bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered serine metabolism promotes drug tolerance in
Mycobacterium abscessus
via a WhiB7-mediated adaptive stress response
Authors: Bernard Célia , Liu Yi , Larrouy-Maumus Gérald , Guilhot Christophe , Cam Kaymeuang , Chalut Christian 
Published: April 2024

ABSTRACT

Mycobacterium abscessus
is an emerging opportunistic pathogen responsible for chronic lung diseases, especially in patients with cystic fibrosis. Treatment failure of
M. abscessus
infections is primarily associated with intrinsic or acquired antibiotic resistance. However, there is growing evidence that antibiotic tolerance, i.e., the ability of bacteria to transiently survive exposure to bactericidal antibiotics through physiological adaptations, contributes to the relapse of chronic infections and the emergence of acquired drug resistance. Yet, our understanding of the molecular mechanisms that underlie antibiotic tolerance in
M. abscessus
remains limited. In the present work, a mutant with increased cross-tolerance to the first- and second-line antibiotics cefoxitin and moxifloxacin, respectively, has been isolated by experimental evolution. This mutant harbors a mutation in
serB2
, a gene involved in L-serine biosynthesis. Metabolic changes caused by this mutation alter the intracellular redox balance to a more reduced state that induces overexpression of the transcriptional regulator WhiB7 during the stationary phase, promoting tolerance through activation of a WhiB7-dependant adaptive stress response. These findings suggest that alteration of amino acid metabolism and, more generally, conditions that trigger
whiB7
overexpression, makes
M. abscessus
more tolerant to antibiotic treatment.
Genomic characterization of two ranavirus isolates identified from a gopher frog (
Lithobates capito
) and a striped newt (
Notophthalmus perstriatus
) during a mass mortality event in Florida
Authors: Hartmann Arik , Subramaniam Kuttichantran , Conrad Cody , Viadanna Pedro H.O. , Waltzek Thomas B. , Longo Ana V. 
Published: April 2024

ABSTRACT

Two ranavirus isolates were recovered from anuran and salamander samples collected during an amphibian mass mortality event in North-Central Florida in 2021. Phylogenetic analyses of the full genomes confirmed that the two isolates were nearly identical and strains of the species
Frog virus 3
.
SILAC analysis of
Escherichia coli
proteome during progression of growth from exponential to prolonged stationary phase
Authors: Reier Kaspar , Liiv Aivar , Remme Jaanus 
Published: April 2024

ABSTRACT

The expression level of individual proteins varies markedly during the progression of the growth phase in bacteria. A set of proteins was quantified in
Escherichia coli
total proteome during 14 days of batch cultivation using pulse stable isotope labeled amino acids in cell culture (SILAC)-based quantitative mass spectrometry.
Emergence of SARS-CoV-2 Omicron sub-lineage JN.1 in Bangladesh
Authors: Jony Manjur Hossain Khan , Alam Ahmed Nawsher , Nasif Md. Abdullah Omar , Sultana Sharmin , Anwar Rubaid , Rudra Mithun , Rahman Mahbubur , Rahman Mustafizur , Qadri Firdausi , Shirin Tahmina 
Published: April 2024

ABSTRACT

We report complete genome sequences of 14 severe acute respiratory syndrome coronavirus 2 Omicron sub-lineage JN.1 obtained from Bangladeshi individuals between 19 December 2023 and 21 January 2024. All sequence data were generated by Oxford Nanopore Sequencing Technology using the amplicon sequencing approach developed by the ARTIC network.
Complete genome sequence of the rumen bacterium
Butyrivibrio fibrisolvens
D1
T
Authors: Palevich Nikola , Palevich Faith P. , Attwood Graeme T. , Kelly William J. 
Published: April 2024

ABSTRACT

Butyrivibrio
are anaerobic bacteria and members of the family
Lachnospiraceae
with important roles in fiber digestion in both animals and humans. This report describes the complete genome of
Butyrivibrio fibrisolvens
type strain D1
T
(DSM 3071) consisting of a chromosome (
CP146963
), megaplasmid (pNP243), and small plasmid (pNP21).
Genome sequences of two
Arthrobacter
phages isolated from soil
Authors: Marchesin-Cupello Dana , Roscales Gabriel , Cobeta Paula , Chaboy-Cansado Ruben , Aguirre de Cárcer Daniel , Rastrojo Alberto 
Published: April 2024

ABSTRACT

The isolation and characterization of additional phages is crucial for adding reliable viral sequences with relevant biological information to viral databases. In this study, we present the complete genomes of two
Arthrobacter
phages obtained from different soil samples.
Detection of Mtb and NTM: preclinical validation of a new asymmetric PCR-binary deoxyribozyme sensor assay
Authors: Neves Yasmin Castillos das , Reis Ana Julia , Rodrigues Marcos Alaniz , Chimara Erica , da Silva Lourenço Maria Cristina , Fountain Jacques , Ramis Ivy Bastos , von Groll Andrea , Gerasimova Yulia , Rohde Kyle H. , Almeida da Silva Pedro Eduardo 
Published: April 2024

ABSTRACT

Tuberculosis (TB) and infectious diseases caused by non-tuberculous mycobacteria (NTM) are global concerns. The development of a rapid and accurate diagnostic method, capable of detecting and identifying different mycobacteria species, is crucial. We propose a molecular approach, the BiDz-TB/NTM, based on the use of binary deoxyribozyme (BiDz) sensors for the detection of
Mycobacterium tuberculosis
(Mtb) and NTM of clinical interest. A panel of DNA samples was used to evaluate Mtb-BiDz,
Mycobacterium abscessus
/
Mycobacterium chelonae
-BiDz,
Mycobacterium avium
-BiDz,
Mycobacterium intracellulare
/
Mycobacterium chimaera
-BiDz, and
Mycobacterium kansasii
-BiDz sensors in terms of specificity, sensitivity, accuracy, and limit of detection. The BiDz sensors were designed to hybridize specifically with the genetic signatures of the target species. To obtain the BiDz sensor targets, amplification of a fragment containing the hypervariable region 2 of the 16S rRNA was performed, under asymmetric PCR conditions using the reverse primer designed based on linear-after-the-exponential principles. The BiDz-TB/NTM was able to correctly identify 99.6% of the samples, with 100% sensitivity and 0.99 accuracy. The individual values of specificity, sensitivity, and accuracy, obtained for each BiDz sensor, satisfied the recommendations for new diagnostic methods, with sensitivity of 100%, specificity and accuracy ranging from 98% to 100% and from 0.98 to 1.0, respectively. The limit of detection of BiDz sensors ranged from 12 genome copies (Mtb-BiDz) to 2,110 genome copies (Mkan-BiDz). The BiDz-TB/NTM platform would be able to generate results rapidly, allowing the implementation of the appropriate therapeutic regimen and, consequently, the reduction of morbidity and mortality of patients.

IMPORTANCE

This article describes the development and evaluation of a new molecular platform for accurate, sensitive, and specific detection and identification of
Mycobacterium tuberculosis
and other mycobacteria of clinical importance. Based on BiDz sensor technology, this assay prototype is amenable to implementation at the point of care. Our data demonstrate the feasibility of combining the species specificity of BiDz sensors with the sensitivity afforded by asymmetric PCR amplification of target sequences. Preclinical validation of this assay on a large panel of clinical samples supports the further development of this diagnostic tool for the molecular detection of pathogenic mycobacteria.
Initial waterline contamination by
Pseudomonas aeruginosa
in newly installed dental chairs
Authors: Baudet Alexandre , Lizon Julie , Florentin Arnaud , Mortier Éric 
Published: April 2024

ABSTRACT

Water contamination in dental unit waterlines (DUWLs) is a potential source of healthcare-associated infection during dental care. The aim of this study was to evaluate the microbiological quality of DUWLs water from newly installed dental chairs in a French University Hospital. The microbiological quality of water from 24 new DUWLs initially disinfected by ICX Renew—prior to use of the dental units for patient treatment—was assessed for total culturable aerobic bacteria at 22°C and 36°C,
Legionella
sp.
, Pseudomonas aeruginosa
, and total coliforms. Among the 24 samples analyzed, 21 were compliant with the water quality levels: 19 had no bacteria, and 2 contained only 4 and 1 CFU/mL for total culturable aerobic bacteria at 22°C and 36°C, respectively. Three samples were non-compliant due to contamination by
P. aeruginosa
(4, 2, and 2 CFU/100 mL). Controlling and preventing the microbiological contamination of DUWLs, especially by pathogenic bacteria, at the time of the installation of the new dental chairs are crucial to prevent healthcare-associated infection in dentistry.

IMPORTANCE
Dental unit waterlines (DUWLs) of new dental chairs may be contaminated before their first clinical use, so an initial shock disinfection is crucial at the time of their installation. The microbiological analyses are crucial to control the water quality of DUWLs before their first clinical use because their disinfection does not guarantee the elimination of all bacteria.
Identification and characterization of a novel antifungal compound tubeimoside I targeting cell wall
Authors: Liu Qiannan , Zhong Zhiqi , Zheng Shunxin , Chu Yunzhuo , Sakamoto Norihiro , Kuno Takayoshi , Fang Yue 
Published: April 2024

ABSTRACT

Due to fungal diseases that threaten immunocompromised patients, along with the limited availability of antifungal agents, there is an urgent need for new antifungal compounds to treat fungal infections. Here, we aimed to identify potential antifungal drugs from natural products using the fission yeast
Schizosaccharomyces pombe
as a model organism since it shares many features with some pathogenic fungi. Here, we identified tubeimoside I (TBMS1), an extract from Chinese herbal medicine, that showed strong antifungal activity against
S. pombe
. To gain insight into the underlying mechanism, we performed transcriptomics analyses of
S. pombe
cells exposed to TBMS1. A significant proportion of the differential expressed genes were involved in cell wall organization or biogenesis. Additionally, TBMS1 treatment of
S. pombe
cells resulted in pleiotropic phenotypes, including increased sensitivity to β-glucanase, enhanced calcineurin activity, translocation of GFP-Prz1 to the nucleus, as well as enhanced dephosphorylation of Prz1, suggesting that TBMS1 disrupted cell wall integrity of
S. pombe
cells. Notably, calcofluor staining showed that abnormal deposits of cell wall materials were observed in the septum and cell wall of the TBMS1-treated cells, which were further corroborated by electron microscopy analysis. We also found that oxidative stress might be involved in the antifungal action of TBMS1. Moreover, we confirmed the antifungal activities of TBMS1 against several clinical isolates of pathogenic fungi. Collectively, our findings suggest that TBMS1, a novel antifungal compound, exerts its antifungal activity by targeting cell walls, which may pave the way for the development of a new class of antifungals.

IMPORTANCE

Fungal infections pose a serious threat to public health and have become an emerging crisis worldwide. The development of new antifungal agents is urgently needed. Here, we identified compound tubeimoside I (TBMS1) for the first time showing strong antifungal activity, and explored the underlying mechanisms of its antifungal action by using the model yeast
Schizosaccharomyces pombe
. Notably, we presented multiple evidence that TBMS1 exerts its antifungal activity through targeting fungal cell walls. Moreover, we verified the antifungal activities of TBMS1 against several pathogenic fungi. Our work indicated that TBMS1 may serve as a novel antifungal candidate, which provides an important foundation for designing and developing new cell wall-targeting agents for combating life-threatening fungal infections.
International circumpolar surveillance: update on the interlaboratory quality control program for
Streptococcus pneumoniae
, 2009 to 2020
Authors: Golden Alyssa R. , Griffith Averil , Simons Brenna C. , Reasonover Alisa , Slotved Hans-Christian , Lefebvre Brigitte , Kristinsson Karl G. , Hurteau Donna , Tyrrell Gregory J. , Bruce Michael G. , Martin Irene 
Published: April 2024

ABSTRACT

The International Circumpolar Surveillance (ICS) program is a population-based surveillance network for invasive bacterial diseases throughout Arctic countries and territories. The ICS quality control program for
Streptococcus pneumoniae
serotyping and antimicrobial susceptibility testing has been ongoing since 1999. Current participating laboratories include the Provincial Laboratory for Public Health in Edmonton, Alberta; Laboratoire de santé publique du Québec in Sainte-Anne-de-Bellevue, Québec; the Centers for Disease Control’s Arctic Investigations Program in Anchorage, Alaska; the Neisseria and Streptococcus Reference Laboratory at Statens Serum Institut in Copenhagen, Denmark; the Department of Clinical Microbiology, Landspitali in Reykjavik, Iceland; and Public Health Agency of Canada’s National Microbiology Laboratory in Winnipeg, Manitoba. From 2009 to 2020, 140 isolates of
S. pneumoniae
were distributed among the six laboratories as part of the quality control program. Overall serotype concordance was 96.9%, with 99.3% concordance to pool level. All participating laboratories had individual concordance rates >92% for serotype and >97% for pool. Overall concordance by modal minimum inhibitory concentration (MIC) for testing done by broth microdilution or Etest was 99.1%, and >98% for all antimicrobials tested. Categorical concordance was >98% by both CLSI and EUCAST criteria. For two laboratories performing disc diffusion, rates of concordance by modal MIC were >97% for most antimicrobials, except chloramphenicol (>93%) and trimethoprim/sulfamethoxazole (>88%). Data collected from 12 years of the ICS quality control program for
S. pneumoniae
demonstrate excellent (≥95%) overall concordance for serotype and antimicrobial susceptibility testing results across six laboratories.

IMPORTANCE

Arctic populations experience several social and physical challenges that lead to the increased spread and incidence of invasive diseases. The International Circumpolar Surveillance (ICS) program was developed to monitor five invasive bacterial diseases in Arctic countries and territories. Each ICS organism has a corresponding interlaboratory quality control (QC) program for laboratory-based typing, to ensure the technical precision and accuracy of reference testing services for these regions, and identify and correct potential problems. Here, we describe the results of the ICS
Streptococcus pneumoniae
QC program, from 2009 to 2020. Excellent overall concordance was achieved for serotype and antimicrobial susceptibility testing results across six laboratories. Ongoing participation in these QC programs ensures the continuation of quality surveillance systems within Arctic populations that experience health disparities.
Qualitative interview study of rheumatology patients’ experiences of COVID-19 shielding to explore the physical and psychological impact and identify associated support needs
Authors: Silverthorne Christine A , Jones Bethan , Brooke Mel , Coates Laura C , Orme Jen , Robson Joanna C , Tillett William , Dures Emma 
Published: April 2024

ObjectiveMany clinically extremely vulnerable rheumatology patients have only recently ceased shielding from COVID-19, while some continue to minimise in-person contact. The objective of this study was to understand the impact of shielding and associated support needs in patients with rheumatic conditions and to understand how rheumatology teams can meet these needs both currently and in future pandemics.Design, participants and settingThe study was conducted in the Southwest of England using a case-study design. The participants were 15 patients with rheumatic conditions who were advised to shield and/or chose to shield at any time during the COVID-19 pandemic.MethodsQualitative data collected via telephone and online semi-structured interviews and analysed using reflexive thematic analysis.ResultsFifteen interviews were conducted. Three main themes represent the data:‘Just shove them over there in the corner’ captures changes in patients’ self-perception. They felt different to most other people, vulnerable and left behind. The initial sense of shock was followed by a sense of loss as changes became long term.‘A long and lonely road’ captures patients’ psychological isolation due to a perceived lack of understanding and support. This included having to prove their health status and justify their shielding behaviours, which impacted their relationships. At times, they felt abandoned by their healthcare providers.‘You can’t just flip a switch’ captures the difficulty of getting back to pre-pandemic normal after shielding. Patients did not recognise themselves physically and mentally. They wanted to collaborate with health professionals and identified the need for specific guidance to support their recovery.ConclusionPatients are dealing with lasting physical and mental effects from shielding and consequences of delayed healthcare. Health professionals need time and resources to ask about patients’ well-being, identify their health needs and refer/signpost to appropriate sources of support.
Association between vitamin D deficiency and benign paroxysmal positional vertigo (BPPV) incidence and recurrence: a systematic review and meta-analysis
Authors: Wood Heather , Kluk Karolina , BinKhamis Ghada 
Published: April 2024

ObjectivesThe objective of this study is to determine the relationship between serum vitamin D level and the risk of developing benign paroxysmal positional vertigo (BPPV) incidence and recurrence in countries in the Northern Hemisphere.DesignSystematic review and meta-analysis.Data sourcesPubMed, Scopus and Web of Science databases were searched for studies published between January 2000 and February 2023.Eligibility criteria for selecting studiesParticipants located in the Northern Hemisphere aged 18 or over with at least one episode of BPPV, serum 25-hydroxyvitamin D levels measured and reported, no comorbidities or history of vitamin D supplementation.Data extraction and synthesisData extraction and synthesis were performed by a single reviewer and checked by a second reviewer. Inclusion and exclusion criteria and risk of bias were assessed by two independent reviewers using the Newcastle Ottawa Tool for Cohort studies and Risk of Bias Assessment Tool for Nonrandomised Studies checklist for case–control studies. Meta-analysis was conducted using random effects models. Standard mean difference with a 95% CI was used to measure the relationship between vitamin D level and BPPV.ResultsThe 35 articles identified by the literature search reported data of 9843 individuals. 19 studies (7387 individuals) were included in the BPPV incidence meta-analysis while 7 studies (622 individuals) were included in the BPPV recurrence meta-analysis. Lower serum vitamin D levels were found in BPPV incidence compared with controls, but the relationship between vitamin D levels in recurrent BPPV compared with non-recurrent disease remained uncertain.ConclusionResults of this systematic review and meta-analysis demonstrated a negative correlation between serum vitamin D and BPPV incidence, while any relationship between serum vitamin D and BPPV recurrence remained uncertain. Risk of bias analysis revealed evidence of variable quality. There were insufficient data available to evaluate seasonal relationships between serum vitamin D and BPPV. Given the potential for this as a confounding factor, future research should aim to investigate this further.PROSPERO registration numberCRD42021271840.
Web-based cognitive rehabilitation intervention for cancer-related cognitive impairment following chemotherapy for aggressive lymphoma: protocol for a randomised pilot trial
Authors: Gates Priscilla , Green Heather J , Gough Karla , Dhillon Haryana , Vardy Janette L , Dickinson Michael , Guarnera Jade , Krishnasamy Meinir , Livingston Patricia M , White Victoria , Ugalde Anna , Caeyenberghs Karen 
Published: April 2024

IntroductionCancer-related cognitive impairment is common among people diagnosed with and treated for cancer. This can be a distressing and disabling side effect for impacted individuals. Interventions to mitigate cognitive dysfunction are available, but, to date, most have been trialled in samples that are largely or exclusively composed of people with solid tumours. Intervention strategies to support cognitive functioning are needed, but there is a paucity of research in this area. The main aim of this study is to test the feasibility and acceptability of methods and procedures intended for use in a definitive trial of a web-based cognitive rehabilitation programme, Responding to Cognitive Concerns (eReCog), in people who have received chemotherapy for aggressive lymphoma.Methods and analysisThe proposed study is a single-site, parallel-group, pilot randomised controlled trial, with one baseline and one follow-up (or postintervention) assessment. 38 people from the target population with low perceived cognitive function based on the Cognitive Change Screen will be recruited from a specialist cancer centre between July 2023 and June 2024. After baseline assessment, participants will be randomised one-to-one to receive usual care only (a factsheet about changes in memory and thinking for people with cancer) or eReCog plus usual care. The 4-week eReCog intervention consists of four online modules offering psychoeducation on cognitive impairment associated with cancer and its treatment, skills training for improving memory, and attention and relaxation training. Study outcomes will include the feasibility of recruitment and retention at follow-up assessment (primary outcomes), as well as adherence to, usability of and intrinsic motivation to engage with eReCog, and compliance with study measures. The potential efficacy of eReCog will also be evaluated.Ethics and disseminationEthical approval was granted by the Peter MacCallum Cancer Centre Human Research Ethics Committee in Victoria, Australia (HREC/97384/PMCC). Study findings will be disseminated via peer-reviewed publications and conference presentations.Trial registration numberAustralian New Zealand Clinical Trials Registry, ACTRN12623000705684.