bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous mutational patterns and novel mutations for bedaquiline and clofazimine resistance in
Mycobacterium tuberculosis
Authors: Shi Jin , Liu Yuanyuan , Wu Tuoya , Li Lu , Han Shujing , Peng Xiao , Shang Yuanyuan , Guo Yongli , Pang Yu , Gao Mengqiu , Lu Jie 
Published: August 2023

ABSTRACT

The 2022 World Health Organization guidelines recommend use of two core anti-tuberculosis (TB) drugs, bedaquiline (BDQ) and clofazimine (CFZ), for treatment of drug-resistant (DR)-TB. However, several mutated
Mycobacterium tuberculosis
(MTB) genes, conferring BDQ and CFZ resistance, have been reported that predominantly arose from sporadic mutations that have not been comprehensively characterized. Herein, MTB clinical isolates collected from drug-susceptible (DS)-, multidrug-resistant (MDR)-, and extensively drug-resistant (XDR)-TB patients were cultured
in vitro
with BDQ or CFZ to generate progeny strains with resistance to these drugs. Progeny strains exposed to CFZ exhibited increased CFZ minimum inhibitory concentrations (MICs) that exceeded MIC increases of BDQ-exposed progeny strains. Notably,
mmpR
and
pepQ
mutations accounted for 83% and 17% of BDQ-induced spontaneous gene mutations, respectively, and 86% and 14% of CFZ-induced spontaneous gene mutations, respectively. Analyses of predicted mutation-induced changes in amino acid sequences and structures of MmpR and PepQ mutants revealed several point mutations affected sequence conversation and functionality as an underlying mechanism for observed acquired BDQ/CFZ resistance. Moreover, our results revealed differences in patterns of BDQ- and CFZ-induced acquired spontaneous mutations that may enhance our understanding of MTB BDQ/CFZ-resistance mechanisms.

IMPORTANCE

This study of MTB drug resistance mechanisms revealed patterns of spontaneous MTB mutations associated with acquired BDQ and CFZ resistance that arose after clinical MTB isolates were cultured
in vitro
with BDQ or CFZ. Results of protein sequence and structural analyses provided insights into potential mechanisms underlying associations between MTB gene mutations and DR phenotypes. Taken together, these results revealed differences in acquired BDQ and CFZ resistance mechanisms as a new perspective that may enhance our understanding of BDQ/CFZ resistance mechanisms and facilitate the development of new methods for detecting MTB drug resistance genes.
Staphylococcus aureus
susceptibility to complestatin and corbomycin depends on the VraSR two-component system
Authors: Gómez-Arrebola Carmen , Hernandez Sara B. , Culp Elizabeth J. , Wright Gerard D. , Solano Cristina , Cava Felipe , Lasa Iñigo 
Published: August 2023

ABSTRACT

The overuse of antibiotics in humans and livestock has driven the emergence and spread of antimicrobial resistance and has therefore prompted research on the discovery of novel antibiotics. Complestatin (Cm) and corbomycin (Cb) are glycopeptide antibiotics with an unprecedented mechanism of action that is active even against methicillin-resistant and daptomycin-resistant
Staphylococcus aureus
. They bind to peptidoglycan and block the activity of peptidoglycan hydrolases required for remodeling the cell wall during growth. Bacterial signaling through two-component transduction systems (TCSs) has been associated with the development of
S. aureus
antimicrobial resistance. However, the role of TCSs in
S. aureus
susceptibility to Cm and Cb has not been previously addressed. In this study, we determined that, among all 16
S. aureus
TCSs, VraSR is the only one controlling the susceptibility to Cm and Cb. Deletion of
vraSR
increased bacterial susceptibility to both antibiotics. Epistasis analysis with members of the vraSR regulon revealed that deletion of spdC, which encodes a membrane protein that scaffolds SagB for cleavage of peptidoglycan strands to achieve physiological length, in the vraSR mutant restored Cm and Cb susceptibility to wild-type levels. Moreover, deletion of either
spdC
or
sagB
in the wild-type strain increased resistance to both antibiotics. Further analyses revealed a significant rise in the relative amount of peptidoglycan and its total degree of cross-linkage in
ΔspdC
and
ΔsagB
mutants compared to the wild-type strain, suggesting that these changes in the cell wall provide resistance to the damaging effect of Cm and Cb.

IMPORTANCE

Although
Staphylococcus aureus
is a common colonizer of the skin and digestive tract of humans and many animals, it is also a versatile pathogen responsible for causing a wide variety and number of infections. Treatment of these infections requires the bacteria to be constantly exposed to antibiotic treatment, which facilitates the selection of antibiotic-resistant strains. The development of new antibiotics is, therefore, urgently needed. In this paper, we investigated the role of the sensory system of
S. aureus
in susceptibility to two new antibiotics: corbomycin and complestatin. The results shed light on the cell-wall synthesis processes that are affected by the presence of the antibiotic and the sensory system responsible for coordinating their activity.
A type I-F CRISPRi system unveils the novel role of CzcR in modulating multidrug resistance of
Pseudomonas aeruginosa
Authors: Chen Shuzhen , Cao Huiluo , Xu Zirui , Huang Jiahui , Liu Zhiqing , Li Ting , Duan Cheng , Wu Weiyan , Wen Yongqi , Zhang Lian-Hui , Xu Zeling 
Published: August 2023

ABSTRACT

Pseudomonas aeruginosa
has abundant signaling systems that exquisitely control its antibiotic resistance in response to different environmental cues. Understanding the regulation of antibiotic resistance will provide important implications for precise antimicrobial interventions. However, efficient genetic tools for functional gene characterizations are sometimes not available, particularly, in clinically isolated strains. Here, we established a type I-F CRISPRi (CSYi) system for programmable gene silencing. By incorporating anti-CRISPR proteins, this system was even applicable to bacterial hosts encoding a native type I-F CRISPR-Cas system. With the newly developed gene-silencing system, we revealed that the response regulator CzcR from the zinc (Zn
2+
)-responsive two-component system CzcS/CzcR is a repressor of efflux pumps MexAB-OprM and MexGHI-OpmD, which inhibits the expression of both operons by directly interacting with their promoters. Repression of MexAB-OprM consequently increases the susceptibility of
P. aeruginosa
to multiple antibiotics such as levofloxacin and amikacin. Together, this study provided a simple approach to study gene functions, which enabled us to unveil the novel role of CzcR in modulating efflux pump genes and multidrug resistance in
P. aeruginosa
.

IMPORTANCE

P. aeruginosa
is a ubiquitous opportunistic pathogen frequently causing chronic infections. In addition to being an important model organism for antibiotic-resistant research, this species is also important for understanding and exploiting CRISPR-Cas systems. In this study, we established a gene-silencing system based on the most abundant type I-F CRISPR-Cas system in this species, which can be readily employed to achieve targeted gene repression in multiple bacterial species. Using this gene-silencing system, the physiological role of Zn
2+
and its responsive regulator CzcR in modulating multidrug resistance was unveiled with great convenience. This study not only displayed a new framework to expand the abundant CRISPR-Cas and anti-CRISPR systems for functional gene characterizations but also provided new insights into the regulation of multidrug resistance in
P. aeruginosa
and important clues for precise anti-pseudomonal therapies.
The IQ-1S JNK (c-Jun N-Terminal Kinase) Inhibitor Suppresses Premature Aging of OXYS Rat Brain
Authors: Zhdankina A. A. , Osipenko A. N. , Tikhonov D. I. , Logvinov S. V. , Plotnikov M. B. , Khlebnikov A. I. , Kolosova N. G. 
Published: August 2023

Abstract—According to the Alzheimer’s Disease International (ADI) international organization about 50 million people in the world suffer from Alzheimer’s disease (AD). However, there are no effective methods for preventing or slowing the progression of AD. Inhibition of the c-Jun N-terminal kinase (JNK) signaling pathway is discussed below as an alternative way to prevent the development of AD and other neurodegenerative diseases. In the present study, we evaluated the ability of a recently synthesized selective JNK3 inhibitor, 11H-indeno[1,2-b]quinoxalin-11-one oxime sodium salt (IQ-1S), to suppress neurodegenerative processes in OXYS rats at an early stage of development of AD at the ages of 4.5 to 6 months. Treatment with IQ-1S (50 mg/kg intragastrically) led to the suppression of the development of neurodegenerative processes in the cerebral cortex of OXYS rats: an increase in the proportion of unchanged neurons, a decrease in the proportion of neurons with signs of destruction and irreversible damage, and a normalization of the glioneuronal index, which was facilitated by a decrease in the severity of hyperviscosity syndrome blood in OXYS rats. The use of the IQ-1S JNK3 inhibitor may be a promising strategy for the prevention of early neurodegenerative disorders and, possibly, the treatment of AD.
Piloting a new method to estimate action thresholds in medicine through intuitive weighing
Authors: Jacobs Bart K M , Keter Alfred Kipyegon , Henriquez-Trujillo Aquiles Rodrigo , Trinchan Paco , de Rooij Madeleine L , Decroo Tom , Lynen Lutgarde 
Published: August 2023

ObjectivesIn clinical decision-making, physicians take actions such as prescribing treatment only when the probability of disease is sufficiently high. The lowest probability at which the action will be considered, is the action threshold. Such thresholds play an important role whenever decisions have to be taken under uncertainty. However, while several methods to estimate action thresholds exist, few methods give satisfactory results or have been adopted in clinical practice. We piloted the adapted nominal group technique (aNGT), a new prescriptive method based on a formal consensus technique adapted for use in clinical decision-making.Design, setting and participantsWe applied this method in groups of postgraduate students using three scenarios: treat for rifampicin-resistant tuberculosis (RR-TB), switch to second-line HIV treatment and isolate for SARS-CoV-2 infection.InterventionsThe participants first summarise all harms of wrongly taking action when none is required and wrongly not taking action when it would have been useful. Then they rate the statements on these harms, discuss their importance in the decision-making process, and finally weigh the statements against each other.Main outcome measuresThe resulting consensus threshold is estimated as the relative weights of the harms of the false positives divided by the total harm, and averaged out over participants. In some applications, the thresholds are compared with an existing method based on clinical vignettes.ResultsThe resulting action thresholds were just over 50% for RR-TB treatment, between 20% and 50% for switching HIV treatment and 43% for COVID-19 isolation. These results were considered acceptable to all participants. Between sessions variation was low for RR-TB and moderate for HIV. Threshold estimates were moderately lower with the method based on clinical vignettes.ConclusionsThe aNGT gives sensible results in our pilot and has the potential to estimate action thresholds, in an efficient manner, while involving all relevant stakeholders. Further research is needed to study the value of the method in clinical decision-making and its ability to generate acceptable thresholds that stakeholders can agree on.
Expansion of non-invasive prenatal screening to the screening of 10 types of chromosomal anomalies: a cost-effectiveness analysis
Authors: Soukkhaphone Bounhome , Baradaran Mohammad , Nguyen Ba Diep , Nshimyumukiza Leon , Little Julian , Rousseau Francois , Audibert Francois , Langlois Sylvie , Reinharz Daniel 
Published: August 2023

ObjectivesTo determine the cost-effectiveness of the addition of chromosomal anomalies detectable by non-invasive prenatal screening (NIPS), in a prenatal screening programme targeting common aneuploidies.Design, setting and participantsA simulation study was conducted to study the addition of chromosomal anomalies detectable by NIPS (sex chromosome aneuploidies, 22q11.2 deletion syndrome, large deletion/duplication >7 Mb and rare autosomal trisomies) to five basic strategies currently aiming the common trisomies: three strategies currently offered by the public healthcare systems in Canada, whose first-tier test is performed with biochemical markers, and two programmes whose first-tier test consists of NIPS-based methods.Outcome measuresThe total number of cases of chromosomal anomalies detected and the costs related to the consumption of medical services.ResultsThe most effective and the most cost-effective option in almost all prenatal screening strategies is the option that includes all targeted additional conditions. In the strategies where NIPS is used as first-tier testing, the cost per additional case detected by adding all possible additional anomalies to a programme that currently targets only common trisomies is $C25 710 (95% CI $C25 489 to $C25 934) for massively parallel shotgun sequencing and $C57 711 (95% CI $C57 141 to $C58 292) for targeted massively parallel sequencing, respectively. The acceptability curves show that at a willingness-to-pay of $C50 000 per one additional case detected, the expansion of NIPS-based methods for the detection of all possible additional conditions has a 90% probability of being cost-effective.ConclusionFrom an economic perspective, in strategies that use NIPS as a first-tier screening test, expanding the programmes to detect any considered chromosomal anomalies other than the three common trisomies would be cost-effective. However, the potential expansion of prenatal screening programmes also requires consideration of societal issues, including ethical ones.
Prognostic factors associated with failure of total elbow replacement: a protocol for a systematic review
Authors: Hamoodi Zaid , Gehringer Celina K , Bull Lucy M , Hughes Tom , Kearsley-Fleet Lianne , Sergeant Jamie C , Watts Adam C 
Published: August 2023

IntroductionTotal elbow replacement (TER) has higher failure rates requiring revision surgery compared with the replacement of other joints. Understanding the factors associated with failure is essential for informed decision-making between patients and clinicians, and for reducing the failure rate. This review aims to identify, describe and appraise the literature examining prognostic factors for failure of TER.Methods and analysisThis systematic review will be conducted and reported in line with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols guidelines. Electronic literature searches will be conducted using Medline, EMBASE, PubMed and Cochrane. The search strategy will be broad, including a combination of subject headings (MESH) and free text search. This search will be supplemented with a screening of reference lists of the included studies and relevant reviews. Two independent reviewers will screen all search results in two stages (title and abstract, and full text) based on the Population, Index prognostic factor, Comparator prognostic factor, Outcome, Time and Setting criteria. The types of evidence included will be randomised trials, non-randomised trials, prospective and retrospective cohort studies, registry studies and case–control studies. If the literature lacks enough studies, then case series with 50 or more TERs will be considered for inclusion. Data extraction and risk of bias assessment for included studies will be performed by two independent reviewers using the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies for Prognostic Factors and Quality In Prognostic Studies tools.Meta-analyses of prognostic estimates for each factor will be undertaken for studies that are deemed to be sufficiently robust and comparable. Several challenges are likely to arise due to heterogeneity between studies, therefore, subgroup and sensitivity analyses will be performed to account for the differences between studies. Heterogeneity will be assessed using Q and I2statistics. If I2>40% then pooled estimates will not be reported. When quantitative synthesis is not possible, a narrative synthesis will be undertaken. The quality of the evidence for each prognostic factor will be assessed using the Grades of Recommendation Assessment, Development and Evaluation tool.PROSPERO registration numberCRD42023384756.
Gender-based discrimination and son preference in Punjabi-Canadian families: a community-based participatory qualitative research study
Authors: Wanigaratne Susitha , Januwalla Alia , Bhangu Manvir , Uppal Pamela , Kumar-Ratta Amrita , Brar Amanpreet , Dennis Cindy-Lee , Urquia Marcelo 
Published: August 2023

ObjectivesTo conduct a qualitative study, guided by the principles of community-based participatory research, with the following objectives: (1) to provide a conceptual framework describing the drivers of son preference; (2) to understand experiences of son preference among Punjabi-Canadians and (3) with this understanding, identify and co-design an appropriate educational tool.Design, setting, participants, methodsQualitative study consisting of four bilingual (Punjabi and English) focus group discussions with 11 mothers, 4 fathers and 17 grandmothers in Toronto and Brampton, Canada. Participants were queried about experiences and perspectives related to reproductive decision-making, gender equity and son preference, and for appropriate approaches to reducing inequities. Transcripts were simultaneously translated and written in English and thematic analysis was conducted. An infoposter was identified as a feasible educational tool and was co-designed by researchers and community partners.ResultsParticipants identified patrilocality (ie, married sons reside with parents, married daughters with in-laws) and patrilineality (ie, sons inherit assets, daughters’ husband receives a dowry) as structural precursors to proximal drivers (ie, old-age security) of son preference. Mothers’ and grandmothers’ value to their families depended strongly on having a son but did not guarantee security. Pressures (ie, internalised discrimination, reproductive coercion) to conceive a son were common after the birth of at least one daughter in the absence of sons. Participants did not know anyone who had a sex selective abortion in Canada; however, traditional sex selection methods (eg, herbal medicines) were mentioned. Our co-designed infoposter entitled ‘Truths About Son Preference’ addressed three misconceptions identified in discussions.ConclusionThis study may be useful to health and social care providers in providing structurally competent and culturally humble counselling and care, particularly after the birth of daughters in the absence of sons. Community engagement is necessary for future intervention development.
Development of a risk prediction tool for patients with locally advanced and recurrent rectal cancer undergoing pelvic exenteration: protocol for a mixed-methods study
Authors: Brown Kilian , Solomon Michael , Ng Kheng-Seong , Sutton Paul , Koh Cherry , White Kate , Steffens Daniel 
Published: August 2023

IntroductionPelvic exenteration (PE) surgery represents the only potentially curative treatment option for patients with locally advanced or recurrent rectal cancer (LARRC). Given the potential morbidity, whether or not PE should be recommended for an individual patient presents a major decisional conflict. This study aims to identify the outcomes of PE for which there is consensus among patients, carers and clinicians regarding their importance in guiding treatment decision-making, and to develop a risk prediction tool which predicts these outcomes.Methods and analysisThis study will be conducted at a specialist PE centre, and employ a mixed-methods study design, divided into three distinct phases. In phase 1, outcomes of PE will be identified through a comprehensive systematic review of the literature (phase 1a), followed by exploration of the experiences of individuals who have undergone PE for LARRC and their carers (phase 1b, target sample size 10–20 patients and 5–10 carers). In phase 2, a survey of patients, their carers and clinicians will be conducted using Delphi methodology to explore consensus around the outcomes of highest priority and the level of influence each outcome should have on treatment decision-making. In phase 3 a, risk prediction tool will be developed using data from a single PE referral centre (estimated sample size 500 patients) to predict priority outcomes using multivariate modelling, and externally validated using data from an international PE collaboration.Ethics and disseminationEthical approval has been granted for phases 1 and 2 (X22-0422 and 2022/ETH02659) and for maintenance of the database used in phase 3 (X13-0283 and HREC/13/RPAH/504). Informed consent will be obtained from participants in phases 1b and 2; a waiver of consent for secondary use of data in phase 3 will be sought. Study results will be submitted for publication in international and/or national peer reviewed journals.PROSPERO registration numberCRD42022351909.
Association between residential greenness and severe psychological distress and the moderating role of ‘stay-at-home’ status: a population-based cross-sectional study during the COVID-19 pandemic in Japan
Authors: Nishimura Hisaaki , Nawa Nobutoshi , Yamaoka Yui , Koyama Yuna , Kuramochi Jin , Fujiwara Takeo 
Published: August 2023

ObjectiveThere is a need for public health strategies to address the negative psychological consequences of the COVID-19 pandemic, and the role of residential green exposure has gained prominence, particularly in the context of the ‘new normal’ and the prevailing ‘stay-at-home’ policies. This study aimed to evaluate the association between residential greenness and severe psychological distress during the COVID-19 pandemic in Japan. We also investigated the association stratified by ‘stay-at-home’ status, a proxy for exposure to residential greenness.Methods and analysisWe used data from a population-based cohort study conducted in Utsunomiya City, Japan. Residential greenness was measured by the normalised difference vegetation index (NDVI) averaged over circular buffers around residence. Severe psychological distress was defined as a Kessler Psychological Distress Scale (K6) score ≥13. ‘Stay-at-home’ status was categorised as either ‘not stay-at-home’ (individuals working outside the home or self-employed) or ‘stay-at-home’ (working from home or not working), based on the working status. Logistic regression analysis was performed to examine the association between residential greenness and severe psychological distress.ResultsA total of 615 participants were analysed. Among the ‘stay-at-home’ group, an IQR increase in NDVI was inversely associated with severe psychological distress (100 m buffer: OR=0.27, 95% CI 0.10 to 0.77; 250 m buffer: OR=0.26, 95% CI 0.10 to 0.69; 500 m buffer: OR=0.33, 95% CI 0.11 to 0.95). However, no significant association was observed for the ‘not stay-at-home’ group.ConclusionResidential greenness was a protective factor for severe psychological distress among the ‘stay-at-home’ group, who were assumed to have spent more time in their residence.