bluuebunny/crossref_metadata_2025_split huggingface dataset:
Campylobacter jejuni
resistance to human milk involves the acyl carrier protein AcpP
Authors: Zhou Bibi , Garber Jolene M. , Butcher James , Muszynski Artur , Casey Rebekah L. , Huynh Steven , Archer-hartmann Stephanie , Porfírio Sara , Rogers Ashley M. , Azadi Parastoo , Parker Craig T. , Ng Kenneth K. S. , Hines Kelly M. , Stintzi Alain , Szymanski Christine M. 
Published: February 2025

ABSTRACT

Campylobacter jejuni
is a common foodborne pathogen worldwide that is associated with high rates of morbidity and mortality among infants in low- to middle-income countries (LMICs). Human milk provides infants with an important source of nutrients and contains antimicrobial components for protection against infection. However, recent studies, including our own, have found significantly higher levels of
Campylobacter
in diarrheal stool samples collected from breastfed infants compared to non-breastfed infants in LMICs. We hypothesized that
C. jejuni
has unique strategies to resist the antimicrobial properties of human milk. Transcriptional profiling found human milk exposure induces genes associated with ribosomal function, iron acquisition, and amino acid utilization in
C. jejuni
strains 81–176 and 11168. However, unidentified proteinaceous components of human milk prevent bacterial growth. Evolving both
C. jejuni
isolates to survive in human milk resulted in mutations in genes encoding the acyl carrier protein (AcpP) and the major outer membrane porin (PorA). Introduction of the PorA/AcpP amino acid changes into the parental backgrounds followed by electron microscopy showed distinct membrane architectures, and the AcpP changes not only significantly improved growth in human milk, but also yielded cells surrounded with outer membrane vesicles. Analyses of the phospholipid and lipooligosaccharide (LOS) compositions suggest an imbalance in acyl chain distributions. For strain 11168, these changes protect both evolved and 11168∆
acpP
G33R
strains from bacteriophage infection and polymyxin killing. Taken together, this study provides insights into how
C. jejuni
may evolve to resist the bactericidal activity of human milk and flourish in the hostile environment of the gastrointestinal tract.

IMPORTANCE

In this study, we evolved
C. jejuni
strains which can grow in the presence of human milk and found that cell membrane alterations may be involved in resistance to the antimicrobial properties of human milk. These bacterial membrane changes are predominantly linked to amino acid substitutions within the acyl carrier protein, AcpP, although other bacterial components, including PorA, are likely involved. This study provides some insights into possible strategies for
C. jejuni
survival and propagation in the gastrointestinal tract of breastfed infants.
Investigation of the
Cyanothece
nitrogenase cluster in
Synechocystis
: a blueprint for engineering nitrogen-fixing photoautotrophs
Authors: Liu Deng , Bandyopadhyay Anindita , Liberton Michelle , Pakrasi Himadri B. , Bhattacharyya-Pakrasi Maitrayee 
Published: February 2025

ABSTRACT

The nitrogenase gene cluster of unicellular diazotrophic cyanobacteria, such as
Cyanothece
, is frequently selected by nature for nitrogen-fixing partnerships with eukaryotic phototrophs. The essential cluster components that confer an advantage in such partnerships remain underexplored. To use this cluster for the development of synthetic, phototrophic nitrogen-fixing systems, a thorough and systematic analysis of its constituent genes is necessary. An initial effort to assess the possibility of engineering this cluster into non-diazotrophic phototrophs led to the generation of a
Synechocystis
6803 strain with significant nitrogenase activity. In the current study, a refactoring approach was taken to determine the dispensability of the non-structural genes in the cluster and define a minimal gene set for constructing a functional nitrogenase for phototrophs. Using a bottom-up strategy, the
nif
genes from
Cyanothece
51142 were re-organized to form new operons. The genes were then seamlessly removed to determine their essentiality in the nitrogen fixation process. We demonstrate that besides the structural genes
nifHDK
,
nifBSUENPVZTXW
, as well as
hesAB
, are important for optimal nitrogenase function in a phototroph. We also show that optimal expression of these genes is crucial for efficient nitrogenase activity. Our findings provide a solid foundation for generating synthetic systems that will facilitate solar-powered conversion of atmospheric nitrogen into nitrogen-rich compounds, a stride toward a greener world.

IMPORTANCE
Integrating nitrogen fixation genes into various photosynthetic organisms is an exciting strategy for converting atmospheric nitrogen into nitrogen-rich products in a green and energy-efficient way. In order to facilitate this process, it is essential that we understand the fundamentals of the functioning of a prokaryotic nitrogen-fixing machinery in a non-diazotrophic, photoautotrophic cell. This study examines a nitrogenase gene cluster that has been naturally selected on multiple occasions for a nitrogen-fixing partnership by eukaryotic photoautotrophs and provides a basic blueprint for designing a photosynthetic organism with nitrogen-fixing ability.
CsrA-mediated regulation of a virulence switch in
Acinetobacter baumannii
Authors: Singh Raja , Pérez-Varela María , Colquhoun Jennifer M. , Kröger Carsten , Hamrock Fergal J. , Shaibah Ali , Neidle Ellen L. , Rather Philip N. 
Published: February 2025

ABSTRACT

CsrA is an RNA binding protein that functions as a global regulator in bacteria. We demonstrate that, in
Acinetobacter baumannii
, CsrA acts as a positive regulator of the switch from virulent (VIR-O) to avirulent (AV-T) subpopulations. This regulation is mediated, in part, by CsrA interfering with Rho-dependent termination in the mRNA leader region of the
ABUW_1645
gene, encoding the primary TetR-type transcriptional regulator that drives cells from the VIR-O to the AV-T state. We demonstrate that CsrA directly binds to the
ABUW_1645
mRNA leader region and interferes with Rho binding. We identify three small RNAs (sRNAs) designated CsrB, CsrC, and CsrD that bind to CsrA and inhibit its activity. Individual overexpression of each sRNA greatly decreased the rate of VIR-O to AV-T switching. Individual deletions of each sRNA increased the frequency of VIR-O to AV-T switching, with loss of CsrB giving the highest increase at 2.4-fold. The expression of each sRNA was strongly dependent on the GacA response regulator and the expression of each sRNA was higher in VIR-O cells than in AV-T variants. This regulation provides a mechanism for the differential control of CsrA activity between VIR-O and AV-T variants.

IMPORTANCE

The World Health Organization has ranked
Acinetobacter baumannii
atop its “priority pathogens” list highlighting the urgent need for new therapeutics against this pathogen. Many
A. baumannii
strains including AB5075 can rapidly switch between cell subpopulations that are virulent or avirulent. In this study, we identify the RNA binding protein CsrA as an important regulator of this switch. Since this switch represents an “Achilles Heel” for pathogenesis, our work may shed light on new mechanisms to lock cells into the avirulent state to block disease.
Draft genomes of six methicillin-resistant
Staphylococcus aureus
in a Philippine tertiary hospital with insights on putative antimicrobial and phage resistance mechanisms
Authors: Carascal Mark B. , Gonzales Jo-Eliz M. , Tañedo Ma. Mona Joy T. , Papa Donna May D. , Destura Raul V. , Henson Karl Evans R. 
Published: February 2025

ABSTRACT

The genomes of six methicillin-resistant
Staphylococcus aureus
(MRSA) revealed CC5(ST5)-SCC
mec
-IVc-
spa
-t105-PVL
+
(
n
= 3), CC5(ST6)-SCC
mec
-IVc-
spa
-t10002 (
n
= 1), CC5(ST5)-SCC
mec
-IVa-
spa
-t002 (
n
= 1), and CC8(ST8)-SCC
mec
-IVa-
spa
-t008-PVL
+
(
n
= 1) genotypes. All possessed multiple antibiotic resistance genes (putative
mecA
and
blaZ,
and
dfrG
for cotrimoxazole-resistant strains), intact staphylococcal prophages, and putative antiphage systems. The results could aid in MRSA infection management and control.
Complete genome sequence of
Veillonella parvula
strain PK1910
Authors: Naumann Allison A. , Siddiqui Danyal , Kerns Kristopher A. , Hendrickson Erik L. , Kotsakis Georgios A. , McLean Jeffrey S. 
Published: February 2025

ABSTRACT

Here, we announce the complete genome sequence of
Veillonella parvula
strain PK1910, obtained from a frozen stock. The genome is composed of one closed contig with a length of 2,213,486 bp, resulting in 98.0× coverage containing 1,979 protein-coding genes, with a GC content of 38.74%.
Metagenome-assembled genomes of acetogenic enrichment obtained from deep subsurface archean granitoids of Koyna Seismogenic Zone, Koyna, India
Authors: Sahu Rajendra Prasad , Sar Pinaki 
Published: February 2025

ABSTRACT

We report 14 metagenome-assembled genomes (MAGs) of acetogenic bacteria (acetogens) enriched from deep (1,679–2,912 m below surface), hot (55°C–74 °C) granitoids of the Koyna Seismogenic Zone, India. These MAGs include
Thermoanaerobacter pseudethanolicus, Exiguobacterium alkaliphilum, Moorella humiferrea, Caldanaerobacter subterraneus
, etc. The study allowed access to the genomes of deep biosphere acetogens.
Draft genome sequence of
Solimonas
sp. strain SE-A11 isolated from the rhizosphere of feral
Brassica napus
in South Korea
Authors: Kim Jihoon , Nam Kyong-Hee , Lee Jun-Woo , Chun Seong-Jun 
Published: February 2025

ABSTRACT

The draft genome of
Solimonas
sp. strain SE-A11 bacterium isolated from the rhizosphere of feral
Brassica napus
in South Korea, represents the first isolate of the genus
Solimonas
obtained from a plant rhizosphere. The strain has a genome size of 4,937,440  bp, a G + C content of 66.5%, and 281 predicted subsystems.
Whole genome sequences of eight
Erwinia amylovora
phages isolated from South Korea
Authors: Roh Eunjung , Duffy Madison E. , Ewool Leslie M. , Grose Julianne H. 
Published: February 2025

ABSTRACT

The gram-negative
Enterobacteriaceae Erwinia amylovora
is the causative agent of fire blight. Herein, we announce the full genome sequencing and annotation of eight
E. amylovora
bacteriophages from apple and pear orchards in South Korea, which have remarkable similarity to
Erwinia
phages previously isolated from the Americas.
Complete genome of the mutualistic symbiont “
Candidatus
Nardonella sp.” Pin-AIST from the black hard weevil
Pachyrhynchus infernalis
Authors: Mizutani Masaki , Moriyama Minoru , Fukatsu Takema , Kakizawa Shigeyuki 
Published: February 2025

ABSTRACT

The complete genome, 226,287 bps in size, of “
Candidatus
Nardonella sp.” Pin-AIST, an obligatory bacterial endosymbiont of the black hard weevil
Pachyrhynchus infernalis
, was sequenced. The extremely reduced endosymbiont genome is specialized for tyrosine synthesis, which contributes to the hardness of the beetle’s exoskeleton.
Near-complete genome of medusavirus euryale, putative third species of the genus
Medusavirus
, isolated from the TaeHwaGang river, Ulsan, South Korea
Authors: Bae Jiwan , Takemura Masaharu 
Published: February 2025

ABSTRACT

We report the isolation and near-complete genome sequencing of medusavirus euryale, a putative third species of the genus
Medusavirus
in the family
Mamonoviridae
, from the TaeHwaGang river in Ulsan, South Korea. Medusavirus euryale has a genome size of approximately 369 kb and contains 446 open reading frames, including two tRNA genes.
Complete genome sequence of
Microbacterium
sp. strain Clip185
Authors: Mitra Mautusi , Stanescu Ana 
Published: February 2025

ABSTRACT

A xenobiotic-degrader and heavy metal-tolerant
Microbacterium sp. strain Clip185
was isolated from a contaminated Tris-Acetate-Phosphate medium culture plate of a green micro-alga,
Chlamydomonas reinhardtii
. Here, we report the complete genome sequence of this strain to provide insights into its metabolic potential and nearest taxonomic neighbor.
In vitro
assays for clinical isolates of sequence type 131
Escherichia coli
do not recapitulate
in vivo
infectivity using a murine model of urinary tract infection
Authors: Rudick Courtney P. , Cox Rachel S. , Bourret Travis J. , Hanson Nancy D. 
Published: February 2025

ABSTRACT

Sequence type 131 isolates are a major cause of cystitis and pyelonephritis. Many studies rely solely on
in vitro
assays to screen for bacterial virulence factors associated with the pathogenicity of clinical isolates of
Escherichia coli
. Few studies have compared
in vitro
findings with
in vivo
infectivity of clinical isolates. The purpose of this study was to evaluate the correlation between
in vitro
assays with the ability to cause cystitis and pyelonephritis in a murine model of urinary tract infection.
In vitro
assays were conducted according to the published protocols and included motility assays, biofilm formation, epithelial cell adhesion and invasion, and curli production. Twenty-one uropathogenic
E. coli
(UPEC) isolates of
E. coli
ST131 and non-ST131 were used for both
in vivo
and
in vitro
studies. Six mice per isolate were inoculated via urethral catheterization. Colony forming units (CFUs) were determined from bladder and kidneys.
In vitro
and
in vivo
correlations were evaluated by multiple linear regression analysis. Pairwise linear regressions showed trendlines with weak positive correlations for motility, adhesion, and invasion and weak negative correlations for hemagglutination, biofilm, and curli production. The ability of
E. coli
ST131 and non-ST131 clinical isolates to cause cystitis and pyelonephritis varied among strains. The
R
2
Pearson correlation value was less than ±0.5 for any pair, indicating little to no statistical association between
in vitro
and
in vivo
findings. These data show that
in vitro
data are not predictive of the ability of ST131
E. coli
to infect and/or cause disease in a mouse model.

IMPORTANCE

Urinary tract infections (UTIs) affect 150 million people annually, and
E. coli
ST131, a pandemic clone, has become responsible for a significant portion of those UTIs. How ST131
E. coli
has become such a successful strain remains to be elucidated. When evaluating bacterial pathogenicity, it is customary to use
in vitro
assays to predict isolate virulence and fitness due to lower cost and ease of experimentation compared with
in vivo
models. It is common to use model organisms like pathogenic
E. coli
CFT073 or a non-pathogenic K12 lab strain as representatives for the entire species. However, our research has shown that model organisms differ from ST131
E. coli,
and
in vitro
assays are poor predictors of ST131 isolate infectivity in a murine model of UTI. As such, research into the mechanisms of fitness/pathogenesis for ST131 infectivity needs to focus on these organisms rather than other types of UPEC.
Virus-neutralizing monoclonal antibodies against bovine viral diarrhea virus and classical swine fever virus target conformational and linear epitopes on E2 glycoprotein subdomains
Authors: Roman-Sosa Gleyder , Meyer Denise , Dellarole Mariano , Wengen Doris à , Lerch Susanne , Postel Alexander , Becher Paul 
Published: February 2025

ABSTRACT

The envelope glycoprotein E2 of pestiviruses plays a crucial role in viral entry and elicits a virus-neutralizing humoral immune response. Consequently, the epitopes recognized by monoclonal antibodies (mAbs) on E2 are a significant focus in pestivirus research and diagnostics. In this study, we characterized a panel of murine mAbs against the E2 protein of classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), two major pathogens for swine and cattle, respectively. The majority of mAbs neutralized the virus
in vitro
and recognized conformational epitopes, which were also detected by sera from infected animals. Notably, binding to these epitopes was retained after low-pH treatment, although conformational epitopes were disrupted upon disulfide bond reduction. The epitopes of the anti-CSFV mAbs were located in various domains of E2, including the interdomain linker sequences. Conversely, all but one of the anti-BVDV mAb epitopes were located in domain A. Moreover, the reactivity of one mAb suggests a conformational interdependence among the linker sequences of pestivirus E2. The panel of mAbs characterized in this study holds potential to support basic research on the mechanism of early pestivirus invasion and to assist in the design of E2-based diagnostic tools and vaccines.

IMPORTANCE

Classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), which belong to the family Flaviviridae, cause economically significant diseases in pigs and cattle. The pestivirus glycoprotein E2 is located on the viral surface and is targeted by antibodies that neutralize virus infection. Due to its variability, E2 is a useful antigen for the development of diagnostic tests to differentiate between infections caused by different pestiviruses. In the present study, two panels of monoclonal antibodies (mAbs) specifically reactive with either CSFV or BVDV E2 were characterized. Interestingly, the majority of mAbs neutralized the respective virus
in vitro
. Epitope mapping revealed that the mAbs recognized low-pH-resistant epitopes of conformational nature located in different domains of CSFV E2 (anti-CSFV mAbs) or in domain A of BVDV E2 (anti-BVDV mAbs). The recombinant proteins along with the characterized mAbs have the potential to develop improved pestivirus-specific diagnostic tests and vaccines.
Association of infection-induced antibody levels with risk of subsequent SARS–COV-2 reinfection among healthcare professionals, Rhode Island, 1 March 2020–17 February 2021
Authors: Shi Jianrong , Gabriel M. Gayle , Epperson Monica , Chan Phil A. , Jones Jefferson M. , Petersen Lyle R. , Briggs Hagen Melissa , Thornburg Natalie J. , Saydah Sharon , Midgley Claire M. 
Published: February 2025

ABSTRACT

Numerous studies have investigated vaccine-induced correlates of protection (CoP) against severe acute respiratory syndrome–coronavirus 2 (SARS–CoV-2) infection, but data on infection-induced CoP are limited. Given differences between vaccine- and infection-induced immune responses, in conjunction with low vaccination in many US populations, a better understanding of infection-induced CoP is needed. We used residual sera from a mid-2020 Rhode Island serosurvey of healthcare professionals (HCP) and corresponding state-collected SARS–CoV-2 testing data through February 2021 to generate an analytic cohort of HCP with a first SARS–CoV-2 infection prior to serosurvey blood collection and multiple viral tests after blood collection to assess for reinfection (defined as a positive viral test ≥90 days after their first positive). We tested sera for levels of IgG and IgA targeting ancestral spike (S), receptor-binding domain (RBD), or nucleocapsid (N). We used adjusted Cox proportional hazard ratios to assess the association between categorical antibody level and the risk of subsequent reinfection. Among 170 HCP included in this analysis (median age = 47 years; interquartile range: 35–55 years), 30 were reinfected during the analytic period. Adjusted Cox proportional hazard ratios indicated that higher levels of anti-S or anti-RBD IgG were significantly associated with a lower risk of reinfection. These findings support the use of anti-S or anti-RBD IgG levels as markers of immunologic protection, such as in population serosurveys, or immune-bridging studies in settings of high prevalence of prior infection.

IMPORTANCE
The measurement of antibodies in blood is a relatively simple process and commonly used to estimate overall levels of past infection in populations. But, if someone has antibodies, does this mean that they are protected from being infected again? And are people with higher levels of antibody better protected? There are good data in the literature exploring how antibodies from the coronavirus disease 2019 (COVID-19) vaccination are associated with protection. But, there is still a lot to learn about protection conferred by antibodies that develop after a severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) infection. In our study, we measure the levels of six different antibody types developed after infection and compare levels to the risk of subsequent infection to better understand which antibody types are best associated with protection. Our data are important for improving studies that use antibodies as proxies for protection, such as population immunity estimates, or those assessing new prevention products.
Pathological characterization of female reproductive organs prior to miscarriage induced by Zika virus infection in the pregnant common marmoset
Authors: Imagawa Toshifumi , Tanaka Kazuo , Ito Masahiko , Matsuda Mami , Suzuki Tadaki , Ando Tsuyoshi , Yaguchi Chizuko , Miyamoto Kazuyoshi , Takabayashi Shuji , Suzuki Ryosuke , Takasaki Tomohiko , Itoh Hiroaki , Kosugi Isao , Suzuki Tetsuro 
Published: February 2025

ABSTRACT

While Zika virus (ZIKV) infection in pregnant women is known to increase the risk of miscarriage and stillbirth, the mechanism by which ZIKV infection leads to the inability to continue a pregnancy is not clear. In our common marmoset models of ZIKV infection in pregnant individuals, miscarriage was observed in dams infected in the first or second trimester, and preterm delivery was observed in a dam infected in the third trimester. Serum progesterone levels were significantly lower prior to miscarriage or preterm delivery in the infected marmosets. To elucidate the pathology of the placental region just before the onset of ZIKV-induced miscarriage, we newly prepared an infected marmoset in the first trimester of pregnancy and euthanized it when the serum progesterone concentration was markedly reduced. Pathological analysis revealed significant degeneration in cells at the maternal-fetal interface, presumably trophoblasts. Cleaved-caspase was widely observed in the endometrial to placental region, and TNFα at 200 pg/mL was detected in the amniotic fluid, suggesting that apoptosis may progress in the endometrium and placenta, leading to decreased trophoblast function and miscarriage. ZIKV NS1 protein was found sporadically in the cellular degeneration area and widely in the basal layer of the endometrium. Furthermore, the viral protein was frequently detected in the follicles and corpus luteum of the ovary. The developed ZIKV infection model in pregnant marmosets would be useful not only to better understand the mechanism of ZIKV-induced miscarriage but also to analyze the effects of the viral infection on female reproductive tissues.

IMPORTANCE
Although several viruses, including Zika virus (ZIKV), are known to increase the risk of miscarriage upon viral infection, the mechanism by which miscarriage is induced by viral infection is largely unknown. This is partly due to the difficulty of pathological analysis of maternal tissues in the period following viral infection and prior to miscarriage. In this study, we predicted the occurrence of miscarriage by monitoring serum progesterone levels and performed pathological analysis of peri-placental tissues at a time point assumed to be just before miscarriage. This is the first report of trophoblast degeneration prior to miscarriage, suggesting that the experimental method used here is useful for analyzing the pathogenesis of virus infection-related miscarriage. Further immunostaining revealed that ZIKV NS1 was distributed not only in the uterus but also in the ovaries, with particularly pronounced staining of oocytes. Whether ZIKV infection affects female reproductive function should be clarified in the future.