bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance and phylogenetic analysis of a pathogenic bacterium candidate in nasal discharge from children
Authors: Fukuda Kazumasa , Haro Kaoru , Yamasaki Kei , Ikegami Hiroaki , Saito Mitsumasa 
Published: May 2024

ABSTRACT

“The infectious organism lurking in human airways (IOLA)” is a candidate pathogenic bacterium detected in bronchoalveolar lavage fluid specimens derived from adult patients with chronic lower respiratory tract infections. Genomic analyses of IOLA have revealed that it possesses the smallest and most AT-rich genome among human-derived bacteria. However, its biological properties remain unclear because no culture method has been established for IOLA. Here, we conducted a large-scale IOLA surveillance study of nasal discharge specimens from children in Japan and investigated the correlation between IOLA detection frequency and patient characteristics. We detected IOLA in 5.4% (103 of 1,920) of pediatric nasal discharge samples. No significant differences were observed in the frequency of detection based on the patient’s background. However, with respect to age, the frequency of detection tended to be significantly high at 2–3 and 6 years old. Phylogenetic analysis revealed five phylotypes in the IOLA 16S rRNA gene sequences, and the sequences detected in adult patients with respiratory infections in a previous study belonged to one of the five phylotypes. The involvement of IOLA in the symptoms is not clear, but IOLA is detected at a relatively high frequency in pediatric nasal discharge. Many subjects with detected IOLA were not always IOLA positive, and IOLA was detected transiently. Our findings suggest that IOLA is horizontally transmitted through groups in nursery and elementary schools, and there are differences in biological characteristics among the IOLA phylotypes.

IMPORTANCE
“The infectious organism lurking in human airways (IOLA)” is a candidate pathogenic bacterium strongly suspected to be infectious to the respiratory tracts of humans and animals. However, a culture method for IOLA has not been established yet, and its properties remain unclear. In this study, IOLA was detected at a relatively high frequency in the nasal discharge of children, and five phylotypes of IOLA were identified. One of these phylotypes was found in the bronchoalveolar lavage fluid from adult patients, suggesting lineage-specific differences in the pathogenicity of IOLA. Moreover, it was suggested that IOLA is horizontally transmitted when children gather in groups such as nursery and elementary schools. These findings strongly indicate that IOLAs have been clinically undetected so far but are spreading among children, with one lineage being involved in respiratory diseases in adults. Examining the presence of IOLA in clinical specimens may help to understand the etiology of respiratory diseases with unknown causes.
Gut and respiratory tract microbiota in children younger than 12 months hospitalized for bronchiolitis compared with healthy children: can we predict the severity and medium-term respiratory outcome?
Authors: Cabrera-Rubio Raul , Calvo Cristina , Alcolea Sonia , Bergia María , Atucha Jorge , Pozo Francisco , Casas Inmaculada , Arroyas María , Collado Maria Carmen , García-García Maria Luz 
Published: May 2024

ABSTRACT

Growing evidence indicates that gut and respiratory microbiota have a potential key effect on bronchiolitis, mainly caused by respiratory syncytial virus (RSV). This was a prospective study of 96 infants comparing infants with bronchiolitis (
n
= 57, both RSV and non-RSV associated) to a control group (
n
= 39). Gut (feces) and respiratory [nasopharyngeal aspirate (NPA)] microbial profiles were analyzed by 16S rRNA amplicon sequencing, and respiratory viruses were identified by PCR. Clinical data of the acute episode and follow-up during the first year after infection were recorded. Pairwise comparisons showed significant differences in the gut (
R
2
= 0.0639,
P
= 0.006) and NPA (
R
2
= 0.0803,
P
= 0.006) microbiota between cases and controls. A significantly lower gut microbial richness and an increase in the NPA microbial diversity (mainly due to an increase in
Haemophilus
,
Streptococcus,
and
Neisseria
) were observed in the infants with bronchiolitis, in those with the most severe symptoms, and in those who subsequently developed recurrent wheezing episodes after discharge. In NPA, the higher microbial richness differed significantly between the control group and the non-RSV bronchiolitis group (
P
= 0.01) and between the control group and the RSV bronchiolitis group (
P
= 0.001). In the gut, the richness differed significantly between the control group and the non-RSV group (
P
= 0.01) and between the control group and the RSV bronchiolitis group (
P
= 0.001), with higher diversity in the RSV group. A distinct respiratory and intestinal microbial pattern was observed in infants with bronchiolitis compared with controls. The presence of RSV was a main factor for dysbiosis. Lower gut microbial richness and increased respiratory microbial diversity were associated with respiratory morbidity during follow-up.

IMPORTANCE
Both the intestinal and respiratory microbiota of children with bronchiolitis, especially those with respiratory syncytial virus infection, are altered and differ from that of healthy children. The microbiota pattern in the acute episode could identify those children who will later have other respiratory episodes in the first year of life. Preventive measures could be adopted for this group of infants.
Detection of
Bartonella
spp. in farmed deer (Artiodactyla: Cervidae) using multiplex assays in the Qinghai-Tibet Plateau, China
Authors: Miao Yu , Guo Wentao , Zhang Wen , Chen Zhizheng , Mian Delan , Li Ruixiao , Xu Ailing , Chen Min , Li Dongmei 
Published: May 2024

ABSTRACT

In this study, we investigated the prevalence of
Bartonella
in deer from Qilian County, Qinghai Province, China. Blood samples were collected from 69 red deer, 40 white-lipped deer, and 27 sika deer. The detection of
Bartonella
spp. has been conducted. The overall prevalence of
Bartonella
was 33.6% (46/135). Species-specific prevalence was 50.72% in red deer (35/69), 20.00% in white-lipped deer (8/40), and 11.11% in sika deer (3/27). There were significant differences in the prevalence rates among the different species of deer. The amplicon sequence comparison revealed a high homology of the ruminant-associated
Bartonella
spp. Nanopore sequencing further confirmed the results.
Bartonella
reads were presented in each of the qPCR-positive samples. Phylogenetic analysis indicated that the
Bartonella
sequences detected in deer blood were closely related to ruminant-borne
Bartonella
spp. In summary, we reported the
Bartonella
prevalence of different deer species in Qinghai, and there were at least one species of ruminant-associated
Bartonella
,
B. schoenbuchensis
.

IMPORTANCE

This is the first report about
Bartonella
infections in the deer population from China. We found that there were two species of
Bartonella
and an unidentified species of
Bartonella
among the unculturing strains carried by these deer populations. We first used Nanopore sequencing to detect
Bartonella
from deer blood samples and indicated that Nanopore sequencing is beneficial to detect pathogens due to its advantage of real-time and high sensitivity.
Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from
Zymomonas mobilis
Authors: Misra Jyotsna , Mettert Erin L. , Kiley Patricia J. 
Published: May 2024

ABSTRACT

Isoprenoids are a diverse family of compounds that are synthesized from two isomeric compounds, isopentenyl diphosphate and dimethylallyl diphosphate. In most bacteria, isoprenoids are produced from the essential methylerythritol phosphate (MEP) pathway. The terminal enzymes of the MEP pathway IspG and IspH are [4Fe-4S] cluster proteins, and in
Zymomonas mobilis,
the substrates of IspG and IspH accumulate in cells in response to O
2
, suggesting possible lability of their [4Fe-4S] clusters. Here, we show using complementation assays in
Escherichia coli
that even under anaerobic conditions,
Z. mobilis
IspG and IspH are not as functional as their
E. coli
counterparts, requiring higher levels of expression to rescue viability. A deficit of the sulfur utilization factor (SUF) Fe-S cluster biogenesis pathway did not explain the reduced function of
Z. mobilis
IspG and IspH since no improvement in viability was observed in
E. coli
expressing the
Z. mobilis
SUF pathway or having increased expression of the
E. coli
SUF pathway. Complementation of single and double mutants with various combinations of
Z. mobilis
and
E. coli
IspG and IspH indicated that optimal growth required the pairing of IspG and IspH from the same species. Furthermore,
Z. mobilis
IspH conferred an O
2
-sensitive growth defect to
E. coli
that could be partially rescued by co-expression of
Z. mobilis
IspG.
In vitro
analysis showed O
2
sensitivity of the [4Fe-4S] cluster of both
Z. mobilis
IspG and IspH. Altogether, our data indicate an important role of the cognate protein IspG in
Z. mobilis
IspH function under both aerobic and anaerobic conditions.

IMPORTANCE

Isoprenoids are one of the largest classes of natural products, exhibiting diversity in structure and function. They also include compounds that are essential for cellular life across the biological world. In bacteria, isoprenoids are derived from two precursors, isopentenyl diphosphate and dimethylallyl diphosphate, synthesized primarily by the methylerythritol phosphate pathway. The aerotolerant
Z. mobilis
has the potential for methylerythritol phosphate pathway engineering by diverting some of the glucose that is typically efficiently converted into ethanol to produce isoprenoid precursors to make bioproducts and biofuels. Our data revealed the surprising finding that
Z. mobilis
IspG and IspH need to be co-optimized to improve flux via the methyl erythritol phosphate pathway in part to evade the oxygen sensitivity of IspH.
Genomic epidemiology of
Streptococcus pyogenes
from pharyngeal and skin swabs in Gabon
Authors: Boutin Sébastien , Arnold Benjamin , Alabi Abraham Sunday , Bélard Sabine , Toepfner Nicole , Nurjadi Dennis 
Published: May 2024

ABSTRACT

The disease burden of
Streptococcus pyogenes
is particularly high in low- and middle-income countries. However, data on the molecular epidemiology of
S. pyogenes
in such regions, especially sub-Saharan Africa, are scarce. To address this, whole-genome sequencing (WGS) of
S. pyogenes
from Gabon was performed to identify transmission clusters and provide valuable genomic data for public repositories. A total of 76
S
.
pyogenes
isolates from 73 patients, collected between September 2012 and January 2013, were characterized by short-read whole-genome sequencing. The predominant emm types were
emm
58.0,
emm
81.2 and
emm
223.0 with 9.2% (7 of 76), 7.9% (6 of 76), and 6.6% (5 of 76), respectively. Single-nucleotide polymorphism analysis revealed 16 putative transmission clusters. Four of these were household transmissions. Four antimicrobial genes (
lmrP
,
tetM
,
tetL
, and
thfT
) were found in the
S. pyogenes
isolates from this study. All strains carried
lmrP
. Of the 76 isolates, 64 (84.2%) carried at least one tetracycline resistance gene (
tetM
or
tetL
). Comparisons with other publicly available African genomic data revealed a significant correlation between geographical location and genetic diversity of
S. pyogenes
, with Gabonese strains showing similarities to those from Kenya and certain Oceanian regions. Our study showed that transmission of
S. pyogenes
can occur at the community/household level and that high-resolution molecular typing is needed to monitor changes in circulating clones and to detect community outbreaks. Advocacy for the adoption of WGS for comprehensive molecular characterization of
S. pyogenes
and data sharing through public repositories should be encouraged to understand the molecular epidemiology and evolutionary trajectory of
S. pyogenes
in sub-Saharan Africa.

IMPORTANCE

The study conducted in Gabon underscores the critical importance of addressing the limited knowledge of the molecular epidemiology of
Streptococcus pyogenes
in low- and middle-income countries, particularly sub-Saharan Africa. Our molecular analysis identified predominant
emm
types and unveiled 16 putative transmission clusters, four involving household transmissions. Furthermore, the study revealed a correlation between geographical location and genetic diversity, emphasizing the necessity for a comprehensive understanding of the molecular epidemiology and evolutionary trajectory of
S. pyogenes
in various regions. The call for advocacy in adopting whole-genome sequencing for molecular characterization and data sharing through public repositories is crucial for advancing our knowledge and implementing effective strategies to combat the spread of
S. pyogenes
in sub-Saharan Africa.
Mycobacterium tuberculosis
is less likely to acquire pathogenic mutations during latent infection than during active disease
Authors: Osugi Asami , Tamaru Aki , Yoshiyama Takashi , Iwamoto Tomotada , Mitarai Satoshi , Murase Yoshiro 
Published: May 2024

ABSTRACT

Most people infected with
Mycobacterium tuberculosis
(
Mtb
) are believed to be in a state of latent tuberculosis (TB) infection (LTBI). Although LTBI is asymptomatic and not infectious, there is a risk of developing active disease even decades after infection. Here, to characterize mutations acquired during LTBI, we collected and analyzed
Mtb
genomes from seven Japanese patient pairs, each pair consisting of two active TB patients whose starting dates of developing active disease were >3 years apart; one had a high suspicion of LTBI before developing active disease, whereas the other did not. Thereafter, we compared these genomes with those of longitudinal sample pairs within a host of chronic active TB infections combined with public data. The bacterial populations in patients with LTBI were genetically more homogeneous and accumulated single nucleotide polymorphisms (SNPs) slower than those from active disease. Moreover, the lower proportion of nonsynonymous SNPs indicated weaker selective pressures during LTBI than active disease. Finally, the different mutation spectrums indicated different mutators between LTBI and active disease. These results suggest that the likelihood of the acquisition of mutations responsible for antibiotic resistance and increased virulence was lower in the
Mtb
population from LTBI than active disease.

IMPORTANCE

Controlling latent tuberculosis (TB) infection (LTBI) activation is an effective strategy for TB elimination, where understanding
Mycobacterium tuberculosis
(
Mtb
) dynamics within the host plays an important role. Previous studies on chronic active disease reported that
Mtb
accumulated genomic mutations within the host, possibly resulting in acquired drug resistance and increased virulence. However, several reports suggest that fewer mutations accumulate during LTBI than during the active disease, but the associated risk is largely unknown. Here, we analyzed the genomic dynamics of
Mtb
within the host during LTBI. Our results statistically suggest that
Mtb
accumulates mutations during LTBI, but most mutations are under low selective pressures, which induce mutations responsible for drug resistance and virulence. Thus, we propose that LTBI acts as a source for new TB disease rather than as a period for in-host genome evolution.
Clinical, endoscopic and therapeutic features of bleeding Dieulafoy’s lesions: case series and literature review
Authors: Aabdi Basma , Kharrasse Ghizlane , Zazour Abdelkrim , Koulali Hajar , Elmqaddem Ouiam , Zahi Ismaili 
Published: May 2024

ObjectiveDieulafoy’s lesions (DLs) are a rare but potentially life-threatening source of gastrointestinal (GI) haemorrhage. They are responsible for roughly 1%–6.5% of all cases of acute non-variceal GI bleeding.Here, we describe retrospectively the clinical and endoscopic features, review the short-term and long-term outcomes of endoscopic management of bleeding DLs and we identify rate and risk factors, of recurrence and mortality in our endoscopic unit.DesignData were collected from patients presenting with GI haemorrhagic secondary to DLs between January 2018 and August 2023. Patients’ medical records as well as endoscopic databases were retrospectively reviewed. Demographic data, risk factors, bleeding site, outcomes of endoscopy techniques, recurrence and mortality rate were taken into account.ResultsAmong 1170 cases of GI bleeding, we identified only seven cases involving DLs. Median age was 74 years, with a male-to-female ratio of 2.5. 75% of patients had significant comorbidities, mainly cardiovascular diseases. Only anticoagulant and antiplatelet agents were significantly associated with DLs. All patients were presented with GI bleeding as their initial symptom. The initial endoscopy led to a diagnosis in 85% of the cases. Initial haemostasis was obtained in all patients treated endoscopically. Nevertheless, the study revealed early recurrence in two out of three patients treated solely with epinephrine injection or argon plasma coagulation. In contrast, one of three patients who received combined therapy, experienced late recurrence (average follow-up of 1 year). Pathological diagnosis was necessary in one case. One patient (14%) died of haemorrhagic shock. Average length of hospital stay was 3 days.ConclusionAlthough rare, DLs may be responsible for active, recurrent and unexplained GI bleeding. Thanks to the emergence of endoscopic therapies, the recurrence rate has decreased and the prognosis has highly improved. Therefore, the endoscopic approach remains the first choice to manage bleeding DLs.
Adverse pregnancy outcomes in gestational diabetes mellitus: a systematic review and meta-analysis protocol
Authors: Chukwuemeka Scholarstica , Chivese Tawanda , Gopinath Aswathy , Obikeze Kenechukwu 
Published: May 2024

IntroductionGestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes, including adverse outcomes for both the mother and the fetus. Different diagnostic criteria are used for GDM, and it is not clear how these affect the reported prevalence of adverse pregnancy outcomes. This protocol is for a systematic review to describe and compare the prevalence of adverse pregnancy outcomes in GDM using the different diagnostic criteria applied in various countries/regions of the world.Methods and analysisA systematic review and meta-analysis will be carried out. A comprehensive search of observational studies that report the outcomes of interest to this review from 2010 to 2021 will be conducted. We will search the major electronic databases such as PubMed, Scopus, CINHAL and Google Scholar, and screen references of included studies for additional studies. Meta-analyses will be performed, if there is low heterogeneity, and pooled estimates per outcome reported. We will use the bias-adjusted inverse variance heterogeneity model and random effects models, depending on the heterogeneity observed, to pool prevalence estimates and perform subgroup analyses by region, by age group, by diagnostic criteria and by GDM screening method if sufficient data are available. We will also compare the prevalence of adverse outcomes by diagnostic method and report prevalence ratios. We will report 95% confidence estimates for all estimates.Ethics and disseminationEthical approval is not required as the review uses published data. Findings will be published in peer-reviewed journals and presented at conferences.PROSPERO registration numberCRD42020155061.
Population density and receipt of care for common mental disorders: a cross-sectional analysis of English household data from the 2014 Adult Psychiatric Morbidity Survey
Authors: Hiepko Alexander Thomas , Shoham Natalie , McManus Sally , Cooper Claudia 
Published: May 2024

ObjectivesPeople living in less urban areas in the UK may have reduced access to mental healthcare compared with people in urban areas. Although this was not reported in the 2000 Adult Psychiatric Morbidity Survey (APMS) data, subsequent changes to mental health provision and economic recession may have impacted care inequalities. We re-examined this, hypothesising that those living in less urban areas of England received less antidepressant medication and psychological interventions, compared with those living in urban areas, after adjusting for covariates including common mental disorders (CMDs) and socioeconomic status.DesignNational cross-sectional study.SettingHouseholds in England.ParticipantsWe analysed data from 7455 participants aged 16 and above from the 2014 English APMS.ExposuresResidence in an urban or less urban area.Primary outcomeCurrent receipt of any antidepressant medication or any psychological intervention.ResultsParticipants living in less urban areas were half as likely to be in receipt of any psychological intervention relative to those living in urban areas (adjusted OR (aOR) 0.49; 95% CI 0.30 to 0.79; p=0.004). There was no association between urbanisation and antidepressant receipt (aOR 1.01; 95% CI 0.81 to 1.25; p=0.944).ConclusionPeople living in less urban areas have a lower likelihood of being in receipt of psychological treatment for CMDs, which may indicate barriers to care access. Our findings differ from the results of a study using a comparable sample conducted 14 years previously. While Improving Access to Psychological Therapies services have increased therapy access nationwide, this may have had more impact in urban areas, potentially widening urban/rural inequalities. Further research is needed to understand how to address such geographical inequalities in access to mental healthcare.
Quality of aerobic training description and its relation to intervention efficacy in chronic obstructive pulmonary disease trials: study protocol for a systematic review, meta-analysis and meta-regression
Authors: Jakobsson Johan , Stoffels Anouk A F , van Hees Hieronymus W H , De Brandt Jana , Nyberg André , Klijn Peter 
Published: May 2024

IntroductionChronic obstructive pulmonary disease (COPD) is a major global health concern, characterised by ventilatory constraints, decreased cardiovascular fitness and reduced limb muscle function, profoundly affecting patients’ quality of life. Aerobic training plays a crucial role in the treatment of COPD, but the variability in methodologies and incomplete reporting of key components in aerobic training trials limits the assessment of their effectiveness. This systematic review aims to critically evaluate the application of training principles and reporting of key components in aerobic training trials in randomised controlled trials (RCTs) in the COPD literature.Methods and analysisThe protocol adheres to the Preferred Reporting Items for Systematic reviews and Meta-Analyses Protocol guidelines. The review will include RCTs utilising aerobic training in individuals with COPD. A comprehensive search, following a predefined search strategy will identify studies published from 2007 to 2024 in English from MEDLINE, Embase, CINAHL, CENTRAL and PEDro. Studies including people with COPD and any aerobic training intervention will be included. Two reviewers will independently screen abstracts and titles for inclusion. Two reviewers will independently conduct the screening of full-text documents and data extraction. Study quality will be assessed using the Tool for the assESsment of sTudy quality and bias in Exercise, specifically developed for exercise training studies. The certainty of the evidence will be evaluated using the Grading of Recommendations Assessment, Development and Evaluation approach. A systematic synthesis will be provided, with meta-analyses and meta-regression when appropriate.Ethics and disseminationAs this review will involve the analysis of published data, ethical approval is not required. The findings of this review will be disseminated through peer-reviewed publications and conference presentations.PROSPERO registration numberCRD42021247343.