bluuebunny/crossref_metadata_2025_split huggingface dataset:
The L-lactate dehydrogenases of
Pseudomonas aeruginosa
are conditionally regulated but both contribute to survival during macrophage infection
Authors: Florek Lindsey C. , Lin Xi , Lin Yu-Cheng , Lin Min-Han , Chakraborty Arijit , Price-Whelan Alexa , Tong Liang , Rahme Laurence , Dietrich Lars E. P. 
Published: August 2024

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it can serve as a carbon source for
P. aeruginosa
in the diverse settings that it inhabits. In this study, we evaluate the production and use of two redundant
P. aeruginosa
L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses
lldD
and identify a new transcription factor, called LldS, that activates
lldA
; these distinct regulators and the genomic contexts of
lldD
and
lldA
contribute to their differential expression. We demonstrate that the
lldD
and
lldA
genes are conditionally controlled in response to lactate isomers as well as to glycolate and ɑ-hydroxybutyrate, which, like lactate, are ɑ-hydroxycarboxylates. We also show that
lldA
is induced when iron availability is low. Our examination of
lldD
and
lldA
expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays reveal that both
lldD
and
lldA
contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during
P. aeruginosa–
eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote
P. aeruginosa
’s success as a resident of contaminated environments and animal hosts.

IMPORTANCE

Pseudomonas aeruginosa
is a major cause of lung infections in people with cystic fibrosis, of hospital-acquired infections, and of wound infections. It consumes L-lactate, which is found at substantial levels in human blood and tissues. In this study, we investigated the spatial regulation of two redundant enzymes, called LldD and LldA, which enable L-lactate metabolism in
P. aeruginosa
biofilms. We uncovered mechanisms and identified compounds that control the preference of
P. aeruginosa
for LldD versus LldA. We also showed that both enzymes contribute to its ability to survive within macrophages, a behavior that is thought to augment the chronicity and recalcitrance of infections. Our findings shed light on a key metabolic strategy used by
P. aeruginosa
and have the potential to inform the development of therapies targeting bacterial metabolism during infection.
Gut bacterial community profile of frugivorous bats from Cathedral Cave in Cavinti, Laguna, Philippines
Authors: Datul Bonie B. , Flores Ronilo Jose D. , Montecillo Andrew D. , De Leon Marian P. 
Published: August 2024

ABSTRACT

Here we report the 16S rRNA gene amplicon analysis of the gut microbiota of three frugivorous cave bat species from the Cathedral Cave in Cavinti, Laguna, Philippines. Among the bat species, the most abundant phyla are Proteobacteria and Firmicutes D.
Draft genome sequence of rhamnolipid-producing bacteria
Thermoanaerobacter thermocopriae
strain CM-CNRG TB177 isolated from an oil reservoir in Mexico
Authors: Segovia Veronica , Martínez Pedro , Hernández-Gama Regina 
Published: August 2024

ABSTRACT

The draft genome of
Thermoanaerobacter thermocopriae
CM-CNRG TB177 isolated from an oil reservoir in Mexico was determined and annotated. The organism is a thermophilic and strict anaerobe bacterium that produces rhamnolipids, using glucose as a carbon source. The predicted genome size is 2,496,169 bp and 2,550 genes.
Complete genome sequence of
Klebsiella pneumoniae
RX.G5M15, a methanol-metabolizing strain recovered from the sole of a shoe
Authors: Xu D. Y. , Leung K. M. , Lai G. K. K. , Leung F. C. C. , Griffin S. D. J. 
Published: August 2024

ABSTRACT

The methanol-metabolizing strain
Klebsiella pneumoniae
RX.G5M15 was isolated from the sole of a shoe in Hong Kong. Its complete genome, a single chromosome and two plasmids totaling 5,381,940 bp (G+C 57.43%), was established through the hybrid assembly.
Draft genome sequence of
Priestia megaterium
strain IMGN3 derived from soil
Authors: Choi Sejin , Jung Hoseong , Kim Yeongjun , Han Jeong A. , Kim Eun Yu , Lee Ho-Seok 
Published: August 2024

ABSTRACT

Priestia megaterium
sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic studies, particularly focusing on plant growth promotion and biocontrol.
Two draft genome assemblies of
Staphylococcus aureus
strains isolated from a cheek swab of a healthy female participant
Authors: Kula Alex , Jablonska Sandra , Avalos Lexi , Jensen Tyler , Appleberry Helen , Putonti Catherine 
Published: August 2024

ABSTRACT

Staphylococcus aureus
is an opportunistic pathogen often commensal within the nasal and oral cavities. Here we present the genomes of
S. aureus
O139-S and O139-NS, both isolated from the cheek swab of a healthy female participant. While found in the same sample, the two strains displayed distinct colony morphologies.
Epigenetic programming of host lipid metabolism associated with resistance to TST/IGRA conversion after exposure to
Mycobacterium tuberculosis
Authors: Dill-McFarland Kimberly A. , Simmons Jason D. , Peterson Glenna J. , Nguyen Felicia K. , Campo Monica , Benchek Penelope , Stein Catherine M. , Vaisar Tomas , Mayanja-Kizza Harriet , Boom W. Henry , Hawn Thomas R. 
Published: August 2024

ABSTRACT

Mycobacterium tuberculosis
(Mtb) exposure leads to a range of outcomes including clearance, latent TB infection (LTBI), and pulmonary tuberculosis (TB). Some heavily exposed individuals resist tuberculin skin test (TST) and interferon-gamma (IFNγ) release assay (IGRA) conversion (RSTR), which suggests that they employ IFNγ-independent mechanisms of Mtb control. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. Chromatin accessibility did not differ between uninfected RSTR and LTBI monocytes. By contrast, methylation significantly differed at 174 CpG sites and across 63 genomic regions. Consistent with previous transcriptional findings in this cohort, differential methylation was enriched in lipid- and cholesterol-associated pathways including the genes APOC3, KCNQ1, and PLA2G3. In addition, methylation was enriched in Hippo signaling, which is associated with cholesterol homeostasis and includes CIT and SHANK2. Lipid export and Hippo signaling pathways were also associated with gene expression in response to Mtb in RSTR as well as IFN stimulation in monocyte-derived macrophages (MDMs) from an independent healthy donor cohort. Moreover, serum-derived high-density lipoprotein from RSTR had elevated ABCA1-mediated cholesterol efflux capacity (CEC) compared to LTBI. Our findings suggest that resistance to TST/IGRA conversion is linked to regulation of lipid accumulation in monocytes, which could facilitate early Mtb clearance among RSTR subjects through IFNγ-independent mechanisms.

IMPORTANCE

Tuberculosis (TB) remains an enduring global health challenge with millions of deaths and new cases each year. Despite recent advances in TB treatment, we lack an effective vaccine or a durable cure. While heavy exposure to
Mycobacterium tuberculosis
often results in latent TB latent infection (LTBI), subpopulations exist that are either resistant to infection or contain Mtb with interferon-gamma (IFNγ)-independent mechanisms not indicative of LTBI. These resisters provide an opportunity to investigate the mechanisms of TB disease and discover novel therapeutic targets. Here, we compare monocyte epigenetic profiles of RSTR and LTBI from a Ugandan household contact cohort. We identify methylation signatures in host lipid and cholesterol pathways with potential relevance to early TB clearance before the sustained IFN responses indicative of LTBI. This adds to a growing body of literature linking TB disease outcomes to host lipids.
Deeply branching
Bacillota
species exhibit atypical Gram-negative staining
Authors: Choi Jessica K. , Poudel Saroj , Yee Nathan , Goff Jennifer L. 
Published: August 2024

ABSTRACT

The Gram staining method differentiates bacteria based on their cell envelope structure, with the monoderm and diderm cell envelope types traditionally being synonymous with Gram-positive and Gram-negative stain results, respectively. Monoderms have a single phospholipid membrane surrounded by a thick layer of peptidoglycan, while diderms have a lipopolysaccharide outer membrane exterior to a thin peptidoglycan layer. The
Bacillota
(formerly
Firmicutes
) phylum has members with both cell wall types, and recent phylogenetic analyses have shown that monoderm
Bacillota
evolved from diderm ancestors on multiple occasions. Here, we compiled Gram staining and ultrastructural data for
Bacillota
species with complete genomes to further investigate the evolution of Gram-positive and Gram-negative cell wall types. The results indicate that many deeply branching lineages at the root of
Bacillota
phylum stain Gram-negative but do not harbor genes for outer membrane protein or lipopolysaccharide biosynthesis. Phylogenetic reconstructions suggest that several deeply branching
Bacillota
species have retained a thin peptidoglycan layer in their cell walls, which was inherited from a diderm ancestor. Taxa with this atypical Gram-negative-staining cell wall structure include the thermophilic anaerobe
Symbiobacterium thermophilum
and members of the
Desulfotomaculia, Syntrophamonadia, Desulfitobacteriia, Thermosediminibacteria,
and
Thermoanaerobacteria
. Using Gram-staining results as a proxy for cell wall thickness, our analysis indicates that several independent peptidoglycan thickening events may have occurred in the evolution of the Gram-positive cell envelope.

IMPORTANCE

In this study, we examined the evolution of bacterial cell envelopes, specifically focusing on Gram-positive and Gram-negative cell wall types in the
Bacillota
phylum. Our results indicate that certain bacteria can stain Gram-negative despite having a monoderm cell wall structure, thus challenging the conventional interpretation of Gram-staining results. Our observations also question the assumption that Gram-negative staining is always indicative of a diderm structure. These findings have broader implications for understanding how and when cell walls thicken during the evolution of bacterial cell envelopes.
Genotypic characterization and antimicrobial susceptibility of human
Campylobacter jejuni
isolates in Southern Spain
Authors: Fernández-Palacios Pablo , Galán-Sánchez Fátima , Casimiro-Soriguer Carlos S. , Jurado-Tarifa Estefanía , Arroyo Federico , Lara María , Chaves J. Alberto , Dopazo Joaquín , Rodríguez-Iglesias Manuel A. 
Published: August 2024

ABSTRACT

Campylobacter jejuni
is the main cause of bacterial gastroenteritis and a public health problem worldwide. Little information is available on the genotypic characteristics of human
C. jejuni
in Spain. This study is based on an analysis of the resistome, virulome, and phylogenetic relationship, antibiogram prediction, and antimicrobial susceptibility of 114 human isolates of
C. jejuni
from a tertiary hospital in southern Spain from October 2020 to June 2023. The isolates were sequenced using Illumina technology, and a bioinformatic analysis was subsequently performed. The susceptibility of
C. jejuni
isolates to ciprofloxacin, tetracycline, and erythromycin was also tested. The resistance rates for each antibiotic were 90.3% for ciprofloxacin, 66.7% for tetracycline, and 0.88% for erythromycin. The fluoroquinolone resistance rate obtained is well above the European average (69.1%). CC-21 (
n
= 23), ST-572 (
n
= 13), and ST-6532 (
n
= 13) were the most prevalent clonal complexes (CCs) and sequence types (STs). In the virulome, the
cadF, ciaB
, and
cdtABC
genes were detected in all the isolates. A prevalence of 20.1% was obtained for the genes
wlaN
and
cstIII
, which are related to the pathogenesis of Guillain-Barré syndrome (GBS). The prevalence of the main antimicrobial resistance markers detected were CmeABC (92.1%), RE-cmeABC (7.9%), the T86I substitution in
gyrA
(88.9%),

bla
OXA-61

(72.6%)
, tet(O)
(65.8%), and

ant (
6
)-Ia

(17.1%). High antibiogram prediction rates (>97%) were obtained, except for in the case of the erythromycin-resistant phenotype. This study contributes significantly to the knowledge of
C. jejuni
genomics for the prevention, treatment, and control of infections caused by this pathogen.

IMPORTANCE

Despite being the pathogen with the greatest number of gastroenteritis cases worldwide,
Campylobacter jejuni
remains a poorly studied microorganism. A sustained increase in fluoroquinolone resistance in human isolates is a problem when treating
Campylobacter
infections. The development of whole genome sequencing (WGS) techniques has allowed us to better understand the genotypic characteristics of this pathogen and relate them to antibiotic resistance phenotypes. These techniques complement the data obtained from the phenotypic analysis of
C. jejuni
isolates. The zoonotic transmission of
C. jejuni
through the consumption of contaminated poultry supports approaching the study of this pathogen through “One Health” approach. In addition, due to the limited information on the genomic characteristics of
C. jejuni
in Spain, this study provides important data and allows us to compare the results with those obtained in other countries.
Investigating the role of
MAB_1915
in intrinsic resistance to multiple drugs in
Mycobacterium abscessus
Authors: Yusuf Buhari , Wang Shuai , Alam Md Shah , Zhang Jingran , Liu Zhiyong , Lu Ziwen , Ding Jie , Chiwala Gift , Gao Yamin , Fang Cuiting , Khan Shahzad Akbar , Tian Xirong , Islam Md Mahmudul , Hameed H. M. Adnan , Maslov Dmitry A. , Zhong Nanshan , Hu Jinxing , Zhang Tianyu 
Published: August 2024

ABSTRACT

The increasing clinical significance of
Mycobacterium abscessus
is owed to its innate high-level, broad-spectrum resistance to antibiotics and therefore rapidly evolves as an important human pathogen. This warrants the identification of novel targets for aiding the discovery of new drugs or drug combinations to treat
M. abscessus
infections. This study is inspired by the drug-hypersensitive profile of a mutant
M. abscessus
(U14) with transposon insertion in
MAB_1915
. We validated the role of
MAB_1915
in intrinsic drug resistance in
M. abscessus
by constructing a selectable marker-free in-frame deletion in
MAB_1915
and complementing the mutant with the same or extended version of the gene and then followed by drug susceptibility testing. Judging by the putative function of MAB_1915, cell envelope permeability was studied by ethidium bromide accumulation assay and susceptibility testing against dyes and detergents. In this study, we established genetic evidence of the role of
MAB_1915
in intrinsic resistance to rifampicin, rifabutin, linezolid, clarithromycin, vancomycin, and bedaquiline. Disruption of
MAB_1915
has also been observed to cause a significant increase in cell envelope permeability in
M. abscessus
. Restoration of resistance is observed to depend on at least 27 base pairs upstream of the coding DNA sequence of
MAB_1915
. MAB_1915 could therefore be associated with cell envelope permeability, and hence its role in intrinsic resistance to multiple drugs in
M. abscessus
, which presents it as a novel target for future development of effective antimicrobials to overcome intrinsic drug resistance in
M. abscessus
.

IMPORTANCE

This study reports the role of a putative fadD (MAB_1915) in innate resistance to multiple drugs by
M. abscessus
, hence identifying MAB_1915 as a valuable target and providing a baseline for further mechanistic studies and development of effective antimicrobials to check the high level of intrinsic resistance in this pathogen.
Evaluating decision regret after extremely preterm birth
Authors: Belden Laura , Kaempf Joseph , Mackley Amy , Kernan-Schloss Finley , Chen Chiayi , Sturtz Wendy , Tomlinson Mark W , Guillen Ursula 
Published: August 2024

Objectives
Little is known about decision regret following extremely premature birth. We assessed decision regret in women who delivered an extremely premature infant, comparing decision regret scores based on resuscitation decision.

Methods
Electronic survey assessment of decision regret using a validated tool included women who delivered at 22–25 completed weeks of gestation at two hospitals 2004–2019. Comparison of ‘active care’, ‘comfort care’ and ‘other’ groups was quantified and comments reviewed.

Results
442 of 787 (56%) eligible women were contacted, 242 of 442 (55%) completed surveys, response rate 242 of 787 (31%). Women not contacted were younger (p=0.0001) and/or delivered in an earlier year (p=0.002). There was a higher percentage of white women who completed the survey (p=0.004). Decision regret was elevated in all groups, varied widely, but was lower in ‘active care’ compared with ‘comfort care’ (Decision Regret Score 14 vs 39, p<0.0001). Lower decision regret occurred in women who recalled a prenatal consult (p=0.014) or identified as the primary decision-maker compared with women who perceived the doctor had a major role (p=0.02) or made the decision (p<0.0001). Lower decision regret occurred in women whose infant was alive at survey completion compared with women whose infant died in the hospital (p<0.0001) or after discharge (p=0.01).

Conclusions
Decision regret was elevated in all groups. Women who recalled prenatal consultation, identified as the primary decision-maker, chose intensive care and/or whose infant survived had lower regret scores.

Clinical trial registration

NCT04074525
.
Medical malpractice claims and state medical board complaints among United States neurointerventionalists
Authors: Fargen Kyle M , Iyer Ankitha M , Mocco J , Fifi Johanna T , Dabus Guilherme , Fraser Justin F , Hirsch Joshua A , Jayaraman Mahesh V 
Published: August 2024

BackgroundSurgeons are at high risk for malpractice claims, which can significantly impact physician quality of life and risk of burnout. There are few published data reporting the incidence, outcomes, and repercussions of malpractice lawsuits on neurointerventionalists.MethodsA survey of senior members of the United States Society of Neurointerventional Surgery (SNIS) was performed to study malpractice litigation and medical board complaints.ResultsIn total, 173 responses were obtained. Of the total sample, 66 respondents (38.2%) reported being subject to a total of 84 malpractice claims during independent practice over the last 10 years, amounting to a malpractice claim annual incidence of 5.9% (84 cases per 1423 years of practice). The majority of claims involved either brain aneurysms (34.5%) or arteriovenous malformations (23.8%), with most alleging either intra-procedural (38.1%) or post-procedural (27.3%) complications. Only three of the 58 claims that had concluded ended in court settlements (5.2%). The majority (78.3%) of claims resulted in no consequences to physician practice. Fourteen respondents (8.1%) reported being subject to a total of 16 state medical board complaints over the previous decade, with most resulting in no significant repercussions.ConclusionMalpractice claims are common among neurointerventionalists and often cause significant physician distress, yet most result in claims being dropped or no paid damages, and the majority conclude without practice repercussions for the named physicians.
Magnitude of systolic blood pressure reduction following endovascular treatment and clinical outcomes in acute large artery occlusion stroke
Authors: Huang Xianjun , Ding Xianhui , Wang Hao , Cai Qiankun , Xu Junfeng , Li Zibao , Yang Qian , Zhou Zhiming , Xu Jie 
Published: August 2024

BackgroundThe impact of lowering systolic blood pressure (SBP) following endovascular treatment (EVT) in acute large vessel occlusion stroke (LVOS) patients remains unclear. We aimed to explore the effect of the magnitude of SBP reduction (SBPr) after EVT on outcomes in LVOS patients.MethodsWe consecutively registered patients at three comprehensive stroke centres who had experienced EVT as a result of acute anterior circulation LVOS. SBPr was calculated as follows: (baseline SBP−mean SBP/baseline SBP)×100%. The 90-day modified Rankin Scale score ranging from 0 to 2 was defined as a favourable functional outcome. Based on CT scans obtained within 24 hours after procedure, symptomatic intracranial haemorrhage (sICH) was assessed according to the criteria of the European Cooperative Acute Stroke Study III.ResultsWe enrolled 1080 patients, of which 908 (84.1%) had successful recanalisation. In the overall cohort, SBPr was correlated with lower odds of sICH (SBPr±10% as a reference, 20%–30%: OR 0.460; 95% CI: 0.245 to 0.864; p=0.016; >30%: OR 0.304; 95% CI 0.123 to 0.749; p=0.010). In patients who achieved successful reperfusion, SBPr>30% was correlated with higher odds of a poor outcome (SBPr±10% as a reference, OR 2.150; 95% CI 1.268 to 3.645; p=0.004) and SBPr has a similar tendency towards reducing the incidence of sICH. In the subgroup analyses, baseline Alberta Stroke Programme Early CT (ASPECT) score (pinteract=0.024) modified the effect of SBPr on the 90-day outcome.ConclusionAmong patients with EVT, a significant drop in SBP may be related to a poor functional outcome and a reduced incidence of sICH. Baseline ASPECT score may be an important interacting factor in the association of SBPr with the 90-day outcome. This study provides new insights for individualised BP management in patients with EVT.
The influence of experimental conditions on absolute beam density measurements for NH$$_3$$ and H
Authors: Pandey Rahul , Wu Lok Yiu , Morris Lucy , Regan Paul , Heazlewood Brianna R. 
Published: August 2024

Abstract
In order to establish important reaction properties, such as rate coefficients, it is often necessary to know the number of reactants that are present in an interaction region. The absolute number densities of pulsed supersonic molecular (NH$$_3$$

3

) and atomic (H) beams are reported using a laser-based detection method, under a range of experimental conditions including photolysis, Zeeman deceleration, and magnetic focusing. Time-averaged densities of (3.6 ± 2.7) $$\times $$
×
10$$^4$$

4

cm$$^{-3}$$

-
3

are reported for successfully Zeeman-decelerated and magnetically focused H atoms, generated by the photodissociation of precursor NH$$_3$$

3

molecules. Without the magnetic guide components in the beamline, the density of the target radicals of interest is somewhat lower, at (2.5 ± 1.8) $$\times $$
×
10$$^4$$

4

cm$$^{-3}$$

-
3

. The average density of the undecelerated H atom beam is approximately an order of magnitude higher (2.9 ± 1.9) $$\times $$
×
10$$^5$$

5

cm$$^{-3}$$

-
3

, with the average density of the molecular ammonia beam over two orders of magnitude higher again (5.1 ± 2.9) $$\times $$
×
10$$^7$$

7

cm$$^{-3}$$

-
3

. The average number densities measured for the two different species of interest in this work span more than three orders of magnitude. These findings highlight the need for accurate and precise experimental measurements of number densities—for each species of interest, under the appropriate experimental conditions—before doing absolute rate coefficient calculations.

Graphical abstract