bluuebunny/crossref_metadata_2025_split huggingface dataset:
LiaX is a surrogate marker for cell envelope stress and daptomycin non-susceptibility in
Enterococcus faecium
Authors: Axell-House Dierdre B. , Simar Shelby R. , Panesso Diana , Rincon Sandra , Miller William R. , Khan Ayesha , Pemberton Orville A. , Valdez Lizbet , Nguyen April H. , Hood Kara S. , Rydell Kirsten , DeTranaltes Andrea M. , Jones Mary N. , Atterstrom Rachel , Reyes Jinnethe , Sahasrabhojane Pranoti V. , Suleyman Geehan , Zervos Marcus , Shelburne Samuel A. , Singh Kavindra V. , Shamoo Yousif , Hanson Blake M. , Tran Truc T. , Arias Cesar A. 
Published: January 2024

ABSTRACT

Daptomycin (DAP) is often used as a first-line therapy to treat vancomycin-resistant
Enterococcus faecium
infections, but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP minimum inhibitory concentrations (MICs) have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system, and deletion of
liaR
encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated
liaXYZ
. In
Enterococcus faecalis
, LiaX is surface-exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in
E. faecalis
, LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in
E. faecium
. Here, we found that
liaX
is essential in
E. faecium
with an activated LiaFSR system. Unlike
E. faecalis
,
E. faecium
LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX enzyme-linked immunosorbent assay (ELISA). We then assessed 86 clinical
E. faecium
bloodstream isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-resistant clinical strains of
E. faecium
exhibited elevated LiaX levels. Strikingly, 73% of DAP-susceptible isolates by standard MIC determination also had elevated LiaX ELISAs compared to a well-characterized DAP-susceptible strain. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many
E. faecium
isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.
In vitro
activity of sulbactam-durlobactam against colistin-resistant and/or cefiderocol-non-susceptible, carbapenem-resistant
Acinetobacter baumannii
collected in U.S. hospitals
Authors: Iovleva Alina , McElheny Christi L. , Fowler Erin L. , Cober Eric , Herc Erica S. , Arias Cesar A. , Hill Carol , Baum Keri , Fowler Vance G. , Chambers Henry F. , Greenwood-Quaintance Kerryl E. , Patel Robin , van Duin David , Bonomo Robert A. , Doi Yohei 
Published: January 2024

ABSTRACT

The activity of a novel β-lactamase inhibitor combination, sulbactam-durlobactam (SUL-DUR), was tested against 87 colistin-resistant and/or cefiderocol-non-susceptible carbapenem-resistant
Acinetobacter baumannii
clinical isolates collected from U.S. hospitals between 2017 and 2019. Among them, 89% and 97% were susceptible to SUL-DUR and imipenem plus SUL-DUR, with MIC
50
/MIC
90
values of 2 µg/mL/8 µg/mL and 1 µg/mL/4 µg/mL, respectively. The presence of amino acid substitutions in penicillin-binding protein 3, including previously reported A515V or T526S, was associated with SUL-DUR non-susceptibility.
Transcriptional heterogeneity of catabolic genes on the plasmid pCAR1 causes host-specific carbazole degradation
Authors: Suzuki-Minakuchi Chiho , Yamamoto Natsumi , Takahira Saki , Yamaguchi Masataka , Takeda Yutaro , Okada Kazunori , Shigeto Shinsuke , Nojiri Hideaki 
Published: January 2024

ABSTRACT

To elucidate why plasmid-borne catabolic ability differs among host bacteria, we assessed the expression dynamics of the P

ant

promoter on the carbazole-degradative conjugative plasmid pCAR1 in
Pseudomonas putida
KT2440(pCAR1) (hereafter, KTPC) and
Pseudomonas resinovorans
CA10. The P

ant

promoter regulates the transcription of both the
car
and
ant
operons, which are responsible for converting carbazole into anthranilate and anthranilate into catechol, respectively. In the presence of anthranilate, transcription of the P

ant

promoter is induced by the AraC/XylS family regulator AntR, encoded on pCAR1. A reporter cassette containing the P

ant

promoter followed by
gfp
was inserted into the chromosomes of KTPC and CA10. After adding anthranilate, GFP expression in the population of CA10 showed an unimodal distribution, whereas a small population with low GFP fluorescence intensity appeared for KTPC. CA10 has a gene,
antR
CA
, that encodes an iso-functional homolog of AntR on its chromosome. When
antR
CA
was disrupted, a small population with low GFP fluorescence intensity appeared. In contrast, overexpression of pCAR1-encoded AntR in KTPC resulted in unimodal expression under the P

ant

promoter. These results suggest that the expression of pCAR1-encoded AntR is insufficient to ameliorate the stochastic expression of the P

ant

promoter. Raman spectra of single cells collected using deuterium-labeled carbazole showed that the C–D Raman signal exhibited greater variability for KTPC than CA10. These results indicate that heterogeneity at the transcriptional level of the P

ant

promoter due to insufficient AntR availability causes fluctuations in the pCAR1-borne carbazole-degrading capacity of host bacterial cells.

IMPORTANCE

Horizontally acquired genes increase the competitiveness of host bacteria under selective conditions, although unregulated expression of foreign genes may impose fitness costs. The “appropriate” host for a plasmid is empirically known to maximize the expression of plasmid-borne traits. In the case of pCAR1-harboring
Pseudomonas
strains,
P. resinovorans
CA10 exhibits strong carbazole-degrading capacity, whereas
P. putida
KT2440 harboring pCAR1 exhibits low degradation capacity. Our results suggest that a chromosomally encoded transcription factor affects transcriptional and metabolic fluctuations in host cells, resulting in different carbazole-degrading capacities as a population. This study may provide a clue for determining appropriate hosts for a plasmid and for regulating the expression of plasmid-borne traits, such as the degradation of xenobiotics and antibiotic resistance.
Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy
Authors: Op De Beeck Michiel , Troein Carl , Peterson Carsten , Tunlid Anders , Persson Per 
Published: January 2024

ABSTRACT

In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus
Paxillus involutus
and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that
P. involutus
has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of
P. involutus
to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.

IMPORTANCE

Infrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus
Paxillus involutus
at the interface between individual fungal hyphae and cellulose substrates.
Simultaneous glucose and xylose utilization by an
Escherichia coli
catabolite repression mutant
Authors: Kaplan Nicholas A. , Islam Khondokar Nowshin , Kanis Fiona C. , Verderber Jack R. , Wang Xin , Jones J. Andrew , Koffas Mattheos A. G. 
Published: January 2024

ABSTRACT

As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including
Escherichia coli
, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation of the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutant of the gene encoding the cyclic AMP receptor protein,
crp*
, has been shown to disable CCR and improve the co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site-specific
crp*
chromosomal mutant in
E. coli
BL21 star (DE3). The
crp*
mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomics further showed that glucose was routed to the C5 carbon utilization pathways to support both
de novo
nucleotide synthesis and energy production in the
crp*
mutant strain. Metabolite analyses further show that overflow metabolism contributes to the slower growth in the
crp*
mutant. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.

IMPORTANCE

As the need for renewable biofuel and biochemical production processes continues to grow, there is an associated need for microbial technology capable of utilizing cheap, widely available, and renewable carbon substrates. This work details the construction and characterization of the first B-lineage
Escherichia coli
strain with mutated cyclic AMP receptor protein, Crp*, which deregulates the carbon catabolite repression (CCR) system and enables the co-utilization of multiple sugar sources in the growth medium. In this study, we focus our analysis on glucose and xylose utilization as these two sugars are the primary components in lignocellulosic biomass hydrolysate, a promising renewable carbon feedstock for industrial bioprocesses. This strain is valuable to the field as it enables the use of mixed sugar sources in traditional fed-batch based approaches, whereas the wild-type carbon catabolite repression system leads to biphasic growth and possible buildup of non-preferential sugars, reducing process efficiency at scale.
Cell surface architecture of the cultivated DPANN archaeon
Nanobdella aerobiophila
Authors: Kato Shingo , Tahara Yuhei O. , Nishimura Yuki , Uematsu Katsuyuki , Arai Takahiro , Nakane Daisuke , Ihara Ayaka , Nishizaka Takayuki , Iwasaki Wataru , Itoh Takashi , Miyata Makoto , Ohkuma Moriya 
Published: January 2024

ABSTRACT

The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon
Nanobdella aerobiophila
strain MJ1
T
and its host
Metallosphaera sedula
strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1
T
were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1
T
gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on
in silico
3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1
T
and MJ1HA were motile, but sole MJ1
T
cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of
Nanobdella aerobiophila
.

IMPORTANCE

DPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon,
Nanobdella aerobiophila
, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of
Nanobdella aerobiophila
, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
Genetic characterization and pathogenicity in a mouse model of newly isolated bat-originated mammalian orthoreovirus in South Korea
Authors: Do Hai Quynh , Yeom Minjoo , Moon Suyun , Lee Hanbyeul , Chung Chul-un , Chung Hee-chun , Park Jun Won , Na Woonsung , Song Daesub 
Published: January 2024

ABSTRACT

Mammalian orthoreoviruses (MRVs) infect a wide range of hosts, including humans, livestock, and wildlife. In the present study, we isolated a novel
Mammalian orthoreovirus
from the intestine of a microbat (
Myotis aurascens
) and investigated its biological and pathological characteristics. Phylogenetic analysis indicated that the new isolate was serotype 2, sharing the segments with those from different hosts. Our results showed that it can infect a wide range of cell lines from different mammalian species, including human, swine, and non-human primate cell lines. Additionally, media containing trypsin, yeast extract, and tryptose phosphate broth promoted virus propagation in primate cell lines and most human cell lines, but not in A549 and porcine cell lines. Mice infected with this strain via the intranasal route, but not via the oral route, exhibited weight loss and respiratory distress. The virus is distributed in a broad range of organs and causes lung damage.
In vitro
and
in vivo
experiments also suggested that the new virus could be a neurotropic infectious strain that can infect a neuroblastoma cell line and replicate in the brains of infected mice. Additionally, it caused a delayed immune response, as indicated by the high expression levels of cytokines and chemokines only at 14 days post-infection (dpi). These data provide an important understanding of the genetics and pathogenicity of mammalian orthoreoviruses in bats at risk of spillover infections.

IMPORTANCE
Mammalian orthoreoviruses (MRVs) have a broad range of hosts and can cause serious respiratory and gastroenteritis diseases in humans and livestock. Some strains infect the central nervous system, causing severe encephalitis. In this study, we identified BatMRV2/SNU1/Korea/2021, a reassortment of MRV serotype 2, isolated from bats with broad tissue tropism, including the neurological system. In addition, it has been shown to cause respiratory syndrome in mouse models. The given data will provide more evidence of the risk of mammalian orthoreovirus transmission from wildlife to various animal species and the sources of spillover infections.
Antimicrobial properties of tomato juice and peptides against typhoidal
Salmonella
Authors: Kwon Ryan S. , Lee Gi Young , Lee Sohyoung , Song Jeongmin 
Published: January 2024

ABSTRACT

Tomatoes are readily available and affordable vegetables that offer a range of health benefits due to their bioactive molecules, such as antioxidants and antimicrobials. In contrast to the widely recognized antioxidant properties of tomatoes, their antimicrobial properties remain largely unexplored. Here, we present our findings on the antimicrobial properties of tomato juice and peptides, namely, tomato-derived antimicrobial peptides (tdAMPs), in relation to their effectiveness against typhoidal
Salmonella
. Our research has revealed that tomato juice demonstrates significant antimicrobial properties against
Salmonella
Typhi, a pathogen that specifically affects humans and is responsible for causing typhoid fever. By employing computational analysis of the tomato genome sequence, conducting molecular dynamics simulation, and performing functional analyses, we have successfully identified two tdAMPs, namely, tdAMP-1 and tdAMP-2. These tdAMPs have demonstrated potent antimicrobial properties by effectively disrupting bacterial membranes. The efficacy of tdAMP-2 is shown to be more effective than tdAMP-1. The efficacy of tdAMP-1 and tdAMP-2 has been demonstrated against drug-resistant
S
. Typhi, as well as hyper-capsular
S
. Typhi variants that possess hypervirulent characteristics, which are presently circulating in countries with endemicity. Tomato juice, along with the two tdAMPs, has demonstrated effectiveness against uropathogenic
Escherichia coli
as well. This underscores their potential as viable agents in combating certain Gram-negative pathogens. This study provides valuable insights into the development of effective and sustainable public health strategies that utilize tomato and its derivatives as lifestyle interventions.

IMPORTANCE

In this study, we investigate the antimicrobial properties of tomato juice, the most widely consumed affordable vegetables, as well as tomato-derived antimicrobial peptides, in relation to their effectiveness against foodborne pathogens with an emphasis on
Salmonella
Typhi, a deadly human-specific pathogen.
Description of maternal and neonatal adverse events in pregnant people immunised with COVID-19 vaccines during pregnancy in the CLAP NETWORK of sentinel sites: nested case–control analysis of the immunization-associated risk – a study protocol
Authors: Macías Saint-Gerons Diego , Castro José Luis , Colomar Mercedes , Rojas-Cortés Robin , Sosa Claudio , Ropero Alba Maria , Serruya Suzanne Jacob , Pastor Desiré , Chiu Monica , Velandia-Gonzalez Martha , Abalos Edgardo , Durán Pablo , Gomez Ponce de León Rodolfo , Tomasso Giselle , Mainero Luis , Rubino Marcelo , De Mucio Bremen 
Published: January 2024

IntroductionCOVID-19 is associated with higher morbimortality in pregnant people compared with non-pregnant people. At present, the benefits of maternal immunisation are considered to outweigh the risks, and therefore, vaccination is recommended during pregnancy. However, additional information is needed on the safety of the vaccines in this population.Methods and analysisThis a retrospective cohort nested case–control study in pregnant people who attended maternity hospitals from eight Latin American and Caribbean countries. A perinatal electronic clinical history database with neonatal and obstetric information will be used. The proportion of pregnant people immunised with COVID-19 vaccines of the following maternal and neonatal events will be described: preterm infant, small for gestational age, low birth weight, stillbirth, neonatal death, congenital malformations, maternal near miss and maternal death. Moreover, the risk of prematurity, small for gestational age and low birth weight associated with exposure to COVID-19 vaccines will be estimated. Each case will be matched with two groups of three randomly selected controls. Controls will be matched by hospital and mother’s age (±3 years) with an additional matching by delivery date and conception time in the first and second control groups, respectively. The estimated required sample size for the main analysis (exposure to any vaccine) concerning ‘non-use’ is at least 1009 cases (3027 controls) to detect an increased probability of vaccine-associated event risk of 30% and at least 650 cases (1950 controls) to detect 30% protection. Sensitivity and secondary analyses considering country, type of vaccine, exposure windows and completeness of immunisation will be reported.EthicsThe study protocol was reviewed by the Ethical Review Committee on Research of the Pan American Health Organization. Patient informed consent was waived due to the retrospective design and the utilisation of anonymised data (Ref. No: PAHOERC.0546.01). Results will be disseminated in open access journals.