bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of a 6-Week Repeated-Sprint Training With Voluntary Hypoventilation at Low and High Lung Volume on Repeated-Sprint Ability in Female Soccer Players
Authors: Ait Ali Braham Mounir , Ouchen Youva , Woorons Xavier
Published: February 2024

Purpose: To investigate the effects of repeated-sprint training with voluntary hypoventilation at low (RSH-VHL) and high (RS-VHH) lung volume on repeated-sprint ability (RSA) in female athletes. Methods: Over a 6-week period, 24 female soccer players completed 12 sessions of repeated 30-m running sprints with end-expiratory breath holding (RSH-VHL, n = 8), end-inspiratory breath holding (RS-VHH, n = 8), or unrestricted breathing (RS-URB, n = 8). Before and after training, a running RSA test consisting of performing 30-m all-out sprints until exhaustion was implemented. Results: From before to after training, the number of sprints completed during the RSA test was increased in both RSH-VHL (19.3 [0.9] vs 22.6 [0.9]; P < .01) and RS-VHH (19.3 [1.5] vs 20.5 [1.7]; P < .01) but not in RS-URB (19.4 [1.3] vs 19.5 [1.7]; P = .67). The mean velocity and the percentage decrement score calculated over sprints 1 to 17 were, respectively, higher (82.2% [1.8%] vs 84.6% [2.1%] of maximal velocity) and lower (23.7% [3.1%] vs 19.4% [3.2%]) in RSH-VHL (P < .01), whereas they remained unchanged in RS-VHH and RS-URB. The mean arterial oxygen saturation recorded during training at the end of the sprints was lower in RSH-VHL (92.1% [0.4%]) than in RS-VHH (97.3% [0.1%]) and RS-URB (97.8% [0.1%]). Conclusions: This study shows that female athletes can benefit from the RSH-VHL intervention to improve RSA. The performance gains may have been limited by the short sprinting distance with end-expiratory breath holding, which provoked only moderate hypoxemia. The increase in the number of sprints in RS-VHH seems to show that factors other than hypoxia may have played a role in RSA improvement.
Sequential Mapping of Game Patterns in Men and Women Professional Padel Players
Authors: Conde-Ripoll Rafael , Muñoz Diego , Escudero-Tena Adrián , Courel-Ibáñez Javier
Published: February 2024

Purpose: This study analyzed the sequences of actions in professional men and women padel players to identify common game patterns. Methods: The sample comprised 17,557 stroke-by-stroke actions (N = 1640 rallies) of the championship World Padel Tour. Multistep Markov chains were used to calculate the conditional probabilities of occurrence of actions during the rally. Results: Results revealed that men’s and women’s padel is mainly defined by 36 patterns constituting 55% and 63% of all actions in the game, respectively, with the 10 most common sequences accounting for 42% to 45% of the game. There were recurrent technical–tactical actions with specific offensive and defensive functions that were constantly reiterated during the rallies. In men, the use of smash, volley, bandeja, direct, back wall, back-wall lobs, and direct lobs followed a foreseeable pattern up to 8 lags, whereas women described predictable interactions for volley, bandeja, direct, lobs, and direct lobs up to 5 lags and for smash and back wall up to 4 lags. Conclusions: The ability of padel players to recall these patterns and enhance their anticipation skills may potentially improve their performance. These findings contribute to a better knowledge of professional padel game dynamics while providing coaches and players with useful information to optimize training and decision-making strategies.
Balancing the scales: achieving the optimal beta-lactam to beta-lactamase inhibitor ratio with continuous infusion piperacillin/tazobactam against extended spectrum beta-lactamase producing
Enterobacterales
Authors: Cojutti Pier Giorgio , Pai Manjunath P. , Tonetti Tommaso , Siniscalchi Antonio , Viale Pierluigi , Pea Federico
Published: February 2024

Piperacillin/tazobactam (TZP) is administered intravenously in a fixed ratio (8:1) with the potential for inadequate tazobactam exposure to ensure piperacillin activity against
Enterobacterales
. Adult patients receiving continuous infusion (CI) of TZP and therapeutic drug monitoring (TDM) of both agents were evaluated. Demographic variables and other pertinent laboratory data were collected retrospectively. A population pharmacokinetic approach was used to select the best kidney function model predictive of TZP clearance (CL). The probability of target attainment (PTA), cumulative fraction of response (CFR) and the ratio between piperacillin and tazobactam were computed to identify optimal dosage regimens by continuous infusion across kidney function. This study included 257 critically ill patients (79.3% male) with intra-abdominal, bloodstream, and hospital-acquired pneumonia infections in 89.5% as the primary indication. The median (min-max range) age, body weight, and estimated glomerular filtration rate (eGFR) were 66 (23–93) years, 75 (39–310) kg, and 79.2 (6.4–234) mL/min, respectively. Doses of up to 22.5 g/day were used to optimize TZP based on TDM. The 2021 chronic kidney disease epidemiology equation in mL/min best modeled TZP CL. The ratio of piperacillin:tazobactam increased from 6:1 to 10:1 between an eGFR of <20 mL/min and >120 mL/min. At conventional doses, the PTA is below 90% when eGFR is ≥100 mL/min. Daily doses of 18 g/day and 22.5 g/day by CI are expected to achieve a >80% CFR when eGFR is 100–120 mL/min and >120–160 mL/min, respectively. Inadequate piperacillin and tazobactam exposure is likely in patients with eGFR ≥ 100 mL/min. Dose regimen adjustments informed by TDM should be evaluated in this specific population.
Ex vivo
drug susceptibility and resistance mediating genetic polymorphisms of
Plasmodium falciparum
in Bobo-Dioulasso, Burkina Faso
Authors: Somé A. Fabrice , Conrad Melissa D. , Kabré Zachari , Fofana Aminata , Yerbanga R. Serge , Bazié Thomas , Neya Catherine , Somé Myreille , Kagambega Tegawinde Josue , Legac Jenny , Garg Shreeya , Bailey Jeffrey A. , Ouédraogo Jean-Bosco , Rosenthal Philip J. , Cooper Roland A.
Published: February 2024

Malaria remains a leading cause of morbidity and mortality in Burkina Faso, which utilizes artemether–lumefantrine as the principal therapy to treat uncomplicated malaria and seasonal malaria chemoprevention with monthly sulfadoxine–pyrimethamine plus amodiaquine in children during the transmission season. Monitoring the activities of available antimalarial drugs is a high priority. We assessed the
ex vivo
susceptibility of
Plasmodium falciparum
to 11 drugs in isolates from patients presenting with uncomplicated malaria in Bobo-Dioulasso in 2021 and 2022. IC
50
values were derived using a standard 72 h growth inhibition assay. Parasite DNA was sequenced to characterize known drug resistance-mediating polymorphisms. Isolates were generally susceptible, with IC
50
values in the low-nM range, to chloroquine (median IC
50
10 nM, IQR 7.9–24), monodesethylamodiaquine (22, 14–46) piperaquine (6.1, 3.6–9.2), pyronaridine (3.0, 1.3–5.5), quinine (50, 30–75), mefloquine (7.1, 3.7–10), lumefantrine (7.1, 4.5–12), dihydroartemisinin (3.7, 2.2–5.5), and atovaquone (0.2, 0.1–0.3) and mostly resistant to cycloguanil (850, 543–1,290) and pyrimethamine (33,200, 18,400–54,200), although a small number of outliers were seen. Considering genetic markers of resistance to aminoquinolines, most samples had wild-type PfCRT K76T (87%) and PfMDR1 N86Y (95%) sequences. For markers of resistance to antifolates, established PfDHFR and PfDHPS mutations were highly prevalent, the PfDHPS A613S mutation was seen in 19% of samples, and key markers of high-level resistance (PfDHFR I164L; PfDHPS K540E) were absent or rare (A581G). Mutations in the PfK13 propeller domain known to mediate artemisinin partial resistance were not detected. Overall, our results suggest excellent susceptibilities to drugs now used to treat malaria and moderate, but stable, resistance to antifolates used to prevent malaria.
Lineage-specific evolution of
Aquibium
, a close relative of
Mesorhizobium
, during habitat adaptation
Authors: Kim Minkyung , Kim Wonjae , Park Yerim , Jung Jaejoon , Park Woojun
Published: February 2024

The novel genus
Aquibium
that lacks nitrogenase was recently reclassified from the
Mesorhizobium
genus. The genomes of
Aquibium
species isolated from water were smaller and had higher GC contents than those of
Mesorhizobium
species. Six
Mesorhizobium
species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24
Mesorhizobium
species. Therefore, they were classified as the non-N
2
-fixing
Mesorhizobium
lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific
fur/mur
indicated that
Mesorhizobium
species may have evolved from
Aquibium
species through an ecological transition. Halotolerant and alkali-resistant
Aquibium
and
Mesorhizobium microcysteis
belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (
mrpABCDEFG
). These genes were not present in the N
2
-fixing
Mesorhizobium
lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in
Aquibium
species, close relatives of
Mesorhizobium
species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.

IMPORTANCE

Phylogenetic analyses revealed that the
Aquibium
lineage (AL) and non-N
2
-fixing
Mesorhizobium
lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N
2
-fixing
Mesorhizobium
lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
Japanese encephalitis virus inhibits superinfection of Zika virus in cells by the NS2B protein
Authors: Yuan Honggen , Rao Jingwei , Zhang Jinhua , Ye Jing , Cao Shengbo , Chen Huanchun , Song Yunfeng
Published: February 2024

Superinfection exclusion (SIE) is a phenomenon in which a preexisting infection prevents a secondary infection. SIE has been described for several flaviviruses, such as West Nile virus vs Nhumirim virus and Dengue virus vs yellow fever virus. Zika virus (ZIKV) is an emerging flavivirus posing threats to human health. The SIE between ZIKV and Japanese encephalitis virus (JEV) is investigated in this study. Our results demonstrate for the first time that JEV inhibits ZIKV infection in both mammalian and mosquito cells, whether co-infects or subsequently infects after ZIKV. The exclusion effect happens at the stage of ZIKV RNA replication. Further studies show that the expression of JEV NS2B protein is sufficient to inhibit the replication of ZIKV, and the outer membrane region of NS2B (46–103 aa) is responsible for this SIE. JEV infection and NS2B expression also inhibit the infection of the vesicular stomatitis virus. In summary, our study characterized a SIE caused by JEV NS2B. This may have potential applications in the prevention and treatment of ZIKV or other RNA viruses.

IMPORTANCE

The reemerged Zika virus (ZIKV) has caused severe symptoms in humans and poses a continuous threat to public health. New vaccines or antiviral agents need to be developed to cope with possible future pandemics. In this study, we found that infection of Japanese encephalitis virus (JEV) or expression of NS2B protein well inhibited the replication of ZIKV. It is worth noting that both the P3 strain and vaccine strain SA14-14-2 of JEV exhibited significant inhibitory effects on ZIKV. Additionally, the JEV NS2B protein also had an inhibitory effect on vesicular stomatitis virus infection, suggesting that it may be a broad-spectrum antiviral factor. These findings provide a new way of thinking about the prevention and treatment of ZIKV.
Oncolytic Newcastle disease virus induced degradation of YAP through E3 ubiquitin ligase PRKN to exacerbate ferroptosis in tumor cells
Authors: Sun Yifan , Tang Lanlan , Kan Xianjin , Tan Lei , Song Cuiping , Qiu Xusheng , Liao Ying , Nair Venugopal , Ding Chan , Liu Xiufan , Sun Yingjie
Published: February 2024

Ferroptosis, a form of programmed cell death characterized by iron-dependent lipid peroxidation, has recently gained considerable attention in the field of cancer therapy. There is significant crosstalk between ferroptosis and several classical signaling pathways, such as the Hippo pathway, which suppresses abnormal growth and is frequently aberrant in tumor tissues. Yes-associated protein 1 (YAP), the core effector molecule of the Hippo pathway, is abnormally expressed and activated in a variety of malignant tumor tissues. We previously proved that the oncolytic Newcastle disease virus (NDV) activated ferroptosis to kill tumor cells. NDV has been used in tumor therapy; however, its oncolytic mechanism is not completely understood. In this study, we demonstrated that NDV exacerbated ferroptosis in tumor cells by inducing ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Blocking YAP degradation suppressed NDV-induced ferroptosis by suppressing the expression of Zrt/Irt-like protein 14 (ZIP14), a metal ion transporter that regulates iron uptake. These findings demonstrate that NDV exacerbated ferroptosis in tumor cells by inducing YAP degradation. Our study provides new insights into the mechanism of NDV-induced ferroptosis and highlights the critical role that oncolytic viruses play in the treatment of drug-resistant cancers.

IMPORTANCE

The oncolytic Newcastle disease virus (NDV) is being developed for use in cancer treatment; however, its oncolytic mechanism is still not completely understood. The Hippo pathway, which is a tumor suppressor pathway, is frequently dysregulated in tumor tissues due to aberrant yes-associated protein 1 (YAP) activation. In this study, we have demonstrated that NDV degrades YAP to induce ferroptosis and promote virus replication in tumor cells. Notably, NDV was found to induce ubiquitin-mediated degradation of YAP at Lys90 through E3 ubiquitin ligase parkin (PRKN). Our study reveals a new mechanism by which NDV induces ferroptosis and provides new insights into NDV as an oncolytic agent for cancer treatment.
HIV-1 RNA genome packaging: it’s G-rated
Authors: Duchon Alice , Hu Wei-Shau
Published: February 2024

A member of the Retroviridae, human immunodeficiency virus type 1 (HIV-1), uses the RNA genome packaged into nascent virions to transfer genetic information to its progeny. The genome packaging step is a highly regulated and extremely efficient process as a vast majority of virus particles contain two copies of full-length unspliced HIV-1 RNA that form a dimer. Thus, during virus assembly HIV-1 can identify and selectively encapsidate HIV-1 unspliced RNA from an abundant pool of cellular RNAs and various spliced HIV-1 RNAs. Several “

G

” features facilitate the packaging of a dimeric RNA genome. The viral polyprotein

G

ag orchestrates virus assembly and mediates RNA genome packaging. During this process, Gag preferentially binds unpaired

g

uanosines within the highly structured 5′ untranslated region (UTR) of HIV-1 RNA. In addition, the HIV-1 unspliced RNA provides a scaffold that promotes Gag:Gag interactions and virus assembly, thereby ensuring its packaging. Intriguingly, recent studies have shown that the use of different

g

uanosines at the junction of U3 and R as transcription start sites results in HIV-1 unspliced RNA species with 99.9% identical sequences but dramatically distinct 5′ UTR conformations. Consequently, one species of unspliced RNA is preferentially packaged over other nearly identical RNAs. These studies reveal how conformations affect the functions of HIV-1 RNA elements and the complex regulation of HIV-1 replication. In this review, we summarize
cis
- and
trans
-acting elements critical for HIV-1 RNA packaging, locations of Gag:RNA interactions that mediate genome encapsidation, and the effects of transcription start sites on the structure and packaging of HIV-1 RNA.
CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells
Authors: Rathore Ujjwal , Haas Paige , Easwar Kumar Vigneshwari , Hiatt Joseph , Haas Kelsey M. , Bouhaddou Mehdi , Swaney Danielle L. , Stevenson Erica , Zuliani-Alvarez Lorena , McGregor Michael J. , Turner-Groth Autumn , Ochieng' Olwal Charles , Bediako Yaw , Braberg Hannes , Soucheray Margaret , Ott Melanie , Eckhardt Manon , Hultquist Judd F. , Marson Alexander , Kaake Robyn M. , Krogan Nevan J.
Published: February 2024

During HIV infection of CD4+ T cells, ubiquitin pathways are essential to viral replication and host innate immune response; however, the role of specific E3 ubiquitin ligases is not well understood. Proteomics analyses identified 116 single-subunit E3 ubiquitin ligases expressed in activated primary human CD4+ T cells. Using a CRISPR-based arrayed spreading infectivity assay, we systematically knocked out 116 E3s from activated primary CD4+ T cells and infected them with NL4-3 GFP reporter HIV-1. We found 10 E3s significantly positively or negatively affected HIV infection in activated primary CD4+ T cells, including UHRF1 (pro-viral) and TRAF2 (anti-viral). Furthermore, deletion of either TRAF2 or UHRF1 in three JLat models of latency spontaneously increased HIV transcription. To verify this effect, we developed a CRISPR-compatible resting primary human CD4+ T cell model of latency. Using this system, we found that deletion of TRAF2 or UHRF1 initiated latency reactivation and increased virus production from primary human resting CD4+ T cells, suggesting these two E3s represent promising targets for future HIV latency reversal strategies.

IMPORTANCE

HIV, the virus that causes AIDS, heavily relies on the machinery of human cells to infect and replicate. Our study focuses on the host cell’s ubiquitination system which is crucial for numerous cellular processes. Many pathogens, including HIV, exploit this system to enhance their own replication and survival. E3 proteins are part of the ubiquitination pathway that are useful drug targets for host-directed therapies. We interrogated the 116 E3s found in human immune cells known as CD4+ T cells, since these are the target cells infected by HIV. Using CRISPR, a gene-editing tool, we individually removed each of these enzymes and observed the impact on HIV infection in human CD4+ T cells isolated from healthy donors. We discovered that 10 of the E3 enzymes had a significant effect on HIV infection. Two of them, TRAF2 and UHRF1, modulated HIV activity within the cells and triggered an increased release of HIV from previously dormant or “latent” cells in a new primary T cell assay. This finding could guide strategies to perturb hidden HIV reservoirs, a major hurdle to curing HIV. Our study offers insights into HIV-host interactions, identifies new factors that influence HIV infection in immune cells, and introduces a novel methodology for studying HIV infection and latency in human immune cells.
The dCas9-based genome editing in
Plasmodium yoelii
Authors: Zhang Chao , Yang Shijie , Quansah Elvis , Zhang Ziyu , Da Weiran , Wang Bingjie
Published: February 2024

Genetic editing is a powerful tool for functional characterization of genes in various organisms. With its simplicity and specificity, the CRISPR-Cas9 technology has become a popular editing tool, which introduces site-specific DNA double-strand breaks (DSBs), and then leverages the endogenous repair pathway for DSB repair
via
homology-directed repair (HDR) or the more error-prone non-homologous end joining (NHEJ) pathways. However, in the
Plasmodium
parasites, the lack of a typical NHEJ pathway selects for DSB repair through the HDR pathway when a homologous DNA template is available. The AT-rich nature of the
Plasmodium
genome exacerbates this drawback by making it difficult to clone longer homologous repair DNA templates. To circumvent these challenges, we adopted the hybrid catalytically inactive Cas9 (dCas9)-microbial single-stranded annealing proteins (SSAP) editor to the
Plasmodium
genome. In
Plasmodium yoelii
, we demonstrated the use of the dCas9-SSAP, as the cleavage-free gene editor, by targeted gene deletion and gene tagging, even using shorter homologous DNA templates. This dCas9-SSAP method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, would be a great addition to the existing genetic toolbox and could be deployed for the functional characterization of genes in
Plasmodium
, contributing to improving the ability of the malaria research community in characterizing more than half of genes with unknown functions.

IMPORTANCE

Malaria caused by
Plasmodium
parasites infection remains a serious threat to human health, with an estimated 249 million malaria cases and 608,000 deaths worldwide in 2022, according to the latest report from the World Health Organization (WHO). Here, we demonstrated the use of dCas9-single-stranded annealing protein, as the cleavage-free gene editor in
Plasmodium yoelii
, by targeted deletion and gene tagging, even using shorter homologous DNA templates. This method with a shorter DNA template, which did not require DSBs, independent of HDR and NHEJ, showing the potential significance in greatly improving our ability to elucidate gene functions, would contribute to assisting the malaria research community in deciphering more than half of genes with unknown functions to identify new drug and vaccine targets.
Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species
Authors: Mann Allison E. , Chakraborty Brinta , O'Connell Lauren M. , Nascimento Marcelle M. , Burne Robert A. , Richards Vincent P.
Published: February 2024

Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS-competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remain an open question. Here, we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic and
in vitro
citrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping and
de novo
assembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low-abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups.

IMPORTANCE

Tooth decay is the most common preventable chronic disease, affecting more than two billion people globally. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of arginine deiminase system (ADS) activity among oral bacteria in a community context remain an open question. In the current study, we use a multi-omics approach to document the pervasiveness of the expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.
Distribution and genetic characterization of fluoroquinolone resistance gene
qnr
among
Salmonella
strains from chicken in China
Authors: Chen Yang , Liu Lihui , Guo Yali , Chu Jinhua , Wang Bangjuan , Sui Yuxin , Wei Hanqi , Hao Haihong , Huang Lingli , Cheng Guyue
Published: February 2024

The prevalence and dissemination of the plasmid-mediated fluoroquinolone (FQ) resistance gene
qnr
in
Salmonella
are considered serious public health concerns worldwide. So far, no comprehensive large-scale studies have focused on the prevalence and genetic characteristics of the
qnr
gene in
Salmonella
isolated from chickens. Herein, this study aimed to investigate the prevalence, antimicrobial resistance (AMR) patterns, and molecular characteristics of chicken-originated
qnr
-positive
Salmonella
strains from chicken farms, slaughterhouses, and markets in 12 provinces of China in 2020–2021. The overall prevalence of the
qnr
gene was 21.13% (56/265), with the highest prevalence in markets (36.11%, 26/72), followed in farms (17.95%, 21/117), and slaughterhouses (10.53%, 9/76). Only the
qnrS
and
qnrB
genes were detected, and the prevalence rate of the
qnrS
gene (19.25%, 51/265) was higher than that of the
qnrB
gene (1.89%, 5/265). Whole genome sequencing identified 37 distinct AMR genes and 15 plasmid replicons, and the most frequent mutation in quinolone resistance determining regions was
parC
(T57S; 91.49%, 43/47). Meanwhile, four different
qnrS
and two
qnrB
genetic environments were discovered among 47
qnr
-positive
Salmonella
strains. In total, 21.28% (10/47) of the strains were capable of conjugative transfer, and all were
qnrS1
-positive strains, with the majority of transferable plasmids being IncHI2 types (
n
= 4). Overall, the prevalence of
qnr
-positive
Salmonella
strains from chickens in China and their carriage of multiple resistance and virulence genes and transferable plasmids is a major concern, which calls for continuous surveillance of
qnr
-positive
Salmonella
and the development of measures to control its prevalence and transmission.

IMPORTANCE

Salmonella
is a common foodborne pathogen responsible for 155,000 deaths annually worldwide. Fluoroquinolones (FQs) are used as first-line drugs for the treatment of
Salmonella
infections in several countries and regions. However, the emergence and increasing prevalence of the FQ-resistant gene
qnr
in
Salmonella
isolated from chickens have been widely reported. Gaining insight into the genetic mechanisms of AMR genes in chicken could lead to the development of preventive measures to control and reduce the risk of drug resistance. In this study, we identified
qnr
-positive
Salmonellae
isolated from chickens in different regions of China and their AMR patterns and genome-wide characteristics, providing a theoretical basis for further control of their prevalence and transmission.
Validation of a real-time polymerase chain reaction for the detection and quantification of the nucleic acid of
Histoplasma
from equine clinical samples
Authors: Fisher Lewis W. S. , Ceesay Abdou , Jallow Demba , Hawkes Sophie F. , Showering Alicia , Kane Yaghouba , Doumbia Amadou , Stringer Andrew P. , Scantlebury Claire E.
Published: February 2024

Histoplasma capsulatum
var
. farciminosum
(HCF) is a dimorphic fungus that causes epizootic lymphangitis in equids. Current diagnostic approaches, including culture, microscopy, and clinical presentation, lack speed, sensitivity, and specificity when diagnosing clinical cases. In this study, equine blood and pus samples on Whatman FTA cards from Senegal (
n
= 3), The Gambia (
n
= 19), Ethiopia (
n
= 16), and Mali (
n
= 13) were tested using a real-time PCR (qPCR) protocol. The assay was optimized and tested for its suitability to detect and quantify HCF in blood and pus loaded onto Whatman FTA cards at sampling. Whatman FTA cards were tested for their suitability for use with qPCR and were found to recover DNA more efficiently than from direct extraction. Using TaqMan fluorescent probes and specific primers, the assay demonstrated 100% analytical specificity when detecting multiple strains of
Histoplasma
and no false positives with off-target organisms. The assay’s diagnostic performance was measured against an existing nested internal transcribed spacer PCR protocol using a receiver operating characteristic curve. The test was found to have a diagnostic specificity and sensitivity of 100% and 71.4%, respectively, when analyzing pus samples using a cycle threshold (Ct) cutoff determined by Youden’s index (27.75). Blood sample cutoff Ct value was proposed at 34.55. Further optimization is required to improve the performance of the protocol when applied to blood samples. This study has, for the first time, demonstrated the ability to detect and quantify the DNA of
Histoplasma
spp. in equine blood and pus samples with a high degree of accuracy, providing a platform to further investigate the pathogenesis and epidemiology of this disease.

IMPORTANCE

Histoplasmosis is a neglected yet major cause of morbidity and mortality in both equids and people in resource-scarce settings. One of the major hindrances to the control of histoplasmosis is a lack of readily available diagnostic tests. Tests are needed to support clinical decision-making and to be applied in population-based research to further understand this disease
in situ
. This paper reports, for the first time, the validation and application of a qPCR to detect
Histoplasma
directly from equine clinical samples, bypassing the need to culture this notoriously difficult organism. We report and comment on the performance of the qPCR in comparison with our previously developed nested PCR.
In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing
Klebsiella pneumoniae
bloodstream isolates from Italian hospital patients
Authors: Posteraro Brunella , De Maio Flavio , Motro Yair , Menchinelli Giulia , De Lorenzis Desy , Marano Roberto B. M. , Aljanazreh Bessan , Errico Federica Maria , Massaria Giuseppe , Spanu Teresa , Posteraro Patrizia , Moran-Gilad Jacob , Sanguinetti Maurizio
Published: February 2024

Bloodstream infection (BSI) caused by carbapenem-resistant
Klebsiella pneumoniae
(KP) poses significant challenges, particularly when the infecting isolate carries multiple antimicrobial resistance (AMR) genes/determinants. This study, employing short- and long-read whole-genome sequencing, characterizes six New Delhi metallo-β-lactamase (NDM) 1 and KP carbapenemase (KPC) 3 co-producing KP isolates, the largest cohort investigated in Europe to date. Five [sequence type (ST) 512] and one (ST11) isolates were recovered from patients who developed BSI from February to August 2022 or February 2023 at two different hospitals in Rome, Italy. Phylogenetic analysis revealed two distinct clusters among ST512 isolates and a separate cluster for the ST11 isolate. Beyond
bla
NDM-1
and
bla
KPC-3
, various AMR genes, indicative of a multidrug resistance phenotype, including colistin resistance, were found. Each cluster-representative ST512 isolate harbored a
bla
NDM-1
plasmid (IncC) and a
bla
KPC-3
plasmid [IncFIB(pQil)/IncFII(K)], while the ST11 isolate harbored a
bla
NDM-1
plasmid [IncFII(pKPX1)] and a
bla
KPC-3
plasmid [IncFIB(K)/IncFII(K)]. The
bla
NDM-1
plasmids carried genes conferring resistance to clinically relevant antimicrobial agents, and the aminoglycoside resistance gene
aac
(
6
′)-
Ib
was found on different plasmids. Colistin resistance-associated
mgrB
/
pmrB
gene mutations were present in all isolates, and the yersiniabactin-encoding
ybt
gene was unique to the ST11 isolate. In conclusion, our findings provide insights into the genomic context of
bla
NDM-1
/
bla
KPC-3
carbapenemase-producing KP isolates.

IMPORTANCE

This study underscores the critical role of genomic surveillance as a proactive measure to restrict the spread of carbapenemase-producing KP isolates, especially when key antimicrobial resistance genes, such as
bla
NDM-1
/
bla
KPC-3
, are plasmid borne. In-depth characterization of these isolates may help identify plasmid similarities contributing to their intra-hospital/inter-hospital adaptation and transmission. Despite the lack of data on patient movements, it is possible that carbapenem-resistant isolates were selected to co-produce KP carbapenemase and New Delhi metallo-β-lactamase via plasmid acquisition. Studies employing long-read whole-genome sequencing should be encouraged to address the emergence of KP clones with converging phenotypes of virulence and resistance to last-resort antimicrobial agents.
Bacteroides fragilis
aggravates high-fat diet-induced non-alcoholic fatty liver disease by regulating lipid metabolism and remodeling gut microbiota
Authors: Huang Yumei , Cao Jiali , Zhu Mengpei , Wang Ziwen , Jin Ze , Xiong Zhifan
Published: February 2024

Gut microbiota dysbiosis is a prominent determinant that significantly contributes to the disruption of lipid metabolism. Consequently, it is essential to the occurrence and development of non-alcoholic fatty liver disease (NAFLD). Nevertheless, the connection between diet and symbiotic gut microbiota in the progression of NAFLD remains uncertain. The purpose of this study was to explore the role of supplementing commensal
Bacteroides fragilis
(
B. fragilis
) on lipid metabolism, gut microbiota, and metabolites in high-fat diet (HFD)-fed mice, elucidating the impact of gut microbiota and metabolites on the development of NAFLD. Our study revealed that supplementation with
B. fragilis
exacerbated both weight gain and obesity in mice.
B. fragilis
exacerbated blood glucose levels and liver dysfunction in mice. Furthermore, an increase in liver lipid accumulation and the upregulation of genes correlated with lipid metabolism were observed in mice. Under an HFD, supplementation of commensal
B. fragilis
resulted in alterations in the gut microbiota, notably a significant increase in
Desulfovibrionaceae
, which led to elevated endotoxin levels and thereby influenced the progression of NAFLD. It was interesting that the simultaneous examination of gut microbiota metabolites revealed a more pronounced impact of diet on short-chain fatty acids. This study represented the pioneering investigation into the impact of
B. fragilis
on NAFLD. Our findings demonstrated that
B. fragilis
induced dysregulation in the intestinal microbiota, leading to elevated levels of lipopolysaccharide and dysfunction in glucose and lipid metabolism, thereby exacerbating NAFLD.

IMPORTANCE

Some intestinal symbiotic microbes are involved in the occurrence of the metabolic disorders. Our study investigated the impact of supplementing commensal
Bacteroides fragilis
on host metabolism in high-fat diet-fed mice. Research results indicated that adding a specific bacterial strain to the complex intestinal microecology can worsen metabolic conditions. This effect mainly affects the structural diversity of intestinal microorganisms, the increase in harmful bacteria in the gut, and the elevation of endotoxin levels, blood glucose, and lipid metabolism, thereby impacting the progression of non-alcoholic fatty liver disease (NAFLD). Understanding the principles that govern the establishment of microbial communities comprising multiple species is crucial for preventing or repairing dysfunctions in these communities, thereby enhancing host health and facilitating disease treatment. This study demonstrated that gut microbiota dysbiosis could contribute to metabolic dysfunction and provides new insights into how to promote gut microbiota in the prevention and therapy of NAFLD.
Christmas tree fir green is not the intensive care unit’s favourite colour
Authors: Hatab Sultan , Waraich Manprit , Amin Danyal , Mahon Ciara
Published: February 2024

A patient in her 60s presented to a district general hospital with headache, loss of consciousness, and vomiting. She was diagnosed with a subarachnoid haemorrhage secondary to an anterior communicating artery aneurysm and was transferred to a tertiary unit for coiling of the aneurysm under the neurosurgical team. She was intubated and had close observational monitoring, where it was noted that her oxygen saturations, obtained using finger-pulse oximetry, varied between 94% and 100%. Each fingernail had a different acrylic nail polish colour which we believe resulted in these inconsistent readings. The dark forest green colour consistently gave a significantly lower oxygen saturation reading when compared with our control, which was the arterial blood gas oxygen saturation, whereas orange and purple were most like our control. We therefore found that the varied colours painted on acrylic nails affected oxygen saturation readings differently. This difference could affect treatment pathways for patients in theatre and the intensive care unit.
Pelvic floor muscle training in female functional fitness exercisers: an assessor-blinded randomised controlled trial
Authors: Skaug Kristina Lindquist , Engh Marie Ellström , Bø Kari
Published: February 2024

Objective

Stress urinary incontinence (SUI) is common among females during functional fitness training, such as CrossFit. The aim of this study was to assess the effect of pelvic floor muscle training (PFMT) on SUI in female functional fitness exercisers.

Methods

This was an assessor-blinded randomised controlled trial with a PFMT group (n=22) and a control group (n=25). The PFMT group followed a 16-week home-training programme with 3 sets of 8–12 maximum pelvic floor muscle (PFM) contractions daily and weekly follow-up/reminders by phone. The primary outcome was change in a total score of the International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form (ICIQ-UI-SF). The secondary outcomes were perceived change of symptoms of SUI, change of PFM strength measured by vaginal manometry and symptoms of anal incontinence (AI) and pelvic organ prolapse (POP).

Results

47 women, mean age of 33.5 years (SD: 8.1), participated. At 16 weeks, there was a mean difference between groups of −1.4 (95% CI: −2.6 to −0.2) in the change of the ICIQ-UI-SF score in favour of the PFMT group. The PFMT group completed a mean of 70% (SD: 23) of the prescribed protocol. 64% in the PFMT group versus 8% in the control group reported improved symptoms of SUI (p<0.001, relative risk: 7.96, 95% CI, 2.03 to 31.19). There were no group differences in the change of PFM strength or AI/POP symptoms.

Conclusion

A 16-week home-training programme of the PFM led to improvements in SUI in female functional fitness exercisers. However, PFM strength and AI and POP symptoms did not improve significantly in the PFMT group compared with the control group.
Review of the direct and indirect effects of hyperglycemia on the HPA axis in T2DM and the co-occurrence of depression
Authors: Mosili Palesa , Mkhize Bongeka Cassandra , Sibiya Ntethelelo Hopewell , Ngubane Phikelelani Sethu , Khathi Andile
Published: February 2024

Type 2 diabetes mellitus (T2DM) is characterized by persistent hyperglycemia which is further associated with hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis. Several studies have shown that HPA axis hyperactivity is heightened in the chronic hyperglycemic state with severe hyperglycemic events more likely to result in a depressive disorder. The HPA axis is also regulated by the immune system. Upon stress, under homeostatic conditions, the immune system is activated via the sympatho-adrenal-medullary axis resulting in an immune response which secretes proinflammatory cytokines. These cytokines aid in the activation of the HPA axis during stress. However, in T2DM, where there is persistent hyperglycemia, the immune system is dysregulated resulting in the elevated concentrations of these cytokines. The HPA axis, already activated by the hyperglycemia, is further activated by the cytokines which all contribute to a diagnosis of depression in patients with T2DM. However, the onset of T2DM is often preceded by pre-diabetes, a reversible state of moderate hyperglycemia and insulin resistance. Complications often seen in T2DM have been reported to begin in the pre-diabetic state. While the current management strategies have been shown to ameliorate the moderate hyperglycemic state and decrease the risk of developing T2DM, research is necessary for clinical studies to profile these direct effects of moderate hyperglycemia in pre-diabetes on the HPA axis and the indirect effects moderate hyperglycemia may have on the HPA axis by investigating the components of the immune system that play a role in regulating this pathway.
In search of a ‘good number’: knowledge controversy and population estimates in the endgame of hepatitis C elimination
Authors: Rhodes Tim , Lancaster Kari , Adams Sophie
Published: February 2024

We explore the contentious life of a metric used to assess a country’s progress in relation to global disease elimination targets. Our topic is hepatitis C elimination, and our context is Australia. A fundamental metric in the calculation of progress toward hepatitis C elimination targets, as set by the WHO, is the population prevalence of people living with hepatitis C. In Australia, this modelled estimate has generated some controversy, largely through its repeated downsizing as an effect of calculus. The 2015 baseline population estimate in Australia, from which measures of current elimination progress are assessed, has reduced, over time, by around 30%. Informed by a social study of science approach, we used qualitative interviews with 32 experts to explore the knowledge controversy. The controversy is narrated through the core concerns of ‘scale’ and ‘care’, with narratives aligning differently to imaginaries of ‘science’ and ‘community’. We trace how constitutions of ‘estimate’ and ‘number’ circulate in relation to ‘population’ and ‘people’, and as affective values. We show how enactments of estimates and numbers materialise hepatitis elimination in different ways, with policy implications. The event of the knowledge controversy opens up the social and political life of enumerations—for science and community—inviting deliberation on how to make ‘good numbers’ in the race to eliminate hepatitis C.
Single-shot liposomal bupivacaine in place of rectus sheath catheters to provide non-opiate analgesia after laparotomy: a quality improvement project to reduce the need for ongoing nursing input
Authors: Matthews Edward , Ragatha Pranu , Smart Neil , Bethune Rob
Published: February 2024

Opioid-sparing pain management is an integral component of enhanced recovery after colonic and rectal surgery. In our hospital, rectus sheath catheters (RSCs) are routinely placed during emergency laparotomy for colorectal procedures to allow a postoperative compartmental block of the surgical site with repeated doses of bupivacaine. However, RSCs require a significant amount of clinical nursing time to maintain and ‘top-up’. We present a quality improvement project in which we administered single-shot liposomal bupivacaine (LB) intraoperatively as an alternative to bolus doses of conventional bupivacaine delivered through RSCs. Having thereby reduced the demands placed on nursing time through a reduction in the use of RSCs, we sought to establish whether there was any associated change in analgesic efficacy. Patient pain scores, use of patient-controlled analgesia (PCA) and length of stay following surgery were analysed before and after the introduction of LB. No disruption in these outcomes was identified using statistical process control analysis. A direct comparison of results for patients who received LB versus those who received bolus dosing of bupivacaine via RSCs found no significant differences, with a median total PCA dose of 270 mg oral morphine equivalents (OME) for patients who received LB versus 396 mg OME for patients who had RSCs (p=0.54). The median length of stay for patients who received LB was 15.5 days versus 16 days for those who had RSCs (p=0.87). We conclude that LB represents a viable alternative to boluses of conventional bupivacaine via RSCs in promoting enhanced recovery after emergency laparotomy and look to extend its use locally.
Safety on the ground: using critical incident technique to explore the factors influencing medical registrars’ provision of safe care
Authors: Ralston Katherine , Smith Samantha Eve , Kerins Joanne , Clark-Stewart Saskia , Tallentire Victoria
Published: February 2024

Background

Avoidable patient harm in hospitals is common, and doctors in training can provide underused but crucial insights into the influencers of patient safety as those working ‘on the ground’ within the system. This study aimed to explore the factors that influence safe care from the perspective of medical registrars, to identify targets for safety-related improvements.

Methods

This study used enhanced critical incident technique (CIT), a qualitative methodology that results in a focused understanding of significant factors influencing an activity, to identify practical solutions. We interviewed 12 out of 17 consenting medical registrars in Scotland, asking them to recount their observations during clinical experiences where something happened that positively or negatively impacted on patient safety. Data were analysed manually using a modified content analysis with credibility checks as per enhanced CIT, with data exhaustiveness reached after six registrars.

Results

A total of 221 critical incidents impacting patient safety were identified. These were inductively placed into 24 categories within 4 overarching categories:Individual skills, encompassing individual behavioural and technical skills;Collaboration, regarding how communication, trust, support and flexibility shape interprofessional collaboration;Organisation, concerning organisational systems and staffing andTraining environment, relating to culture, civility, having a voice and learning at work. Practical targets for safety-related interventions were identified, such as clear policies for patient care ownership or educational interventions to foster civility.

Conclusions

This study provides a rigorous and focused understanding of the factors influencing patient safety in hospitals, using the ‘insider’ perspective of the medical registrar. Safety goes beyond the individual and is reliant on safe system design, interprofessional collaboration and a culture of support, learning and respect. Organisations should also promote flexibility within clinical practice when patient needs do not conform to standardised care pathways. We suggest targeted interventions within educational and organisational priorities to improve safety in hospitals.