bluuebunny/crossref_metadata_2025_split huggingface dataset:
From wolves to humans: oral microbiome resistance to transfer across mammalian hosts
Authors: Podar Nicholas A. , Carrell Alyssa A. , Cassidy Kira A. , Klingeman Dawn M. , Yang Zamin , Stahler Erin A. , Smith Douglas W. , Stahler Daniel R. , Podar Mircea 
Published: February 2024

ABSTRACT

The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.

IMPORTANCE
Numerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
Annotated whole-genome sequences of fermentative and spoilage associated Bacilli and proteobacteria autochthonous to commercial cucumber fermentation
Authors: Page Clinton A. , Simpson Sheron , Pérez-Díaz Ilenys M. , Rivers Adam R. 
Published: February 2024

ABSTRACT

We report 36 whole-genome sequences, along with annotations, of fermentative (
n
= 12) and spoilage associated (
n
= 6) lactic acid bacteria,
Lysinibacillus
(
n
= 3),
Streptococcus
(
n
= 1), and Proteobacteria (
n
= 14) isolated from commercial cucumber fermentations. Fifty-three percent of the genome sequence assemblies consist of 1–4 contigs, and the remainder have fewer than 16.
Complete genome sequence of a novel papillomavirus in Siamese fighting fish (
Betta splendens
) from Trinidad and Tobago
Authors: Blake Lemar , Phillips Savage A. Carla , Soto Esteban , Oura Christopher , Brown-Jordan Arianne , Raines Clayton , Buck Christopher B. , Iwanowicz Luke R. 
Published: February 2024

ABSTRACT

Here, we announce the complete genome of a previously undescribed papillomavirus from a betta fish,
Betta splendens
. The genome is 5,671 bp with a GC content of 38.2%. Variants were detected in public databases. This genome is most similar to papillomaviruses that infect sea bass (52.9 % nucleotide identity).
Complete reference genomes of two ceftriaxone-resistant
Neisseria gonorrhoeae
strains identified in routine surveillance in Bangkok, Thailand, using Nanopore Q20+ chemistry, VolTRAX V2b, and Illumina sequencing
Authors: Sangprasert Pongsathorn , Golparian Daniel , Paopang Porntip , Girdthep Natnaree , Lawung Ratana , Gopinath Deyer , Thammawijaya Panithee , Kittiyaowanarn Rossaphorn , Unemo Magnus 
Published: February 2024

ABSTRACT

Ceftriaxone-resistant
Neisseria gonorrhoeae
strains, mostly associated with Asia, threaten gonorrhea treatment. We report the reference genomes of two ceftriaxone-resistant isolates found in routine surveillance in Bangkok, Thailand. The genomes belonged to the more antimicrobial-susceptible genomic lineage B, illustrating that both ceftriaxone-resistant strains and the mosaic
penA
-60.001 ceftriaxone-resistance determinant are spreading.
Resistance, mechanism, and fitness cost of specific bacteriophages for
Pseudomonas aeruginosa
Authors: Feng Luozhu , Chen Huanchang , Qian Changrui , Zhao Yining , Wang Weixiang , Liu Yan , Xu Mengxin , Cao Jianming , Zhou Tieli , Wu Qing 
Published: February 2024

ABSTRACT

The bacteriophage is an effective adjunct to existing antibiotic therapy; however, in the course of bacteriophage therapy, host bacteria will develop resistance to bacteriophages, thus affecting the efficacy. Therefore, it is important to describe how bacteria evade bacteriophage attack and the consequences of the biological changes that accompany the development of bacteriophage resistance before the bacteriophage is applied. The specific bacteriophage vB3530 of
Pseudomonas aeruginosa
(
P. aeruginosa
) has stable biological characteristics, short incubation period, strong
in vitro
cleavage ability, and absence of virulence or resistance genes. Ten bacteriophage-resistant strains (TL3780-R) were induced using the secondary infection approach, and the plaque assay showed that vB3530 was less sensitive to TL3780-R. Identification of bacteriophage adsorption receptors showed that the bacterial surface polysaccharide was probably the adsorption receptor of vB3530. In contrast to the TL3780 parental strain, TL3780-R is characterized by the absence of long lipopolysaccharide chains, which may be caused by base insertion of
wzy
or deletion of
galU
. It is also intriguing to observe that, in comparison to the parent strain, the bacteriophage-resistant strains TL3780-R mostly exhibited a large cost of fitness (growth rate, biofilm formation, motility, and ability to produce enhanced pyocyanin). In addition, TL3780-R9 showed increased susceptibility to aminoglycosides and chlorhexidine, which may be connected to the loss and down-regulation of
mexX
expression. Consequently, these findings fully depicted the resistance mechanism of
P. aeruginosa
to vB3530 and the fitness cost of bacteriophage resistance, laying a foundation for further application of bacteriophage therapy.

IMPORTANCE

The bacteriophage is an effective adjunct to existing antibiotic therapy; However, bacteria also develop defensive mechanisms against bacteriophage attack. Thus, there is an urgent need to deeply understand the resistance mechanism of bacteria to bacteriophages and the fitness cost of bacteriophage resistance so as to lay the foundation for subsequent application of the phage. In this study, a specific bacteriophage vB3530 of
P. aeruginosa
had stable biological characteristics, short incubation period, strong
in vitro
cleavage ability, and absence of virulence or resistance genes. In addition, we found that
P. aeruginosa
may lead to phage resistance due to the deletion of
galU
and the base insertion of
wzy
, involved in the synthesis of lipopolysaccharides. Simultaneously, we showed the association with the biological state of the bacteria after bacteria acquire bacteriophage resistance, which is extremely relevant to guide the future application of therapeutic bacteriophages.
Genomic epidemiology and antifungal-resistant characterization of
Candida auris
, Colombia, 2016–2021
Authors: Misas Elizabeth , Escandón Patricia L. , Gade Lalitha , Caceres Diego H. , Hurst Steve , Le Ngoc , Min Brian , Lyman Meghan , Duarte Carolina , Chow Nancy A. 
Published: February 2024

ABSTRACT

Since 2016, in Colombia, ongoing transmission of
Candida auris
has been reported in multiple cities. Here, we provide an updated description of
C. auris
genomic epidemiology and the dynamics of antifungal resistance in Colombia. We sequenced 99 isolates from
C. auris
cases with collection dates ranging from June 2016 to January 2021; the resulting sequences coupled with 103 previously generated sequences from
C. auris
cases were described in a phylogenetic analysis. All
C. auris
cases were clade IV. Of the 182 isolates with antifungal susceptibility data, 67 (37%) were resistant to fluconazole, and 39 (21%) were resistant to amphotericin B. Isolates predominately clustered by country except for 16 isolates from Bogotá, Colombia, which grouped with isolates from Venezuela. The largest cluster (
N
= 166 isolates) contained two subgroups. The first subgroup contained 26 isolates, mainly from César; of these, 85% (
N
= 22) were resistant to fluconazole. The second subgroup consisted of 47 isolates from the north coast; of these, 81% (
N
= 38) were resistant to amphotericin B. Mutations in the
ERG11
and
TAC1B
genes were identified in fluconazole-resistant isolates. This work describes molecular mechanisms associated with
C. auris
antifungal resistance in Colombia. Overall,
C. auris
cases from different geographic locations in Colombia exhibited high genetic relatedness, suggesting continued transmission between cities since 2016. These findings also suggest a lack of or minimal introductions of different clades of
C. auris
into Colombia.

IMPORTANCE

Candida auris
is an emerging fungus that presents a serious global health threat and has caused multiple outbreaks in Colombia. This work discusses the likelihood of introductions and local transmission of
C. auris
and provides an updated description of the molecular mechanisms associated with antifungal resistance in Colombia. Efforts like this provide information about the evolving
C. auris
burden that could help guide public health strategies to control
C. auris
spread.
Cathodic voltage-controlled electrical stimulation and betadine decontaminate nosocomial pathogens from implant surfaces
Authors: Gupta Tripti Thapa , Zumpano Bernadette , Opalinski Jacob , Ritchey Riley , Winter Nathan , Nodzo Scott R. , Canty Mary 
Published: February 2024

ABSTRACT

Periprosthetic joint infection (PJI) after total joint arthroplasty is a major concern requiring multiple surgeries and antibiotic interventions.
Staphylococcus aureus
,
Pseudomonas aeruginosa
, and
Escherichia coli
are the predominant causes of these infections. Due to biofilm formation, antibiotic treatment for patients with PJI can prolong resistance, further complicating the use of current treatments. Previous research has shown that cathodic voltage-controlled electrical stimulation (CVCES) is an effective technique to prevent/treat implant-associated biofilm infections on titanium (Ti) surfaces. This study thus evaluated the efficacy of CVCES via the use of 10% betadine alone and in combination with CVCES to eradicate lab-grown biofilms on cemented and cementless cobalt–chromium (CoCr) and Ti surfaces. CVCES treatment alone for 24 hours demonstrated no detectable CFU for
E. coli
and
P. aeruginosa
biofilms on cementless CoCr implants. In the presence of cement,
E. coli
biofilms had 10
6
CFUs/implant remaining after CVCES treatment alone; however,
P. aeruginosa
biofilms on cemented implants were reduced to below detectable limits. The use of 10% betadine treatment for 3 minutes followed by 24-hour CVCES treatment brought CFU levels to below detectable limits in
E. coli
and
P. aeruginosa
. The same was true for
S. aureus
biofilms on cementless patellofemoral implants as well as femoral and tibial implants. These treatment methods were not sufficient for eradication of
S. aureus
biofilms on cemented implants. These results suggest that CVCES alone and CVCES with 10% betadine are effective approaches to treating biofilms formed by certain bacterial species potentially leading to the treatment of PJI.

IMPORTANCE
Periprosthetic joint infections (PJIs) are problematic due to requiring multiple surgeries and antibiotic therapies that are responsible for increased patient morbidity and healthcare costs. These infections become resistant to antibiotic treatment due to the formation of biofilms on the orthopedic surfaces. Cathodic voltage-controlled electrical stimulation (CVCES) has previously been shown to be an effective technique to prevent and treat biofilm infections on different surfaces. This study shows that CVCES can increase the efficacy of 10% betadine irrigation used in debridement, antibiotics, and implant retention by 99.9% and clear infection to below detection limits. PJI treatments are at times limited, and CVCES could be a promising technology to improve patient outcomes.
Pericardiocentesis versus window formation in malignant pericardial effusion: trends and outcomes
Authors: Lee Jaeoh , Kim Kyu , Gwak Seo-Yeon , Lee Hyun-Jung , Cho Iksung , Hong Geu-Ru , Ha Jong-Won , Shim Chi Young 
Published: February 2024

ObjectivesMalignant pericardial effusion (MPE) in patients with cancer is associated with poor prognosis. This study aimed to compare clinical outcomes in patients with cancer who underwent pericardiocentesis versus pericardial window formation.MethodsIn the present study, 765 consecutive patients with cancer (mean age 58.4 years, 395 men) who underwent pericardial drainage between 2003 and 2022 were retrospectively analysed. All-cause death and MPE recurrence were compared based on the drainage method (pericardiocentesis vs pericardial window formation) and time period (period 1: 2003–2012; period 2: 2013–2022).ResultsPericardiocentesis was performed in 639 (83.5%) patients and pericardial window formation in 126 (16.5%). There was no difference in age, sex distribution, proportion of metastatic or relapsed cancer, and chemotherapy status between the pericardiocentesis and pericardial window formation groups. Difference was not found in all-cause death between the two groups (log-rank p=0.226) regardless of the period. The pericardial window formation group was associated with lower MPE recurrence than the pericardiocentesis group (6.3% vs 18.0%, log-rank p=0.001). This advantage of pericardial window formation was more significant in period 2 (18.1%vs1.3%, log-rank p=0.005). In multivariate analysis, pericardial window formation was associated with lower MPE recurrence (HR: 0.31, 95% CI: 0.15 to 0.63, p=0.001); younger age, metastatic or relapsed cancer, and positive malignant cells in pericardial fluid were associated with increased recurrence.ConclusionIn patients undergoing pericardial drainage for MPE, pericardial window formation showed mortality outcomes comparable with pericardiocentesis and was associated with lower incidence of MPE recurrence.
Improved methods to estimate days and temperature to fifty percent mortality of winter wheat (Triticum aestivum L.) under low-temperature flooding and ice encasement
Authors: Husiny Jaber , Ficht Alexandra , Whiting Rachel , Booker Helen , Hooker David C. , McElroy Michel , Lyons Eric 
Published: February 2024

Low-temperature flooding and ice encasement (LTFIE) cause variable survival of winter wheat ( Triticum aestivum L.) in Ontario, which limits the adoption of wheat into crop rotations by growers. The development of novel cultivars capable of withstanding LTFIE is a promising avenue for improvement, but the methods used to assess the survival of winter wheat under LTFIE are restricted. This study developed updated methods to determine the survival of wheat cultivars under LTFIE using controlled environments and, to our knowledge, is the first method since the 1980s to use Canadian eastern soft red winter wheat (CESRW) to conduct cold tolerance studies. Chamber-acclimated plants of AC Carberry (spring wheat control), Branson (CESRW), CM614 (CESRW), and Norstar (hardy Canadian western red winter control) cultivars were used to estimate the days (LD50) and temperature (LT50) to reach 50% mortality under ice and without ice treatments. Norstar had the longest LD50 at 33 days, Branson and CM614 had similar LD50 of 18 and 20 days, and AC Carberry did not reach an LD50 as it died early in both treatments. The LT50 of each cultivar was different; Norstar had the lowest LT50 (−13.6 °C day 0 and −13.2 °C day 7), and AC Carberry had the highest LT50 (−6.6 °C day 0 and −2.7 °C day 7). The detailed methods developed in this study were more reliable compared to older methods based on the more accurate reported LD50 and LT50 of the cultivars, therefore, these methods can be used to screen winter cereals for LTFIE in the future.
Antisymmetric tensor field and Cheshire Cat smile of the local conformal symmetry
Authors: Shapiro Ilya L. 
Published: February 2024

AbstractThe conformal version of the antisymmetric second-order tensor field in four spacetime dimensions does not have gauge invariance extensively discussed in the literature for more than half a century. Our first observation is that, when coupled to fermions, only the conformal version provides renormalizability of the theory at the one-loop level. General considerations are supported by the derivation of one-loop divergences in the fermionic sector, indicating good chances for asymptotic freedom. The arguments concerning one-loop renormalizability remain valid in the presence of self-interactions and the masses for both fermion and antisymmetric tensor fields. In the flat spacetime limit, even regardless the conformal symmetry has gone, there is an expectation to meet renormalizability in all loop orders.
Efficacy of Minimally Invasive Ulnar Superficialis Slip Resection for Unfavourable Results after Trigger Finger Release
Authors: USAMI Satoshi , KAWAHARA Sanshiro , INAMI Kohei , SONOKI Kentaro , TAKEMITSU Masashi 
Published: February 2024

Background: This study aimed to evaluate the efficacy of ulnar superficial slip resection (USSR) for improving hand function after unfavourable results after triggering finger release using a minimally invasive approach. Methods: We evaluated 17 consecutive fingers of 16 patients who complained of unfavourable outcomes after primary trigger finger release. The chief complaints of the two index and 15 middle fingers were proximal interphalangeal (PIP) joint pain during movement, flexion contracture of the PIP joint and snapping at the A2 pulley in eight, seven and two fingers, respectively. The joint arc of the active range of motion and extension loss of the PIP joint, grip strength, visual analogue score (VAS) of PIP joint pain and Quick Disability of the Arm, Shoulder and Hand were evaluated before and after surgery. Results: Thirteen fingers could release joint contracture and snapping by the USSR procedure. However, four fingers of three patients required total flexor digitorum superficialis resection to resolve the unsatisfactory conditions of the intraoperative decision. The joint arc of active range of motion and extension loss of the PIP joint, grip strength and VAS score significantly improved (mean of 16.1 months follow-up). Finally, 15 patients (88.2%) were satisfied with the symptom relief outcomes. Conclusions: USSR is an effective and satisfactory procedure for unfavourable conditions after trigger finger release, including PIP joint pain, joint contracture and snapping at the A2 pulley. Level of Evidence: Level IV (Therapeutic)
Abstract A069: The molecular landscape of injury-induced mammary epithelial cell fate switching
Authors: Vallmajo-Martin Queralt , Lytle Nikki K. , Murali Divya , Srinivasan Sumana , Ma Zhibo , Mukund Kavitha , Dravis Christopher , Zamora Liliana , Peterson Ana , Khramtsova Galina , Olopade Funmi , Subramaniam Shankar , Wahl Geoffrey M. 
Published: February 2024

Abstract
The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression.
Citation Format: Queralt Vallmajo-Martin, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A069.