bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vivo
Application of Bacteriophage as a Potential Therapeutic Agent To Control OXA-66-Like Carbapenemase-Producing Acinetobacter baumannii Strains Belonging to Sequence Type 357
Authors: Jeon Jongsoo , Ryu Choong-Min , Lee Jun-Young , Park Jong-Hwan , Yong Dongeun , Lee Kyungwon 
Published: May 2016

ABSTRACT

The increasing prevalence of carbapenem-resistant
Acinetobacter baumannii
(CRAB) strains in intensive care units has caused major problems in public health worldwide. Our aim was to determine whether this phage could be used as an alternative therapeutic agent against multidrug-resistant bacterial strains, specifically CRAB clinical isolates, using a mouse model. Ten bacteriophages that caused lysis in CRAB strains, including
bla
OXA-66-like
genes, were isolated. YMC13/01/C62 ABA BP (phage Bϕ-C62), which showed the strongest lysis activity, was chosen for further study by transmission electron microscopy (TEM), host range test, one-step growth and phage adsorption rate, thermal and pH stability, bacteriolytic activity test, genome sequencing and bioinformatics analysis, and therapeutic effect of phage using a mouse intranasal infection model. The phage Bϕ-C62 displayed high stability at various temperatures and pH values and strong cell lysis activity
in vitro
. The phage Bϕ-C62 genome has a double-stranded linear DNA with a length of 44,844 bp, and known virulence genes were not identified
in silico. In vivo
study showed that all mice treated with phage Bϕ-C62 survived after intranasal bacterial challenge. Bacterial clearance in the lung was observed within 3 days after bacterial challenge, and histologic damage also improved significantly; moreover, no side effects were observed.

IMPORTANCE
In our study, the novel
A. baumannii
phage Bϕ-C62 was characterized and evaluated
in vitro
,
in silico
, and
in vivo
. These results, including strong lytic activities and the improvement of survival rates, showed the therapeutic potential of the phage Bϕ-C62 as an antimicrobial agent. This study reports the potential of a novel phage as a therapeutic candidate or nontoxic disinfectant against CRAB clinical isolates
in vitro
and
in vivo
.
Degradation Pathways of 2- and 4-Nitrobenzoates in Cupriavidus sp. Strain ST-14 and Construction of a Recombinant Strain, ST-14::3NBA, Capable of Degrading 3-Nitrobenzoate
Authors: Basu Soumik , Pal Chowdhury Piyali , Deb Satamita , Dutta Tapan K. 
Published: May 2016

ABSTRACT

Strain ST-14, characterized as a member of the genus
Cupriavidus
, was capable of utilizing 2- and 4-nitrobenzoates individually as sole sources of carbon and energy. Biochemical studies revealed the assimilation of 2- and 4-nitrobenzoates via 3-hydroxyanthranilate and protocatechuate, respectively. Screening of a genomic fosmid library of strain ST-14 constructed in
Escherichia coli
identified two gene clusters,
onb
and
pob-pca
, to be responsible for the complete degradation of 2-nitrobenzoate and protocatechuate, respectively. Additionally, a gene segment (
pnb
) harboring the genes for the conversion of 4-nitrobenzoate to protocatechuate was unveiled by transposome mutagenesis. Reverse transcription-PCR analysis showed the polycistronic nature of the gene clusters, and their importance in the degradation of 2- and 4-nitrobenzoates was ascertained by gene knockout analysis. Cloning and expression of the relevant pathway genes revealed the transformation of 2-nitrobenzoate to 3-hydroxyanthranilate and of 4-nitrobenzoate to protocatechuate. Finally, incorporation of functional 3-nitrobenzoate dioxygenase into strain ST-14 allowed the recombinant strain to utilize 3-nitrobenzoate via the existing protocatechuate metabolic pathway, thereby allowing the degradation of all three isomers of mononitrobenzoate by a single bacterial strain.

IMPORTANCE
Mononitrobenzoates are toxic chemicals largely used for the production of various value-added products and enter the ecosystem through industrial wastes. Bacteria capable of degrading mononitrobenzoates are relatively limited. Unlike other contaminants, these man-made chemicals have entered the environment since the last century, and it is believed that bacteria in nature evolved not quite efficiently to assimilate these compounds; as a consequence, to date, there are only a few reports on the bacterial degradation of one or more isomers of mononitrobenzoate. In the present study, fortunately, we have been able to isolate a
Cupriavidus
sp. strain capable of assimilating both 2- and 4-nitrobenzoates as the sole carbon source. Results of the biochemical and molecular characterization of catabolic genes responsible for the degradation of mononitrobenzoates led us to manipulate a single enzymatic step, allowing the recombinant host organism to expand its catabolic potential to assimilate 3-nitrobenzoate.
Fast, Continuous, and High-Throughput (Bio)Chemical Activity Assay forN-Acyl-l-Homoserine Lactone Quorum-Quenching Enzymes
Authors: Last Daniel , Krüger Georg H. E. , Dörr Mark , Bornscheuer Uwe T. 
Published: May 2016

ABSTRACTQuorum sensing, the bacterial cell-cell communication by small molecules, controls important processes such as infection and biofilm formation. Therefore, it is a promising target with several therapeutic and technical applications besides its significant ecological relevance. Enzymes inactivatingN-acyl-l-homoserine lactones, the most common class of communication molecules among Gram-negative proteobacteria, mainly belong to the groups of quorum-quenching lactonases or quorum-quenching acylases. However, identification, characterization, and optimization of these valuable biocatalysts are based on a very limited number of fundamentally different methods with their respective strengths and weaknesses. Here, a (bio)chemical activity assay is described, which perfectly complements the other methods in this field. It enables continuous and high-throughput activity measurements of purified and unpurified quorum-quenching enzymes within several minutes. For this, the reaction products released by quorum-quenching lactonases and quorum-quenching acylases are converted either by a secondary enzyme or by autohydrolysis tol-homoserine. In turn,l-homoserine is detected by the previously described calcein assay, which is sensitive to α-amino acids with free N and C termini. Besides its establishment, the method was applied to the characterization of three previously undescribed quorum-quenching lactonases and variants thereof and to the identification of quorum-quenching acylase-expressingEscherichia coliclones in an artificial library. Furthermore, this study indicates that porcine aminoacylase 1 is not active towardN-acyl-l-homoserine lactones as published previously but instead converts the autohydrolysis productN-acyl-l-homoserine.IMPORTANCEIn this study, a novel method is presented for the identification, characterization, and optimization of quorum-quenching enzymes that are active towardN-acyl-l-homoserine lactones. These are the most common communication molecules among Gram-negative proteobacteria. The activity assay is a highly valuable complement to the available analytical tools in this field. It will facilitate studies on the environmental impact of quorum-quenching enzymes and contribute to the development of therapeutic and technical applications of this promising enzyme class.
Thermal Stability of Hepatitis E Virus as Estimated by a Cell Culture Method
Authors: Johne Reimar , Trojnar Eva , Filter Matthias , Hofmann Jörg 
Published: May 2016

ABSTRACT
Hepatitis E virus (HEV) is an increasingly recognized zoonotic pathogen. Transmission is suspected to occur from infected pigs or wild boars to humans through direct contact, environmental pathways, or contaminated food. However, the physical and chemical stability of HEV is largely unknown, because suitable cell culture methods for infectivity measurement are missing. Here, we developed a titration method using infection of the cell line A549/D3 with HEV genotype 3 strain 47832c and subsequent counting of focus-forming units by immunofluorescence, which allowed HEV infectivity measurements within a 4-log-dilution range. Long-term storage of HEV in cell culture medium at different temperatures indicated a phase of rapid virus inactivation, followed by a slower progression of virus inactivation. Infective HEV was detected up to 21 days at 37°C, up to 28 days at room temperature, and until the end of the experiment (56 days) with a 2.7-log decrease of infectious virus at 4°C. Heat treatment for 1 min resulted in moderate decreases of infectivity up to 60°C, 2- to 3.5-log decreases between 65°C and 75°C, and no remaining virus was detected at temperatures of ≥80°C. Heating for 70°C resulted in a 3.6-log decrease after 1.5 min and the absence of detectable virus (>3.9-log decrease) after 2 min. The data were used to calculate predictive heat inactivation models for HEV. The results may help estimate HEV stability in the environment or food. The established method may be used to study other aspects of HEV stability in the future.

IMPORTANCE
In this study, a cell culture method was developed which allows the measurement of hepatitis E virus (HEV) infectivity. Using this system, the stability of HEV at different time-temperature combinations was assessed, and a predictive model was established. The obtained data may help estimate HEV stability in the environment or food, thus enabling an assessment of the relative risks of HEV infection through distinct routes and by distinct types of food in the future.
Isolation of Nontuberculous Mycobacteria from the Environment of Ghanian Communities Where Buruli Ulcer Is Endemic
Authors: Aboagye Samuel Yaw , Danso Emelia , Ampah Kobina Assan , Nakobu Zuliehatu , Asare Prince , Otchere Isaac Darko , Röltgen Katharina , Yirenya-Tawiah Dzidzo , Yeboah-Manu Dorothy 
Published: May 2016

ABSTRACT

This study aimed to isolate nontuberculous mycobacterial species from environmental samples obtained from some selected communities in Ghana. To optimize decontamination, spiked environmental samples were used to evaluate four decontamination solutions and supplemented media, after which the best decontamination solution and media were used for the actual analysis. The isolates obtained were identified on the basis of specific genetic sequences, including heat shock protein 65, IS
2404
, IS
2606
,
rpoB
, and the ketoreductase gene, as needed. Among the methods evaluated, decontamination with 1 M NaOH followed by 5% oxalic acid gave the highest rate of recovery of mycobacteria (50.0%) and the lowest rate of contamination (15.6%). The cultivation medium that supported the highest rate of recovery of mycobacteria was polymyxin B-amphotericin B-nalidixic acid-trimethoprim-azlocillin–supplemented medium (34.4%), followed by isoniazid-supplemented medium (28.1%). Among the 139 samples cultivated in the main analysis, 58 (41.7%) yielded mycobacterial growth, 70 (50.4%) had no growth, and 11 (7.9%) had all inoculated tubes contaminated. A total of 25 different mycobacterial species were identified. Fifteen species (60%) were slowly growing (e.g.,
Mycobacterium ulcerans
,
Mycobacterium avium
,
Mycobacterium mantenii
, and
Mycobacterium malmoense
), and 10 (40%) were rapidly growing (e.g.,
Mycobacterium chelonae
,
Mycobacterium fortuitum
, and
Mycobacterium abscessus
). The occurrence of mycobacterial species in the various environmental samples analyzed was as follows: soil, 16 species (43.2%); vegetation, 14 species (38.0%); water, 3 species (8.0%); moss, 2 species (5.4%); snail, 1 species (2.7%); fungi, 1 species (2.7%). This study is the first to report on the isolation of
M. ulcerans
and other medically relevant nontuberculous mycobacteria from different environmental sources in Ghana.

IMPORTANCE
Diseases caused by mycobacterial species other than those that cause tuberculosis and leprosy are increasing. Control is difficult because the current understanding of how the organisms are spread and where they live in the environment is limited, although this information is needed to design preventive measures. Growing these organisms from the environment is also difficult, because the culture medium becomes overgrown with other bacteria that also live in the environment, such as in soil and water. We aimed to improve the methods for growing these organisms from environmental sources, such as soil and water samples, for better understanding of important mycobacterial ecology.
Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments
Authors: Tully Benjamin J. , Heidelberg John F. 
Published: May 2016

ABSTRACT

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching
Alphaproteobacteria
, two novel organisms within the
Proteobacteria
, and new members of the
Nitrospirae
,
Nitrospinae
, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.

IMPORTANCE
This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1
Thaumarchaeota
,
Nitrospinae
, and
Nitrospirae
and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium.
Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid
Authors: Leonard Susan R. , Mammel Mark K. , Rasko David A. , Lacher David W. 
Published: May 2016

ABSTRACT

Hybrid isolates of Shiga toxin-producing
Escherichia coli
(STEC) and enterotoxigenic
E. coli
(ETEC) encoding heat-stable enterotoxin (ST) are being reported with increasing frequency from a variety of sources. However, information regarding the plasmids that these strains harbor is scarce. In this study, we sequence and characterize a plasmid, p7v, from the STEC/ETEC hybrid strain 7v. Whole-genome phylogenetic analyses of STEC/ETEC hybrid strains and prototype
E. coli
isolates of other pathotypes placed 7v in the
Escherichia
sp. cryptic lineage 1 (CL1) clade. The complete plasmid, p7v, was determined to be 229,275 bp and encodes putative virulence factors that are typically carried on STEC plasmids as well as those often carried on ETEC plasmids, indicating that the hybrid nature of the strain extends beyond merely encoding the two toxins. Plasmid p7v carries two copies of
sta
with identical sequences, which were discovered to be divergent from the
sta
sequences found in the prototype human ETEC strains. Using a nomenclature scheme based on a phylogeny constructed from
sta
and
stb
sequences, the
sta
encoded on p7v is designated STa4.
In silico
analysis determined that p7v also encodes the K88 fimbria, a colonization factor usually associated with porcine ETEC plasmids. The p7v sequence and the presence of plasmid-encoded virulence factors are compared to those of other STEC/ETEC CL1 hybrid genomes and reveal gene acquisition/loss at the strain level. In addition, the interrogation of 24 STEC/ETEC hybrid genomes for identification of plasmid replicons, colonization factors, Stx and ST subtypes, and other plasmid-encoded virulence genes highlights the diversity of these hybrid strains.

IMPORTANCE
Hybrid Shiga toxin-producing
Escherichia coli
/enterotoxigenic
Escherichia coli
(STEC/ETEC) strains, which have been isolated from environmental, animal, and human clinical samples, may represent an emerging threat as food-borne pathogens. Characterization of these strains is important for assessing virulence potential, aiding in the development of pathogen detection methods, and understanding how the hybrid strains evolve to potentially have a greater impact on public health. This study represents, to our knowledge, both the first characterization of a closed plasmid sequence from a STEC/ETEC hybrid strain and the most comprehensive phylogenetic analysis of available STEC/ETEC hybrid genomes to date. The results demonstrate how the mobility of plasmid-associated virulence genes has resulted in the creation of a diverse plasmid repertoire within the STEC/ETEC hybrid strains.
Athletic groin pain: a systematic review of surgical diagnoses, investigations and treatment
Authors: de SA Darren , Hölmich Per , Phillips Mark , Heaven Sebastian , Simunovic Nicole , Philippon Marc J , Ayeni Olufemi R 
Published: May 2016

IntroductionAthletic groin pain requiring surgery remains a diagnostic and therapeutic challenge. This systematic review aims to identify the most common causes of groin pain in athletes requiring surgery. Additionally, it aims to further characterise their susceptible athlete profiles, common physical examination and imaging techniques, and surgical procedures performed. This will enable the orthopaedic sports medicine clinician/surgeon to best treat these patients.Materials and methodsThe electronic databases MEDLINE, PubMed and EMBASE were searched from database inception to 13 August 2014 for studies in the English language that addressed athletic groin pain necessitating surgery. The search was updated on 4 August 2015 to find any articles published after the original search. The studies were systematically screened and data were abstracted in duplicate, with descriptive data presented.ResultsA total of 73 articles were included within our study, with data from 4655 patients abstracted. Overall, intra-articular and extra-articular causes of groin pain in athletes requiring surgery were equal. The top five causes for pain were: femoroacetabular impingement (FAI) (32%), athletic pubalgia (24%), adductor-related pathology (12%), inguinal pathology (10%) and labral pathology (5%), with 35% of this labral pathology specifically attributed to FAI.ConclusionsGiven the complex anatomy, equal intra-articular and extra-articular contribution, and potential for overlap of clinical entities causing groin pain leading to surgery in athletes, further studies are required to ascertain the finer details regarding specific exam manoeuvres, imaging views and surgical outcomes to best treat this patient population.
What is the association between sedentary behaviour and cognitive function? A systematic review
Authors: Falck Ryan S , Davis Jennifer C , Liu-Ambrose Teresa 
Published: May 2016

AimThe increasing rate of all-cause dementia worldwide and the lack of effective pharmaceutical treatments emphasise the value of lifestyle approaches as prevention strategies. Emerging evidence suggests sedentary behaviour is associated with impaired cognitive function. A better understanding of this association would significantly add to our knowledge of how to best promote healthy cognitive ageing. Thus, we conducted a systematic review ascertaining the contribution of sedentary behaviour towards associated changes in cognitive function over the adult lifespan.Study designSystematic review of peer-reviewed literature examining the association of sedentary behaviour with cognition.Data sourcesWe searched PubMed, PsycINFO, EBSCO and Web of Science, and reference lists of relevant reviews on sedentary behaviour. Two independent reviewers extracted (1) study characteristics and (2) information regarding measurement of sedentary behaviour and cognitive function. We also assessed study quality using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist.Eligibility criteriaWe limited search results to adults ≥40 years, observational studies published in English since 1990 and studies investigating associations between sedentary behaviour and cognitive function.Results8 studies examined the association of sedentary behaviour with cognitive function. 6 studies reported significant negative associations between sedentary behaviour and cognitive function. 8 different measures of sedentary behaviour and 13 different measures of cognitive function were used across all eight studies.SummarySedentary behaviour is associated with lower cognitive performance, although the attributable risk of sedentary time to all-cause dementia incidence is unclear. Our systematic review provides evidence that limiting sedentary time and concomitantly engaging in regular moderate-to-vigorous physical activity may best promote healthy cognitive ageing.
Prediction of protective sensory loss, neuropathy and foot ulceration in type 2 diabetes
Authors: Paisey R B , Darby T , George A M , Waterson M , Hewson P , Paisey C F , Thomson M P 
Published: May 2016

ObjectivesTo prospectively determine clinical and biochemical characteristics associated with the development of peripheral neuropathy, loss of protective sensation, and foot ulceration in persons with type 2 diabetes mellitus (DM) over 7 years.Research design and methodsGraded monofilament (MF) testing, vibration perception threshold, and neuropathy symptom questionnaires were undertaken in 206 participants with type 2 DM without peripheral vascular disease or history of foot ulceration and 71 healthy participants without DM at baseline and after 7 years. 6 monthly glycosylated hemoglobin (HbA1c) levels and annual serum lipid profiles were measured during follow-up of those with DM. Incident foot ulceration was recorded at follow-up.ResultsTaller stature and higher quartiles of serum triglyceride and HbA1c levels were associated with neuropathy at follow-up (p=0.008). Remission of baseline neuropathy was observed in 7 participants at follow-up. 9 participants with type 2 DM developed foot ulcers by the end of the study, only 1 at low risk. Mean HbA1c levels were higher in those who developed foot ulceration (p<0.0001). 1 participant with neuropathy throughout developed a Charcot foot. Failure to perceive 2 or more 2, 4 and 6 g MF stimuli at baseline predicted loss of protective sensation at follow-up.ConclusionsTall stature and worse metabolic control were associated with progression to neuropathy. Mean HbA1c levels were higher in those who developed foot ulcers. Graded MF testing may enrich recruitment to clinical trials and assignation of high risk for foot ulceration.