bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth defect of domain III glycoprotein B mutants of human cytomegalovirus reverted by compensatory mutations co-localizing in post-fusion conformation
Authors: Mollik Madlen , Rohorzka Andreas , Chen Xiaohan , Kropff Barbara , Eisler Lukas , Külekci Büsra , Puchhammer-Stöckl Elisabeth , Thomas Marco , Görzer Irene 
Published: September 2024

ABSTRACT

Cell entry is a crucial step for a virus to infect a host cell. Human cytomegalovirus utilizes glycoprotein B (gB) to fuse the viral and host cell membranes upon receptor binding of gH/gL-containing complexes. Fusion is mediated by major conformational changes of gB from a metastable pre-fusion to a stable post-fusion state whereby the central trimeric coiled-coils, formed by domain (Dom)III α helices, remain structurally nearly unchanged. To better understand the role of the stable core, we individually introduced three potentially helix-breaking or one disulfide bond-breaking mutation in the DIII α3 to study different aspects of the viral behavior upon long-term culturing. Two of the three helix-breaking mutations, gB_Y494P and gB_I495P, were lethal for the virus in either fibroblasts or epithelial cells. The third substitution, gB_G493P, on the other hand, displayed a delayed replication and spread, which was more pronounced in epithelial cells, hinting at an impaired fusion. Interestingly, the disulfide bond-breaker mutation, gB_C507S, performed strikingly differently in the two cell types - lethal in epithelial cells and an atypical phenotype in fibroblasts, respectively. Replication curve analyses paired with the infection efficiency, the spread morphology, and the cell–cell fusogenicity suggest a dysregulated fusion process, which could be reverted by second-site mutations mapping predominantly to gB DomV. Our findings underline the functional importance of a stable DomIII core for a well-regulated DomV rearrangement during fusion.

IMPORTANCE
Human cytomegalovirus (HCMV) can establish a lifelong infection. In most people, the infection follows an asymptomatic course; however, it is a major cause of morbidity and mortality in immunocompromised patients or neonates. HCMV has a very broad cell tropism, ranging from fibroblasts to epi- and endothelial cells. The virus uses different entry pathways utilizing the core fusion machinery consisting of glycoprotein complexes gH/gL and glycoprotein B (gB). The fusion protein gB undergoes fundamental rearrangements from a metastable pre-fusion to a stable post-fusion conformation. Here, we characterized the viral behavior after the introduction of four single-point mutations in the gB central core. These led to various cell type-specific atypical phenotypes and the emergence of compensatory mutations, demonstrating an important interaction between domains III and V. We provide a new basis for the development of a structurally and functionally altered gB, which can further serve as a tool for drug and vaccine development.
Investigation of Zur-regulated metal transport systems reveals an unexpected role of pyochelin in zinc homeostasis
Authors: Secli Valerio , Michetti Emma , Pacello Francesca , Iacovelli Federico , Falconi Mattia , Astolfi Maria Luisa , Visaggio Daniela , Visca Paolo , Ammendola Serena , Battistoni Andrea 
Published: September 2024

ABSTRACT

Limiting the availability of transition metals at infection sites serves as a critical defense mechanism employed by the innate immune system to combat microbial infections.
Pseudomonas aeruginosa
exhibits a remarkable ability to thrive in zinc-deficient environments, facilitated by intricate cellular responses governed by numerous genes regulated by the zinc-responsive transcription factor Zur. Many of these genes have unknown functions, including those within the predicted
PA2911-PA2914
and
PA4063-PA4066
operons. A structural bioinformatics investigation revealed that
PA2911-PA2914
comprises a TonB-dependent outer membrane receptor and inner membrane ABC-permeases responsible for importing metal-chelating molecules, whereas
PA4063-PA4066
contains genes encoding a MacB transporter, likely involved in the export of large molecules. Molecular genetics and biochemical experiments, feeding assays, and intracellular metal content measurements support the hypothesis that
PA2911-PA2914
and
PA4063-PA4066
are engaged in the import and export of the pyochelin-cobalt complex, respectively. Notably, cobalt can reduce zinc demand and promote the growth of
P. aeruginosa
strains unable to import zinc, highlighting pyochelin-mediated cobalt import as a novel bacterial strategy to counteract zinc deficiency. These results unveil an unexpected role for pyochelin in zinc homeostasis and challenge the traditional view of this metallophore exclusively as an iron transporter.

IMPORTANCE

The mechanisms underlying the remarkable ability of
Pseudomonas aeruginosa
to resist the zinc sequestration mechanisms implemented by the vertebrate innate immune system to control bacterial infections are still far from being fully understood. This study reveals that the Zur-regulated gene clusters
PA2911-2914
and
PA4063-PA4066
encode systems for the import and export of cobalt-bound pyochelin, respectively. This proves to be a useful strategy to counteract conditions of severe zinc deficiency since cobalt can replace zinc in many proteins. The discovery that pyochelin may contribute to cellular responses to zinc deficiency leads to a reevaluation of the paradigm that pyochelin is a siderophore involved exclusively in iron acquisition and suggests that this molecule has a broader role in modulating the homeostasis of multiple metals.
Draft genome sequence of
Achromobacter aegrifaciens
BAW48 isolated from arsenic-contaminated tubewell water in Bangladesh
Authors: Hossain Anamica , Hoque M. Nazmul , Bukharid Momtaz Zamila , Hossain M. Anwar , Sultana Munawar 
Published: September 2024

ABSTRACT

We report the draft genome of
Achromobacter aegrifaciens
strain BAW48, a bacterium with a genome size of 6,877,653 bp. This genome comprises gene clusters for arsenic conversion, such as arsenic resistance (
arsHCsO
), arsenite oxidation (
aioBA
), and arsenate reduction (
arsRCDAB
), along with genes for heavy metal and antibiotic resistance.
Draft genome sequence of an arsenotrophic
Achromobacter aegrifaciens
strain isolated from soil in Bangladesh
Authors: Hoque M. Nazmul , Hossain Anamica , Faisal Golam Mahbub , Bukharid Momtaz Zamila , Hossain M. Anwar , Sultana Munawar 
Published: September 2024

ABSTRACT

We report the draft genome of an arsenotrophic
Achromobacter aegrifaciens
BAS32 isolated from arsenic (As)-contaminated soil in Bangladesh. This genome contains several predicted gene clusters for As-conversion, namely, As resistance (
ars
HCsO), arsenite-oxidizing (
aio
BA), and arsenate-reducing (
ars
RCDAB) gene clusters along with antibiotic resistance genes (ARGs).
Genome sequencing of
Enterococcus faecalis
strain 13, an oral strain isolated from C57BL/6 mice
Authors: Vazquez-Munoz Roberto , Russell Jordan T. , Thompson Angela , Dongari-Bagtzoglou Anna 
Published: September 2024

ABSTRACT

Enterococcus faecalis
strain 13 (Ef#13) is a tongue isolate from a C57BL/6 mouse with experimental oropharyngeal candidiasis. Short-read sequencing revealed a genome of 2,767,598 bp with a GC content of 38.4%, and 2,649 genes were predicted.
Preexisting cell state rather than stochastic noise confers high or low infection susceptibility of human lung epithelial cells to adenovirus
Authors: Petkidis Anthony , Suomalainen Maarit , Andriasyan Vardan , Singh Abhyudai , Greber Urs F. 
Published: September 2024

ABSTRACT

Viruses display large variability across all stages of their life cycle, including entry, gene expression, replication, assembly, and egress. We previously reported that the immediate early adenovirus (AdV) E1A transcripts accumulate in human lung epithelial A549 cancer cells with high variability, mostly independent of the number of incoming viral genomes, but somewhat correlated to the cell cycle state at the time of inoculation. Here, we leveraged the classical Luria–Delbrück fluctuation analysis to address whether infection variability primarily arises from the cell state or stochastic noise. The E1A expression was measured by the expression of green fluorescent protein (GFP) from the endogenous E1A promoter in AdV-C5_E1A-FS2A-GFP and found to be highly correlated with the viral plaque formation, indicating reliability of the reporter virus. As an ensemble, randomly picked clonal A549 cell isolates displayed significantly higher coefficients of variation in the E1A expression than technical noise, indicating a phenotypic variability larger than noise. The underlying cell state determining infection variability was maintained for at least 9 weeks of cell cultivation. Our results indicate that preexisting cell states tune adenovirus infection in favor of the cell or the virus. These findings have implications for antiviral strategies and gene therapy applications.

IMPORTANCE
Viral infections are known for their variability. Underlying mechanisms are still incompletely understood but have been associated with particular cell states, for example, the eukaryotic cell division cycle in DNA virus infections. A cell state is the collective of biochemical, morphological, and contextual features owing to particular conditions or at random. It affects how intrinsic or extrinsic cues trigger a response, such as cell division or anti-viral state. Here, we provide evidence that cell states with a built-in memory confer high or low susceptibility of clonal human epithelial cells to adenovirus infection. Results are reminiscent of the Luria–Delbrück fluctuation test with bacteriophage infections back in 1943, which demonstrated that mutations, in the absence of selective pressure prior to infection, cause infection resistance rather than being a consequence of infection. Our findings of dynamic cell states conferring adenovirus infection susceptibility uncover new challenges for the prediction and treatment of viral infections.
A “plus one” strategy impacts replication of felid alphaherpesvirus 1,
Mycoplasma
and
Chlamydia,
and the metabolism of coinfected feline cells
Authors: Klose Sara M. , De Souza David P. , Devlin Joanne M. , Bushell Rhys , Browning Glenn F. , Vaz Paola K. 
Published: September 2024

ABSTRACT

Coinfections are known to play an important role in disease progression and severity. Coinfections are common in cats, but no coinfection studies have investigated the
in vitro
dynamics between feline viral and bacterial pathogens. In this study, we performed co-culture and invasion assays to investigate the ability of common feline bacterial respiratory pathogens,
Chlamydia felis
and
Mycoplasma felis
, to replicate in and invade into Crandell–Rees feline kidney cells. We subsequently investigated how coinfection of these feline cells with each bacterium (
C. felis
or
M. felis
) and the common feline viral pathogen, felid alphaherpesvirus 1 (FHV-1), affects replication of each agent in this cell culture system. We also investigated the metabolic impact of each co-pathogen using metabolomic analysis of infected and coinfected cells.
C. felis
was able to invade and replicate in CRFKs, while
M. felis
had little capacity to invade. During coinfection, FHV-1 replication was minimally affected by the presence of either bacterial pathogen, but bacterial replication kinetics were more affected, particularly in
M. felis
. Both
C. felis
and
M. felis
replicated to higher levels in the presence of a secondary pathogen. Coinfections resulted in reprogramming of the glycolysis pathway, the pentose phosphate pathway, and the tricarboxylic acid cycle. The distinct metabolic profiles of coinfected cells compared to those of cells infected with just one of these three pathogens, as well as the impact of coinfections on viral or bacterial load, suggest strong interactions between these three pathogens and possible synergistic mechanisms enhancing virulence that need further investigation.

IMPORTANCE
In the natural world, respiratory pathogens coexist within their hosts, but their dynamics and interactions remain largely unexplored. Herpesviruses, mycoplasmas, and chlamydias are common and significant causes of acute and chronic respiratory and system disease in animals and people, and these diseases are increasingly found to be polymicrobial. This study investigates how coinfection of feline cells between three respiratory pathogens of cats impact each other as well as the host innate metabolic response to infection. Each of these pathogens have been implicated in the induction of feline upper respiratory tract disease in cats, which is the leading cause of euthanasia in shelters. Understanding how coinfection impacts co-pathogenesis and host responses is critical for improving disease management.
Clinical prediction model for bacterial co-infection in hospitalized COVID-19 patients during four waves of the pandemic
Authors: Elbaz Meital , Moshkovits Itay , Bar-On Tali , Goder Noam , Lichter Yael , Ben-Ami Ronen 
Published: September 2024

ABSTRACT

The reported estimates of bacterial co-infection in COVID-19 patients are highly variable. We aimed to determine the rates and risk factors of bacterial co-infection and develop a clinical prediction model to support early decision-making on antibiotic use. This is a retrospective cohort study conducted in a tertiary-level academic hospital in Israel between March 2020 and May 2022. All adult patients with severe COVID-19 who had a blood or lower respiratory specimen sent for microbiological analyses within 48 h of admission were included. The primary study endpoint was the prevalence of bacterial co-infection at the time of hospital admission. We created a prediction model using the R XGBoost package. The study cohort included 1,050 patients admitted with severe or critical COVID-19. Sixty-two patients (5.9%) had a microbiologically proven bacterial infection on admission. The variables with the greatest impact on the prediction model were age, comorbidities, functional capacity, and laboratory parameters. The model achieved perfect prediction on the training set (area under the curve = 1.0). When applied to the test dataset, the model achieved 56% and 78% specificity with the area under the receiver operating curve of 0.784. The negative and positive predictive values were 0.975 and 0.105, respectively. Applying the prediction model would have resulted in a 2.5-fold increase in appropriate antibiotic use and an 18% reduction in inappropriate use in patients with severe and critical COVID-19. The use of a clinical prediction model can support decisions to withhold empiric antimicrobial treatment at the time of hospital admission without adversely affecting patient outcomes.

IMPORTANCE
Estimates of bacterial coinfection in COVID-19 patients are highly variable and depend on many factors. Patients with severe or critical COVID-19 requiring intensive care unit admission have the highest risk of infection-related complications and death. Thus, the study of the incidence and risk factors for bacterial coinfection in this population is of special interest and may help guide empiric antibiotic therapy and avoid unnecessary antimicrobial treatment. The prediction model based on clinical criteria and simple laboratory tests may be a useful tool to predict bacterial co-infection in patients hospitalized with severe COVID-19.
Role of rectal colonization by third-generation cephalosporin-resistant Enterobacterales on the risk of surgical site infection after hepato-pancreato-biliary surgery
Authors: Rodríguez-Fernández Miguel , Trigo-Rodríguez Marta , Martínez-Baena Darío , Herrero Rocío , Espíndola-Gómez Reinaldo , Martínez Pérez-Crespo Pedro , Vela Alberto Gallego , Torres Eva , García Ana Isabel Aller , León Eva M. , Corzo-Delgado Juan E. , Parra-Membrives Pablo , Merchante Nicolás 
Published: September 2024

ABSTRACT

The impact of third-generation cephalosporin-resistant Enterobacterales (3GCR-E) rectal colonization in the development of subsequent infection after surgery is controversial. In particular, there is a lack of data in the context of hepato-pancreato-biliary (HPB) surgery. The objective of this study was to assess the prevalence of 3GCR-E intestinal carriage among patients undergoing elective HPB resection surgery and its impact on the incidence and etiology of surgical site infections (SSIs). This retrospective cohort study (January 2016–December 2022) was performed at Valme University Hospital (Seville, Spain). The inclusion criteria included (i) 18 years of age or older, (ii) undergoing elective HPB resection surgery, and (iii) availability of a periprocedural surveillance rectal swab culture to detect 3GCR-E. The prevalence of 3GCR-E intestinal carriage at elective HPB resection surgery was assessed, as well as SSI incidence at 30 days and possible associated factors. Two hundred nine patients were included. Eleven (5.3%) patients were colonized by 3GCR-E at baseline. According to 3GCR-E carriage status, 6 (55%) of the carriers developed SSI, whereas this occurred in 50 (25%) of non-carriers (
P
= 0.033). Likewise, the rates of SSI caused specifically by 3GCR-E were 83% (5 of 6) in 3GCR-E carriers and 6% (3 of 50) in non-carriers (
P
< 0.001). After multivariate analyses, 3GCR-E colonization at the time of surgery was identified as an independent predictor for developing SSI (adjusted odds ratio 4.63, 95% confidence interval: 1.177–18.232,
P
= 0.028). Despite a low prevalence of 3GCR-E intestinal carriage at surgery, 3GCR-E rectal colonization is associated with a higher risk of SSI among patients undergoing elective HPB resection surgery, with most SSIs being caused by the colonizing bacteria.

IMPORTANCE
In this Spanish retrospective cohort study, previous 3GCR-E rectal colonization was associated with a higher risk of SSI after hepato-pancreato-biliary resection surgeries. Most of SSIs were caused by the colonizing bacteria, suggesting a rationale for adapted perioperative antibiotic prophylaxis in known 3GCR-E colonized patients.
Selection of marine bacterial consortia efficient at degrading chitin leads to the discovery of new potential chitin degraders
Authors: Meunier Laurence , Costa Rodrigo , Keller-Costa Tina , Cannella David , Dechamps Etienne , George Isabelle F. 
Published: September 2024

ABSTRACT

Chitin degradation is a keystone process in the oceans, mediated by marine microorganisms with the help of several enzymes, mostly chitinases. Sediment, seawater, and filter-feeding marine invertebrates, such as sponges, are known to harbor chitin-degrading bacteria and are presumably hotspots for chitin turnover. Here, we employed an artificial selection process involving enrichment cultures derived from microbial communities associated with the marine sponge
Hymeniacidon perlevis
, its surrounding seawater and sediment, to select bacterial consortia capable of degrading raw chitin. Throughout the artificial selection process, chitin degradation rates and the taxonomic composition of the four successive enrichment cultures were followed. To the best of our knowledge, chitin degradation was characterized for the first time using size exclusion chromatography, which revealed significant shifts in the numbered average chitin molecular weight, strongly suggesting the involvement of endo-chitinases in the breakdown of the chitin polymer during the enrichment process. Concomitantly with chitin degradation, the enrichment cultures exhibited a decrease in alpha diversity compared with the environmental samples. Notably, some of the dominant taxa in the enriched communities, such as
Motilimonas
,
Arcobacter
, and
Halarcobacter
, were previously unknown to be involved in chitin degradation. In particular, the analysis of published genomes of these genera suggests a pivotal role of
Motilimonas
in the hydrolytic cleavage of chitin. This study provides context to the microbiome of the marine sponge
Hymeniacidon perlevis
in light of its environmental surroundings and opens new ground to the future discovery and characterization of novel enzymes of marine origin involved in chitin degradation processes.

IMPORTANCE
Chitin is the second most abundant biopolymer on Earth after cellulose, and the most abundant in the marine environment. At present, industrial processes for the conversion of seafood waste into chitin, chitosan, and chitooligosaccharide (COS) rely on the use of high amounts of concentrated acids or strong alkali at high temperature. Developing bio-based methods to transform available chitin into valuable compounds, such as chitosan and COS, holds promise in promoting a more sustainable, circular bioeconomy. By employing an artificial selection procedure based on chitin as a sole C and N source, we discovered microorganisms so-far unknown to metabolize chitin in the rare microbial biosphere of several marine biotopes. This finding represents a first important step on the path towards characterizing and exploiting potentially novel enzymes of marine origin with biotechnological interest, since products of chitin degradation may find applications across several sectors, such as agriculture, pharmacy, and waste management.
First report of IS
Kpn26
element mediating
mgrB
gene disruption in the ST1 colistin- and carbapenem-resistant
Klebsiella pneumoniae
cluster isolated from a patient with chest infection
Authors: Li Xiaosi , Shen Siquan , Feng Yan , Shen Heping , Hu Fupin , Wu Xiaoyan 
Published: September 2024

ABSTRACT

Colistin is used as a last-line therapy against carbapenem-resistant
Klebsiella pneumoniae
(CRKP). However, colistin resistance in
Klebsiella pneumoniae
is increasingly reported worldwide. This study aims to investigate the instrumental role of insertion sequence (IS) elements in colistin resistance through
mgrB
disruption in
K. pneumoniae
during treatment. Five clinical isolates of CRKP, designated KPN1~KPN5 were collected from the lower respiratory tract of a patient with chest infection before and after treatment with colistin. Antimicrobial susceptibility testing was performed using the broth microdilution method. Whole genome sequencing and bioinformatics were used to analyze the sequence types (STs), resistance genes, and genetic characteristics of the five isolates of
K. pneumoniae
. Antimicrobial susceptibility testing indicated that all five
K. pneumoniae
isolates were resistant to cephalosporins (ceftriaxone, ceftazidime, and cefepime), several carbapenems (imipenem, meropenem), cefoperazone–sulbactam, piperacillin–tazobactam, ciprofloxacin, and fosfomycin, whereas they were sensitive to amikacin and tigecycline. In addition, three of these isolates were resistant to colistin, with minimum inhibitory concentration values of >8 mg/L. Whole genome sequencing revealed that all five
K. pneumoniae
isolates belonged to sequence type 1 (ST1), which shared an identical
bla
KPC-2
. Notably, disruption of
mgrB
by the IS
Kpn26
insertion sequence was shown to be the primary colistin resistance mechanism during the treatment. To our knowledge, this is the first report of IS
Kpn26
element mediating
mgrB
disruption in the ST1 colistin and CRKP obtained from a patient with chest infection in mainland China. This study provides new research ideas to explore the clinical drug resistance mechanism of CRKP and the critical need to monitor and understand resistance mechanisms to preserve the efficacy of last-line antibiotics such as colistin.

IMPORTANCE

Of note, this chapter gives an update on colistin resistance in sequence type 1
Klebsiella pneumoniae
, by focusing on the
mgrB
disrupted by IS
Kpn26
element.