bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global view on carbapenem-resistant
Acinetobacter baumannii
Authors: Müller Carina , Reuter Sandra , Wille Julia , Xanthopoulou Kyriaki , Stefanik Danuta , Grundmann Hajo , Higgins Paul G. , Seifert Harald 
Published: October 2023

ABSTRACT

To give an update on the molecular epidemiology and global distribution of carbapenemase encoding genes, we subjected 313 carbapenem-resistant
Acinetobacter baumannii
isolated from 114 study centers in 47 countries in five world regions, Africa, Asia, Europe, Latin America, and North America, to whole genome sequencing. Numbers of isolates investigated were proportional to the population size of the contributing countries. Molecular epidemiology was investigated using seven-loci and core genome multilocus sequence typing, whole-genome single nucleotide polymorphism phylogenies, and the intrinsic
bla
OXA-51-like
variant. Carbapenemase encoding genes were identified by multiplex PCR and ResFinder. Among the total of 313 isolates, 289 (92.3%) were assigned to
A. baumannii
international clones (IC) IC1–IC8. IC2 predominated with 196 isolates (62.6%) and was spread worldwide, followed by IC5 with 44 isolates (14.1%) mainly confined to Latin America. Six isolates (1.9%) originating from Belgium, Egypt, Italy, and Pakistan represent the novel IC9. Acquired OXA-type carbapenemase genes were found in 300 (96%) isolates with
bla
OXA-23-like
and
bla
OXA-40-like
predominating, which constitutes a significant increase compared to our findings from 2010. Metallo-beta-lactamases were rare with seven isolates (2.2%). The distribution of ICs and carbapenemase determinants can vary widely among different geographical regions.

IMPORTANCE

Carbapenem-resistant
Acinetobacter baumannii
are of increasing public health importance, as they are resistant to last-line antibiotics. International clones with well-characterized resistance genes dominate globally; however, locally, other lineages with different properties may be of importance to consider. This study investigated isolates from a broad geographic origin from 114 hospitals in 47 countries and from five world regions ensuring the greatest possible diversity in an organism known for its propensity for clonal epidemic spread and reflecting the current global epidemiology of carbapenem-resistant
A. baumannii
. In Latin America, a lineage different from other geographic regions circulates, with a different resistance gene profile. This knowledge is important to adjust local infection prevention measures. In a global world with migration and increasing use of antimicrobials, multidrug-resistant bacteria will continue to adapt and challenge our healthcare systems worldwide.
Complete genome sequence of
Paenibacillus
sp. VCA1 isolated from crater lake of the El Chichón Volcano
Authors: Martínez-López Nancy Abril , Peña-Ocaña Betsy Anaid , García-Contreras Rodolfo , Maeda Toshinari , Rincón-Rosales Reiner , Cazares Adrián , Hoshiko Yuki , Ruíz-Valdiviezo Víctor Manuel 
Published: October 2023

ABSTRACT

We report the complete genome of
Paenibacillus
sp. strain VCA1, which was isolated from sediment from El Chichón Volcano. This genome consists of 6,690,819 bp and 6,312 coding sequences, with 51.8% G+C content. Whole-genome sequencing was performed to explore the strain’s biocontrol and plant growth promotion properties.
Draft genome sequence of aWolbachiaendosymbiont fromSyringophilopsis turdi(Fritsch, 1958) (Acari, Syringophilidae)
Authors: Głowska Eliza , Gerth Michael 
Published: October 2023

ABSTRACTWe present the draft genome of aWolbachiaendosymbiont from quill mites. This is the first representative of a recently discovered distinctWolbachialineage (supergroup P). We hope the genome will be a useful resource for comparative evolutionary and genomic studies across the globally distributed symbiontWolbachia.
Proteomes reveal metabolic capabilities of
Yarrowia lipolytica
for biological upcycling of polyethylene into high-value chemicals
Authors: Walker Caleb , Mortensen Max , Poudel Bindica , Cotter Christopher , Myers Ryan , Okekeogbu Ikenna O. , Ryu Seunghyun , Khomami Bamin , Giannone Richard J. , Laursen Siris , Trinh Cong T. 
Published: October 2023

ABSTRACT

Polyolefins derived from plastic wastes are recalcitrant for biological upcycling. However, chemical depolymerization of polyolefins can generate depolymerized plastic (DP) oil, comprising of a complex mixture of saturated, unsaturated, even, and odd hydrocarbons suitable for biological conversion. While DP oil contains a rich carbon and energy source, it is inhibitory to cells. Understanding and harnessing robust metabolic capabilities of microorganisms to upcycle the hydrocarbons in DP oil, both naturally and unnaturally occurring, into high-value chemicals are limited. Here, we discovered that an oleaginous yeast,
Yarrowia lipolytica,
undergoing short-term adaptation to DP oil robustly utilized a wide range of hydrocarbons for cell growth and production of citric acid and neutral lipids. When growing on hydrocarbons,
Y. lipolytica
partitioned into planktonic and oil-bound cells with each exhibiting distinct proteomes and amino acid distributions invested in establishing these proteomes. Significant proteome reallocation toward energy and lipid metabolism, belonging to 2 of the 23 Eukaryotic Orthologous Groups classes C and I, enabled robust growth of
Y. lipolytica
on hydrocarbons, with n-hexadecane as the preferential substrate. This investment was even higher for growth on DP oil where classes C and I were ranked one and two, respectively, and many associated proteins and pathways were expressed and upregulated including the hydrocarbon degradation pathway, Krebs cycle, glyoxylate shunt and, unexpectedly, propionate metabolism. However, a reduction in proteome allocation for protein biosynthesis, at the expense of the observed increase toward energy and lipid metabolisms, might have caused the inhibitory effect of DP oil on cell growth.

IMPORTANCE

Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of
Yarrowia lipolytica
to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how
Y. lipolytica
activates its metabolism to utilize DP oil and establishes
Y. lipolytica
as a promising host for the upcycling of plastic wastes.
A single dietary factor, daily consumption of a fermented beverage, can modulate the gut bacteria and fecal metabolites within the same ethnic community
Authors: Das Santanu , Özkurt Ezgi , Joishy Tulsi Kumari , Mukherjee Ashis K. , Hildebrand Falk , Khan Mojibur R. 
Published: October 2023

ABSTRACT

In this study, the impact of traditional rice-based fermented alcoholic beverages (two types of Apong drink: Poro and Nogin) on the gut microbiome and health of the Mishing community in India was examined. Two groups (
n
= 71 in each group, 58 females and 84 males) that consumed one of these beverages were compared to a control group (
n
= 24, all males) that did not consume either beverage. Gut microbial composition was analyzed by sequencing 16S rRNA of fecal metagenomes and analyzing untargeted fecal metabolites, and short-chain fatty acids (SCFAs). We also collected data on anthropometric measures and serum biochemical markers. Our results showed that Apong drinkers had higher blood pressure, but lower blood glucose and total protein levels than other non-drinkers. Also, gut microbiome composition was found to be affected by the choice of Apong
,
with Apong drinkers having a more diverse and distinct microbiome compared to non-drinkers. Apong drink type or being a drinker or not explained even a higher variation of fecal metabolome composition than microbiome composition and Apong drinkers had lower levels of the SCFA isovaleric acid than non-drinkers. Overall, this study shows that a single dietary factor can significantly impact the gut microbiome of a community and highlights the potential role of traditional fermented beverages in modulating gut bacteria.

IMPORTANCE
Our study investigated how a traditional drink called Apong, made from fermented rice, affects the gut and health of the Mishing community in India. We compared two groups of people who drink Apong to a group of people who do not drink it. To accomplish this, we studied the gut bacteria, fecal metabolites, and blood samples of the participants. It was found that the people who drank Apong had higher blood pressure but lower blood sugar and protein levels than people who did not drink it. We also found that the gut microbiome composition of people who drank Apong was different from those who did not drink it. Moreover, people who drank Apong had lower levels of isovaleric acid in their feces. Overall, this study shows that a traditional drink like Apong can affect the gut bacteria of a community.
Identification of key residues of B cell epitopes in hemagglutinin of H6 influenza A virus
Authors: Wan Zhimin , Gong Jianxi , Sang Jianjun , Jiang Wenjie , Zhao Zhehong , Tang Ting , Li Yafeng , Zhao Yichao , Kan Qiuqi , Xie Quan , Li Tuofan , Shao Hongxia , Gao Wei , Qin Aijian , Ye Jianqiang 
Published: October 2023

ABSTRACT
H6 influenza A viruses are enzootic and genetically diverse in both domestic poultry and wild birds, occasionally causing spillovers to mammals, including humans, posing threat to public health. However, the antigenic sites of the hemagglutinin (HA) of H6 are poorly understood. In this study, a panel of murine monoclonal antibodies (MAbs) with different reactivity spectra against HA of H6 was generated and nine key residues of antigenic epitopes in H6 were identified through escape mutants of these MAbs. Of these, residues 139 and 140 belonged to antigenic Sa, residue 89 belonged to antigenic Cb, residue 149 belonged to Ca2, while residue 221 belonged to Ca1 regarding the H1 antigenic sites. However, the other four residues 69, 120, 124, and 246 were not located in the identified antigenic regions of H1. Although most HA variants of the escape mutants had the preference for avian-like receptor, whereas escape mutants m3B9 and m4C2 increased the binding affinity for both avian and human-like receptors, and m1A5 and m6D11 decreased the binding affinity for avian-like receptors. Moreover, a single dose of MAbs 4C2 or 6E3 could fully protect mice against lethal challenge of mouse-adapted A/Eurasian teal/Jiangxi/2018WB0417(H6N2) (MA E-Teal/417) in the prophylactic treatment and also could provide partial protection in the therapeutic treatment. Overall, the generated MAbs and the identified key residues of antigenic epitopes not only provide novel insights into the key markers for monitoring the antigenic variation of H6 but also demonstrate the potential for developing MAb-based passitive treatments for H6.

IMPORTANCE
Since the escape immunity of influenza A viruses (IAVs) is mainly caused by the continuous antigenic variations in HA, the identification of key antigenic epitopes is crucial for better understanding of the escape immunity and vaccine development for IAVs. The antigenic sites of several HA subtypes, including H1, H3, H5, and H9, have been well characterized, whereas those of H6 subtype are poorly understood. Here, we mapped nine key residues of antigenic epitopes in H6 through escape mutants using a panel of MAbs. Moreover, MAbs 4C2 and 6E3, targeting 140 and 89 residues, respectively, could protect mice against lethal challenge of MA E-Teal/417. These key residues of antigenic epitopes identified here provide the molecular targets for further elucidating the antigenic evolution of H6 and better preparing the vaccine against H6 IAV.
Chlamydia suisdisplays high transformation capacity with complete cloning vector integration into the chromosomalrrn-nqrFplasticity zone
Authors: Marti Hanna , Biggel Michael , Shima Kensuke , Onorini Delia , Rupp Jan , Charette Steve J. , Borel Nicole 
Published: October 2023

ABSTRACTChlamydia, comprising several human and zoonotic pathogens, is a genus of the conserved bacterial phylum Chlamydiota. Their obligate intracellular niche serves as a barrier for natural genetic exchange via horizontal gene transfer (HGT), and further limits the development and application of genetic tools. To date, the only example for recent inter-phylum HGT among the Chlamydiota is tetracycline resistance in the potentially zoonotic speciesChlamydia suis, a close phylogenetic relative of humanC. trachomatis, which causes bacterial sexually transmitted infections and ocular trachoma. Tetracycline resistance in porcineC. suisstrains has been described worldwide and is always part of a genomic island dividinginvasin(inv), located within a chromosomal region between the rRNA operon (rrn) and thenqrFreductase. Here, we aimed to expand the still modest number of available genetic manipulation systems forChlamydiaby generating allele-replacement and integration vectors forC. suis. These vectors comprised homologousC. suissequences of the chromosomal region of interest, anE. coliorigin of replication (ori) and selection markers but lacked the native chlamydial plasmids or itsori. We first recovered allele-replacement mutants using a vector that targets the tryptophan (trp) operon ofC. suis. The vector was further successfully maintained as a free plasmid inC. trachomatiswithout allele replacement, suggesting complex plasmid dynamics in the absence of a chlamydialori. Moreover, we showed that the hypervariablerrn-nqrFintergenic region ofC. suisis highly susceptible to transformation, resulting in complete vector integration upstream ofnqrFwithout interruption of the targetedinvgene.IMPORTANCEThe obligate intracellularChlamydiagenus contains many pathogens with a negative impact on global health and economy. Despite recent progress, there is still a lack of genetic tools limiting our understanding of these complex bacteria. This study provides new insights into genetic manipulation ofChlamydiawith the opportunistic porcine pathogenChlamydia suis, the only chlamydial species naturally harboring an antibiotic resistance gene, originally obtained by horizontal gene transfer.C. suisis transmissible to humans, posing a potential public health concern. We report thatC. suiscan take up vectors that lack the native plasmid, a requirement for most chlamydial transformation systems described to date. Additionally, we show thatC. trachomatis, the most common cause for bacterial sexually transmitted infections and infectious blindness worldwide, can be transformed withC. suisvectors. Finally, the chromosomal region that harbors the resistance gene ofC. suisis highly susceptible to complete vector integration.
Brucella
spp. are facultative anaerobic bacteria under denitrifying conditions
Authors: Freddi Luca , de la Garza-García Jorge A. , Al Dahouk Sascha , Occhialini Alessandra , Köhler Stephan 
Published: October 2023

ABSTRACT

Bacteria of the genus
Brucella
are responsible for human and animal brucellosis worldwide and comprise the well-characterized, so-called classical species belonging to the core clade, with a host range limited to mammals, and the novel atypical strains mainly considered as non-zoonotic to date, but able to colonize non-traditional hosts such as amphibians. Despite marked phenotypical differences between the two groups,
Brucella
species display a high degree of genome identity, including genes encoding reductases involved in the denitrification pathway, a respiratory process able to reduce nitrate to nitrogen under anoxic conditions.
Brucella
spp. have always been considered as strictly aerobic pathogens. Our study, however, describes for the first time that atypical
Brucella
spp. grow well under anoxia, but in a strictly nitrate-dependent manner, whereas classical species show a heterogeneous behavior. The rate of anaerobic growth of the atypical species
Brucella microti
was dependent on nitrate concentration, highlighting a more efficient denitrification pathway with rapid consumption of intermediate nitrite, whereas the classical species
Brucella suis
exhibited lower, nitrate concentration-independent growth coupled with nitrite accumulation. Transcriptional studies performed under anoxic conditions revealed a higher expression of genes participating in the last three denitrification steps in
B. microti
, as compared to
B. suis
, which correlates with the rapid and efficient consumption of nitrite in this atypical species and its rapid growth.

IMPORTANCE

Respiration is a fundamental and complex process that bacteria use to produce energy. Despite aerobic respiration being the most common, some bacteria make use of a mode of respiration in the absence of oxygen, called anaerobic respiration, which can yield advantages in adaptation to various environmental conditions. Denitrification is part of this respiratory process ensuring higher respiratory flexibility under oxygen depletion. Here, we report for the first time the evidence of anaerobic growth of
Brucella
spp. under denitrifying conditions, which implies that this genus should be reconsidered as facultative anaerobic. Our study further describes that efficient denitrification is not equally found within the
Brucella
genus, with atypical species showing a greater ability to denitrify, correlated with higher expression of the genes involved, as compared to classical species.
PRMT5 regulates the polysaccharide content by controlling the splicing of thaumatin-like protein in
Ganoderma lucidum
Authors: Liu Rui , Yang Zhengyan , Yang Tao , Wang Zi , Chen Xin , Zhu Jing , Ren Ang , Shi Liang , Yu Hanshou , Zhao Mingwen 
Published: October 2023

ABSTRACT

In the current study, the silencing of protein arginine methyltransferase 5 (PRMT5) decreased the polysaccharide content of
Ganoderma lucidum
compared to that of the wild-type (WT) strain. Furthermore, RNA-seq screening showed that the glycan degradation process-related gene thaumatin-like protein (
TLP
) was alternatively spliced in WT strains via retained introns, leading to the production of a longer
TLP1
isoform and a shorter
TLP2
isoform; however, only the
TLP2
isoform was observed in
PRMT5
i strains. Experiments examining the polysaccharide content of the TLP silencing,
TLP1
overexpression (OE-
TLP1
), and
TLP2
overexpression (OE-
TLP2
) transformants revealed that
TLP2
plays a more important role than
TLP1
in polysaccharide degradation. Through a combination of yeast two-hybrid, bimolecular fluorescence complementation and surface plasmon resonance assays, we found that
TLP2
directly physically interacted with phosphoglucose isomerase (PGI), a key enzyme in polysaccharide synthesis, and thereby increased PGI activity. However, TLP1 failed to interact with PGI, and PGI activity was not affected. Further inspection showed that the polysaccharide content was decreased in the OE-
TLP2
strains but not significantly changed in the OE-
TLP1
strains compared with that in the WT strains. In addition, the polysaccharide content of the
PRMT5-TLP
-cosilenced strains was not significantly different from that of the WT strains. These results demonstrate that PRMT5 modulates
TLP
processing of pre-mRNA transcripts and thereby decreases the polysaccharide content.

IMPORTANCE

PRMT5 contributes to secondary metabolite biosynthesis in
Ganoderma lucidum
. However, the mechanism through which PRMT5 regulates the biosynthesis of secondary metabolites remains unclear. In the current study,
PRMT5
silencing led to a significant decrease in the biosynthesis of polysaccharides from
G. lucidum
through the action of the alternative splicing of
TLP
. A shorter
TLP2
isoform can directly bind to PGI and regulated polysaccharide biosynthesis. These results suggest that PRMT5 enhances PGI activity by regulating TLP binding to PGI. The results of the current study reveal a novel target gene for PRMT5-mediated alternative splicing and provide a reference for the identification of PRMT5 regulatory target genes.
Racial differences in low value care among older adult Medicare patients in US health systems: retrospective cohort study
Authors: Ganguli Ishani , Mackwood Matthew B , Yang Ching-Wen Wendy , Crawford Maia , Mulligan Kathleen L , O’Malley A James , Fisher Elliott S , Morden Nancy E 
Published: October 2023

Abstract

Objective
To characterize racial differences in receipt of low value care (services that provide little to no benefit yet have potential for harm) among older Medicare beneficiaries overall and within health systems in the United States.

Design
Retrospective cohort study

Setting
100% Medicare fee-for-service administrative data (2016–18).

Participants
Black and White Medicare patients aged 65 or older as of 2016 and attributed to 595 health systems in the United States.

Main outcome measures
Receipt of 40 low value services among Black and White patients, with and without adjustment for patient age, sex, and previous healthcare use. Additional models included health system fixed effects to assess racial differences within health systems and separately, racial composition of the health system’s population to assess the relative contributions of individual patient race and health system racial composition to low value care receipt.

Results

The cohort included 9 833 304 patients (6.8% Black; 57.9% female). Of 40 low value services examined, Black patients had higher adjusted receipt of nine services and lower receipt of 20 services than White patients. Specifically, Black patients were more likely to receive low value acute diagnostic tests, including imaging for uncomplicated headache (6.9%
v
3.2%) and head computed tomography scans for dizziness (3.1%
v
1.9%). White patients had higher rates of low value screening tests and treatments, including preoperative laboratory tests (10.3%
v
6.5%), prostate specific antigen tests (31.0%
v
25.7%), and antibiotics for upper respiratory infections (36.6%
v
32.7%; all P<0.001). Secondary analyses showed that these differences persisted within given health systems and were not explained by Black and White patients receiving care from different systems.

Conclusions
Black patients were more likely to receive low value acute diagnostic tests and White patients were more likely to receive low value screening tests and treatments. Differences were generally small and were largely due to differential care within health systems. These patterns suggest potential individual, interpersonal, and structural factors that researchers, policy makers, and health system leaders might investigate and address to improve care quality and equity.