bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonal Dissemination of Pseudomonas aeruginosa Sequence Type 235 Isolates Carrying
bla
IMP-6
and Emergence of
bla
GES-24
and
bla
IMP-10
on Novel Genomic Islands PAGI-15 and -16 in South Korea
Authors: Hong Jun Sung , Yoon Eun-Jeong , Lee Hyukmin , Jeong Seok Hoon , Lee Kyungwon 
Published: September 2016

ABSTRACT

A total of 431
Pseudomonas aeruginosa
clinical isolates were collected from 29 general hospitals in South Korea in 2015. Antimicrobial susceptibility was tested by the disk diffusion method, and MICs of carbapenems were determined by the agar dilution method. Carbapenemase genes were amplified by PCR and sequenced, and the structures of class 1 integrons surrounding the carbapenemase gene cassettes were analyzed by PCR mapping. Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed for strain typing. Whole-genome sequencing was carried out to analyze
P. aeruginosa
genomic islands (PAGIs) carrying the
bla
IMP-6
,
bla
IMP-10
, and
bla
GES-24
genes. The rates of carbapenem-nonsusceptible and carbapenemase-producing
P. aeruginosa
isolates were 34.3% (148/431) and 9.5% (41/431), respectively. IMP-6 was the most prevalent carbapenemase type, followed by VIM-2, IMP-10, and GES-24. All carbapenemase genes were located on class 1 integrons of 6 different types on the chromosome. All isolates harboring carbapenemase genes exhibited genetic relatedness by PFGE (similarity > 80%); moreover, all isolates were identified as sequence type 235 (ST235), with the exception of two ST244 isolates by MLST. The
bla
IMP-6
,
bla
IMP-10
, and
bla
GES-24
genes were found to be located on two novel PAGIs, designated PAGI-15 and PAGI-16. Our data support the clonal spread of an IMP-6-producing
P. aeruginosa
ST235 strain, and the emergence of IMP-10 and GES-24 demonstrates the diversification of carbapenemases in
P. aeruginosa
in Korea.
Transposition of Tn
125
Encoding the NDM-1 Carbapenemase in Acinetobacter baumannii
Authors: Bontron Séverine , Nordmann Patrice , Poirel Laurent 
Published: September 2016

ABSTRACT

The
bla
NDM-1
gene encodes a carbapenemase that confers resistance to almost all β-lactams, including last-resort carbapenems. This is increasingly reported worldwide in nosocomial and community-acquired Gram-negative bacteria.
Acinetobacter baumannii
is an important opportunistic pathogen that is considered an intermediate reservoir for the
bla
NDM-1
gene. In this species, the
bla
NDM-1
gene is located within the Tn
125
composite transposon. The mechanism driving the mobility of Tn
125
has not yet been elucidated. Here we experimentally demonstrated the transposition of Tn
125
in
A. baumannii
. Systematic 3-bp duplication of the target site, being the signature of transposition, was evidenced. The target site consensus sequence for Tn
125
transposition was found to be GC enriched at the duplicated 3 bp and AT rich in the vicinity. Transposition frequency was not influenced by temperature changes or by exposure to subinhibitory concentrations of various antibiotics. This work is the first direct evidence of the functionality of a composite transposon in
A. baumannii
. It provides a mechanistic clue for the dissemination of the
bla
NDM-1
gene in
Acinetobacter
spp. and subsequently among
Enterobacteriaceae
.
Fluorescent Reporter DS6A Mycobacteriophages Reveal Unique Variations in Infectibility and Phage Production in Mycobacteria
Authors: Mayer Oren , Jain Paras , Weisbrod Torin R. , Biro Daniel , Ho Libby , Jacobs-Sera Deborah , Hatfull Graham F. , Jacobs William R. 
Published: September 2016

ABSTRACT

Mycobacteriophage DS6A is unique among the more than 8,000 isolated mycobacteriophages due to its ability to form plaques exclusively on mycobacteria belonging to the
Mycobacterium tuberculosis
complex (MTBC). Speculation surrounding this specificity has led to unsupported assertions in published studies and patents that nontuberculous mycobacteria (NTM) are wholly resistant to DS6A infection. In this study, we identified two independent nonessential regions in the DS6A genome and replaced them with an mVenus-expressing plasmid to generate fluorescent reporter phages Φ
2
GFP12 and Φ
2
GFP13. We show that even though DS6A is able to form plaques only on MTBC bacteria, infection of various NTM results in mVenus expression in transduced cells. The efficiency of DS6A in delivering DNA varied between NTM species. Additionally, we saw a striking difference in the efficiency of DNA delivery between the closely related members of the
Mycobacterium abscessus
complex,
M. abscessus
and
Mycobacterium massiliense
. We also demonstrated that TM4 and DS6A, two phages that do not form plaques on
M. massiliense
, differ in their ability to deliver DNA, suggesting that there is a phage-specific restriction between mycobacterial species. Phylogenetic analysis reveals that the DS6A genome has a characteristically mosaic structure but provided few insights into the basis for the specificity for MTBC hosts. This study demonstrates that the inability of the MTBC-specific phage DS6A to form plaques on NTM is more complex than previously thought. Moreover, the DS6A-derived fluorophages provide important new tools for the study of mycobacterial biology.

IMPORTANCE
The coevolution of bacteria and their infecting phages involves a constant arms race for bacteria to prevent phage infection and phage to overcome these preventions. Although a diverse array of phage defense systems is well characterized in bacteria, very few phage restriction systems are known in mycobacteria. The DS6A mycobacteriophage is unique in the mycobacterial world in that it forms plaques only on members of the
Mycobacterium tuberculosis
complex. However, the novel DS6A reporter phages developed in this work demonstrate that DS6A can infect nontuberculous mycobacteria at various efficiencies. By comparing the abilities of DS6A and another phage, TM4, to infect and form plaques on various mycobacterial species, we can begin to discern new phage restriction systems employed within the genus.
The Adc/Lmb System Mediates Zinc Acquisition in Streptococcus agalactiae and Contributes to Bacterial Growth and Survival
Authors: Moulin Pauline , Patron Kévin , Cano Camille , Zorgani Mohamed Amine , Camiade Emilie , Borezée-Durant Elise , Rosenau Agnès , Mereghetti Laurent , Hiron Aurélia 
Published: September 2016

ABSTRACT

The Lmb protein of
Streptococcus agalactiae
is described as an adhesin that binds laminin, a component of the human extracellular matrix. In this study, we revealed a new role for this protein in zinc uptake. We also identified two Lmb homologs, AdcA and AdcAII, redundant binding proteins that combine with the AdcCB translocon to form a zinc-ABC transporter. Expression of this transporter is controlled by the zinc concentration in the medium through the zinc-dependent regulator AdcR. Triple deletion of
lmb
,
adcA
, and
adcAII
, or that of the
adcCB
genes, impaired growth and cell separation in a zinc-restricted environment. Moreover, we found that this Adc zinc-ABC transporter promotes
S. agalactiae
growth and survival in some human biological fluids, suggesting that it contributes to the infection process. These results indicated that zinc has biologically vital functions in
S. agalactiae
and that, under the conditions tested, the Adc/Lmb transporter constitutes the main zinc acquisition system of the bacterium.

IMPORTANCE
A zinc transporter, composed of three redundant binding proteins (Lmb, AdcA, and AdcAII), was characterized in
Streptococcus agalactiae
. This system was shown to be essential for bacterial growth and morphology in zinc-restricted environments, including human biological fluids.
Paleomicrobiology of Human Tuberculosis
Authors: Donoghue Helen D. 
Published: September 2016

ABSTRACT

Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is
Mycobacterium tuberculosis
, an obligate pathogen in the
M. tuberculosis
complex that also contains closely related species, such as
Mycobacterium bovis
, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of
M. tuberculosis
ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments,
M. tuberculosis
cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified
M. tuberculosis
lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different
M. tuberculosis
strains and other pathogens. Identification of
M. tuberculosis
lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.
Sources of Materials for Paleomicrobiology
Authors: Aboudharam Gérard 
Published: September 2016

ABSTRACT
The Paleomicrobiology establishes the diagnosis of ancient infectious diseases by studying ancient pathogens. This recent science also analyzes the evolution of these pathogens, virulence, and their adaptation to their habitat and their vectors. The DNA persists a long time after the death of an organism despite the chemical and enzymatic degradation. The possibility of sequencing bacterial, viral, parasitic and archaeal DNA molecules persists over time.
Various sources are used for these studies: frozen tissue and particularly human tissue are a exceptional source for the analysis because at very low temperatures, all biological activity is suspended. The coprolites are a source of choice for studying the human microbiome. Other sources, the ancient bones are the most abundant, however, they may contain only small amounts of DNA due to natural leaching. When the use of the tooth is possible, is a particularly interesting source because of its highly mineralized structure, which gives greater persistence than bone. The calcified tartar deposited on teeth is a source of interest for the study of oral microbiome.
All these sources are subject to precautions (gloves and masks hat) at the time of sampling to avoid cross contamination and also be listed in the most precise way because they are precious and rare.
Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution
Authors: Abi-Rached Laurent , Raoult Didier 
Published: September 2016

ABSTRACT

With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent
Yersinia pestis
or to
Mycobacterium tuberculosis
, which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.
Early puberty in 11-year-old girls: Millennium Cohort Study findings
Authors: Kelly Yvonne , Zilanawala Afshin , Sacker Amanda , Hiatt Robert , Viner Russell 
Published: September 2016

ObjectiveEarly puberty in girls is linked to some adverse outcomes in adolescence and mid-life. We address two research questions: (1) Are socioeconomic circumstances and ethnicity associated with early onset puberty? (2) Are adiposity and/or psychosocial stress associated with observed associations?DesignLongitudinal data on 5839 girls from the UK Millennium Cohort Study were used to estimate associations between ethnicity, family income, adiposity and psychosocial stress with a marker of puberty.Main outcome measureReported menstruation at age 11 years.ResultsAll quoted ORs are statistically significant. Girls in the poorest income quintile were twice as likely (OR=2.1), and the second poorest quintile nearly twice as likely (OR=1.9) to have begun menstruation compared with girls in the richest income quintile. Estimates were roughly halved on adjustment for Body Mass Index and markers of psychosocial stress (poorest, OR=1.5; second poorest, OR=1.5). Indian girls were over 3 times as likely compared with whites to have started menstruation (OR=3.5) and statistical adjustments did not attenuate estimates. The raised odds of menstruation for Pakistani (OR=1.9), Bangladeshi (OR=3.3) and black African (OR=3.0) girls were attenuated to varying extents, from about a third to a half, on adjustment for income and adiposity.ConclusionsIn contemporary UK, excess adiposity and psychosocial stress were associated with social inequalities in early puberty, while material disadvantage and adiposity were linked to ethnic inequalities in early puberty among girls.
Partnering with consumers to develop and evaluate a Vietnamese Dementia Talking-Book to support low health literacy: a qualitative study incorporating codesign and participatory action research
Authors: Goeman Dianne , Michael J , King J , Luu Huy , Emmanuel Claire , Koch S 
Published: September 2016

ObjectiveThe aim of the Vietnamese Dementia talking-book was to address low health literacy in older people of Vietnamese background living with dementia through the provision of an online resource to help individuals, their families and carers better understand and manage this condition and provide information about available dementia services.DesignThis qualitative study used codesign and participatory action research to develop and refine the talking-book in consultation with expert stakeholders, a consumer advocacy group and the Vietnamese community to assess its utility and ensure cultural and linguistic appropriateness and relevance.Participants59 members of the Vietnamese community, 11 stakeholders from community health services and ethnic agencies, consumer advocacy groups and the research team participated in the codesign and refinement of the talking-book. 22 members of the Vietnamese community appraised the final product.SettingVietnamese community planned activity groups in the Western, Northern and Southern suburbs of Melbourne, Australia.ResultsOur codesign study outlines the process required to develop a Vietnamese Dementia Talking-Book resource partnering with consumers and expert stakeholders to identify consumer need, selection of the content and appropriate language level, construction of the book, measuring acceptability of the talking-book, modification based on feedback and production and dissemination. Feedback on the final version of the talking-book revealed widespread consensus that the book enhanced the knowledge of members of the Vietnamese community in regard to understanding dementia and navigation and accessing of available services.ConclusionsThis free internationally available online Vietnamese Dementia Talking-Book facilitates improved dementia-related health literacy in the Vietnamese community. The book also serves as a tool to facilitate the provision of care to Vietnamese people living with memory loss by assisting health professional staff to develop relationships with Vietnamese clients, their families and carers in a culturally appropriate manner.
Knee osteoarthritis in traumatic knee symptoms in general practice: 6-year cohort study
Authors: Kastelein Marlous , Luijsterburg Pim A J , Koster Ingrid M , Verhaar Jan A N , Koes Bart W , Vroegindeweij Dammis , Bierma-Zeinstra Sita M A , Oei Edwin H G 
Published: September 2016

AimTo identify degenerative knee abnormalities using MRI and radiography 6 years after knee trauma, their relation with persistent knee symptoms and baseline prognostic factors.MethodsAdults (18–65 years) with incident traumatic knee symptoms visiting their general practitioner were followed up for 6 years and underwent baseline MRI and 6-year follow-up MRI and radiography. Logistic regression was used to analyse associations between various degenerative abnormalities on 6-year MRI and radiography, persistent knee symptoms and baseline prognostic factors for knee osteoarthritis (OA) on 6-year MRI.ResultsOn 6-year radiography, 60% of patients showed no OA, 28% showed OA with Kellgren&Lawrence (K&L) grade 1 and 13% showed with K&L grade 2. On 6-year MRI, 55% of patients showed cartilage defect(s), 45% showed osteophyte(s), 36% showed subchondral cyst(s), 40% showed bone marrow oedema, 21% showed meniscal subluxation, 83% showed meniscal degeneration,11% showed effusion and 11% showed a Baker's cyst. Of these, most were significantly related with 6-year radiographic K&L grade, while only lateral cartilage defect(s), medial osteophyte(s) and medial meniscal subluxation were significantly related with persistent knee symptoms. 32% of patients showed new onset or progressive knee OA on 6-year MRI, for which age, history of non-traumatic knee symptoms and bone marrow oedema at baseline were independent prognostic factors.ConclusionsDegenerative knee abnormalities on MRI are related to the K&L score; however, not all abnormalities are reflected in clinical outcome. Age, history of non-traumatic knee symptoms and bone marrow oedema predict knee OA 6 years after knee trauma, present in 32% of the patients.
Which unscheduled return visits indicate a quality-of-care issue?
Authors: Jiménez-Puente Alberto , del Río-Mata José , Arjona-Huertas José Luís , Mora-Ordóñez Begoña , Martínez-Reina Alfonso , Martínez del Campo Miguel , Nieto-de Haro Lourdes , Lara-Blanquer Antonio 
Published: September 2016

BackgroundThe rate of unscheduled return visits is often used as a quality-of-care indicator in EDs, although its validity is not yet fully established. Our aim was to identify the characteristics of return visits that may be attributed to problems in quality of care.MethodsRetrospective paired review of medical charts in a random sample of return visits during the 72 hours following discharge from the ED in three hospitals of Andalusia, Spain in 2013. Charts were reviewed by senior medical physicians to determine which return visits reflected quality-of-care problems. Time frame for return visit, index and return visit acuity, disposition and diagnosis were compared with determine which variables were associated with a quality problem. Sensitivity and specificity for each variable to indicate a quality problem were determined.ResultsWe studied the causes of 895 return visits, finding that 65 (7.3%) were due to inadequate quality of care in the index visit. Potentially avoidable return visits were more common in more severely ill patients, in those with greater severity in the return than in the index visit and in patients hospitalised after the return. The combination of this three variables presented sensitivity 66% and specificity 68% in identification of quality-related returns.ConclusionsThe overall level of return visits cannot be considered a valid indicator of quality of care. However, certain specific variables, including the level of severity of the patient's condition or the discharge destination following the return visits, could be considered valid in this respect.
First-lineHelicobacter pylorieradication therapies in countries with high and low clarithromycin resistance: a systematic review and network meta-analysis
Authors: Yeo Yee Hui , Shiu Sz-Iuan , Ho Hsiu J , Zou Biyao , Lin Jaw-Town , Wu Ming-Shiang , Liou Jyh-Ming , Wu Chun-Ying 
Published: September 2016

ObjectiveTo determine the optimal regimen of different first-lineHelicobacter pylorieradication therapies according to the clarithromycin resistance rate.DesignElectronic search for articles published between January 2005 and April 2016. Randomised, controlled trials that reported the effectiveness of first-line eradication therapies in treatment-naïve adults were included. Two independent reviewers performed articles screening and data extraction. Network and traditional meta-analyses were conducted using the random effect model. Subgroup analyses were performed to determine the ranking of regimens in countries with high (>15%) and low (<15%) clarithromycin resistance. Data including adverse events and therapeutic cure rate were also extracted and analysed.Results117 trials (totally 32 852 patients) for 17H. pylorieradication regimens were eligible for inclusion. Compared with 7-day clarithromycin-based triple therapy, sequential therapy (ST) for 14 days had the highest effectiveness (OR=3.74, 95% CrI 2.37 to 5.96). ST-14 (OR=6.53, 95% CrI 3.23 to 13.63) and hybrid therapy (HY) for 10 days or more (OR=2.85, 95% CrI 1.58 to 5.37) represented the most effective regimen in areas with high and low clarithromycin resistance, respectively. The effectiveness of standard triple therapy was below therapeutic eradication rate in most of the countries. Longer duration was associated with higher eradication rate, but with a higher risk of events that lead to discontinuation.ConclusionsST and HY appeared to be the most effective therapies in countries with high and low clarithromycin resistance, respectively. The clinical decision for optimal regimen can be supported by referring to the rank ordering of relative efficacies stratified by local eradication rates, antibiotic resistance and safety profile.Trial registration numberCRD42015025445.