bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes
Authors: Hu Yongfei , Yang Xi , Li Jing , Lv Na , Liu Fei , Wu Jun , Lin Ivan Y. C. , Wu Na , Weimer Bart C. , Gao George F. , Liu Yulan , Zhu Baoli 
Published: September 2016

ABSTRACT

Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in
Proteobacteria
. The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.

IMPORTANCE
The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.
Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution
Authors: Peabody George , Winkler James , Fountain Weston , Castro David A. , Leiva-Aravena Enzo , Kao Katy C. 
Published: September 2016

ABSTRACT

Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of
Escherichia coli
engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load.

IMPORTANCE
Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual
Escherichia coli
and determine if a sexual strain of
E. coli
can become an effective tool for strain development.
Expression of Surface Protein LapB by a Wide Spectrum of Listeria monocytogenes Serotypes as Demonstrated with Anti-LapB Monoclonal Antibodies
Authors: Boivin Teela , Elmgren Cathie , Brooks Brian W. , Huang Hongsheng , Pagotto Franco , Lin Min 
Published: September 2016

ABSTRACT

Protein antigens expressed on the surface of all strains of
Listeria monocytogenes
and absent from nonpathogenic
Listeria
spp. are presumably useful targets for pathogen identification, detection, and isolation using specific antibodies (Abs). To seek such surface proteins expressed in various strains of
L. monocytogenes
for diagnostic applications, we focused on a set of surface proteins known to be involved or putatively involved in
L. monocytogenes
virulence and identified
Listeria
adhesion protein B (LapB) as a candidate based on the bioinformatics analysis of whole-genome sequences showing that the gene coding for LapB was present in
L. monocytogenes
strains and absent from strains of other
Listeria
spp. Immunofluorescence microscopy (IFM), performed with rabbit polyclonal antibodies against the recombinant LapB protein (rLapB) of
L. monocytogenes
serotype 4b strain L10521, confirmed expression of LapB on the surface. A panel of 48 mouse monoclonal antibodies (MAbs) to rLaB was generated, and 7 of them bound strongly to the surface of
L. monocytogenes
cells as demonstrated using IFM. Further characterization of these 7 anti-LapB MAbs, using an enzyme-linked immunosorbent assay (ELISA), revealed that 6 anti-LapB MAbs (M3484, M3495, M3500, M3509, M3517, and M3519) reacted strongly with 46 (86.8%) of 53 strains representing 10 of the 12 serotypes tested (1/2a, 1/2b, 1/2c, 3a, 3b, 3c, 4ab, 4b, 4d, and 4e). These results indicate that LapB, together with companion anti-LapB MAbs, can be targeted as a biomarker for the detection and isolation of various
L. monocytogenes
strains from contaminated foods.

IMPORTANCE
Strains of
L. monocytogenes
are traditionally grouped into serotypes. Identification of a surface protein expressed in all or the majority of at least 12 serotypes would aid in the development of surface-binding monoclonal antibodies (MAbs) for detection and isolation of
L. monocytogenes
from foods. Bioinformatics analysis revealed that the gene coding for
Listeria
adhesion protein B (LapB), a surface protein involved in
L. monocytogenes
virulence, was present in
L. monocytogenes
strains and absent from other
Listeria
spp. Polyclonal antibodies against recombinant LapB (rLapB) detected the exposed epitopes on the surface of
L. monocytogenes
. Production and extensive assessment of 48 MAbs to rLapB showed that 6 anti-LapB MAbs (M3484, M3495, M3500, M3509, M3517, and M3519) detected the expression of LapB in a wide range of
L. monocytogenes
isolates representing 10 of 12 serotypes tested, suggesting that LapB, together with specific MAbs, can be targeted as a biomarker for pathogen detection and isolation.
Epithelial Coculture and
l
-Lactate Promote Growth of Helicobacter cinaedi under H
2
-Free Aerobic Conditions
Authors: Schmitz Jonathan E. , Taniguchi Takako , Misawa Naoaki , Cover Timothy L. 
Published: September 2016

ABSTRACT

Helicobacter cinaedi
is an emerging opportunistic pathogen associated with infections of diverse anatomic sites. Nevertheless, the species demonstrates fastidious axenic growth; it has been described as requiring a microaerobic atmosphere, along with a strong preference for supplemental H
2
gas. In this context, we examined the hypothesis that
in vitro
growth of
H. cinaedi
could be enhanced by coculture with human epithelial cells. When inoculated (in Ham's F12 medium) over Caco-2 monolayers, the type strain (ATCC BAA-847) gained the ability to proliferate under H
2
-free aerobic conditions. Identical results were observed during coculture with several other monolayer types (LS-174T, AGS, and HeLa). Under chemically defined conditions, 40 amino acids and carboxylates were screened for their effect on the organism's atmospheric requirements. Several molecules promoted H
2
-free aerobic proliferation, although it occurred most prominently with millimolar concentrations of
l
-lactate. The growth response of
H. cinaedi
to Caco-2 cells and
l
-lactate was confirmed with a collection of 12 human-derived clinical strains. mRNA sequencing was next performed on the type strain under various growth conditions. In addition to providing a whole-transcriptome profile of
H. cinaedi
, this analysis demonstrated strong constitutive expression of the
l
-lactate utilization locus, as well as differential transcription of terminal respiratory proteins as a function of Caco-2 coculture and
l
-lactate supplementation. Overall, these findings challenge traditional views of
H. cinaedi
as an obligate microaerophile.

IMPORTANCE
H. cinaedi
is an increasingly recognized pathogen in people with compromised immune systems. Atypical among other members of its bacterial class,
H. cinaedi
has been associated with infections of diverse anatomic sites. Growing
H. cineadi
in the laboratory is quite difficult, due in large part to the need for a specialized atmosphere. The suboptimal growth of
H. cinaedi
is an obstacle to clinical diagnosis, and it also limits investigation into the organism's biology. The current work shows that
H. cinaedi
has more flexible atmospheric requirements in the presence of host cells and a common host-derived molecule. This nutritional interplay raises new questions about how the organism behaves during human infections and provides insights for how to optimize its laboratory cultivation.
Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii
Authors: Kirs Marek , Caffaro-Filho Roberto A. , Wong Mayee , Harwood Valerie J. , Moravcik Philip , Fujioka Roger S. 
Published: September 2016

ABSTRACT

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated
Bacteroides
spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [
n
= 11], 30% of mongoose [
n
= 10], and 10% of feline [
n
= 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii.

IMPORTANCE
This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and
Escherichia coli
). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers.
Aerosol and Surface Deposition Characteristics of Two Surrogates for Bacillus anthracis Spores
Authors: Bishop Alistair H. , Stapleton Helen L. 
Published: September 2016

ABSTRACT

Spores of an acrystalliferous derivative of
Bacillus thuringiensis
subsp.
kurstaki
, termed
Btcry
−, are morphologically, aerodynamically, and structurally indistinguishable from
Bacillus anthracis
spores.
Btcry
− spores were dispersed in a large, open-ended barn together with spores of
Bacillus atrophaeus
subsp.
globigii
, a historically used surrogate for
Bacillus anthracis
. Spore suspensions (2 × 10
12
CFU each of
B. atrophaeus
subsp.
globigii
and
Btcry
−) were aerosolized in each of five spray events using a backpack misting device incorporating an air blower; a wind of 4.9 to 7.6 m s
−1
was also flowing through the barn in the same direction. Filter air samplers were situated throughout the barn to assess the aerosol density of the spores during each release. Trays filled with a surfactant in aqueous buffer were placed on the floor near the filter samplers to assess spore deposition. Spores were also recovered from arrays of solid surfaces (concrete, aluminum, and plywood) that had been laid on the floor and set up as a wall at the end of the barn.
B. atrophaeus
subsp.
globigii
spores were found to remain airborne for significantly longer periods, and to be deposited on horizontal surfaces at lower densities, than
Btcry
− spores, particularly near the spray source. There was a 6-fold-higher deposition of
Btcry
− spores than of
B. atrophaeus
subsp.
globigii
spores on vertical surfaces relative to the surrounding airborne density. This work is relevant for selecting the best
B. anthracis
surrogate for the prediction of human exposure, hazard assessment, and hazard management following a malicious release of
B. anthracis
.

IMPORTANCE
There is concern that pathogenic bacteria could be maliciously disseminated in the air to cause human infection and disruption of normal life. The threat from spore-forming organisms, such as the causative agent of anthrax, is particularly serious. In order to assess the extent of this risk, it is important to have a surrogate organism that can be used to replicate the dispersal characteristics of the threat agent accurately. This work compares the aerosol dispersal and deposition behaviors of the surrogates
Btcry
− and
B. atrophaeus
subsp.
globigii
.
Btcry
− spores remained in the air for a shorter time, and were markedly more likely to adhere to vertical surfaces, than
B. atrophaeus
subsp.
globigii
spores.
Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine
Authors: Trachsel Julian , Bayles Darrell O. , Looft Torey , Levine Uri Y. , Allen Heather K. 
Published: September 2016

ABSTRACT

Studying the host-associated butyrate-producing bacterial community is important, because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl coenzyme A (CoA):acetate-CoA transferase (EC 2.3.8.3) as a gene of primary importance for butyrate production in intestinal ecosystems; however, this gene family (
but
) remains poorly defined. We developed tools for the analysis of butyrate-producing bacteria based on 12 putative
but
genes identified in the genomes of nine butyrate-producing bacteria obtained from the swine intestinal tract. Functional analyses revealed that eight of these genes had strong But enzyme activity. When
but
paralogues were found within a genome, only one gene per genome encoded strong activity, with the exception of one strain in which no gene encoded strong But activity. Degenerate primers were designed to amplify the functional
but
genes and were tested by amplifying environmental
but
sequences from DNA and RNA extracted from swine colonic contents. The results show diverse
but
sequences from swine-associated butyrate-producing bacteria, most of which clustered near functionally confirmed sequences. Here, we describe tools and a framework that allow the bacterial butyrate-producing community to be profiled in the context of animal health and disease.

IMPORTANCE
Butyrate is a compound produced by the microbiota in the intestinal tracts of animals. This compound is of critical importance for intestinal health, and yet studying its production by diverse intestinal bacteria is technically challenging. Here, we present an additional way to study the butyrate-producing community of bacteria using one degenerate primer set that selectively targets genes experimentally demonstrated to encode butyrate production. This work will enable researchers to more easily study this very important bacterial function that has implications for host health and resistance to disease.
Laser Acupuncture Attenuates Oxaliplatin-Induced Peripheral Neuropathy in Patients with Gastrointestinal Cancer: A Pilot Prospective Cohort Study
Authors: Hsieh Yueh-Ling , Chou Li-Wei , Hong Shao-Fu , Chang Fei-Chi , Tseng Szu-Wen , Huang Chi-Chou , Yang Ching-Hsiang , Yang Chen-Chia , Chiu Wei-Feng 
Published: September 2016

Background Oxaliplatin is a platinum compound that is widely used in the treatment of some solid tumours. Oxaliplatin-induced peripheral neuropathy (OIPN) in the upper and lower extremities is the major adverse side effect and represents the main dose-limiting factor of this drug. The aim of this single-arm study was to evaluate the feasibility and effects of laser acupuncture (LA) in the treatment of OIPN in patients with advanced gastrointestinal cancers. Methods 17 gastrointestinal cancer survivors (14 colorectal and 3 gastric cancers), who had been treated with oxaliplatin-based chemotherapies, were recruited. Low-level laser stimulation (50 mW) bilaterally at PC6, PC7, PC8, P9, LU11, SP6, KI3, BL60, KI1, and KI2 was administered for 20 min/point for 12 sessions over 4 weeks. The pain quality assessment scale (PQAS), chemotherapy-induced neurotoxicity questionnaire (CINQ), oxaliplatin-specific neurotoxicity scale (OSNS), quantitative touch-detection threshold (using von Frey filaments), and cold-triggered pain withdrawal latency (using the cold-water immersion test) were measured before and after completion of the 12 treatment sessions. Results PQAS, CINQ, and OSNS scores, as well as touch-detection threshold and cold-trigger pain withdrawal latency all improved significantly after LA in the cancer patients with OIPN (p<0.05). LA significantly relieved both oxaliplatin-induced cold and mechanical allodynia and also decreased the incidence and severity of neurotoxicity symptoms in the patients’ upper and lower extremities and impact on their daily activities (all p<0.05). Conclusions Following treatment with LA, neurotoxicity symptoms were significantly improved in cancer patients with OIPN. Further randomised controlled trials are needed to evaluate the role of LA as a therapeutic option in the management of OIPN.
New clinical decision rule to exclude subarachnoid haemorrhage for acute headache: a prospective multicentre observational study
Authors: Kimura Akio , Kobayashi Kentaro , Yamaguchi Hitoshi , Takahashi Takeshi , Harada Masahiro , Honda Hideki , Mori Yoshio , Hirose Keika , Tanaka Noriko 
Published: September 2016

ObjectiveTo ensure good outcomes in the management of subarachnoid haemorrhage (SAH), accurate prediction is crucial for initial assessment of patients presenting with acute headache. We conducted this study to develop a new clinical decision rule using only objectively measurable predictors to exclude SAH, offering higher specificity than the previous Ottawa SAH Rule while maintaining comparable sensitivity.DesignMulticentre prospective cohort study.SettingTertiary-care emergency departments of five general hospitals in Japan from April 2011 to March 2014.ParticipantsEligible patients comprised 1781 patients aged >15 years with acute headache, excluding trauma or toxic causes and patients who presented in an unconscious state.Main outcome measuresDefinitive diagnosis of SAH was based on confirmation of SAH on head CT or lumbar puncture findings of non-traumatic red blood cells or xanthochromia.ResultsA total of 1561 patients were enrolled in this study, of whom 277 showed SAH. Using these enrolled patients, we reached a rule with mainly categorical predictors used in previous reports, called the ‘Ottawa-like rule’, offering 100% sensitivity when using any of age ≥40 years, neck pain or stiffness, altered level of consciousness or onset during exertion. Using the 1317 patients from whom blood samples were obtained, a new rule using any of systolic blood pressure >150 mm Hg, diastolic blood pressure >90 mm Hg, blood sugar >115 mg/dL or serum potassium <3.9 mEq/L offered 100% sensitivity (95% CI 98.6% to 100%) and 14.5% specificity (12.5% to 16.9%), while the Ottawa-like rule showed the same sensitivity with a lower specificity of 8.8% (7.2% to 10.7%).ConclusionsWhile maintaining equal sensitivity, our new rule seemed to offer higher specificity than the previous rules proposed by the Ottawa group. Despite the need for blood sampling, this method can reduce unnecessary head CT in patients with acute headache.Trial registration numberUMIN 00004871.