bluuebunny/crossref_metadata_2025_split huggingface dataset:
How accurate is ceftriaxone at predicting susceptibility of enterobacterales isolates to oral higher-generation cephalosporins?
Authors: Claeys Kimberly C. , Simner Patricia J. , Tekle Tsigereda , Harris Anthony D. , Jacobs Emily , Cosgrove Sara E. , Tamma Pranita D. 
Published: December 2024

ABSTRACT

The reliability of ceftriaxone for inferring susceptibility to higher-generation oral cephalosporins is unknown. Overall, ceftriaxone susceptibility predicted susceptibility to cefuroxime (89%), cefdinir (86%), cefpodoxime (90%), and cefixime (94%) based on disk diffusion results for 409 consecutive Enterobacterales bloodstream isolates from unique patients. Susceptibility percentages to the four oral cephalosporins ranged from 92% to 99% when limited to
Escherichia coli
,
Klebsiella pneumoniae, Klebsiella oxytoca, or Proteus mirabilis
isolates susceptible to ceftriaxone.
Treatment with BKI-1748 after
Toxoplasma gondii
systemic dissemination in experimentally infected pregnant sheep improves fetal and lamb mortality and morbidity and prevents congenital infection
Authors: Sánchez-Sánchez Roberto , Huertas-López Ana , Largo-de la Torre Andrea , Ferre Ignacio , Dini Filippo Maria , Re Michela , Moreno-Gonzalo Javier , Choi Ryan , Hulverson Matthew A. , Ojo Kayode K. , Arnold Samuel L. M. , Hemphill Andrew , Van Voorhis Wesley C. , Ortega-Mora Luis Miguel 
Published: December 2024

ABSTRACT

Drug development for congenital toxoplasmosis is challenging since first-line therapy has a high rate of adverse effects and exhibits suboptimal efficacy. Bumped kinase inhibitors (BKIs), targeting protein kinases with small gatekeeper residues, have been found to be effective against
Toxoplasma gondii
. The efficacy of BKI-1748 administered later than 2 days post-infection (p.i.), a scenario that may better reflect its real-world use as a therapeutic candidate, has not been investigated in
T. gondii
-infected pregnant sheep. For this purpose, 19 pregnant sheep were assigned to three experimental groups. Group 1 (G1,
n
= 8) and group 2 (G2,
n
= 8) were dosed orally with 10 TgShSp1 sporulated oocysts at 90 days of gestation (dg). Animals from group 3 (G3,
n
= 3) were simultaneously mock dosed with phosphate-buffered solution (PBS). In G1, BKI-1748 was administered orally from day 7 p.i. (fever and increased serum IFNγ levels) onward, maintaining drug exposure for 20 days (10 doses at 15 mg/kg every 2 days). Treated animals (G1) exhibited significantly lower rectal temperatures (on days 8 and 9 p.i.), serum IFNγ levels (on day 10 p.i.), and specific IgG levels when compared with non-treated animals (G2). At delivery, significantly higher percentages of healthy lambs were found in infected/treated sheep in G1 (73.3%) and in uninfected sheep in G3 (80%) compared with infected/untreated sheep in G2 (31.3%). Concerning congenital transmission, parasite DNA was neither detected in placenta nor target tissues (brain and lungs) from the fetuses/lambs in G1(infected/treated) and G3 (uninfected). By contrast, parasite DNA was detected in all placentas and lambs from G2 (infected/untreated), except for one sheep that aborted on day 13 p.i.
A
Clostridioides difficile
cell-free gene expression system for prototyping and gene expression analysis
Authors: Zeng Ji , Wang Hao , Xu Yuxi , Han Jianying , Li Yannan , Wen Shu'an , Wu Changbu , Li Dani , Liu Zheng , Zhang Xiaokang , Tian Guo-Bao , Dong Min 
Published: December 2024

ABSTRACT

Clostridioides difficile
is an obligate anaerobic, Gram-positive bacterium that produces toxins. Despite technological progress, conducting gene expression analysis of
C. difficile
under different conditions continues to be labor-intensive. Therefore, there is a demand for simplified tools to investigate the transcriptional and translational regulation of
C. difficile
. The cell-free gene expression (CFE) system has demonstrated utility in various applications, including prototyping, protein production, and
in vitro
screening. In this study, we developed a
C. difficile
CFE system capable of
in vitro
transcription and translation (TX-TL) in the presence of oxygen. Through optimization of cell extract preparation and reaction systems, we increased the protein yield significantly. Furthermore, our observations indicated that this system exhibited higher protein yield using linear DNA templates than circular plasmids for
in vitro
expression. The prototyping capability of the
C. difficile
CFE system was assessed using a series of synthetic
Clostridium
promoters, demonstrating a good correlation between
in vivo
and
in vitro
expression. Additionally, we tested the expression of
tcdB
and
tcdR
from clinically relevant
C. difficile
strains using the CFE system, confirming higher toxin expression of the hypervirulent strain R20291. We believe that the CFE system can not only serve as a platform for
in vitro
protein synthesis and genetic part prototyping but also has the potential to be a simplified model for studying metabolic regulations in
Clostridioides difficile
.

IMPORTANCE

Clostridioides difficile
has been listed as an urgent threat due to its antibiotic resistance, and it is crucial to conduct gene expression analysis to understand gene functionality. However, this task can be challenging, given the need to maintain the bacterium in an anaerobic environment and the inefficiency of introducing genetic material into
C. difficile
cells. Conversely, the
C. difficile
cell-free gene expression (CFE) system enables
in vitro
transcription and translation in the presence of oxygen within just half an hour. Furthermore, the composition of the CFE system is adaptable, permitting the addition or removal of elements, regulatory proteins for example, during the reaction. As a result, this system could potentially offer an efficient and accessible approach to accelerate the study of gene expression and function in
Clostridioides difficile
.
Absence of biofilm adhesin proteins changes surface attachment and cell strategy for
Desulfovibrio vulgaris
Hildenborough
Authors: Pickens C. Pete , Wang Dongyu , Pan Chongle , De León Kara B. 
Published: December 2024

ABSTRACT

Ubiquitous in nature, biofilms provide stability in a fluctuating environment and provide protection from stressors. Biofilms formed in industrial processes are exceedingly problematic and costly. While biofilms of sulfate-reducing bacteria in the environment are often beneficial because of their capacity to remove toxic metals from water, in industrial pipelines, these biofilms cause a major economic impact due to their involvement in metal and concrete corrosion. The mechanisms by which biofilms of sulfate-reducing bacteria form, however, are not well understood. Our previous work identified two proteins, named by their gene loci DVU1012 and DVU1545, as adhesins in the model sulfate-reducing bacterium,
Desulfovibrio vulgaris
Hildenborough. Both proteins are localized to the cell surface and the presence of at least one of the proteins, with either being sufficient, is necessary for biofilm formation to occur. In this study, differences in cell attachment and early biofilm formation in single deletion mutants of these adhesins were identified. Cells lacking DVU1012 had a different attachment strategy from wild-type (WT) and ΔDVU1545 cells, more often attaching as single cells than aggregates, which indicated that DVU1012 was more important for cell-to-cell attachment. ΔDVU1545 cells had increased cell attachment compared to WT cells when grown in static cultures. To date, comparisons of the
D. vulgaris
Hildenborough have been made to the large adhesion protein system in environmental pseudomonads. Yet, we and others have shown distinct mechanistic differences in the systems. We propose to name these proteins in
D. vulgaris
Hildenborough biofilm formation system to facilitate comparisons.

IMPORTANCE

Biofilms of sulfate-reducing bacteria contribute to biocorrosion, costing the United States hundreds of millions of dollars annually. In contrast, these biofilms can be used to bioremediate toxic heavy metals and to generate bioelectricity. As one of the most abundant groups of organisms on Earth, it is pertinent to better understand mechanistically how the biofilms of sulfate-reducing bacteria form so we may use this knowledge to help in efforts to mitigate biocorrosion, to promote bioremediation, and to produce clean energy. This study shows that the absence of either one of two biofilm adhesins impacts surface colonization by a sulfate-reducing bacterium, and that these two biofilm adhesins differ in their effect on cell attachment compared to other well-documented bacteria such as
Pseudomonas
species.
Assembly and performance of a cholera RDT prototype that detects both
Vibrio cholerae
and associated bacteriophage as a proxy for pathogen detection
Authors: Sayeed Md. Abu , Nabil Imrul Kayes , Bhattacharjee Piyash , Hossain Md. Shawkat , Akter Noor Jahan , Akter Romana , Kelley Karen L. , Karim Mahbubul , Begum Yasmin Ara , Bhuiyan Taufiqur Rahman , Qadri Firdausi , Khan Ashraful Islam , Nelson Eric J. 
Published: December 2024

ABSTRACT

Cholera rapid diagnostic tests (RDTs) are vulnerable to virulent bacteriophage predation. We hypothesized that an enhanced cholera RDT that detects the common virulent bacteriophage ICP1 might serve as a proxy for pathogen detection. We previously developed a monoclonal antibody (mAb) to the ICP1 major capsid protein. Our objective was to design and assemble a first-of-its-kind RDT that detects both a bacterial pathogen (
Vibrio cholerae
) and associated virulent bacteriophage (ICP1). Candidate mAbs were expanded to increase design options and evaluated by immunological assays (ELISA; western blot). A subset of mAbs were selected for gold conjugation and printing on the RDT. The detection limit of the prototype RDTs was determined in diarrheal stools with the addition of ICP1. Three mAb candidates were developed and evaluated for the capsid decoration protein (ORF123) and tail fiber protein (ORF93), and the prior mAb for the major capsid protein (ORF122). A single mAb sandwich RDT prototype for ORF122 was able to detect ICP1; RDTs with mAbs to ORF123 and ORF93 failed to detect ICP1 in single- or dual-sandwich configurations. Biologically relevant concentrations for ICP1 were detected only after boiling the stool with ICP1; analysis by electron microscopy (EM) suggested increased epitope availability after boiling. In this study, we demonstrate a proof of concept for a functional RDT that can detect both the primary pathogen and a common virulent bacteriophage as a proxy for pathogen detection. Further optimization is required before scaled production and implementation.

IMPORTANCE

This paper represents an important step forward to address the vulnerability of cholera RDTs to the effects of phage predation on the target
Vibrio cholerae
. The assembly and evaluation of an RDT that detects both the primary pathogen and a phage as a proxy for the primary pathogen is an innovative solution. When optimized and evaluated in clinical studies, this tool may become critical in the cholera response tool kit as well as represent a diagnostic proof-of-concept for other infectious agents.
Validation of a simplified HPV genotyping assay designed for cervical screening in low-resource settings
Authors: Desai Kanan T. , Ajenifuja Kayode O. , Adepiti Clement A. , Inturrisi Federica , Dagnall Casey , Hoffman Amanda C. , Egemen Didem , Gage Julia C. , Wentzensen Nicolas , de Sanjose Silvia , Schiffman Mark 
Published: December 2024

ABSTRACT

Human papillomavirus (HPV) genotype predicts cervical cancer risk, and genotyping could help guide the management of HPV positives as part of cervical screening. An isothermal amplification HPV extended genotyping test (ScreenFire HPV RS assay) can assay up to 96 samples/controls in 1 hour plus preparation time. A novel format with pre-aliquoted reagents and an anti-contamination component (Zebra BioDome) could simplify the HPV testing process and reduce the chances of post-amplification contamination. We validated the Zebra BioDome formulation prior to its clinical use. Residual provider-collected cervical samples (
n
= 450) from a population-based study in rural Nigeria were retested with ScreenFire, once using the standard assay version (liquid reagents combined onsite) and twice with Zebra BioDome. HPV results with adequate DNA (
N
= 427) were analyzed channel-by-channel and using the cervical cancer risk-based hierarchy of HPV type channels (HPV16, else 18/45, else 31/33/35/52/58, else 39/51/56/59/68, else high-risk HPV negative) to evaluate Zebra BioDome repeatability and accuracy against the standard version. Zebra BioDome reduced the number of pipetting steps to run the ScreenFire HPV assay. Following amplification, the BioDome material formed a sealant layer above the reaction components. Zebra BioDome had excellent repeatability and agreement with the standard version, both at the channel-specific analysis (positive percent agreement between 88.4% [HPV39/51/56/59/68] and 100% [HPV16]; negative percent agreement between 97.8% [HPV31/33/35/52/58] and 100% [HPV39/51/56/59/68]) and hierarchical analysis (overall agreement 97.2%). The assay version utilizing Zebra BioDome performed similarly to the previously validated standard version of the ScreenFire HPV assay and is now undergoing field evaluation. This solution has the potential to reduce assay preparation time and risk of contamination, providing a simpler, low-cost, near-point-of-care HPV testing and extended genotyping solution for cervical screening in lower-resource settings. The potential application of Zebra BioDome technology to other PCR assays should be considered.

IMPORTANCE
This work validates a novel pre-packed formulation for the ScreenFire human papillomavirus (HPV) assay, which has the potential to simplify the HPV testing process and to reduce the chances of post-amplification contamination, providing a simpler, low-cost, near-point-of-care HPV testing, and extended genotyping solution for cervical screening in resource-limited settings as part of the ultimate public health goal to accelerate cervical cancer prevention. This technology can also have broad applications for other DNA amplification assays beyond HPV.
Delivery determinants of an
Acinetobacter baumannii
type VI secretion system bifunctional peptidoglycan hydrolase
Authors: Bezkorovayna Valeriya , Hayes Brooke K. , Gillett Francesca N. , Wright Amy , Roper David I. , Harper Marina , McGowan Sheena , Boyce John D. 
Published: December 2024

ABSTRACT

Acinetobacter baumannii
is a Gram-negative opportunistic pathogen and is a common cause of nosocomial infections. The increasing development of antibiotic resistance in this organism is a global health concern. The
A. baumannii
clinical isolate AB307-0294 produces a type VI secretion system (T6SS) that delivers three antibacterial effector proteins that give this strain a competitive advantage against other bacteria in polymicrobial environments. Each effector, Tse15, Tde16, and Tae17, is delivered
via
a non-covalent interaction with a specific T6SS VgrG protein (VgrG15, VgrG16, and VgrG17, respectively). Here we define the regions of interaction between Tae17 and its cognate delivery protein VgrG17 and identify that amino acids G1069 and W1075 in VgrG17 are essential for Tae17 delivery
via
the T6SS, the first time such specific delivery determinants of T6SS cargo effectors have been defined. Furthermore, we determine that the Tae17 effector is a multidomain, bifunctional, peptidoglycan-degrading enzyme that has both amidase activity, which targets the sugar-peptide bonds, and lytic transglycosylase activity, which targets the peptidoglycan sugar backbone. Moreover, we show that the Tae17 transglycosylase activity is more important than amidase activity for the killing of
Escherichia coli
. This study provides molecular insight into how the T6SS allows
A. baumannii
strains to gain dominance in polymicrobial communities and thus improve their chances of survival and transmission.

IMPORTANCE

We have shown that the
Acinetobacter baumannii
T6SS effector Tae17 is a modular, bifunctional, peptidoglycan-degrading enzyme that has both lytic transglycosylase and amidase activities. Both activities contribute to the ability to degrade peptidoglycan, but the transglycosylase activity was more important for the killing of
Escherichia coli
. We have defined the specific regions of Tae17 and its cognate delivery protein VgrG17 that are necessary for the non-covalent interactions and, for the first time, identified specific amino acids essential for T6SS cargo effector delivery. This work contributes to our molecular understanding of bacterial competition strategies in polymicrobial environments and may provide a window to design new therapeutic approaches for combating infection by
A. baumannii
.
Transposon-sequencing across multiple
Mycobacterium abscessus
isolates reveals significant functional genomic diversity among strains
Authors: Akusobi Chidiebere , Choudhery Sanjeevani , Benghomari Bouchra S. , Wolf Ian D. , Singhvi Shreya , Ioerger Thomas R. , Rubin Eric J. 
Published: December 2024

ABSTRACT

Mycobacterium abscessus (Mab
) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in
Mab
have been primarily performed on reference strains. Given the growing public health threat of
Mab
infections, understanding the functional genomic differences among
Mab
clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among
Mab
strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15
M
.
abscessus
subsp.
abscessus
isolates and 6
M
.
abscessus
subsp.
massiliense
isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3,845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the
Mab
core genome. We also identified genes whose requirements were subspecies, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in
Mab
. Altogether, we find that
Mab
clinical isolates are not only genetically diverse but functionally diverse as well.

IMPORTANCE

This study investigates the genetic diversity of
Mycobacterium abscessus
(
Mab
), a bacteria known for causing difficult-to-treat infections. Researchers performed transposon-sequencing (TnSeq) on 21 different clinical isolates of
Mab
to identify essential and non-essential genes in each strain. Through this analysis, they identified core genes required for growth across all strains. Interestingly, they also identified genes whose requirement for growth or “essentiality” were subspecies, lineage, and isolate-specific. This study reveals that
Mab’
s genetic diversity translates into significant functional differences among clinical isolates. Insights from this paper lay essential groundwork for future studies exploring the biological and clinical implications of genetic diversity in
Mab
clinical isolates. Understanding this diversity could guide targeted therapies and offer new insights into managing infections caused by
Mab
, a growing public health concern.
Complete genome sequence of
Prevotella spp
. GTC17253 isolated from equine in Japan
Authors: Hayashi Masahiro , Yonetamari Jun , Muto Yoshinori , Niwa Hidekazu , Tanaka Kaori 
Published: December 2024

ABSTRACT

Prevotella
is one of the major clinical anaerobic bacteria belonging to the family
Prevotellaceae
. Herein, we report the complete genome sequence of a clinical isolate of new
Prevotella
species obtained from equine bronchial lavage fluid in Japan. The genome comprised a circular chromosome with a length of 2,948,037 bp.
Metagenome-assembled genomes from irradiated human dental plaque
Authors: Filho Romualdo M. , Mengoni Claudia , Bruno Julia S. , Fregnani Eduardo R. , Segata Nicola , Camargo Anamaria A. , Heidrich Vitor 
Published: December 2024

ABSTRACT

We provide 309 quality-controlled bacterial metagenome-assembled genomes recovered from supragingival plaque metagenomes. Samples were collected from head and neck cancer patients following radiotherapy, so the recovered genomes can be useful to investigate the effects of oral cavity irradiation on oral microbiome members.
Complete genome sequence of
Schlesneria
sp. strain DSM 10557, isolated from the leachate of an industrial compost heap
Authors: Friedrich Ines , Klassen Anna , Poehlein Anja , Hertel Robert , Daniel Rolf 
Published: December 2024

ABSTRACT

We present the complete genome of
Schlesneria
sp. DSM 10557, isolated from compost heap leakage (leachate). The genome consists of a single chromosome (7,067,087 bp) with a GC content of 56.48%. Genome-based phylogenetic analysis revealed that strain DSM 10557 is most closely related to members of the genus
Schlesneria
.
Two complete genome sequences of antimonite-oxidizing bacteria,
Mesorhizobium
sp. strain ANAO-SY3R2 and
Hydrogenophaga
sp. strain ANAO-22, isolated from mine tailing soil
Authors: Yamashita Yoriko , Hamamura Natsuko 
Published: December 2024

ABSTRACT

We report the complete genome sequences of two antimony-oxidizing bacteria,
Mesorhizobium
sp. strain ANAO-SY3R2, comprising one chromosome (4.3 Mbp) and four circular plasmids, and
Hydrogenophaga
sp. strain ANAO-22, comprising one chromosome (5.8 Mbp) and two circular plasmids. These genome information extend our understanding of physiological versatility of antimony-transforming microorganisms.