bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of the resistome and predominant genetic lineages of Gram-positive bacteria causing keratitis
Authors: André Camille , Van Camp Andrew G. , Ung Lawson , Gilmore Michael S. , Bispo Paulo J. M.
Published: January 2024

Bacterial keratitis is a vision-threatening infection mainly caused by Gram-positive bacteria (GPB). Antimicrobial therapy is commonly empirical using broad-spectrum agents with efficacy increasingly compromised by the emergence of antimicrobial resistance. We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of GPB causing keratitis and to characterize their antimicrobial resistance patterns. A total of 161 isolates, including
Staphylococcus aureus
(
n
= 86), coagulase-negative staphylococci (CoNS;
n
= 34),
Streptococcus
spp. (
n
= 34), and
Enterococcus faecalis
(
n
= 7), were included. The population of
S. aureus
isolates consisted mainly of clonal complex 5 (CC5) (30.2%). Similarly, the population of
Staphylococcus epidermidis
was homogenous with most of them belonging to CC2 (78.3%). Conversely, the genetic population of
Streptococcus pneumoniae
was highly diverse. Resistance to first-line antibiotics was common among staphylococci, especially among CC5
S. aureus
. Methicillin-resistant
S. aureus
was commonly resistant to fluoroquinolones and azithromycin (78.6%) and tobramycin (57%). One-third of the CoNS were resistant to fluoroquinolones and 53% to azithromycin. Macrolide resistance was commonly caused by
erm
genes in
S. aureus
,
mphC
and
msrA
in CoNS, and
mefA and msr(D
) in streptococci. Aminoglycoside resistance in staphylococci was mainly associated with genes commonly found in mobile genetic elements and that encode for nucleotidyltransferases like
ant(4′)-Ib
and
ant(9)-Ia
. Fluroquinolone-resistant staphylococci carried from 1 to 4 quinolone resistance-determining region mutations, mainly in the
gyrA
and
parC
genes. We found that GPB causing keratitis are associated with strains commonly resistant to first-line topical therapies, especially staphylococcal isolates that are frequently multidrug-resistant and associated with major hospital-adapted epidemic lineages.
A single locus determines praziquantel response in
Schistosoma mansoni
Authors: Chevalier Frédéric D. , Le Clec’h Winka , Berriman Matthew , Anderson Timothy J.C.
Published: January 2024

We previously performed a genome-wide association study (GWAS) to identify the genetic basis of praziquantel (PZQ) response in schistosomes, identifying two quantitative trait loci situated on chromosomes 2 and 3. We reanalyzed this GWAS using the latest (version 10) genome assembly showing that a single locus on chromosome 3, rather than two independent loci, determines drug response. These results reveal that PZQ response is monogenic and demonstrates the importance of high-quality genomic information.
High performance
Legionella pneumophila
source attribution using genomics-based machine learning classification
Authors: Buultjens Andrew H. , Vandelannoote Koen , Mercoulia Karolina , Ballard Susan , Sloggett Clare , Howden Benjamin P. , Seemann Torsten , Stinear Timothy P.
Published: January 2024

Identifying the sources of Legionnaires’ disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of
Legionella pneumophila
, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires’ disease outbreaks. Developed using cross-validation on environmental
L. pneumophila
genomes, our models demonstrate excellent predictive sensitivity and specificity. Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires’ disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.
Effect of glutathione-transport-related gene
gsiD
on desiccation tolerance of
Cronobacter sakazakii
and its related regulatory mechanism
Authors: Wang Xiao-yi , Li Ping , Du Xin-jun , Wang Shuo
Published: January 2024

The outstanding desiccation tolerance of
Cronobacter sakazakii
(
C. sakazakii
) enables long-term persistence in food products with low-water activity to increase the infection risk, especially in low-birth-weight, immuno-compromised neonates, and infants less than 4 weeks of age. In our previous study, the disruption of glutathione transport-related gene
gsiD
by transposon was found to significantly increase its inactivation rate under drying stress challenges. However, the mechanism underlying the association between glutathione transport and desiccation tolerance of
C. sakazakii
remains to be clarified. In this study, the mechanism underlying their association was investigated in detail by constructing the
gsiD
gene deletion mutant.
gsiD
gene deletion was found to cause the dysfunction of the glutathione transport system GsiABCD and the limitation of glutathione import. The resulting decrease in intracellular glutathione caused the decreased potassium ions uptake and increased potassium ions efflux, inhibited the proline synthesis process, limited extracellular glutathione utilization, increased oxidant stress, reduced biofilm formation, and increased outer membrane permeability, which may be the main reasons for the significant reduction of the desiccation tolerance of
C. sakazakii
.

IMPORTANCE

Contributing to its superior environmental adaptability,
Cronobacter sakazakii
can survive under many abiotic stress conditions. The outstanding desiccation tolerance makes this species persist in low-water activity foods, which increases harm to humans. For decades, many studies have focused on the desiccation tolerance of
C. sakazakii
, but the existing research is still insufficient. Our study found that
gsiD
gene deletion inhibited glutathione uptake and further decreased intracellular glutathione content, causing a decrease in desiccation tolerance and biofilm formation and an increase in outer membrane permeability. Moreover, the expression level of relative genes verified that
gsiD
gene deletion made the mutant not conducive to surviving in dry conditions due to restricting potassium ions uptake and efflux, inhibiting the conversion of glutamate to compatible solute proline, and increasing the oxidative stress of
C. sakazakii
. The above results enrich our knowledge of the desiccation tolerance mechanism of
C. sakazakii
.
HtrAs are essential for the survival of the haloarchaeon
Natrinema gari
J7-2 in response to heat, high salinity, and toxic substances
Authors: Luo Hongyi , Qu Xiaoyi , Deng Xi , He Liping , Wu Yi , Liu Yang , He Dan , Yin Jing , Wang Bingxue , Gan Fei , Tang Bing , Tang Xiao-Feng
Published: January 2024

Bacterial and eukaryotic HtrAs can act as an extracytoplasmic protein quality control (PQC) system to help cells survive in stress conditions, but the functions of archaeal HtrAs remain unknown. Particularly, haloarchaea route most secretory proteins to the Tat pathway, enabling them to fold properly in well-controlled cytoplasm with cytosolic PQC systems before secretion. It is unclear whether HtrAs are required for haloarchaeal survival and stress response. The haloarchaeon
Natrinema gari
J7-2 encodes three Tat signal peptide-bearing HtrAs (NgHtrA, NgHtrB, and NgHtrC), and the signal peptides of NgHtrA and NgHtrC contain a lipobox. Here, the
in vitro
analysis reveals that the three HtrAs show different profiles of temperature-, salinity-, and metal ion-dependent proteolytic activities and could exhibit chaperone-like activities to prevent the aggregation of reduced lysozyme when their proteolytic activities are inhibited at low temperatures or the active site is disrupted. The gene deletion and complementation assays reveal that NgHtrA and NgHtrC are essential for the survival of strain J7-2 at elevated temperature and/or high salinity and contribute to the resistance of this haloarchaeon to zinc and inhibitory substances generated from tryptone. Mutational analysis shows that the lipobox mediates membrane anchoring of NgHtrA or NgHtrC, and both the membrane-anchored and free extracellular forms of the two enzymes are involved in the stress resistance of strain J7-2, depending on the stress conditions. Deletion of the gene encoding NgHtrB in strain J7-2 causes no obvious growth defect, but NgHtrB can functionally substitute for NgHtrA or NgHtrC under some conditions.

IMPORTANCE

HtrA-mediated protein quality control plays an important role in the removal of aberrant proteins in the extracytoplasmic space of living cells, and the action mechanisms of HtrAs have been extensively studied in bacteria and eukaryotes; however, information about the function of archaeal HtrAs is scarce. Our results demonstrate that three HtrAs of the haloarchaeon
Natrinema gari
J7-2 possess both proteolytic and chaperone-like activities, confirming that the bifunctional nature of HtrAs is conserved across all three domains of life. Moreover, we found that NgHtrA and NgHtrC are essential for the survival of strain J7-2 under stress conditions, while NgHtrB can serve as a substitute for the other two HtrAs under certain circumstances. This study provides the first biochemical and genetic evidence of the importance of HtrAs for the survival of haloarchaea in response to stresses.
Impaired neutrophil extracellular trap-forming capacity contributes to susceptibility to chronic vaginitis in a mouse model of vulvovaginal candidiasis
Authors: Yano Junko , Fidel Paul L.
Published: January 2024

Vulvovaginal candidiasis (VVC), caused by
Candida albicans,
is characterized by aberrant inflammation by polymorphonuclear neutrophils (PMNs) in the vaginal lumen. Data from the established murine model shows that despite potent antifungal properties, PMNs fail to clear
C. albicans
due to local heparan sulfate that inhibits the interaction between PMNs and
C. albicans
, resulting in chronic vaginal immunopathology. To understand the role of neutrophil extracellular traps (NETs) in defense against
C. albicans
at the vaginal mucosa, we investigated the NET-forming capacity of PMNs in chronic VVC-susceptible (CVVC-S/C3H) and -resistant (CVVC-R/CD-1) mouse strains. Immunofluorescence revealed the formation of NETs (release of DNA with PMN-derived antimicrobial proteins) in PMN
–C. albicans
cocultures using vaginal conditioned medium (VCM) generated from CVVC-R/CD-1 mice, similar to NET-inducing positive controls. Under these NETotic conditions, PMNs released high levels of double-stranded DNA bound with NET-associated proteins, concomitant with substantial
C. albicans
killing activity. In contrast, PMN
–C. albicans
cocultures in VCM from CVVC-S/C3H mice lacked NET formation together with reduced antifungal activity. Similar results were observed
in vivo
: active NET
–C. albicans
interaction followed by fungal clearance in inoculated CVVC-R/CD-1 mice, and sustained high vaginal fungal burden and no evidence of NETs in inoculated CVVC-S/C3H mice. Furthermore, the level of Ki67 expression, a putative NETotic PMN marker, was significantly reduced in vaginal lavage fluid from CVVC-S/C3H mice compared to CVVC-R/CD-1 mice. Finally, scanning electron microscopy revealed that PMNs in CVVC-R, but not CVVC-S, conditions exhibited NETs in direct contact with
C. albicans
hyphae
in vitro
and
in vivo
. These results suggest that VVC-associated immunopathology includes impaired NET-mediated antifungal activity.
Layering vaccination with antibiotic therapy results in protection and clearance of
Burkholderia pseudomallei
in Balb/c mice
Authors: Barnes Kay B. , Brett Paul , Burtnick Mary , Vente Andreas , Bentley Christine , Richards Mark I. , Flick-Smith Helen C. , Burgess Gary , Thwaite Joanne E. , Laws Thomas R. , Maishman Thomas C. , Nelson Michelle , Harding Sarah V.
Published: January 2024

Melioidosis is a disease that is difficult to treat due to the causative organism,
Burkholderia pseudomallei
being inherently antibiotic resistant and it having the ability to invade, survive, and replicate in an intracellular environment. Combination therapy approaches are routinely being evaluated in animal models with the aim of improving the level of protection and clearance of colonizing bacteria detected. In this study, a subunit vaccine layered with the antibiotic finafloxacin was evaluated
in vivo
against an inhalational infection with
B. pseudomallei
in Balb/c mice. Groups of mice vaccinated, infected, and euthanized at antibiotic initiation had a reduced bacterial load compared to those that had not been immunized. In addition, the subunit vaccine provided a synergistic effect when it was delivered with a CpG ODN and finafloxacin was initiated at 48 h post-challenge. Vaccination was also shown to improve the outcome, in a composite measure of survival and clearance. In summary, layering a subunit vaccine with the antibiotic finafloxacin is a promising therapeutic alternative for use in the treatment of
B. pseudomallei
infections.
MicroRNA-22-3p displaces critical host factors from the 5′ UTR and inhibits the translation of Coxsackievirus B3 RNA
Authors: Rani Priya , George Biju , V Sabarishree , Biswas Somarghya , V Madhurya , Pal Apala , Rajmani Raju S. , Das Saumitra
Published: January 2024

CVB3 infection is associated with the development of end-stage heart diseases. Lack of effective anti-viral treatments and vaccines for CVB3 necessitates comprehensive understanding of the molecular players during CVB3 infection. miRNAs have emerged as promising targets for anti-viral strategies. Here, we demonstrate that miR-22-3p binds to 5′ UTR and inhibits viral RNA translation at the later stage of infection to promote viral RNA replication. Conversely, as host response, it targets PCDH1, a proviral factor, to discourage viral propagation. miR-22-3p also influences CVB3 tissue tropism. Deciphering the multifaced role of miR-22-3p during CVB3 infection unravels the necessary molecular insights, which can be exploited for novel intervening strategies to curb infection and restrict viral pathogenesis.
Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells
Authors: Wang Qian , Zhang Shijian , Nguyen Hanh T. , Sodroski Joseph
Published: January 2024

The Env trimers on the HIV-1 mediate virus entry into host cells. Env is synthesized in infected cells, modified by complex sugars, and cleaved to form a mature, functional Env, which is incorporated into virus particles. Env elicits antibodies in infected individuals, some of which can neutralize the virus. We found that antibodies co-expressed in the virus-producing cell can disrupt Env transit to the proper compartment for cleavage and sugar modification and, in some cases, block incorporation into viruses. These studies provide insights into the processes by which Env becomes functional in the virus-producing cell and may assist attempts to interfere with these events to inhibit HIV-1 infection.
Cleavage of HDAC6 to dampen its antiviral activity by nsp5 is a common strategy of swine enteric coronaviruses
Authors: Li Zhuang , Xiao Wenwen , Yang Zhixiang , Guo Jiahui , Zhou Junwei , Xiao Shaobo , Fang Puxian , Fang Liurong
Published: January 2024

Viral infections and host defenses are in constant opposition. Once viruses combat or evade host restriction, productive infection is achieved. HDAC6 is a broad-spectrum antiviral protein that has been demonstrated to inhibit many viruses, including porcine deltacoronavirus (PDCoV). However, whether HDAC6 is reciprocally targeted and disabled by viruses remains unclear. In this study, we used PDCoV as a model and found that HDAC6 is targeted and cleaved by nsp5, a viral 3C-like protease. The cleaved HDAC6 loses its deacetylase activity as well as its ability to degrade viral proteins and activate interferon responses. Furthermore, this cleavage mechanism is shared among other swine enteric coronaviruses. These findings shed light on the intricate interplay between viruses and HDAC6, highlighting the strategies employed by viruses to evade host antiviral defenses.
The subgenomic flaviviral RNA suppresses RNA interference through competing with siRNAs for binding RISC components
Authors: Chen Xiang , Li Rui-Ting , Chen Ru-Yi , Shi Pan-Deng , Liu Zi-Xin , Lou Ya-Nan , Wu Mei , Zhang Rong-Rong , Tang Wei , Li Xiao-Feng , Qin Cheng-Feng
Published: January 2024

Zika virus (ZIKV) infection mainly targets human neural progenitor cells (hNPCs) and induces cell death and dysregulated cell-cycle progression, leading to microcephaly and other central nervous system abnormalities. RNA interference (RNAi) plays critical roles during ZIKV infections in hNPCs, and ZIKV has evolved to encode specific viral proteins to antagonize RNAi. Herein, we first show that abundant sfRNA was produced in ZIKV-infected hNPCs in a similar pattern to that in other cells. Importantly, ZIKV sfRNA acts as a potent viral suppressor of RNAi (VSR) by competing with siRNAs for binding RISC components, RHA and PACT. The 3′SL of sfRNA is responsible for binding RISC components, which is a conserved feature among mosquito-borne flaviviruses. As most known VSRs are viral proteins, our findings highlight the importance of viral non-coding RNAs during the antagonism of host RNAi-based antiviral innate immunity.
Enhanced antigen-specific CD8 T cells contribute to early protection against FMDV through swine DC vaccination
Authors: Mu Suyu , Chen Lingbo , Dong Hu , Li Shuai , Zhang Yun , Yin Shuanghui , Tian Yunfei , Ding Yaozhong , Sun Shiqi , Shang Shaobin , Guo Huichen
Published: January 2024

Foot-and-mouth disease virus (FMDV) remains a challenge for cloven-hooved animals. The currently licensed FMDV vaccines induce neutralizing antibody (NAb)-mediated protection but show defects in the early protection. Dendritic cell (DC) vaccines have shown great potency in inducing rapid T-cell immunity in humans and mice. Whether DC vaccination could enhance early protection against FMDV has not been elaborately explored in domestic pigs. In this study, we employed DC vaccination as an experimental approach to study the roles of cellular immunity in the early protection against FMDV in pigs. Autologous DCs were differentiated from the periphery blood mononuclear cells of each pig, pulsed with inactivated FMDV (iFMDV-DC) and treated with LPS, and then injected into the original pigs. The cellular immune responses and protective efficacy elicited by the iFMDV-DC were examined by multicolor flow cytometry and tested by FMDV challenge. The results showed that autologous iFMDV-DC immunization induced predominantly FMDV-specific IFN-γ-producing CD4
+
T cells and cytotoxic CD8
+
T cells (CTLs), high NAb titers, compared to the inactivated FMDV vaccine, and accelerated the development of memory CD4 and CD8 T cells, which was concomitantly associated with early protection against FMDV virulent strain in pigs. Such early protection was associated with the rapid proliferation of secondary T-cell response after challenge and significantly contributed by secondary CD8 effector memory T cells. These results demonstrated that rapid induction of cellular immunity through DC immunization is important for improving early protection against FMDV. Enhancing cytotoxic CD8
+
T cells may facilitate the development of more effective FMDV vaccines.

IMPORTANCE

Although the currently licensed FMDV vaccines provide NAb-mediated protection, they have defects in early immune protection, especially in pigs. In this study, we demonstrated that autologous swine DC immunization augmented the cellular immune response and induced an early protective response against FMDV in pigs. This approach induced predominantly FMDV-specific IFN-γ-producing CD4
+
T cells and cytotoxic CD8
+
T cells, high NAb titers, and rapid development of memory CD4 and CD8 T cells. Importantly, the early protection conferred by this DC immunization is more associated with secondary CD8
+
T response rather than NAbs. Our findings highlighted the importance of enhancing cytotoxic CD8
+
T cells in early protection to FMDV in addition to Th1 response and identifying a strategy or adjuvant comparable to the DC vaccine might be a future direction for improving the current FMDV vaccines.
Interspecies metabolite transfer fuels the methionine metabolism of
Fusobacterium nucleatum
to stimulate volatile methyl mercaptan production
Authors: Hara Takeshi , Sakanaka Akito , Lamont Richard J. , Amano Atsuo , Kuboniwa Masae
Published: January 2024

Halitosis can have a significant impact on the social life of affected individuals. Among oral odor compounds, CH
3
SH has a low olfactory threshold and halitosis is a result of its production. Recently, there has been a growing interest in the collective properties of oral polymicrobial communities, regarded as important for the development of oral diseases, which are shaped by physical and metabolic interactions among community participants. However, it has yet to be investigated whether interspecies interactions have an impact on the production of volatile compounds, leading to the development of halitosis. The present findings provide mechanistic insights indicating that ornithine, a metabolite excreted by
Streptococcus gordonii
, promotes polyamine synthesis by
Fusobacterium nucleatum
, resulting in a compensatory increase in demand for methionine, which results in elevated methionine pathway activity and CH
3
SH production. Elucidation of the mechanisms related to CH
3
SH production is expected to lead to the development of new strategies for managing halitosis.
The small RNA PrrH aggravates
Pseudomonas aeruginosa
-induced acute lung injury by regulating the type III secretion system activator ExsA
Authors: Shi Qixuan , Zeng Shenghe , Yu Ruiqi , Li Mo , Shen Cong , Zhang Xuan , Zhao Chanjing , Zeng Jianming , Huang Bin , Pu Jieying , Chen Cha
Published: January 2024

Pseudomonas aeruginosa
is an opportunistic pathogen that causes acute and chronic infections in immunocompromised individuals. Small regulatory RNAs (sRNAs) regulate multiple bacterial adaptations to environmental changes, especially virulence. Our previous study showed that sRNA PrrH negatively regulates the expression of a number of virulence factors, such as pyocyanin, rhamnolipid, biofilm, and elastase in the
P. aeruginosa
strain PAO1. However, previous studies have shown that the
prrH
-deficient mutant attenuates virulence in an acute murine lung infection model. All Δ
prrH
-infected mice survived the entire 28-day course of the experiment, whereas all mice inoculated with the wild-type or the complemented mutant succumbed to lung infection within 4 days of injection, but the specific mechanism is unclear. Herein, we explored how PrrH mediates severe lung injury by regulating the expression of virulence factors.
In vivo
mouse and
in vitro
cellular assays demonstrated that PrrH enhanced the pathogenicity of PAO1, causing severe lung injury. Mechanistically, PrrH binds to the coding sequence region of the mRNA of
exsA
, which encodes the type III secretion system master regulatory protein. We further demonstrated that PrrH mediates a severe inflammatory response and exacerbates the apoptosis of A549 cells. Overall, our results revealed that PrrH positively regulates ExsA, enhances the pathogenicity of
P. aeruginosa
, and causes severe lung injury.

IMPORTANCE

Pseudomonas aeruginosa
is a Gram-negative bacterium and the leading cause of nosocomial pneumonia. The pathogenicity of
P. aeruginosa
is due to the secretion of many virulence factors. Small regulatory RNAs (sRNAs) regulate various bacterial adaptations, especially virulence. Therefore, understanding the mechanism by which sRNAs regulate virulence is necessary for understanding the pathogenicity of
P. aeruginosa
and the treatment of the related disease. In this study, we demonstrated that PrrH enhances the pathogenicity of
P. aeruginosa
by binding to the coding sequence regions of the ExsA, the master regulatory protein of type III secretion system, causing severe lung injury and exacerbating the inflammatory response and apoptosis. These findings revealed that PrrH is a crucial molecule that positively regulates ExsA. Type III-positive strains are often associated with a high mortality rate in
P. aeruginosa
infections in clinical practice. Therefore, this discovery may provide a new target for treating
P. aeruginosa
infections, especially type III-positive strains.
Comparative analysis of
Porphyromonas gingivalis
A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems
Authors: Śmiga Michał , Ślęzak Paulina , Olczak Teresa
Published: January 2024

Porphyromonas gingivalis
strains exhibit different phenotypes
in vitro
, different virulence potential in animal models, and different associations with human diseases, with strains classified as virulent/more virulent (e.g., A7436 and W83) or as less virulent/avirulent (e.g., ATCC 33277). In this study, we comparatively analyzed the A7436 and ATCC 33277 strains to better understand their variability. Global gene expression analysis in response to heme and iron limitation revealed more pronounced differences in the A7436 than in the ATCC 33277 strain; however, in both strains, the largest changes were observed in genes encoding hypothetical proteins, genes whose products participate in energy metabolism, and in genes encoding proteins engaged in transport and binding proteins. Our results confirmed that variability between
P. gingivalis
strains is due to differences in the arrangement of their genomes. Analysis of gene expression of heme acquisition systems demonstrated that not only the availability of iron and heme in the external environment but also the ability to store iron intracellularly can influence the
P. gingivalis
phenotype. Therefore, we assume that differences in virulence potential may also be due to differences in the production of systems involved in iron and heme acquisition, mainly the Hmu system. In addition, our study showed that hemoglobin, in a concentration-dependent manner, differentially influences the virulence potential of
P. gingivalis
strains. We conclude that iron and heme homeostasis may add to the variability observed between
P. gingivalis
strains.

IMPORTANCE

Periodontitis belongs to a group of multifactorial diseases, characterized by inflammation and destruction of tooth-supporting tissues.
P. gingivalis
is one of the most important microbial factors involved in the initiation and progression of periodontitis. To survive in the host, the bacterium must acquire heme as a source of iron and protoporphyrin IX.
P. gingivalis
strains respond differently to changing iron and heme concentrations, which may be due to differences in the expression of systems involved in iron and heme acquisition. The ability to accumulate iron intracellularly, being different in more and less virulent
P. gingivalis
strains, may influence their phenotypes, production of virulence factors (including proteins engaged in heme acquisition), and virulence potential of this bacterium.
Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection
Authors: Romani L. , Del Chierico F. , Pane S. , Ristori M. V. , Pirona I. , Guarrasi V. , Cotugno N. , Bernardi S. , Lancella L. , Perno C. F. , Rossi P. , Villani A. , Campana A. , Palma P. , Putignani L. ,   the CACTUS Study Team, Carducci Francesca Calò , Cancrini Caterina , Chiurchiù Sara , degli Atti Marta Ciofi , Cursi Laura , Cutrera Renato , D’Amore Carmen , D’Argenio Patrizia , De Ioris Maria A. , De Luca Maia , Finocchi Andrea , Manno Emma Concetta , Morrocchi Elena , Pansa Paola , Sessa Libera , Zangari Paola
Published: January 2024

The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (
T
0
), 72 h to 7 days (
T
1
), and at the discharge (
T
2
) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (
N
= 71) was characterized by reduction of α-diversity compared to CTRLs (
N
= 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in
Streptococcus
,
Haemophilus
,
Staphylococcus
,
Veillonella
,
Enterococcus
,
Neisseria
,
Moraxella
, Enterobacteriaceae,
Gemella
,
Bacillus
, and reduced in
Faecalibacterium
,
Akkermansia
,
Blautia
,
Bifidobacterium
,
Ruminococcus
, and
Bacteroides,
compared to CTRLs (FDR < 0.001). Exploiting ML models,
Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus
, and
Veillonella
resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL.

IMPORTANCE

Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.
Traditional Chinese medicine bufalin inhibits infectious hematopoietic necrosis virus infection
in vitro
and
in vivo
Authors: Zhao Jing-Zhuang , Xu Li-Ming , Li Lin-Fang , Ren Guang-Ming , Shao Yi-Zhi , Liu Qi , Lu Tong-Yan
Published: January 2024

Infectious hematopoietic necrosis virus (IHNV) causes infectious hematopoietic necrosis and severe economic losses to salmon and trout aquaculture worldwide. Currently, the only commercial vaccine against IHNV is a DNA vaccine with some biosafety concerns. Hence, more effective vaccines and antiviral drugs are needed to prevent IHNV infection. In this study, 1,483 compounds were screened from a traditional Chinese medicine monomer library, and bufalin showed potential antiviral activity against IHNV. The 50% cytotoxic concentration of bufalin was >20 µM, and the 50% inhibitory concentration was 0.1223 µΜ against IHNV. Bufalin showed the inhibition of diverse IHNV strains
in vitro
, which confirmed that it had an inhibitory effect against all IHNV strains, rather than random activity against a single strain. The bufalin-mediated block of IHNV infection occurred at the viral attachment and RNA replication stages, but not internalization. Bufalin also inhibited IHNV infection
in vivo
and significantly increased the survival of rainbow trout compared with the mock drug-treated group, and this was confirmed by
in vivo
viral load monitoring. Our data showed that the anti-IHNV activity of bufalin was proportional to extracellular Na
+
concentration and inversely proportional to extracellular K
+
concentration, and bufalin may inhibit IHNV infection by targeting Na
+
/K
+
-ATPase. The
in vitro
and
in vivo
studies showed that bufalin significantly inhibited IHNV infection and may be a promising candidate drug against the disease in rainbow trout.

IMPORTANCE

Infectious hematopoietic necrosis virus (IHNV) is the pathogen of infectious hematopoietic necrosis (IHN) which outbreak often causes huge economic losses and hampers the healthy development of salmon and trout farming. Currently, there is only one approved DNA vaccine for IHN worldwide, but it faces some biosafety problems. Hence, more effective vaccines and antiviral drugs are needed to prevent IHNV infection. In this study, we report that bufalin, a traditional Chinese medicine, shows potential antiviral activity against IHNV both
in vitro
and
in vivo
. The bufalin-mediated block of IHNV infection occurred at the viral attachment and RNA replication stages, but not internalization, and bufalin inhibited IHNV infection by targeting Na
+
/K
+
-ATPase. The
in vitro
and
in vivo
studies showed that bufalin significantly inhibited IHNV infection and may be a promising candidate drug against the disease in rainbow trout.
Erratum to: Specificities of the Fourier Transform Infrared Spectroscopic Methodology and Interpretation of Spectroscopic Data in Microbiological Analyses
Authors: Kamnev A. A. , Tugarova A. V.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S106193482344003X
Erratum to: Determination of 15 Functional State Biomarkers in Human Urine by High-Performance Liquid Chromatography with Tandem Mass Spectrometric Detection
Authors: Leninskii M. A. , Savel’eva E. I. , Belyakov M. V. , Karakashev G. V. , Samchenko N. A.
Published: January 2024

An Erratum to this paper has been published: https://doi.org/10.1134/S1061934823440053
Patient and parent perspectives on paediatric cancer multidisciplinary team working and national advisory panels in the UK: a qualitative research study
Authors: Brown Sarah , Johnson Katie , Gray Juliet , Bate Jessica
Published: January 2024

Objective

The concept of patient-centred care is central to the role of cancer multidisciplinary teams (MDTs) and particularly pertinent with the recent rise in number of virtual national advisory panels (NAPs) for childhood cancer in the UK. We sought to explore patient and caregiver views regarding MDT working and NAPs.

Methods

Three focus groups were undertaken between March 2019 and January 2020.

Results

Sixteen participants attended. All regarded MDTs and NAPs highly, while highlighting patient involvement in decision-making should not be diluted by this process. The importance of personalised consultations was stressed, acknowledging that information-sharing preferences may change with circumstance and time. Most participants felt they had not been actively involved in decisions, including those made following MDT or NAP discussions. Group suggestions to improve patient-centred care included a clinician knowing them presenting their case, referral proformas to include family-related factors and an advocate attending meetings to represent the patient/family view.

Conclusion

Several changes have been driven forward by this work, including the modification of NAP referral proformas to include additional information. Patient and parent perspectives are now embedded into a best practice model for the NAPs to promote personalised recommendations at national level.
Communicative development inventory in type 1 and presymptomatic infants with spinal muscular atrophy: a cohort study
Authors: Buchignani Bianca , Cicala Gianpaolo , Cumbo Francesca , Ricci Martina , Capasso Anna , Ticci Chiara , Mazzanti Sara , Brolatti Noemi , Tosi Michele , Dosi Claudia , Antonaci Laura , Coratti Giorgia , Pera Maria Carmela , Leone Daniela , Palermo Concetta , Berti Beatrice , Frongia Anna Lia , Sacchini Michele , Bruno Claudio , Masson Riccardo , D’Amico Adele , Battini Roberta , Pane Marika , Mercuri Eugenio
Published: January 2024

Objective

The aim of this study was to assess early language acquisitions in treated individuals with spinal muscular atrophy (SMA) type 1 and in infants identified by newborn screening (NBS).

Methods

Parents of SMA individuals aged between 8 and 36 months were asked to fill in the MacArthur-Bates Communicative Development Inventory (MB-CDI) that assesses comprehension, gesture and expressive skills. A follow-up assessment was performed in 21 of the 36.

Results

The MB-CDI was completed by parents of 24 type 1 and 12 infants identified by NBS. Comprehension skills were preserved in 81% of the type 1 SMA and in 87% infants identified by NBS. Gesture abilities were <5th centile in 55% of the type 1 SMA and in none of those identified by NBS. Lexical expressions were <5th centile in more than 80% type 1 SMA and in 50% of infants identified by NBS. At follow-up, despite an increase in lexical expression skills, the scores remained below the fifth centile in 43% type 1 SMA and in 86% of infants identified by NBS.

Conclusions

These results suggest that language and communication development may follow a similar pattern to that observed in motor function with the possibility to develop skills (eg, ability to say clear words) that are not usually present in untreated infants but with a level of performance that does not reach that of their typically developing peers.
Predictors of 24-month onset of macular fibrosis in type 3 macular neovascularisation
Authors: Forte Paolo , Fontana Vincenzo , Muzio Julia , Di Cello Luca , Corazza Paolo , Rosa Raffaella , Musetti Donatella , Vagge Aldo , Traverso Carlo Enrico , Nicolò Massimo
Published: January 2024

Aims

To explore prognostic multimarker models for progression to macular fibrosis (MF) over 24 months specific to type 3 macular neovascularisation (T3 MNV).

Methods

This retrospective, exploratory, single-centre, cohort study comprised 65 eyes of 43 Caucasian patients with treatment naive T3 MNV, all with a 24-month follow-up post anti-VEGF therapy using a strict pro-re-nata (PRN) regimen. Data on demographic features, clinical findings, frequency of intravitreal treatments and optical coherence tomography biomarkers were collected at baseline and after 12 and 24 months of follow-up. Logistic regression models (LRM) and receiver-operating curve (C-index) analyses were performed to evaluate the prognostic ability of the studied biomarkers in discriminating between MF affected and unaffected patients.

Results

At final follow-up, MF was present in 46.2% of eyes. Subretinal hyper-reflective material (SHRM) and subretinal pigment epithelium multilaminar hyper-reflectivity (multilaminae) emerged as significant predictors for MF, with adjusted odds ratios (OR) of 18.0 (95% CL 13.4 to 24.1) and 11.8 (95% CL 8.66 to 16.0), respectively. Additionally, the presence of multifocal lesions (OR 0.04, 95% CL 0.01 to 0.30) appeared to decrease the likelihood of MF. C-indexes for the selected LRMs ranged between 0.92 and 0.88, indicating a comparably high discriminant ability. Despite consistent treatment schedules between the two groups (MF: median intravitreal treatment (IVT) number=10.5, IQR=7; non-MF: median IVT=10, IQR=6), a decline in best-corrected visual acuity was noted in the group with MF onset over the 24-month follow-up (−13.0 ETDRS letters; 95% CL –22.1 to –3.9; p=0.006).

Conclusion

Our study identifies SHRM and multilaminae as relevant predictors of 24-month onset of MF in patients with T3 MNV. These findings enrich our understanding of the development of MF in T3 MNV and can guide improved risk prognostication. Future research should consider larger samples and prospective designs to validate these predictors.
High-risk factors for zonular complications during cataract surgery in eyes with pseudoexfoliation syndrome
Authors: Hayashi Ken , Yoshida Motoaki , Manabe Shin-ichi , Hirata Akira
Published: January 2024

Aims

To predict high-risk factors for zonular complications during cataract surgery due to pre-existing severe zonular dehiscence in eyes with pseudoexfoliation (PXF) syndrome.

Methods

315 eyes of 315 consecutive patients with PXF scheduled for phacoemulsification surgery underwent preoperative examination of various ocular parameters using an anterior segment-optical coherence tomography and other devices. When zonular complications occurred during surgery due to zonular dehiscence, scleral fixation of the intraocular lens (IOL) or implantation of a capsular tension ring (CTR) was performed. High-risk factors for these intraoperative zonular complications were examined using classification-tree and logistic regression analyses.

Results

Of the 315 eyes, 31 (9.84%) underwent scleral IOL fixation or CTR implantation. High-risk factors identified by classification-tree analysis were a small pupillary diameter after mydriasis <6.30 mm, a shallow anterior chamber depth <2.074 mm and lens decentration >0.260 mm. Based on exact logistic regression analysis, the OR was 4.81-fold higher for eyes with poor mydriasis than for eyes without poor mydriasis (p=0.006, 95% CI 1.49 to 18.23), 23.99-fold higher for eyes with poor mydriasis and a shallow anterior chamber (p<0.001, 5.92 to 109.02) and 287.39-fold higher for eyes with poor mydriasis, a shallow chamber and great lens decentration (p<0.001, 50.46 to infinity).

Conclusion

In eyes with PXF, high-risk factors for zonular complications during cataract surgery due to pre-existing severe zonular dehiscence were poor mydriasis, shallow anterior chamber and large lens decentration, suggesting the importance of evaluating these conditions preoperatively.
Lack of consistency in measurement methods and semantics used for network measures in adolescent health behaviour studies using social network analysis: a systematic review
Authors: Collonnaz Magali , Minary Laetitia , Riglea Teodora , Kalubi Jodi , O'Loughlin Jennifer , Kestens Yan , Agrinier Nelly
Published: January 2024

Background

Social network analysis (SNA) is often used to examine how social relationships influence adolescent health behaviours, but no study has documented the range of network measures used to do so. We aimed to identify network measures used in studies on adolescent health behaviours.

Methods

We conducted a systematic review to identify network measures in studies investigating adolescent health behaviours with SNA. Measures were grouped into eight categories based on network concepts commonly described in the literature: popularity, position within the network, network density, similarity, nature of relationships, peer behaviours, social norms, and selection and influence mechanisms. Different subcategories were further identified. We detailed all distinct measures and the labels used to name them in included articles.

Results

Out of 6686 articles screened, 201 were included. The categories most frequently investigated were peer behaviours (n=201, 100%), position within the network (n=144, 71.6%) and popularity (n=110, 54.7%). The number of measurement methods varied from 1 for ‘similarity on popularity’ (within the ‘similarity’ category) to 28 for the ‘characterisation of the relationship between the respondent and nominated peers’ (within the ‘nature of the relationships’ category). Using the examples of ‘social isolation’, ‘group membership’, ‘individuals in a central position’ (within the ‘position within the network’ category) and ‘nominations of influential peers’ (sub within the ‘popularity’ category), we illustrated the inconsistent reporting and heterogeneity in measurement methods and semantics.

Conclusion

Robust methodological recommendations are needed to harmonise network measures in order to facilitate comparison across studies and optimise public health intervention based on SNA.
Prognostic model for unresectable hepatocellular carcinoma treated with dual PD-1 and angiogenesis blockade therapy
Authors: Mo Zhiqiang , Lv Ling , Mai Qicong , Li Qiao , He Jian , Zhang Tao , Xu Jingwu , Fang Jiayan , Shi Ning , Gou Qing , Chen Xiaoming , Zhang Jing , Zhuang Wenhang , Jin Haosheng
Published: January 2024

Background and aims

Dual programmed death 1 (PD-1) and angiogenesis blockade therapy is a frontline treatment for hepatocellular carcinoma (HCC). An accepted model for survival prediction and risk stratification in individual patients receiving this treatment is lacking. Aimed to develop a simple prognostic model specific to these patients.

Approach and results

Patients with unresectable HCC undergoing dual PD-1 and angiogenesis blockade therapy were included in training cohort (n=168) and validation cohort (n=72). We investigated the prognostic value of clinical variables on overall survival using a Cox model in the training set. A prognostic score model was then developed and validated. Predictive performance and discrimination were also evaluated.Largest tumor size andAlpha-fetoprotein concentration at baseline andNeutrophil count andSpleen volume change after 6 weeks of treatment were identiﬁed as independent predictors of overall survival in multivariable analysis and used to develop LANS score. Time-dependent receiver operating characteristic analysis, calibration curves, and C-index showed LANS score had favorable performance in survival prediction. Patients were divided into three risk categories based on LANS score. Median survival for patients with low, intermediate, and high LANS scores was 31.7, 23.5, and 11.5 months, respectively (p<0.0001). The disease control rates were 96.4%, 64.3%, and 32.1%, respectively (p<0.0001). The predictive performance and risk stratification ability of the LANS score were confirmed in validation and entire cohorts.

Conclusion

The LANS score model can provide individualized survival prediction and risk stratification in patients with unresectable HCC undergoing dual PD-1 and angiogenesis blockade therapy.
Artificial intelligence in medicine and the negative outcome penalty paradox
Authors: Appel Jacob M
Published: January 2024

Artificial intelligence (AI) holds considerable promise for transforming clinical diagnostics. While much has been written both about public attitudes toward the use of AI tools in medicine and about uncertainty regarding legal liability that may be delaying its adoption, the interface of these two issues has so far drawn less attention. However, understanding this interface is essential to determining how jury behaviour is likely to influence adoption of AI by physicians. One distinctive concern identified in this paper is a ‘negative outcome penalty paradox’ (NOPP) in which physicians risk being penalised by juries in cases with negative outcomes, whether they overrule AI determinations or accept them. The paper notes three reasons why AI in medicine is uniquely susceptible to the NOPP and urges serious further consideration of this complex dilemma.