bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PKA-CREB1 axis regulates coronavirus proliferation by viral helicase nsp13 association
Authors: Zheng Tong , Shen Beilei , Bai Yu , Li Entao , Zhang Xun , Hu Yong , Gao Ting , Dong Qincai , Zhu Lin , Jin Rui , Shi Hui , Liu Hainan , Gao Yuwei , Liu Xuan , Cao Cheng 
Published: March 2024

ABSTRACT

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a worldwide threat in the past 3 years. Although it has been widely and intensively investigated, the mechanism underlying the coronavirus-host interaction requires further elucidation, which may contribute to the development of new antiviral strategies. Here, we demonstrated that the host cAMP-responsive element-binding protein (CREB1) interacts with the non-structural protein 13 (nsp13) of SARS-CoV-2, a conserved helicase for coronavirus replication, both in cells and in lung tissues subjected to SARS-CoV-2 infection. The ATPase and helicase activity of viral nsp13 were shown to be potentiated by CREB1 association, as well as by Protein kinase A (PKA)-mediated CREB1 activation. SARS-CoV-2 replication is significantly suppressed by PKA Cα, cAMP-activated protein kinase catalytic subunit alpha (PRKACA), and CREB1 knockdown or inhibition. Consistently, the CREB1 inhibitor 666-15 has shown significant antiviral effects against both the WIV04 strain and the Omicron strain of the SARS-CoV-2. Our findings indicate that the PKA-CREB1 signaling axis may serve as a novel therapeutic target against coronavirus infection.

IMPORTANCE

In this study, we provide solid evidence that host transcription factor cAMP-responsive element-binding protein (CREB1) interacts directly with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) helicase non-structural protein 13 (nsp13) and potentiate its ATPase and helicase activity. And by live SARS-CoV-2 virus infection, the inhibition of CREB1 dramatically impairs SARS-CoV-2 replication
in vivo
. Notably, the IC50 of CREB1 inhibitor 666-15 is comparable to that of remdesivir. These results may extend to all highly pathogenic coronaviruses due to the conserved nsp13 sequences in the virus.
Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice
Authors: Ouwendijk Werner J. D. , Roychoudhury Pavitra , Cunningham Anthony L. , Jerome Keith R. , Koelle David M. , Kinchington Paul R. , Mohr Ian , Wilson Angus C. , Verjans Georges G. M. G. M. , Depledge Daniel P. 
Published: March 2024

ABSTRACT

Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3’ scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1
latency-associated transcript
(
LAT
) intronic RNAs. However,
LAT
reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1
LAT
and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.

IMPORTANCE
Most people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.
Rickettsia rickettsii
virulence determinants RARP2 and RapL mitigate IFN-
β
signaling in primary human dermal microvascular endothelial cells
Authors: Fitzsimmons Liam , Bublitz DeAnna , Clark Tina , Hackstadt Ted 
Published: March 2024

ABSTRACT

We compared the growth characteristics of a virulent
Rickettsia rickettsii
strain (Sheila Smith) to an attenuated
R. rickettsii
stain (Iowa) and a non-pathogenic species (
R. montanensis
) in primary human dermal microvascular endothelial cells (HDMEC). All replicated in Vero cells, however, only the Sheila Smith strain productively replicated in HDMECs. The Iowa strain showed minimal replication over a 24-h period, while
R. montanensis
lost viability and induced lysis of the HDMECs via a rapid programmed cell death response. Both the virulent and attenuated
R. rickettsii
strains, but not
R. montanensis
, induced an interferon-1 response, although the response was of lesser magnitude and delayed in the Sheila Smith strain. IFN-β secretion correlated with increased host cell lysis, and treatment with anti-IFNAR2 antibody decreased lysis from Iowa-infected but not Sheila Smith-infected cells. Both Sheila Smith- and Iowa-infected cells eventually lysed, although the response from Sheila Smith was delayed and showed characteristics of apoptosis. We, therefore, examined whether reconstitution of the Iowa strain with two recently described putative virulence determinants might enhance survival of Iowa within HDMECs. Reconstitution with RARP2, which is inhibitory to anterograde trafficking through the Golgi apparatus, reduced IFN-β secretion but had no effect on cell lysis. RapL, which proteolytically processes surface exposed autotransporters and enhances replication of Iowa in Guinea pigs, suppressed both IFN-β production and host cell lysis. These findings suggest distinct mechanisms by which virulent spotted fever group rickettsiae may enhance intracellular survival and replication.

IMPORTANCE

We examined a naturally occurring non-pathogenic rickettsial species,
R. montanensis
, a laboratory-attenuated
R. rickettsii
strain (Iowa), and a fully virulent
R. rickettsii
strain (Sheila Smith) for growth in human dermal microvascular endothelial cells. The two avirulent strains replicated poorly or not at all. Only the virulent Sheila Smith strain replicated. IFN-β production correlated with the inhibition of
R. rickettsii
Iowa. Reconstitution of Iowa with either of two recently described putative virulence determinants altered the IFN-β response. A rickettsial ankyrin repeat protein, RARP2, disrupts the
trans-
Golgi network and inhibits IFN-β secretion. An autotransporter peptidase, RapL, restores proteolytic maturation of outer membrane autotransporters and diminishes the IFN-β response to enhance cell survival and permit replication of the recombinant strain. These studies point the way toward discovery of mechanisms for innate immune response avoidance by virulent rickettsia.
Inhibition of multiple staphylococcal growth states by a small molecule that disrupts membrane fluidity and voltage
Authors: Dombach Jamie L. , Christensen Grace L. , Allgood Samual C. , Quintana Joaquin L. J. , Detweiler Corrella S. 
Published: March 2024

ABSTRACT

New molecular approaches to disrupting bacterial infections are needed. The bacterial cell membrane is an essential structure with diverse potential lipid and protein targets for antimicrobials. While rapid lysis of the bacterial cell membrane kills bacteria, lytic compounds are generally toxic to whole animals. In contrast, compounds that subtly damage the bacterial cell membrane could disable a microbe, facilitating pathogen clearance by the immune system with limited compound toxicity. A previously described small molecule, D66, terminates
Salmonella enterica
serotype Typhimurium (
S
. Typhimurium) infection of macrophages and reduces tissue colonization in mice. The compound dissipates bacterial inner membrane voltage without rapid cell lysis under broth conditions that permeabilize the outer membrane or disable efflux pumps. In standard media, the cell envelope protects Gram-negative bacteria from D66. We evaluated the activity of D66 in Gram-positive bacteria because their distinct envelope structure, specifically the absence of an outer membrane, could facilitate mechanism of action studies. We observed that D66 inhibited Gram-positive bacterial cell growth, rapidly increased
Staphylococcus aureus
membrane fluidity, and disrupted membrane voltage while barrier function remained intact. The compound also prevented planktonic staphylococcus from forming biofilms and a disturbed three-dimensional structure in 1-day-old biofilms. D66 furthermore reduced the survival of staphylococcal persister cells and of intracellular
S. aureus
. These data indicate that staphylococcal cells in multiple growth states germane to infection are susceptible to changes in lipid packing and membrane conductivity. Thus, agents that subtly damage bacterial cell membranes could have utility in preventing or treating disease.

IMPORTANCE

An underutilized potential antibacterial target is the cell membrane, which supports or associates with approximately half of bacterial proteins and has a phospholipid makeup distinct from mammalian cell membranes. Previously, an experimental small molecule, D66, was shown to subtly damage Gram-negative bacterial cell membranes and to disrupt infection of mammalian cells. Here, we show that D66 increases the fluidity of Gram-positive bacterial cell membranes, dissipates membrane voltage, and inhibits the human pathogen
Staphylococcus aureus
in several infection-relevant growth states. Thus, compounds that cause membrane damage without lysing cells could be useful for mitigating infections caused by
S. aureus
.
The host transcriptional response to superinfection by influenza A virus and
Streptococcus pneumoniae
Authors: Cohn Ofir , Yankovitz Gal , Mandelboim Michal , Peshes-Yaloz Naama , Brandes Rachel , Bacharach Eran , Gat-Viks Irit 
Published: March 2024

ABSTRACT

Secondary bacterial challenges during influenza virus infection “superinfection”) cause excessive mortality and hospitalization. Here, we present a longitudinal study of bulk gene expression changes in murine lungs during superinfection, with an initial influenza A virus infection and a subsequent
Streptococcus pneumoniae
infection. In addition to the well-characterized impairment of the host response, we identified superinfection-specific alterations in the global transcriptional program that are linked to the host’s ability to resist the pathogens. Particularly, whereas superinfected mice manifested an excessive rapid induction of the resistance-to-infection program, there was a substantial tissue-level rewiring of this program: upon superinfection, interferon-regulated genes were switched from positive to negative correlations with the host’s resistance state, whereas genes of fatty acid metabolism switched from negative to positive correlations with resistance states. Thus, the transcriptional resistance state in superinfection is reprogrammed toward repressed interferon signaling and induced fatty acid metabolism. Our findings suggest new insights into a tissue-level remodeling of the host defense upon superinfection, providing promising targets for future therapeutic interventions.

IMPORTANCE

Secondary bacterial infections are the most frequent complications during influenza A virus (IAV) pandemic outbreaks, contributing to excessive morbidity and mortality in the human population. Most IAV-related deaths are attributed to
Streptococcus pneumoniae
(SP) infections, which usually begin within the first week of IAV infection in the respiratory tracts. Here, we focused on longitudinal transcriptional responses during a superinfection model consisting of an SP infection that follows an initial IAV infection, comparing superinfection to an IAV-only infection, an SP-only infection, and control treatments. Our longitudinal data allowed a fine analysis of gene expression changes during superinfection. For instance, we found that superinfected mice exhibited rapid gene expression induction or reduction within the first 12 h after encountering the second pathogen. Cell proliferation and immune response activation processes were upregulated, while endothelial processes, vasculogenesis, and angiogenesis were downregulated, providing promising targets for future therapeutic interventions. We further analyzed the longitudinal transcriptional responses in the context of a previously defined spectrum of the host’s resistance state, revealing superinfection-specific reprogramming of resistance states, such as reprogramming of fatty acid metabolism and interferon signaling. The reprogrammed functions are compelling new targets for switching the pathogenic superinfection state into a single-infection state.
Carbapenemase-producing Enterobacterales strains causing infections in companion animals—Portugal
Authors: Moreira da Silva Joana , Menezes Juliana , Fernandes Laura , Santos Costa Sofia , Amaral Andreia , Pomba Constança 
Published: March 2024

ABSTRACT

An increase in
Klebsiella pneumoniae
carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the
bla
OXA-48-like
and
bla
KPC-like
genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January–December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (
n
= 5/977). Thus, five strains were characterized: (i) one OXA-181-producing
K. pneumoniae
ST273, (ii) two KPC-3-producing
K. pneumoniae
ST147; (iii) one KPC-3-producing
K. pneumoniae
ST392; and (iv) one OXA-48-producing
E. coli
ST127. The
bla
KPC-3
gene was located on transposon Tn
4401d
on IncFIA type plasmid for the
K. pneumoniae
ST147 strains and on a IncN-type plasmid for the
K. pneumoniae
ST392 strain, while
bla
OXA-181
gene was located on an IncX3 plasmid. All
de novo
assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing
E. coli
ST127. The dissemination of carbapenem resistance is occurring horizontally
via
plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed.

IMPORTANCE
This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.
Prevalence and determinants of antibiotics self-medication among indigenous people of Bangladesh: a cross-sectional study
Authors: Mannan Adnan , Chakma Kallyan , Dewan Gourab , Saha Ayan , Chy Naim Uddin Hasan A , Mehedi H M Hamidullah , Hossain Amzad , Wnaiza Jannatun , Ahsan Md Tanveer , Rana Md Mashud , Alam Nazmul 
Published: March 2024

ObjectivesSelf-medication with antibiotics (SMA) contributes significantly to the emergence of antimicrobial resistance (AMR), especially in low-income countries including Bangladesh. This study aimed to generate evidence on the self-reported prevalence of antibiotic self-medication and its determinants among indigenous people residing in Bangladesh’s Chittagong Hill Tracts (CHT) districts.DesignThis study used a cross-sectional design with data collected through a survey using a semi-structured questionnaire.SettingThis study was conducted from late January to early July 2021; among different indigenous group populations aged 18 years or more olders residing in the three districts of CHT.ParticipantsA total of 1336 indigenous people residing in Bangladesh’s CHT districts were included.Primary outcome and explanatory variablesThe primary outcome measure was SMA while explanatory variables were socio-demographic characteristics, health status of participants, and knowledge of antibiotics usage and its side effects.ResultsAmong the study participants, more males (60.54%) than females (51.57%) reported using antibiotics. The SMA rate was high among individuals with education levels below secondary (over 50%) and those in the low-income group (55.19%). The most common diseases reported were cough, cold and fever, with azithromycin being the most frequently used antibiotic. Levels of education, family income, having a chronic illness and place of residence were found to be the significant predictors of having good knowledge of antibiotic use as found in the ordered logit model. Findings from a logistic regression model revealed that men had 1.6 times higher odds (adjusted OR (AOR) 1.57; 95% CI 1.12 to 2.19) of SMA than women. Participants with ≥US$893 per month family income had lowest odds (AOR 0.14; 95% CI 0.03 to 0.64) of SMA than those who earned <US$417. Participants living in Rangamati districts had a lower risk of SMA (…) than those in Bandarban district. rate of SMA (AOR 0.52; 95% CI 0.30 to 0.90) than those in Bandarban district.ConclusionMale gender, family income, place of residence and knowledge of antibiotics were the significant predictors of antibiotic self-medication. Hence, it is important to streamline awareness-raising campaigns at the community level to mitigate the practice of SMA in indigenous people and ultimately address the devastating effects of Antimicrobial resistance (AMR) in Bangladesh.
Barriers and facilitators to use of digital health tools by healthcare practitioners and their patients, before and during the COVID-19 pandemic: a multimethods study
Authors: Turnbull Sophie Louise , Dack Charlotte , Lei Jiedi , Aksu Irem , Grant Sabrina , Lasseter Gemma , Silarova Barbora , Ainsworth Ben 
Published: March 2024

ObjectivesTo explore how healthcare practitioners (HCPs) made decisions about the implementation of digital health technologies (DHTs) in their clinical practice before and during the COVID-19 pandemic.DesignA multimethods study, comprising semistructured interviews conducted prior to the COVID-19 pandemic, supplemented with an online survey that was conducted during the pandemic with a different sample, to ensure the qualitative findings remained relevant within the rapidly changing healthcare context. Participants were recruited through HCP networks, snowballing and social media. Data were analysed thematically.SettingPhone interviews and online survey.ParticipantsHCPs represented a range of professions from primary and secondary care across England, with varied socioeconomic deprivation.Results24 HCPs were interviewed, and 16 HCPs responded to the survey. In the interviews, HCPs described three levels where decisions were made, which determined who would have access to what DHTs: health organisation, HCP and patient levels. These decisions resulted in the unequal implementation of DHTs across health services, created barriers for HCPs using DHTs in their practice and influenced HCPs’ decisions on which patients to supply DHTs with. In the survey, HCPs described being provided support to overcome some of the barriers at the organisation and HCP level during the pandemic. However, they cited similar concerns to pre-pandemic about barriers patients faced using DHTs (eg, digital literacy). In the absence of centralised guidance on how to manage these barriers, health services made their own decisions about how to adapt their services for those who struggled with DHTs.ConclusionsDecision-making at the health organisation, HCP and patient levels influences inequalities in access to DHTs for HCPs and patients. The mobilisation of centralised information and resources during the pandemic can be viewed as good practice for reducing barriers to use of DHTs for HCPs. However, attention must also be paid to reducing barriers to accessing DHTs for patients.
Characteristics, treatment patterns and burden of illness in US patients with asthma newly initiating multiple-inhaler triple therapy
Authors: Numbere Beade , Liu Yunhao , Zhang Shiyuan , Czira Alexandrosz , Lu Yifei 
Published: March 2024

IntroductionFor patients with asthma who remain symptomatic on medium-dose inhaled corticosteroid/long-acting β2-agonist, add-on long-acting muscarinic antagonist is a treatment option, which can be administered as multiple-inhaler triple therapy (MITT). A high proportion of patients (61.5%–88.2%) discontinue MITT use within 1 year postinitiation; however, which patients discontinue and their treatment patterns at initiation are unknown. This study aimed to understand the demographic, clinical and treatment-related characteristics of patients with asthma who newly initiated MITT, by discontinuation status.MethodsThis retrospective cohort study used administrative data from IBM Truven MarketScan Commercial Claims and Encounters Database with Medicare supplement between 1 January 2016 and 31 December 2019. Adult patients with asthma who initiated MITT between 1 January 2017 and 31 March 2019 were included and were classified based on their discontinuation status. ‘Continuous users’ had continuous use of MITT and ‘discontinuers’ discontinued treatment within the 6-month period postinitiation. Demographics and clinical characteristics, asthma treatment use prior to MITT initiation (12-month baseline period), mode of MITT initiation and complexity of regimen were described.ResultsOf 4132 patients (mean age: 49.0 years, 67.9% female), 78.0% (n=3224) were discontinuers; 22.0% (n=908) were continuous users. Demographic and other clinical and treatment-related characteristics during baseline were broadly similar between cohorts. A significantly higher proportion of continuous users versus discontinuers had ≥6 dispensed claims for short-acting β2-agonist canisters (16.0% vs 12.5%; p=0.006) during baseline and initiated a once-daily MITT regimen (35.2% vs 26.2%; p<0.001). Fewer continuous MITT users used a mix of once-daily and twice-daily regimens than those who discontinued MITT (64.3% vs 72.3%; p<0.001).ConclusionsMost patients with asthma discontinued MITT within 6 months. Results indicate that patients with a history of uncontrolled, symptomatic asthma and those using less complex triple therapy regimens at initiation are less likely to discontinue MITT than patients with controlled asthma and those using a complex MITT regimen.