bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Epitogen Lyme Detect IgG ELISA: a novel peptide multiplexing approach
Authors: Wang Tiehui , Wang Alex , Zindrili Rodanthi , Melis Elena , Guntupalli Swapna , Brittain-Long Robin , Delibegovic Mirela , Secombes Christopher J. , Mody Nimesh , Mavin Sally , Buks Ralfs 
Published: October 2024

ABSTRACT

Lyme Borreliosis (LB), or Lyme disease, is a growing health concern caused by
Borrelia burgdorferi sensu lato
(Bbsl) bacteria transmitted through tick bites, and untreated cases can lead to severe health complications. Existing serology tests, while valuable, have low sensitivity in early infection stages where diagnosis is vital, interpretation variability, and false positives from cross-reactivity, while direct detection methods also suffer from low sensitivity, due to the inconsistent presence of Bbsl components in clinical samples. This study validated the diagnostic performance of the novel Epitogen Lyme Detect IgG enzyme-linked immunosorbent assay (ELISA) based on scaffold-displayed peptide antigens, using 120 specific immunodominant epitopes selected from 37 antigenic bacterial proteins corresponding to the main pathogenic Bbsl genospecies. Using 220 serum samples from Scottish patients with early, late, and disseminated LB, the assay’s sensitivity was compared with that of the LIAISON Borrelia IgG CLIA, while specificity was assessed with 198 control samples, including healthy individuals and patients with diseases that are humorally similar. The Epitogen Lyme Detect IgG assay demonstrated comparable performance to the LIAISON Borrelia IgG in disseminated and late LB (Lyme neuroborreliosis, acrodermatitis chronica atrophicans, and Lyme arthritis). Notably, the Epitogen Lyme Detect IgG showed significantly higher sensitivity in patients with suspected erythema migrans, while maintaining high specificity. The Epitogen Lyme Detect IgG ELISA offers a promising advancement in LB diagnostics, demonstrating its potential for more accurate and timely diagnosis, particularly in the early stages of LB infection.

IMPORTANCE

Lyme Borreliosis (LB), caused by
Borrelia burgdorferi sensu lato
bacteria, poses significant health risks if undiagnosed or diagnosed late. Current diagnostic tests have limitations, especially in early-stage detection. This study validates the Epitogen Lyme Detect IgG enzyme-linked immunosorbent assay, demonstrating superior sensitivity in early LB detection while maintaining high specificity. The Epitogen Lyme Detect IgG comprises a suite of 120 immunodominant IgG epitopes/peptides from 37 bacterial antigens, covering the main LB-causing species:
Borrelia burgdorferi sensu stricto
,
Borrelia afzelii
,
Borrelia garinii
, and
Borrelia mayonii
. The novel design of multiplexing peptide antigens onto a scaffold to facilitate expression, correct folding, and orientation of the relevant peptides offers a promising advancement, potentially leading to more accurate and timely LB diagnoses and improving patient outcomes.
An
Acinetobacter baumannii
nasal carriage isolate recovered from an asymptomatic patient in Vietnam is extensively antibiotic resistant and produces a rare K71 type capsule
Authors: Shpirt Anna M. , Harmer Christopher J. , Shashkov Alexander S. , Shneider Mikhail M. , Chizhov Alexander O. , Dmitrenok Andrey S. , Popova Anastasiya V. , Kasimova Anastasiya A. , Perepelov Andrei V. , Knirel Yuriy A. , Hall Ruth M. , Kenyon Johanna J. 
Published: October 2024

ABSTRACT

Acinetobacter baumannii
is a leading cause of multidrug-resistant bacterial infections worldwide, and the capsular polysaccharide (CPS) is a major virulence determinant. A previous study of
A. baumannii
from intubated and asymptomatic patients admitted to the intensive care unit (ICU) at the Hospital for Tropical Diseases in Ho Chi Minh City in Vietnam revealed multiple lineages with diverse antibiotic resistance profiles and CPS biosynthesis loci. Here, we show that 48_n, an asymptomatic nasal carriage isolate belonging to ST142, is extensively antibiotic resistant and carries acquired resistance determinants accounting for the resistance profile. 48_n carries the novel KL71 CPS biosynthesis locus in the chromosome. The structure of the CPS produced by 48_n was established using
1
H and
13
C nuclear magnetic resonance spectroscopy, including two-dimensional
1
Н,
1
Н COSY,
1
Н,
1
Н TOCSY,
1
Н,
1
Н ROESY,
1
Н,
13
C HSQC, and
1
Н,
13
C HMBC experiments, and confirmed by Smith degradation. Consistent with the genetic content of KL71, the K71 CPS was found to be made up of octasaccharide K units containing six
l
-rhamnose residues and one residue each of
N
-acetyl-
d
-glucosamine and
d
-glucuronic acid. K71 CPS was branched and closely related to the K74 CPS produced by BAL_309, an antibiotic susceptible ST142 isolate recovered from an intubated patient in the same ICU 7 years later. K71 and K74 differ only in the linkage between K units, and this is due to the replacement of a single gene at the K locus that codes for the Wzy polymerase.

IMPORTANCE

The majority of
Acinetobacter baumannii
genomes sequenced and analyzed to develop an understanding of extensively drug-resistant (XDR) isolates belong to the globally disseminated CC2 clonal complex. While XDR isolates belonging to rarer lineages are often unexplored, detailed analyses could provide novel insights into the spread of resistance, as well as cell surface features such as the CPS that determine the specificity of non-antibiotic therapeutics required to treat XDR infections that resist antimicrobial chemotherapy. Here, we describe the properties of an XDR asymptomatic nasal carriage isolate recovered in Vietnam that belongs to ST142, a rarely encountered sequence type. We report the resistance profile and correlate this with detected resistance determinants. We also solve the structure of the CPS and reveal its relationship with CPS produced by other
A. baumannii
isolates.
Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics
Authors: Hernandez Daniella M. , Marzouk Melissa , Cole Madeline , Fortoul Marla C. , Reddy Kethireddy Saipranavi , Contractor Rehan , Islam Habibul , Moulder Trent , Kalifa Ariane R. , Marin Meneses Estefania , Barbosa Mendoza Maximiliano , Thomas Ruth , Masud Saad , Pubien Sheena , Milanes Patricia , Diaz-Tang Gabriela , Lopatkin Allison J. , Smith Robert P. 
Published: October 2024

ABSTRACT

The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. Previous work found that the relationship between [ATP] and growth rate can account for the strength and occurrence of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. Using a combination of flux balance analysis and experimentation, we show that nucleotide synthesis can determine the relationship between [ATP] and growth and thus the strength of inoculum effect in an antibiotic class-dependent manner. If the [ATP]/growth rate is sufficiently high as determined by exogenously supplied nitrogenous bases, the inoculum effect does not occur. This is consistent for both
Escherichia coli
and
Pseudomonas aeruginosa
. Interestingly, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect, which may pave the way for intervention strategies to reduce the inoculum effect in the clinic.

IMPORTANCE
If a bacterial population can grow and reach a sufficiently high density, routine doses of antibiotics can be ineffective. This phenomenon, called the inoculum effect, has been observed for nearly all antibiotics and bacterial species. It has also been reported to result in antibiotic failure in the clinic. Understanding how to reduce the inoculum effect can make high-density infections easier to treat. Here, we show that purine and pyrimidine synthesis affect the strength of the inoculum effect; as the transcriptional activity of pyrimidine synthesis increases, the strength of the inoculum effect for aminoglycosides decreases. Conversely, as the transcriptional activity of purine synthesis increases, the strength of the inoculum effect for β-lactam antibiotics decreases. Our work highlights the importance of nucleotide synthesis in determining the strength of the inoculum effect, which may lead to the identification of new ways to treat high-density infections in the clinic.
Identification of new SdiA regulon members of
Escherichia coli
,
Enterobacter cloacae
, and
Salmonella enterica
serovars Typhimurium and Typhi
Authors: Schwieters Andrew , Ahmer Brian M. M. 
Published: October 2024

ABSTRACT

Bacteria can coordinate behavior in response to population density through the production, release, and detection of small molecules, a phenomenon known as quorum sensing.
Salmonella enterica
is among a group of Enterobacteriaceae that can detect signaling molecules of the
N
-acyl homoserine lactone (AHL) type but lack the ability to produce them. The AHLs are detected by the LuxR-type transcription factor, SdiA. This enables a behavior known as eavesdropping, where organisms can sense the signaling molecules of other species of bacteria. The role of SdiA remains largely unknown. Here, we use RNA-seq to more completely identify the
sdiA
regulons of two clinically significant serovars of
Salmonella enterica
: Typhimurium and Typhi. We find that their
sdiA
regulons are largely conserved despite the significant differences in pathogenic strategy and host range of these two serovars. Previous studies identified
sdiA
-regulated genes in
Escherichia coli
and
Enterobacter cloacae
, but there is surprisingly no overlap in regulon membership between the different species. This led us to individually test orthologs of each regulon member in the other species and determine that there is indeed some overlap. Unfortunately, the functions of most
sdiA
-regulated genes are unknown, with the overall function of eavesdropping in these organisms remaining unclear.

IMPORTANCE

Many bacterial species detect their own population density through the production, release, and detection of small molecules (quorum sensing).
Salmonella
and other Enterobacteriaceae have a modified system that detects the
N
-acyl-homoserine lactones of other bacteria through the solo quorum sensing receptor SdiA, a behavior known as eavesdropping. The roles of
sdiA
-dependent eavesdropping in the lifecycles of these bacteria are unknown. In this study, we identify
sdiA
-dependent transcriptional responses in two clinically relevant serovars of
Salmonella
, Typhimurium and Typhi, and note that their responses are partially conserved. We also demonstrate for the first time that
sdiA
-dependent regulation of genes is partially conserved in
Enterobacter cloacae
and
Escherichia coli
as well, indicating a degree of commonality in eavesdropping among the Enterobacteriaceae.
Purine limitation prevents the exogenous pyridoxal 5′-phosphate accumulation of
Salmonella enterica yggS
mutants
Authors: Ezekiel Kailey S. , Downs Diana M. 
Published: October 2024

ABSTRACT

YggS belongs to the highly conserved pyridoxal 5′-phosphate (PLP) binding protein family (COG0325) that is found in all domains of life. Though no precise biochemical activity or molecular mechanism has been determined for this protein, an involvement in vitamin B
6
homeostasis has been demonstrated in multiple organisms. In
Salmonella enterica
, loss of YggS results in altered B
6
vitamer pools, including an accumulation of PLP in the growth medium. Transposon mutagenesis identified an insertion upstream of
purC
(encoding 5′-phosphoribosyl-5-aminoimidazole-4-
N
-succinocarboxamide synthetase, EC 6.3.2.6) that eliminated accumulation of PLP in the spent medium. Genetic characterization of the insertion showed the causative effect was reduced expression of
purC
, which limited purine biosynthesis. Data herein shows that purine limitation decreased the exogenous accumulation of B
6
vitamers of a
yggS
mutant but did not suppress other
yggS
mutant phenotypes. Neither limitation for ATP, regulation by PurR, or decreased growth rate, all of which are direct consequences of purine limitation, prevented exogenous B
6
vitamer accumulation of a
yggS
mutant. This work establishes a relationship between the status of purine biosynthesis and the impact of a
yggS
mutation. It lays the foundation for continued efforts to identify the physiological role of YggS and its homologs.

IMPORTANCE

Pyridoxal 5′-phosphate is the active form of vitamin B
6
and is an essential cofactor in all domains of life. PLP can be synthesized
de novo
or salvaged from the environment from one of the six B
6
vitamers. B
6
vitamer levels appear to be tightly regulated, and alterations in their levels can have deleterious effects, most notably being the development of B6-dependent epilepsy in humans. YggS homologs are broadly conserved across multiple organisms and considered to be involved in maintaining B
6
homeostasis, though no specific mechanism has been defined. The current study showed that the exogenous accumulation of PLP caused by a lack of YggS can be prevented by purine limitation. The demonstration that purine limitation impacts exogenous PLP accumulation separates one consequence of a
yggS
mutation for further study and contributes to continuing efforts to define the biochemical and physiological roles of the COG0325 family of proteins.
Optimal 16S rRNA gene amplicon sequencing analysis for oral microbiota to avoid the potential bias introduced by trimming length, primer, and database
Authors: Nagai Takahiko , Shiba Takahiko , Komatsu Keiji , Watanabe Takayasu , Nemoto Takashi , Maekawa Shogo , Kobayashi Ryota , Matsumura Shunsuke , Ohsugi Yujin , Katagiri Sayaka , Takeuchi Yasuo , Iwata Takanori 
Published: October 2024

ABSTRACT

16S rRNA gene amplicon sequencing analysis is used to investigate bacterial communities; however, the estimated bacterial composition can differ from the original due to experimental and analytical biases. Therefore, this study determines the optimal conditions to minimize the potential biases in 16S rRNA gene amplicon sequencing analysis using different DNA samples, trimming lengths, primers, and databases. The results of the mock1 community with 250 and 300 bp paired-end (PE), comprising 15 bacteria from various environments, showed the highest similarity between the theoretical value and the data using the Greengenes2 and the V3 region at the genus level and V5–V6 at the species level. In the 300 bp PE sequencing analysis of the mock2 community, comprising six major oral bacteria, the data using the V3–V4, V4, and V5–V6 regions with the SILVA, Greengenes2, and the Human Oral Microbiome Database (HOMD) showed the highest similarity to the theoretical values at the genus level. At the species level, the data using the V3–V4 and V4 regions with Greengenes2 and the data using the V1–V2 with HOMD exhibited the highest alignment with the theoretical values. In the species analysis of the dental calculus samples with 300 bp PE, the Shannon index value was higher with the V1–V2 region and HOMD than with others. Our results suggest that the optimal conditions for oral microbiome analysis are the combinations of 300 bp PE and the V3–V4 or V4 region with the Greengenes2 and the V1–V2 with HOMD.

IMPORTANCE
The 16S rRNA gene amplicon sequencing analysis is frequently used in oral microbiome research. However, this method can have biases that distort the experimental data, which depend on the methodological steps, including sequencing length, trimming length, selected amplification regions, and referenced databases. In this study, a combination of 300 bp PE and the primer targeting the V3–V4 or V4 regions with the Greengenes2 and the V1–V2 region with the HOMD was the most bias-minimizing condition for oral microbiota analysis. In addition, this is the first report of such analyses in modern Japanese dental calculus. The methods used in this study will aid in setting appropriate conditions for sequence analysis of microbiota obtained not only from the oral cavity but also from any environment.
Twenty year analysis of professional men’s rugby union knee injuries from the English premiership shows high rates and burden
Authors: West Stephen W , Hudson Sam J , Starling Lindsay , Cross Matthew , Williams Sean , McKay Carly D , Cazzola Dario , Brooks John H M , Murray Rory , Williams Andy , Kemp Simon P T , Stokes Keith A 
Published: October 2024

ObjectivesTo determine the rates, severity and burden of knee injuries in professional male rugby union from the English Premiership.MethodsInjury and exposure data were captured over 20 seasons using a prospective cohort design. Knee injury incidence, days’ absence and burden were recorded for each injury type and by pitch surface type for match and training.ResultsThe rate of knee injury in matches was 9.8/1000 hours (95% CIs 9.3–10.3). Mean days lost were 50 (95% CI 46 to 53) in matches and 51 (95% CI 44 to 57) in training. In matches, medial collateral ligament injuries were the most common, while anterior cruciate ligament (ACL) injuries had the highest mean severity and burden. There was no significant change in the count of knee injuries over time; however, average severity increased significantly (annual change: 2.18 days (95% CI 1.60 to 2.77); p<0.001). The incidence of match knee injury was 44% higher on artificial pitches than grass pitches (incidence rate ratio: 1.44 (95% CI 1.21 to 1.69); p<0.01), with no significant difference in severity between surfaces. In matches, the tackle was the event most commonly associated with knee injuries for all diagnoses, except ACL injuries (running). In training, running was a more common injury event than the tackle.ConclusionKnee injuries in matches are common and severe in English professional men’s rugby union. Despite an increased focus on player conditioning and injury prevention throughout the study period, rates of knee injury remained stable, and resulting days’ absence increased. New strategies for the prevention of knee injuries should be considered a priority.
Multicentre study to assess the performance of an artificial intelligence instrument to support qualitative diagnosis of colorectal polyps
Authors: Sato Keigo , Kuramochi Mizuki , Tsuchiya Akihiko , Yamaguchi Akihiro , Hosoda Yasuo , Yamaguchi Norio , Nakamura Naohiro , Itoi Yuki , Hashimoto Yu , Kasuga Kengo , Tanaka Hirohito , Kuribayashi Shiko , Takeuchi Yoji , Uraoka Toshio 
Published: October 2024

ObjectiveComputer-aided diagnosis (CAD) using artificial intelligence (AI) is expected to support the characterisation of colorectal lesions, which is clinically relevant for efficient colorectal cancer prevention. We conducted this study to assess the diagnostic performance of commercially available CAD systems.MethodsThis was a multicentre, prospective performance evaluation study. The endoscopist diagnosed polyps using white light imaging, followed by non-magnified blue light imaging (non-mBLI) and mBLI. AI subsequently assessed the lesions using non-mBLI (non-mAI), followed by mBLI (mAI). Eventually, endoscopists made the final diagnosis by integrating the AI diagnosis (AI+endoscopist). The primary endpoint was the accuracy of the AI diagnosis of neoplastic lesions. The diagnostic performance of each modality (sensitivity, specificity and accuracy) and confidence levels were also assessed.ResultsOverall, 380 lesions from 139 patients were included in the analysis. The accuracy of non-mAI was 83%, 95% CI (79% to 87%), which was inferior to that of mBLI (89%, 95% CI (85% to 92%)) and mAI (89%, 95% CI (85% to 92%)). The accuracy (95% CI) of diagnosis by expert endoscopists using mAI (91%, 95% CI (87% to 94%)) was comparable to that of expert endoscopists using mBLI (91%, 95% CI (87% to 94%)) but better than that of non-expert endoscopists using mAI (83%, 95% CI (75% to 90%)). The level of confidence in making a correct diagnosis was increased when using magnification and AI.ConclusionsThe diagnostic performance of mAI for differentiating colonic lesions is comparable to that of endoscopists, regardless of their experience. However, it can be affected by the use of magnification as well as the endoscopists’ level of experience.
Human papillomavirus nonavalent (HPV9) vaccination and risk of immune mediated diseases, myocarditis, pericarditis, and thromboembolic outcomes in Denmark: self-controlled case series study
Authors: Faksová Kristýna , Laksafoss Anna D , Hviid Anders 
Published: October 2024

ObjectiveTo assess the associations between vaccination with the nonavalent human papillomavirus (HPV9) vaccine and immune mediated diseases, myocarditis, pericarditis, arterial thromboembolism, and venous thromboembolism with or without thrombocytopenia, in adolescent girls and boys in Denmark.DesignSelf-controlled case series study.SettingPopulation based study of linked nationwide health registers in Denmark for HPV vaccination and hospital diagnosis data, 1 October 2017 (or age 10 years) to 31 December 2022 or censored. Personal data were obtained from the Central Person Register. Information on dates of HPV vaccination and type of vaccine were obtained from the Danish Vaccination Register. Primary or secondary diagnoses of inpatient or outpatient hospital contact were sourced from the Danish National Patient Register.ParticipantsSource cohort 854 586. 350 687 individuals aged 10-17 years living in Denmark received at least one dose of HPV9 vaccine. Self-controlled case series analysis of 3354 individuals (1913 girls and 1441 boys) who received at least one dose of HPV9 vaccine and had at least one outcome.Main outcome measuresRate ratios of the study outcomes in a 28 day or 180 day risk period (depending on the type of outcome) after HPV9 vaccination compared with the reference period were calculated. 47 immune mediated diseases, myocarditis, pericarditis, and seven thromboembolic outcomes were assessed. A safety signal for a specific outcome was identified if at least three outcomes were seen in the risk period after vaccination, the rate ratio was significantly increased (lower bound of the 95% confidence interval (CI) for the self-controlled case series rate ratio >1.0), and the false discovery rate adjusted P value was significant (<0.05).Results696 776 doses of any HPV vaccine were given during the study period, including 673 530 doses of HPV9 vaccine in 350 687 individuals who received at least one dose. In the self-controlled case series analysis, rate ratios of all immune mediated outcomes combined were 0.99 (95% CI 0.86 to 1.13) and 1.03 (0.89 to 1.20) in girls and boys, respectively, after HPV9 vaccination. Rate ratios for any of the 47 analysed immune mediated outcomes were not increased in the risk periods in girls after vaccination. The only increased rate ratio seen was for Raynaud's disease (rate ratio 2.62, 95% CI 1.07 to 6.40) after HPV9 vaccination in boys, which did not fulfil the criteria of a safety signal. These findings should be interpreted in the light of the study limitations. None of the other 55 outcomes examined showed an association with HPV9 vaccination.ConclusionsThe results of this study did not suggest an association between HPV9 vaccination and the study outcomes in adolescent boys and girls aged 10-17 years. This study contributes to the evidence on the safety of the HPV9 vaccine.