bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro
activity of cefiderocol, a siderophore cephalosporin, against carbapenem-resistant hypervirulent
Klebsiella pneumoniae
in China
Authors: Zhao Jiankang , Pu Danni , Li Ziyao , Liu Xinmeng , Zhang Yulin , Wu Yongli , Zhang Feilong , Li Chen , Zhuo Xianxia , Lu Binghuai , Cao Bin 
Published: November 2023

ABSTRACT

Cefiderocol is a siderophore cephalosporin that binds ferric iron and utilizes iron transporters to cross the cell membrane. Hypervirulent
Klebsiella pneumoniae
(hvKp) is known to produce more siderophores; in this case, the uptake of cefiderocol may be decreased. Therefore, the objective of this study was to evaluate the
in vitro
activity of cefiderocol against hvKp isolates. A total of 320 carbapenem-resistant
K. pneumoniae
(CRKp) isolates were collected in China between 2014 and 2022, including 171 carbapenem-resistant hvKp (CR-hvKp) and 149 carbapenem-resistant classical
K. pneumoniae
(CR-cKp). Quantitative detection of siderophores showed that the average siderophore production of CR-hvKp (234.6 mg/L) was significantly higher than that of CR-cKp (68.9 mg/L,
P
< 0.001). The overall cefiderocol resistance rate of CR-hvKp and CR-cKp was 5.8% (10/171) and 2.7% (4/149), respectively. The non-susceptible rates of both cefiderocol and siderophore production of CR-hvKp isolates were higher than those of CR-cKp in either NDM-1- or KPC-2-producing groups. The MIC90 and MIC50 for CR-hvKp and CR-cKp were 8 mg/L and 2 mg/L and 4 mg/L and 1 mg/L, respectively. The cumulative cefiderocol MIC distribution for CR-hvKp was significantly lower than that of CR-cKp isolates (
P
= 0.003). KL64 and KL47 consisted of 53.9% (83/154) and 75.7% (53/70) of the ST11 CR-hvKp and CR-cKp, respectively, and the former had significantly higher siderophore production. In summary, cefiderocol might be less effective against CR-hvKp compared with CR-cKp isolates, highlighting the need for caution regarding the prevalence of cefiderocol-resistant
K. pneumoniae
strains, particularly in CR-hvKp isolates.
MmoD regulates soluble methane monooxygenase and methanobactin production in
Methylosinus trichosporium
OB3b
Authors: Peng Peng , Yang Junwon , DiSpirito Alan A. , Semrau Jeremy D. 
Published: November 2023

ABSTRACT

Methane oxidation by aerobic methanotrophs is well known to be strongly regulated by the availability of copper, i.e., the “copper switch.” That is, there are two forms of methane monooxygenase: a cytoplasmic or soluble methane monooxygenase (sMMO) and a membrane-bound or particulate methane monooxygenase (pMMO). sMMO is only expressed and active in the absence of copper, while pMMO requires copper. Previous work has also shown that one gene in the operon of the soluble methane monooxygenase
—mmoD
—also plays a critical role in the “copper switch,” but its function is still vague. Herein, we show that MmoD is not needed for the expression of genes in the sMMO gene cluster but is critical for the formation of sMMO polypeptides and sMMO activity in
Methylosinus trichosporium
OB3b, indicating that MmoD plays a key post-transcriptional role in the maturation of sMMO. Furthermore, data also show that MmoD controls the expression of methanobactin, a copper-binding compound used by some methanotrophs, including
M. trichosporium
OB3b, for copper sequestration. Collectively, these results provide greater insights into the components of the “copper switch” and provide new strategies to manipulate methanotrophic activity.

IMPORTANCE
Aerobic methanotrophs play a critical role in the global carbon cycle, particularly in controlling net emissions of methane to the atmosphere. As methane is a much more potent greenhouse gas than carbon dioxide, there is increasing interest in utilizing these microbes to mitigate future climate change by increasing their ability to consume methane. Any such efforts, however, require a detailed understanding of how to manipulate methanotrophic activity. Herein, we show that methanotrophic activity is strongly controlled by MmoD, i.e., MmoD regulates methanotrophy through the post-transcriptional regulation of the soluble methane monooxygenase and controls the ability of methanotrophs to collect copper. Such data are likely to prove quite useful in future strategies to enhance the use of methanotrophs to not only reduce methane emissions but also remove methane from the atmosphere.
Reduced toxin binding associated with resistance to Vip3Aa in the corn earworm (
Helicoverpa zea
)
Authors: Kerns Dawson D. , Yang Fei , Kerns David L. , Stewart Scott D. , Jurat-Fuentes Juan Luis 
Published: November 2023

ABSTRACT

Transgenic corn and cotton that express Cry and Vip insecticidal proteins from the bacterium,
Bacillus thuringiensis
(Bt), have been valuable tools for the management of lepidopteran pests. In 2019, a Vip3Aa-resistant strain of
Helicoverpa zea
(CEW-Vip-RR) was isolated from F
2
screens of field populations in Texas. Characterizing the resistance mechanism in this strain is important for predicting the sustained efficacy of current commercial Bt traits and guiding the development of future transgenic traits. Resistance to insecticidal proteins in Bt traits is commonly associated with reduced toxin binding, with the exception of Vip3Aa resistance being associated to altered proteolytic processing in the insect host gut. Therefore, Vip3Aa protoxin processing was tested by incubation with midgut fluids from CEW-Vip-RR relative to a susceptible strain (CEW-SS). Finding no significant processing differences, alterations in Vip3Aa binding were tested by comparing binding of radiolabeled and biotinylated Vip3Aa toxin to midgut brush border membrane vesicles (BBMV) from CEW-Vip-RR and CEW-SS larvae. Specific Vip3Aa binding to CEW-Vip-RR BBMV in these experiments was consistently reduced when compared with CEW-SS BBMV. These results support that an altered Vip3Aa-receptor is associated with resistance in CEW-Vip-RR. Understanding this resistance mechanism could have important implications for resistance management decisions, considering widespread Cry1 and Cry2 resistance in
H. zea
populations.

IMPORTANCE

Helicoverpa zea
is a major crop pest in the United States that is managed with transgenic corn and cotton that produce insecticidal proteins from the bacterium,
Bacillus thuringiensis
(Bt). However,
H. zea
has evolved widespread resistance to the Cry proteins produced in Bt corn and cotton, leaving Vip3Aa as the only plant-incorporated protectant in Bt crops that consistently provides excellent control of
H. zea
. The benefits provided by Bt crops will be substantially reduced if widespread Vip3Aa resistance develops in
H. zea
field populations. Therefore, it is important to identify resistance alleles and mechanisms that contribute to Vip3Aa resistance to ensure that informed resistance management strategies are implemented. This study is the first report of reduced binding of Vip3Aa to midgut receptors associated with resistance.
Elizabethkingia anophelis
outer membrane vesicles as a novel vaccine candidate against infection: insights into immune response and potential for passive immunity
Authors: Yang Ya-Sung , Chen Hung-Jui , Chen Xiao-Chun , Tang Hung-Jen , Chang Fang-Ju , Huang Yun-Ling , Pan Yu-Ling , Kesavan Dinesh Kumar , Chen Huan-Yuan , Shang Hung-Sheng , Kuo Shu-Chen , Chen Te-Li , Chiang Ming-Hsien 
Published: November 2023

ABSTRACT

The emerging pathogen
Elizabethkingia anophelis
poses severe threats to public health and has caused several outbreaks. The efficacy of antimicrobials is limited due to the pathogen’s innate multi-drug resistance to most antibiotics. Hence, novel approaches to treat
E. anophelis
infections are urgently needed. This study evaluated the immunogenic and protective effects of the imipenem-induced outer membrane vesicles (iOMVs) of
E. anophelis
as a vaccine. Mice immunized with iOMVs were completely protected during lethal-dose challenges. Passive immunization with hyperimmune sera and splenocytes conferred protection against lethal pneumonia. iOMVs also induced Th1-, Th2-, and Th17-driven immune responses. Immunization with iOMVs increased IgG1 and IgG2c isotype levels, and the antisera from immunized mice promoted complement-dependent bactericidal and opsonophagocytic activities against
E. anophelis
C08. Our study suggests that
E. anophelis
iOMVs are a promising vaccine candidate for preventing and treating
E. anophelis
infections and provides insights into the use of OMVs in vaccine development against the clinically emergent
E. anophelis
.

IMPORTANCE

Elizabethkingia anophelis
, a Gram-negative pathogen, causes infections such as bacteraemia, pneumonia, and neonatal meningitis. The pathogen resists most antimicrobial classes, making novel approaches urgently needed. In natural settings, Gram-negative bacteria secrete outer membrane vesicles (OMVs) that carry important molecules in the bacterial life cycle. These OMVs are enriched with proteins involved in virulence, survival, and carbohydrate metabolism, making them a promising source for vaccine development against the pathogen. This study investigated the efficacy of imipenem-induced OMVs (iOMVs) as a vaccine candidate against
E. anophelis
infection in a mouse pneumonia model. Mice immunized with iOMVs were completely protected during lethal-dose challenges. Passive immunization with hyperimmune sera and splenocytes conferred protection against lethal pneumonia. Further investigation is needed to understand the mechanisms underlying the protective effects of iOMV-induced passive immunity, such as the action on specific antibody subclasses or T cell subsets.
In situ
cell division and mortality rates of SAR11, SAR86,
Bacteroidetes
, and
Aurantivirga
during phytoplankton blooms reveal differences in population controls
Authors: Brüwer Jan D. , Orellana Luis H. , Sidhu Chandni , Klip Helena C. L. , Meunier Cédric L. , Boersma Maarten , Wiltshire Karen H. , Amann Rudolf , Fuchs Bernhard M. 
Published: November 2023

ABSTRACT

Net growth of microbial populations, that is, changes in abundances over time, can be studied using 16S rRNA fluorescence
in situ
hybridization (FISH). However, this approach does not differentiate between mortality and cell division rates. We used FISH-based image cytometry in combination with dilution culture experiments to study net growth, cell division, and mortality rates of four bacterial taxa over two distinct phytoplankton blooms: the oligotrophs SAR11 and SAR86, and the copiotrophic phylum
Bacteroidetes
, and its genus
Aurantivirga
. Cell volumes, ribosome content, and frequency of dividing cells (FDC) co-varied over time. Among the three, FDC was the most suitable predictor to calculate cell division rates for the selected taxa. The FDC-derived cell division rates for SAR86 of up to 0.8/day and
Aurantivirga
of up to 1.9/day differed, as expected for oligotrophs and copiotrophs. Surprisingly, SAR11 also reached high cell division rates of up to 1.9/day, even before the onset of phytoplankton blooms. For all four taxonomic groups, the abundance-derived net growth (−0.6 to 0.5/day) was about an order of magnitude lower than the cell division rates. Consequently, mortality rates were comparably high to cell division rates, indicating that about 90% of bacterial production is recycled without apparent time lag within 1 day. Our study shows that determining taxon-specific cell division rates complements omics-based tools and provides unprecedented clues on individual bacterial growth strategies including bottom–up and top–down controls.

IMPORTANCE

The growth of a microbial population is often calculated from their numerical abundance over time. However, this does not take cell division and mortality rates into account, which are important for deriving ecological processes like bottom–up and top–down control. In this study, we determined growth by numerical abundance and calibrated microscopy-based methods to determine the frequency of dividing cells and subsequently calculate taxon-specific cell division rates
in situ
. The cell division and mortality rates of two oligotrophic (SAR11 and SAR86) and two copiotrophic (
Bacteroidetes
and
Aurantivirga
) taxa during two spring phytoplankton blooms showed a tight coupling for all four taxa throughout the blooms without any temporal offset. Unexpectedly, SAR11 showed high cell division rates days before the bloom while cell abundances remained constant, which is indicative of strong top–down control. Microscopy remains the method of choice to understand ecological processes like top–down and bottom–up control on a cellular level.
Harnessing multiplex crRNA enables an amplification-free/CRISPR-Cas12a-based diagnostic methodology for
Nosema bombycis
Authors: Zhang Huarui , Zhao Huijuan , Cao Lu , Yu Bin , Wei Junhong , Pan Guoqing , Bao Jialing , Zhou Zeyang 
Published: November 2023

ABSTRACT

Nosema bombycis
is transmitted horizontally and vertically from infected female moths to progeny eggs, bringing substantial economic losses to sericulture production. Timely and accurate detection of
N. bombycis
can effectively block the spread of silkworm pébrine disease, which is of great significance for its prevention and control. In this study, we established a multiplex-crRNA CRISPR/Cas12a nucleic acid amplification-free detection method for
N. bombycis
.. Specificity and sensitivity assessments confirmed that this method specifically detects
N. bombycis
without cross-reacting with other pathogens. It can detect
N. bombycis
at levels as low as 2 pg of genomic DNA. This method could also provide information on pathogen quantification, which will be important for in-field applications and promotions.

IMPORTANCE

The multiplex-crRNA CRISPR/Cas12a detection method saves hands-on time, reduces the risk of aerosol pollution, and can be directly applied to detecting silkworms infected with
Nosema bombycis
. This study provides a new approach for the inspection and quarantine of silkworm pébrine disease in sericulture and provides a new method for the detection of other pathogens.
Caregiver knowledge and attitudes relating to paediatric pneumonia and antimicrobial stewardship: a qualitative study
Authors: Huang Nelson , Murphy Lara , Kandasamy Sujane , Wahi Gita , Pernica Jeffrey M 
Published: November 2023

ObjectiveThe objective of this study was to understand caregiver perspectives and experiences relating to the treatment of paediatric community-acquired pneumonia (CAP).Design, setting and patientsThis was a phenomenological qualitative study involving interviews with caregivers of young children in Hamilton, Ontario. Caregivers were asked open-ended questions relating to germ theory, pneumonia and the role of antibiotic treatment. The principles of conventional content analysis guided the coding and synthesis of the transcribed interviews.ResultsEleven caregivers were interviewed. Many knew that antibiotics were not effective against all types of infections and stated that there was an increased risk of developing resistance with frequent use. However, there were misconceptions that probiotics effectively mitigated antibiotic side effects, and few were familiar with the potential long-term consequences of antibiotic use in children.There was variability in the perceived severity of paediatric CAP. Some participants thought that antibiotic treatment would accelerate recovery and prevent caregivers from feeling helpless. However, others also thought it was inappropriate for physicians to prescribe antibiotics solely to make the caregiver feel better. Many caregivers also felt strongly that clinical follow-up and discussions on treatment risks/benefits would be desirable to counteract feelings of helplessness that result from being sent home without a prescription.ConclusionRecognising that parents may have misperceptions about antibiotic use for CAP (and may seek antibiotics without strong rationale) can inform clinicians’ efforts to better educate and support caregivers in the emergency department. Care strategies informed by caregiver experiences can improve parent–provider communication and reduce antibiotic misuse
Liquid embolic surface area as a predictor of chronic subdural hematoma resolution in middle meningeal artery embolization
Authors: John Kevin , Syed Shoaib , Kaestner Thomas , Dashti Reza , Fiorella David , Sadasivan Chander 
Published: November 2023

BackgroundLiquid embolic agents (LEAs) such as ethylene vinyl alcohol (EVOH) are utilized for middle meningeal artery embolization (MMAE) for chronic subdural hematomas (cSDH). LEAs may be advantageous for MMAE as they are permanent and can penetrate the microvasculature of the subdural membranes. LEA surface area (SA) can quantify this penetration. The segmentation of LEA SA is not described in the literature and may be of interest in refining MMAE technique.MethodsWe retrospectively collected computerized tomography (CT) scans from 74 patients (with 95 cSDH) who underwent first-line MMAE with EVOH. Non-contrast head CTs were acquired pre-embolization, immediately post-embolization and at 1-, 3-, and 6 month follow-up. A 3D-Slicer was used to segment hematoma volumes and the liquid embolic cast. We hypothesized that greater LEA SA would be correlated with greater improvements in cSDH volumetric resolution.ResultsThere was significant resolution in cSDH volumes over the follow-up period compared to preoperative volume (p<0.0001). The LEA SA was significantly correlated with the rate of cSDH resolution at 3 months (R2=0.08, p=0.03), and 6 months (R2=0.14, p=0.01).ConclusionsThe correlation of LEA surface area with hematoma resolution at 3-months and 6-months suggests greater LEA penetration may improve radiographic outcomes. This study uniquely provides a quantitative radiological perspective on the effect of LEA penetration on cSDH resolution.
GFAP palmitoylcation mediated by ZDHHC23 in spinal astrocytes contributes to the development of neuropathic pain
Authors: Fan Xiaoqing , Zhang Siyu , Sun Suling , Bi Wenxu , Li Shuyang , Wang Wei , Chen Xueran , Fang Zhiyou 
Published: November 2023

BackgroundCancer pain has a significant impact on patient’s quality of life. Astrocytes play an important role in cancer pain signaling. The direct targeting of astrocytes can effectively suppress cancer pain, however, they can cause many side effects. Therefore, there is an urgent need to identify the specific signaling pathways or proteins involved within astrocytes in cancer pain as targets for treating pain.MethodsA neuropathic cancer pain (NCP) model was established by inoculating mouse S-180 sarcoma cells around the right sciatic nerve in C57BL/6 mice. Spontaneous persistent pain and paw withdrawal thresholds were measured usingvonFrey filaments. The NCP spinal cord dorsal horn (L4–L6) and mouse astrocyte cell line MA-C were used to study protein palmitoylation using acyl-biotin exchange, real-time polymerase chain reaction, ELISA, western blotting, and immunofluorescent staining.ResultsIn a cancer pain model, along with tumor growth, peripheral nerve tissue invasion, and cancer pain onset, astrocytes in the dorsal horn of the spinal cord were activated and palmitoyltransferase ZDHHC23 expression was upregulated, leading to increased palmitoylation levels of GFAP and increased secretion of inflammatory factors, such as (C–X–C motif) ligand (CXCL)10 (CXCL-10), interleukin 6, and granulocyte-macrophage colony-stimulating factor. These factors in turn activate astrocytes by activating the signal transducer and activator of transcription 3 (STAT3) signaling pathway. A competitive peptide targeting GFAP palmitoylations was designed to effectively alleviate morphine tolerance in cancer pain treatment as well as cancer pain signaling and inflammatory factor secretion.ConclusionsIn a rodent model, targeting GFAP palmitoylation appears to be an effective strategy in relieving cancer pain and morphine tolerance. Human translational research is warranted.
A Multiethnic Germline–Somatic Association Database Deciphers Multilayered and Interconnected Genetic Mutations in Cancer
Authors: Xin Junyi , Mo Zongchao , Chai Ruichao , Hua Wei , Wang Jiguang 
Published: November 2023

Abstract

Inherited germline and acquired somatic alterations can both promote human tumor development. Elucidating the cooperation between somatic and germline genetic alterations that drive tumorigenesis could help inform precision cancer prevention and treatment strategies. Here, leveraging genomic genotyping and sequencing data from 9,029 patients with cancer with European, East Asian, and African ancestry, we performed a pan-cancer analysis to evaluate the associations between germline SNPs and somatic alterations, including single-nucleotide variant and small insertion/deletion mutations, copy-number variation, tumor mutational burden, and mutational signatures. Genome-wide significant germline–somatic pairs were abundant, and most of the associations were observed in one cancer type and one ancestry group. A user-friendly interactive Multiethnic Germline–Somatic Association (MGSA) database (http://wanglab-hkust.cn:3838/MGSA/) was developed, which can be used to query, browse, and download the results of the association analyses. Moreover, the MGSA database offers additional survival analysis and functional annotation. Together, this work provides a resource for uncovering the clinical and biological roles of associations between germline variants and somatic alterations in human cancer.

Significance:
Comprehensive analysis of connections between germline variants and somatic events in cancer offers a resource for investigating the functional significance of genetic mutations and exploring genetic factors contributing to racial disparities.
Correlates of Circulating Osteoprotegerin in Women with a Pathogenic or Likely Pathogenic Variant in the BRCA1 Gene
Authors: Park Sarah Sohyun , Zaman Tasnim , Kim Shana J. , Brooks Jennifer D. , Wong Andy Kin On , Lubiński Jan , Narod Steven A. , Salmena Leonardo , Kotsopoulos Joanne 
Published: November 2023

Abstract

Background:
Lower levels of osteoprotegerin (OPG), the decoy receptor for receptor activator of NFκB (RANK)-ligand, have been reported among women with a BRCA1 mutation, suggesting OPG may be marker of cancer risk. Whether various reproductive, hormonal, or lifestyle factors impact OPG levels in these women is unknown.

Methods:
BRCA1 mutation carriers enrolled in a longitudinal study, no history of cancer, and a serum sample for OPG quantification, were included. Exposure information was collected through self-reported questionnaire at study enrollment and every 2 years thereafter. Serum OPG levels (pg/mL) were measured using an ELISA, and generalized linear models were used to assess the associations between reproductive, hormonal, and lifestyle exposures at the time of blood collection with serum OPG. Adjusted means were estimated using the fully adjusted model.

Results:
A total of 701 women with a median age at blood collection of 39.0 years (18.0–82.0) were included. Older age (Spearman r = 0.24; P &lt; 0.001) and current versus never smoking (98.82 vs. 86.24 pg/mL; Pcat &lt; 0.001) were associated with significantly higher OPG, whereas ever versus never coffee consumption was associated with significantly lower OPG (85.92 vs. 94.05 pg/mL; Pcat = 0.03). There were no other significant associations for other exposures (P ≥ 0.06). The evaluated factors accounted for 7.5% of the variability in OPG.

Conclusions:
OPG is minimally influenced by hormonal and lifestyle factors among BRCA1 mutation carriers.

Impact:
These findings suggest that circulating OPG levels are not impacted by non-genetic factors in high-risk women.