bluuebunny/crossref_metadata_2025_split huggingface dataset:
To Modulate Survival under Secondary Stress Conditions, Listeria monocytogenes 10403S Employs RsbX To Downregulate σ
B
Activity in the Poststress Recovery Stage or Stationary Phase
Authors: Xia Ye , Xin Yongping , Li Xiaoliang , Fang Weihuan 
Published: December 2015

ABSTRACT

Listeria monocytogenes
is a saprophytic bacterium that thrives in diverse environments and causes listeriosis via ingestion of contaminated food. RsbX, a putative sigma B (σ
B
) regulator, is thought to maintain the ready state in the absence of stress and reset the bacterium to the initial state in the poststress stage in
Bacillus subtilis
. We wondered whether RsbX is functional in
L. monocytogenes
under different stress scenarios. Genetic deletion and complementation of the
rsbX
gene were combined with survival tests and transcriptional and translational analyses of σ
B
expression in response to stresses. We found that deletion of
rsbX
increased survival under secondary stress following recovery of growth after primary stress or following stationary-phase culturing. The Δ
rsbX
mutant had higher expression of σ
B
than its parent strain in the recovery stage following primary sodium stress and in stationary-phase cultures. Apparently, increased σ
B
expression had contributed to improved survival in the absence of RsbX. There were no significant differences in survival rates or σ
B
expression levels in response to primary stresses between the
rsbX
mutant and its parent strain during the exponential phase. Therefore, we provide clear evidence that RsbX is a negative regulator of
L. monocytogenes
σ
B
during the recovery period after a primary stress or in the stationary phase, thus affecting its survival under secondary stress.
Alterations in the Quinolone Resistance-Determining Regions and Fluoroquinolone Resistance in Clinical Isolates and Laboratory-Derived Mutants of Mycoplasma bovis: Not All Genotypes May Be Equal
Authors: Khalil Dima , Becker Claire A. M. , Tardy Florence 
Published: December 2015

ABSTRACT

Mycoplasma bovis
is considered a major contributor to respiratory diseases in young cattle. Resistant
M. bovis
isolates have increasingly been reported worldwide due to extensive use of antimicrobials to treat bovine pneumonia. The frequency of isolates resistant to fluoroquinolones varies considerably from one country to another. The MICs of isolates collected in France have only increased from “very low” to “low.” The present study was conducted to investigate whether alterations in the quinolone resistance-determining regions (QRDRs) could account for this slight modification in susceptibility. No correlation between QRDR alterations and increased MICs was evidenced in clinical isolates. In addition, all clinical isolates were subtyped, and the tendencies of the different sequence types to develop resistance through mutations in QRDRs under selective pressure
in vitro
were examined.
In vitro
, 3 hot spots for mutations in QRDRs (position 83 in GyrA and positions 80 and 84 in ParC) were associated with a high level of resistance when cumulated. We showed that the point mutations in the QRDRs observed
in vitro
were different (in location and selection rapidity) between the different subtypes. Our
in vitro
observations were corroborated by the recent detection of a clinical isolate highly resistant to fluoroquinolones (MIC ≥ 16 μg/ml) and belonging to the subtype which easily accumulates QRDR alterations
in vitro
. The current increased prevalence of this subtype in clinical isolates highlights the urgent need to control fluoroquinolone usage in veterinary medicine.
Phytic Acid and Sodium Chloride Show Marked Synergistic Bactericidal Effects against Nonadapted and Acid-Adapted Escherichia coli O157:H7 Strains
Authors: Kim Nam Hee , Rhee Min Suk 
Published: December 2015

ABSTRACTThe synergistic antimicrobial effects of phytic acid (PA), a natural extract from rice bran, plus sodium chloride againstEscherichia coliO157:H7 were examined. Exposure to NaCl alone at concentrations up to 36% (wt/wt) for 5 min did not reduce bacterial populations. The bactericidal effects of PA alone were much greater than those of other organic acids (acetic, citric, lactic, and malic acids) under the same experimental conditions (P< 0.05). Combining PA and NaCl under conditions that yielded negligible effects when each was used alone led to marked synergistic effects. For example, whereas 0.4% PA or 3 or 4% NaCl alone had little or no effect on cell viability, combining the two completely inactivated both nonadapted and acid-adapted cells, reducing their numbers to unrecoverable levels (>7-log CFU/ml reduction). Flow cytometry confirmed that PA disrupted the cell membrane to a greater extent than did other organic acids, although the cells remained viable. The combination of PA and NaCl induced complete disintegration of the cell membrane. By comparison, none of the other organic acids acted synergistically with NaCl, and neither did NaCl-HCl solutions at the same pH values as the test solutions of PA plus NaCl. These results suggest that PA has great potential as an effective bacterial membrane-permeabilizing agent, and we show that the combination is a promising alternative to conventional chemical disinfectants. These findings provide new insight into the utility of natural compounds as novel antimicrobial agents and increase our understanding of the mechanisms underlying the antibacterial activity of PA.
Genomic Features of Environmental and Clinical Vibrio parahaemolyticus Isolates Lacking Recognized Virulence Factors Are Dissimilar
Authors: Ronholm J. , Petronella N. , Chew Leung C. , Pightling A. W. , Banerjee S. K. 
Published: December 2015

ABSTRACT

Vibrio parahaemolyticus
is a bacterial pathogen that can cause illness after the consumption or handling of contaminated seafood. The primary virulence factors associated with
V. parahaemolyticus
illness are thermostable direct hemolysin (TDH) and Tdh-related hemolysin (TRH). However, clinical strains lacking
tdh
and
trh
have recently been isolated, and these clinical isolates are poorly understood. To help understand the emergence of clinical
tdh
- and
trh
-negative isolates, a genomic approach was used to comprehensively compare 4 clinical
tdh
- and
trh
-negative isolates with 16 environmental
tdh
- and
trh
-negative isolates and 34 clinical isolates positive for
tdh
or
trh
, or both, with the objective of identifying genomic features that are unique to clinical
tdh
- and
trh
-negative isolates. The prevalence of pathogenicity islands (PAIs) common to clinical isolates was thoroughly examined in each of the clinical
tdh
- and
trh
-negative isolates. The
tdh
PAI was not present in any clinical or environmental
tdh
- and
trh
-negative isolates. The
trh
PAI was not present in any environmental isolates; however, in clinical
tdh
- and
trh
-negative isolate 10-4238, the majority of the
trh
PAI including a partial
trh1
gene was present, which resulted in reclassification of this isolate as a
tdh
-negative and
trh
-positive isolate. In the other clinical
tdh
- and
trh
-negative isolates, neither the
trh
gene nor the
trh
PAI was present. We identified 862 genes in clinical
tdh
- and
trh
-negative isolates but not in environmental
tdh
- and
trh
-negative isolates. Many of these genes are highly homologous to genes found in common enteric bacteria and included genes encoding a number of chemotaxis proteins and a novel putative type VI secretion system (T6SS) effector and immunity protein (T6SS1). The availability of genome sequences from clinical
V. parahaemolyticus
tdh
- and
trh
-negative isolates and the comparative analysis may help provide an understanding of how this pathotype is able to survive
in vivo
during clinical illness.
Secreted Acb1 Contributes to the Yeast-to-Hypha Transition in Cryptococcus neoformans
Authors: Xu Xinping , Zhao Youbao , Kirkman Elyssa , Lin Xiaorong 
Published: December 2015

ABSTRACT

Adaptation to stress by eukaryotic pathogens is often accompanied by a transition in cellular morphology. The human fungal pathogen
Cryptococcus neoformans
is known to switch between the yeast and the filamentous form in response to amoebic predation or during mating. As in the classic dimorphic fungal pathogens, the morphotype is associated with the ability of cryptococci to infect various hosts. Many cryptococcal factors and environmental stimuli, including pheromones (small peptides) and nutrient limitation, are known to induce the yeast-to-hypha transition. We recently discovered that secreted matricellular proteins could also act as intercellular signals to promote the yeast-to-hypha transition. Here we show that the secreted acyl coenzyme A (acyl-CoA)-binding protein Acb1 plays an important role in enhancing this morphotype transition. Acb1 does not possess a signal peptide. Its extracellular secretion and, consequently, its function in filamentation are dependent on an unconventional GRASP (Golgi reassembly stacking protein)-dependent secretion pathway. Surprisingly, intracellular recruitment of Acb1 to the secretory vesicles is independent of Grasp. In addition to Acb1, Grasp possibly controls the secretion of other cargos, because the
grasp
Δ mutant, but not the
acb1
Δ mutant, is defective in capsule production and macrophage phagocytosis. Nonetheless, Acb1 is likely the major or the sole effector of Grasp in terms of filamentation. Furthermore, we found that the key residue of Acb1 for acyl binding, Y80, is critical for the proper subcellular localization and secretion of Acb1 and for cryptococcal morphogenesis.
Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens
Authors: Zhou Yanjiao , Wylie Kristine M. , El Feghaly Rana E. , Mihindukulasuriya Kathie A. , Elward Alexis , Haslam David B. , Storch Gregory A. , Weinstock George M. 
Published: December 2015

ABSTRACT

The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for
Clostridium difficile
identification in diarrhea stool samples. Twenty-two
C. difficile
-positive diarrhea samples identified by PCR and qPCR and five
C. difficile
-negative diarrhea controls were studied.
C. difficile
was detected in 90.9% of
C. difficile
-positive samples using 16S rRNA gene sequencing, and
C. difficile
was detected in 86.3% of
C. difficile
-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of
C. difficile
from 16S rRNA gene sequencing (
r
2
= −0.60) and MSS (
r
2
= −0.55).
C. difficile
was codetected with
Clostridium perfringens
, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of
Candida
spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without
a priori
knowledge.
Evaluation of the BYG Carba Test, a New Electrochemical Assay for Rapid Laboratory Detection of Carbapenemase-Producing Enterobacteriaceae
Authors: Bogaerts Pierre , Yunus Sami , Massart Marion , Huang Te-Din , Glupczynski Youri 
Published: December 2015

ABSTRACT

Accurate detection of carbapenemase-producing
Enterobacteriaceae
(CPE) constitutes a major laboratory diagnostic challenge. We evaluated an electrochemical technique (the BYG Carba test) which allows detection of CPE in less than 35 min. The BYG Carba test was first validated in triplicate against 57 collection isolates with previously characterized β-lactam resistance mechanisms (OXA-48,
n
= 12; KPC,
n
= 8; NDM,
n
= 8; VIM,
n
= 8; IMP,
n
= 3; GIM,
n
= 1; GES-6,
n
= 1; no carbapenemase,
n
= 16) and against a panel of 10 isolates obtained from the United Kingdom National External Quality Assessment Service (NEQAS). The test was then evaluated prospectively against 324 isolates referred to the national reference center for suspicion of CPE. The BYG Carba test results were compared with those obtained with the Carba NP test using multiplex PCR sequencing as the gold standard. Of the 57 collection and the 10 NEQAS isolates, all but one GES-6-producing isolate were correctly identified by the Carba BYG test. Among the 324 consecutive
Enterobacteriaceae
isolates tested prospectively, 146 were confirmed as noncarbapenemase producers by PCR while 178 harbored a carbapenemase gene (OXA-48,
n
= 117; KPC,
n
= 25; NDM,
n
= 23; and VIM,
n
= 13). Prospectively, in comparison with PCR results, the BYG Carba test displayed 95% sensitivity and 100% specificity versus 89% and 100%, respectively, for the Carba NP test. The BYG Carba test is a novel, rapid, and efficient assay based on an electro-active polymer biosensing technology discriminating between CPE and non-CPE. The precise electrochemical signal (electrochemical impedance variations) allows the establishment of real-time objective measurement and interpretation criteria which should facilitate the accreditation process of this technology.
Acute Viral Escape Selectively Impairs Nef-Mediated Major Histocompatibility Complex Class I Downmodulation and Increases Susceptibility to Antiviral T Cells
Authors: Weiler Andrea M. , Das Arpita , Akinyosoye Oluwasayo , Cui Sherry , O'Connor Shelby L. , Scheef Elizabeth A. , Reed Jason S. , Panganiban Antonito T. , Sacha Jonah B. , Rakasz Eva G. , Friedrich Thomas C. , Maness Nicholas J. 
Published: December 2015

ABSTRACT

Nef-specific CD8
+
T lymphocytes (CD8TL) are associated with control of simian immunodeficiency virus (SIV) despite extensive
nef
variation between and within animals. Deep viral sequencing of the immunodominant Mamu-B*017:01-restricted Nef
165–173
IW9 epitope revealed highly restricted evolution. A common acute escape variant, T
170
I, unexpectedly and uniquely degraded Nef's major histocompatibility complex class I (MHC-I) downregulatory capacity, rendering the virus more vulnerable to CD8TL targeting other epitopes. These data aid in a mechanistic understanding of Nef functions and suggest means of immunity-mediated control of lentivirus replication.
Influenza A Virus-Induced Expression of a GalNAc Transferase, GALNT3, via MicroRNAs Is Required for Enhanced Viral Replication
Authors: Nakamura Shoko , Horie Masayuki , Daidoji Tomo , Honda Tomoyuki , Yasugi Mayo , Kuno Atsushi , Komori Toshihisa , Okuzaki Daisuke , Narimatsu Hisashi , Nakaya Takaaki , Tomonaga Keizo 
Published: December 2015

ABSTRACT

Influenza A virus (IAV) affects the upper and lower respiratory tracts and rapidly induces the expression of mucins, which are common O-glycosylated proteins, on the epithelial surfaces of the respiratory tract. Although mucin production is associated with the inhibition of virus transmission as well as characteristic clinical symptoms, little is known regarding how mucins are produced on the surfaces of respiratory epithelial cells and how they affect IAV replication. In this study, we found that two microRNAs (miRNAs), miR-17-3p and miR-221, which target GalNAc transferase 3 (GALNT3) mRNA, are rapidly downregulated in human alveolar basal epithelial cells during the early stage of IAV infection. We demonstrated that the expression of GALNT3 mRNA is upregulated in an IAV replication-dependent fashion and leads to mucin production in bronchial epithelial cells. A lectin microarray analysis revealed that the stable expression of GALNT3 by human alveolar basal epithelial cells induces mucin-type O-glycosylation modifications similar to those present in IAV-infected cells, suggesting that GALNT3 promotes mucin-type O-linked glycosylation in IAV-infected cells. Notably, analyses using short interfering RNAs and miRNA mimics showed that GALNT3 knockdown significantly reduces IAV replication. Furthermore, IAV replication was markedly decreased in embryonic fibroblast cells obtained from
galnt3
-knockout mice. Interestingly, IAV-infected
galnt3
-knockout mice exhibited high mortality and severe pathological alterations in the lungs compared to those of wild-type mice. Our results demonstrate not only the molecular mechanism underlying rapid mucin production during IAV infection but also the contribution of O-linked glycosylation to the replication and propagation of IAV in lung cells.

IMPORTANCE
Viral infections that affect the upper or lower respiratory tracts, such as IAV, rapidly induce mucin production on the epithelial surfaces of respiratory cells. However, the details of how mucin-type O-linked glycosylation is initiated by IAV infection and how mucin production affects viral replication have not yet been elucidated. In this study, we show that levels of two miRNAs that target the UDP-GalNAc transferase GALNT3 are markedly decreased during the early stage of IAV infection, resulting in the upregulation of GALNT3 mRNA. We also demonstrate that the expression of GALNT3 initiates mucin production and affects IAV replication in infected cells. This is the first report demonstrating the mechanism underlying the miRNA-mediated initiation of mucin-type O-glycosylation in IAV-infected cells and its role in viral replication. Our results have broad implications for understanding IAV replication and suggest a strategy for the development of novel anti-influenza approaches.
Antibody Binding Modulates Conformational Exchange in Domain III of Dengue Virus E Protein
Authors: Moraes Adolfo H. , Simonelli Luca , Pedotti Mattia , Almeida Fabio C. L. , Varani Luca , Valente Ana P. 
Published: December 2015

ABSTRACT
Domain III of dengue virus E protein (DIII) participates in the recognition of cell receptors and in structural rearrangements required for membrane fusion and ultimately viral infection; furthermore, it contains epitopes for neutralizing antibodies and has been considered a potential vaccination agent. In this work, we addressed various structural aspects of DIII and their relevance for both the dengue virus infection mechanism and antibody recognition. We provided a dynamic description of DIII at physiological and endosomal pHs and in complex with the neutralizing human antibody DV32.6. We observed conformational exchange in the isolated DIII, in regions important for the packing of E protein dimers on the virus surface. This conformational diversity is likely to facilitate the partial detachment of DIII from the other E protein domains, which is required to achieve fusion to the host cellular membranes and to expose the epitopes of many anti-DIII antibodies. A comparison of DIII of two dengue virus serotypes revealed many common features but also some possibly unexpected differences. Antibody binding to DIII of dengue virus serotype 4 attenuated the conformational exchange in the epitope region but, surprisingly, generated exchange in other parts of DIII through allosteric effects.

IMPORTANCE
Many studies have provided extensive structural information on the E protein and particularly on DIII, also in complex with antibodies. However, there is very scarce information regarding the molecular dynamics of DIII, and almost nothing is available on the dynamic effect of antibody binding, especially at the quantitative level. This work provides one of the very rare descriptions of the effect of antibody binding on antigen dynamics.
Influenza Virus Infection Induces Platelet-Endothelial Adhesion Which Contributes to Lung Injury
Authors: Sugiyama Michael G. , Gamage Asela , Zyla Roman , Armstrong Susan M. , Advani Suzanne , Advani Andrew , Wang Changsen , Lee Warren L. 
Published: December 2015

ABSTRACT

Lung injury after influenza infection is characterized by increased permeability of the lung microvasculature, culminating in acute respiratory failure. Platelets interact with activated endothelial cells and have been implicated in the pathogenesis of some forms of acute lung injury. Autopsy studies have revealed pulmonary microthrombi after influenza infection, and epidemiological studies suggest that influenza vaccination is protective against pulmonary thromboembolism; however, the effect of influenza infection on platelet-endothelial interactions is unclear. We demonstrate that endothelial infection with both laboratory and clinical strains of influenza virus increased the adhesion of human platelets to primary human lung microvascular endothelial cells. Platelets adhered to infected cells as well as to neighboring cells, suggesting a paracrine effect. Influenza infection caused the upregulation of von Willebrand factor and ICAM-1, but blocking these receptors did not prevent platelet-endothelial adhesion. Instead, platelet adhesion was inhibited by both RGDS peptide and a blocking antibody to platelet integrin α
5
β
1
, implicating endothelial fibronectin. Concordantly, lung histology from infected mice revealed viral dose-dependent colocalization of viral nucleoprotein and the endothelial marker PECAM-1, while platelet adhesion and fibronectin deposition also were observed in the lungs of influenza-infected mice. Inhibition of platelets using acetylsalicylic acid significantly improved survival, a finding confirmed using a second antiplatelet agent. Thus, influenza infection induces platelet-lung endothelial adhesion via fibronectin, contributing to mortality from acute lung injury. The inhibition of platelets may constitute a practical adjunctive strategy to the treatment of severe infections with influenza.

IMPORTANCE
There is growing appreciation of the involvement of the lung endothelium in the pathogenesis of severe infections with influenza virus. We have recently shown that the virus can infect human lung endothelial cells, but the functional consequences of this infection are unknown (S. M. Armstrong, C. Wang, J. Tigdi, X. Si, C. Dumpit, S. Charles, A. Gamage, T. J. Moraes, and W. L. Lee, PLoS One 7:e47323, 2012,
http://dx.doi.org/10.1371/journal.pone.0047323
). Here, we show that this infection causes platelets to adhere to the lung endothelium. Importantly, blocking platelets using two distinct antiplatelet drugs improved survival in a mouse model of severe influenza infection. Thus, platelet inhibition may constitute a novel therapeutic strategy to improve the host response to severe infections with influenza.