific volume needed for its protective effect in mixed feeding is unclear. This study aimed to investigate the impact of different HM volumes on BPD risk.MethodsA retrospective cohort study examined the association between HM volume and BPD risk in very low birthweight (VLBW) infants. Dose-dependent analysis with spline smoothing curve and univariate, multivariate analyses and sensitivity analyses were conducted.ResultThe study included 339 VLBW infants. BPD incidence was 4.7% (6 infants) in the high HM group (HM volume≥1190 mL), 27.0% (48 infants) in the low HM group (HM volume<1190 mL) and 9.1% (3 infants) in the exclusive formula group, and the difference is statistically significant. Both univariate and multivariate logistic regression analyses showed significantly higher BPD incidence in the low HM group (OR 3.237, 95% CI 0.81 to 12.89) compared with the exclusive formula group. The sensitivity analysis showed that low HM remained a risk factor for BPD (model I OR 3.26, 95% CI 0.92 to 11.53; model II OR 3.28, 95% CI 0.81 to 13.1).ConclusionHigher HM volumes (≥1190 mL) were associated with decreased BPD risk compared with low HM and formula feeding. Although not statistically significant, the low HM group exhibited increased BPD incidence compared with the exclusive formula group. These findings emphasise the importance of considering HM quantity in mixed feeding practices.