Publications

evolution of metallo-β-lactamases: trends revealed by natural diversity and in vitro evolution.	the production of β-lactamase enzymes is one of the most distributed resistance mechanisms towards β-lactam antibiotics. metallo-β-lactamases constitute a worrisome group of these kinds of enzymes, since they present a broad spectrum profile, being able to hydrolyze not only penicillins, but also the latest generation of cephalosporins and carbapenems, which constitute at present the last resource antibiotics. the vim, imp, and ndm enzymes comprise the main groups of clinically relevant metallo- ...	2014	25364574
novel selective medium for isolation of staphylococcus lugdunensis from wound specimens.	we compared a novel selective staphylococcus lugdunensis (ssl) medium with routine media (blood and chocolate agars) for the detection of s. lugdunensis in 990 clinical specimens (from tissue, pus, or wound swabs). significantly more s. lugdunensis isolates were detected on ssl medium (34/990) than on routine medium (7/990) (p = 0.001, mcnemar's test).	2014	24759715
coeliac disease - new pathophysiological findings and their implications for therapy.	coeliac disease (cd) is one of the most common diseases worldwide, resulting from a combination of environmental (gluten) and genetic (human leucocyte antigen (hla) and non-hla genes) factors. depending on the geographical location, the prevalence of cd has been estimated to approximate 0.5-1%. the only treatment currently available for cd is a gluten-free diet (gfd) excluding gluten-containing cereals such as wheat, rye, and barley, and other foodstuffs with natural or added gluten. however, ad ...	2014	26288589
exploring the role of conformational heterogeneity in cis-autoproteolytic activation of thnt.	in the past decade, there have been major achievements in understanding the relationship between enzyme catalysis and protein structural plasticity. in autoprocessing systems, however, there is a sparsity of direct evidence of the role of conformational dynamics, which are complicated by their intrinsic chemical reactivity. thnt is an autoproteolytically activated enzyme involved in the biosynthesis of the β-lactam antibiotic thienamycin. conservative mutation of thnt results in multiple conform ...	2014	24933323
specific glycosylation of membrane proteins in epithelial ovarian cancer cell lines: glycan structures reflect gene expression and dna methylation status.	epithelial ovarian cancer is the fifth most common cause of cancer in women worldwide bearing the highest mortality rate among all gynecological cancers. cell membrane glycans mediate various cellular processes such as cell signaling and become altered during carcinogenesis. the extent to which glycosylation changes are influenced by aberrant regulation of gene expression is nearly unknown for ovarian cancer and remains crucial in understanding the development and progression of this disease. to ...	2014	24855066
insights from the genome annotation of elizabethkingia anophelis from the malaria vector anopheles gambiae.	elizabethkingia anophelis is a dominant bacterial species in the gut ecosystem of the malaria vector mosquito anopheles gambiae. we recently sequenced the genomes of two strains of e. anophelis, r26t and ag1, isolated from different strains of a. gambiae. the two bacterial strains are identical with a few exceptions. phylogenetically, elizabethkingia is closer to chryseobacterium and riemerella than to flavobacterium. in line with other bacteroidetes known to utilize various polymers in their ec ...	2014	24842809
draft genome sequence of elizabethkingia meningoseptica isolated from a traumatic wound.	we report the draft genome assembly of elizabethkingia meningoseptica strain 502. the sample was isolated from the wound of a repatriated military serviceperson who suffered major trauma from an improvised explosive device (ied), resulting in wounds with extensive environmental contamination. e. meningoseptica was isolated from wounds in both legs. the draft genome assembly has 21 contigs with a total size of 3,960,744 bases. the genome contains genes encoding 26 putative β-lactamases.	2014	24812216
comparative genomic analysis of malaria mosquito vector-associated novel pathogen elizabethkingia anophelis.	acquisition of elizabethkingia infections in intensive care units (icus) has risen in the past decade. treatment of elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. elizabethkingia infections have long been attributed to elizabethkingia meningoseptica. recently, we used whole-genome sequencing to reveal that e. anophelis is the pathogenic agent for an elizabethkingia outbreak at two icus. we performed comparative genom ...	2014	24803570
chryseobacterium indologenes in a woman with acute leukemia in senegal: a case report.	this report documents a rare case of chryseobacterium indologenes urinary tract infection in senegal. chryseobacterium indologenes is an uncommon human pathogen reported in hospital outbreaks in taiwan and there have been some sporadic cases reported in europe and in the usa mainly from immune-suppressed patients.	2014	24886628
the value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in identifying clinically relevant bacteria: a comparison with automated microbiology system.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has been developed as a new-type soft ionization mass spectrometry in the recent year. increasing number of clinical microbiological laboratories consider it as an innovate approach for bacterial identification.	2014	24822117
spectroscopic and mechanistic studies of heterodimetallic forms of metallo-β-lactamase ndm-1.	in an effort to characterize the roles of each metal ion in metallo-β-lactamase ndm-1, heterodimetallic analogues (coco-, znco-, and cocd-) of the enzyme were generated and characterized. uv-vis, (1)h nmr, epr, and exafs spectroscopies were used to confirm the fidelity of the metal substitutions, including the presence of a homogeneous, heterodimetallic cluster, with a single-atom bridge. this marks the first preparation of a metallo-β-lactamase selectively substituted with a paramagnetic metal ...	2014	24754678
quality control and stability studies with the monoclonal antibody, trastuzumab: application of 1d- vs. 2d-gel electrophoresis.	recombinant monoclonal antibodies (rmabs) are medicinal products obtained by rdna technology. consequently, like other biopharmaceuticals, they require the extensive and rigorous characterization of the quality attributes, such as identity, structural integrity, purity and stability. the aim of this work was to study the suitability of gel electrophoresis for the assessment of charge heterogeneity, post-translational modifications and the stability of the therapeutic, recombinant monoclonal anti ...	2014	24739811
multiresistant elizabethkingia meningoseptica infections in tertiary care.		2014	26288498
multiresistant elizabethkingia meningoseptica infections in tertiary care.		2014	26288498
new β-lactamase inhibitors: a therapeutic renaissance in an mdr world.	as the incidence of gram-negative bacterial infections for which few effective treatments remain increases, so does the contribution of drug-hydrolyzing β-lactamase enzymes to this serious clinical problem. this review highlights recent advances in β-lactamase inhibitors and focuses on agents with novel mechanisms of action against a wide range of enzymes. to this end, we review the β-lactamase inhibitors currently in clinical trials, select agents still in preclinical development, and older the ...	2014	24379206
impact of myeloperoxidase-ldl interactions on enzyme activity and subsequent posttranslational oxidative modifications of apob-100.	oxidation of ldl by the myeloperoxidase (mpo)-h2o2-chloride system is a key event in the development of atherosclerosis. the present study aimed at investigating the interaction of mpo with native and modified ldl and at revealing posttranslational modifications on apob-100 (the unique apolipoprotein of ldl) in vitro and in vivo. using amperometry, we demonstrate that mpo activity increases up to 90% when it is adsorbed at the surface of ldl. this phenomenon is apparently reflected by local stru ...	2014	24534704
current and emerging therapy for celiac disease.	at present, strict and lifelong gluten-free diet is the only effective treatment for celiac disease. even small amounts of gluten (50 mg/day) can be immunogenic; therefore all food and food items and drugs that contain gluten and its derivatives must be eliminated completely from the diet. while prescribing gluten-free diet is easy; the key to the success is the dietary counseling by a nutrition specialist and maintenance of adherence to gfd by the patient. in recent times, a number of targets t ...	2014	25705619
endoe from enterococcus faecalis hydrolyzes the glycans of the biofilm inhibiting protein lactoferrin and mediates growth.	glycosidases are widespread among bacteria. the opportunistic human pathogen enterococcus faecalis encodes several putative glycosidases but little is known about their functions. the identified endo-β-n-acetylglucosaminidase endoe has activity on the n-linked glycans of the human immunoglobulin g (igg). in this report we identified the human glycoprotein lactoferrin (hlf) as a new substrate for endoe. hydrolysis of the n-glycans from hlf was investigated using lectin blot, uhplc and mass spectr ...	2014	24608122
bacteriology and drug susceptibility analysis of pus from patients with severe intra-abdominal infection induced by abdominal trauma.	the aim of the present study was to retrospectively analyze the bacteriology and drug susceptibility of pus flora from abdominal trauma patients with severe intra-abdominal infection (siai). a total of 41 patients with siai induced by abdominal trauma were enrolled in the study, from which 123 abdominal pus samples were obtained. the results from laboratory microbiology and drug sensitivity were subjected to susceptibility analysis using whonet software. a total of 297 strains were isolated in w ...	2014	24940451
exploring anopheles gut bacteria for plasmodium blocking activity.	malaria parasite transmission requires the successful development of plasmodium gametocytes into flagellated microgametes upon mosquito blood ingestion, and the subsequent fertilization of microgametes and macrogametes for the development of motile zygotes, called ookinetes, which invade and transverse the anopheles vector mosquito midgut at around 18-36 h after blood ingestion. within the mosquito midgut, the malaria parasite has to withstand the mosquito's innate immune response and the detrim ...	2014	24428613
neonatal meningitis by multidrug resistant elizabethkingia meningosepticum identified by 16s ribosomal rna gene sequencing.	clinical and microbiological profile of 9 neonates with meningitis by elizabethkingia meningosepticum identified by 16s ribosomal gene sequencing was studied. all the clinical isolates were resistant to cephalosporins, aminoglycosides, trimethoprim-sulfamethoxazole, β -lactam combinations, carbapenems and only one isolate was susceptible to ciprofloxacin. all the isolates were susceptible to vancomycin. six of nine neonates died even after using vancomycin, based on susceptibility results. e. me ...	2014	24678326
structural analysis of the endogenous glycoallergen hev b 2 (endo-β-1,3-glucanase) from hevea brasiliensis and its recognition by human basophils.	endogenous glycosylated hev b 2 (endo-β-1,3-glucanase) from hevea brasiliensis is an important latex allergen that is recognized by ige antibodies from patients who suffer from latex allergy. the carbohydrate moieties of hev b 2 constitute a potentially important ige-binding epitope that could be responsible for its cross-reactivity. here, the structure of the endogenous isoform ii of hev b 2 that exhibits three post-translational modifications, including an n-terminal pyroglutamate and two glyc ...	2014	24531467
filter-aided n-glycan separation (fangs): a convenient sample preparation method for mass spectrometric n-glycan profiling.	we have developed a simple method for the release and isolation of glycoprotein n-glycans from whole-cell lysates using less than a million cells, for subsequent implementation with mass spectrometric analysis. cellular protein extracts prepared using sds solubilization were sequentially treated in a membrane filter device to ultimately release glycans enzymatically using pngase f in the volatile buffer ammonium bicarbonate. the released glycans are recovered in the filtrate following centrifuga ...	2014	24450425
low-molecular-mass penicillin binding protein 6b (dacd) is required for efficient gob-18 metallo-β-lactamase biogenesis in salmonella enterica and escherichia coli.	metallo-β-lactamases (mbls) are zn(2+)-containing secretory enzymes of clinical relevance, whose final folding and metal ion assembly steps in gram-negative bacteria occur after secretion of the apo form to the periplasmic space. in the search of periplasmic factors assisting mbl biogenesis, we found that dacd null (δdacd) mutants of salmonella enterica and escherichia coli expressing the pre-gob-18 mbl gene from plasmids showed significantly reduced resistance to cefotaxime and concomitant lowe ...	2014	24145538
structural basis of metallo-β-lactamase inhibition by captopril stereoisomers.	β-lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (mbls). mbls are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for mbls. l-captopril, which is used to treat hypertension via angiote ...	2015	26482303
structural basis of metallo-β-lactamase inhibition by captopril stereoisomers.	β-lactams are the most successful antibacterials, but their effectiveness is threatened by resistance, most importantly by production of serine- and metallo-β-lactamases (mbls). mbls are of increasing concern because they catalyze the hydrolysis of almost all β-lactam antibiotics, including recent-generation carbapenems. clinically useful serine-β-lactamase inhibitors have been developed, but such inhibitors are not available for mbls. l-captopril, which is used to treat hypertension via angiote ...	2015	26482303
the soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance.	the origin of carbapenem-hydrolyzing metallo-β-lactamases (mbls) acquired by clinical bacteria is largely unknown. we investigated the frequency, host range, diversity, and functionality of mbls in the soil microbiota. twenty-five soil samples of different types and geographical origins were analyzed by antimicrobial selective culture, followed by phenotypic testing and expression of mbl-encoding genes in escherichia coli, and whole-genome sequencing of mbl-producing strains was performed. carba ...	2015	26482314
the soil microbiota harbors a diversity of carbapenem-hydrolyzing β-lactamases of potential clinical relevance.	the origin of carbapenem-hydrolyzing metallo-β-lactamases (mbls) acquired by clinical bacteria is largely unknown. we investigated the frequency, host range, diversity, and functionality of mbls in the soil microbiota. twenty-five soil samples of different types and geographical origins were analyzed by antimicrobial selective culture, followed by phenotypic testing and expression of mbl-encoding genes in escherichia coli, and whole-genome sequencing of mbl-producing strains was performed. carba ...	2015	26482314
structure-function characterization reveals new catalytic diversity in the galactose oxidase and glyoxal oxidase family.	alcohol oxidases, including carbohydrate oxidases, have a long history of research that has generated fundamental biological understanding and biotechnological applications. despite a long history of study, the galactose 6-oxidase/glyoxal oxidase family of mononuclear copper-radical oxidases, auxiliary activity family 5 (aa5), is currently represented by only very few characterized members. here we report the recombinant production and detailed structure-function analyses of two homologues from ...	2015	26680532
performances and reliability of bruker microflex lt and vitek ms maldi-tof mass spectrometry systems for the identification of clinical microorganisms.	in clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. matrix assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) technology has been established as a cost effective, reliable, and faster alternative identification platform. in this study, we evaluated the reliability of the two available maldi-tof ms systems for their routine clinical ...	2015	26793718
lysosome associated membrane proteins maintain pancreatic acinar cell homeostasis: lamp-2 deficient mice develop pancreatitis.	the pathogenic mechanism of pancreatitis is poorly understood. recent evidence implicates defective autophagy in pancreatitis responses; however, the pathways mediating impaired autophagy in pancreas remain largely unknown. here, we investigate the role of lysosome associated membrane proteins (lamps) in pancreatitis.	2015	26693174
noncontiguous finished genome sequence and description of weeksella massiliensis sp. nov.	strain ff8(t) (= csur p860 = dsm 28259) was isolated in dakar, senegal, from the urine of a 65-year-old man with acute cystitis. this strain shows a similarity of sequence of 16s rrna of 98.38% with weeksella virosa, and its genbank accession numbers are hg931340 and ccmh00000000. matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. using a polyphasic study made of ph ...	2015	26649182
empirical antibiotic therapy for pneumonia in intensive care units: a multicentre, retrospective analysis of potentially pathogenic microorganisms identified by endotracheal aspirates cultures.	the purpose of this investigation was to explore the presumed relationship between the days of hospitalisation and microorganisms identified by endotracheal aspirate cultures in relation to adequate empirical treatment strategies of pneumonia in the intensive care unit (icu). all potentially pathogenic microorganisms identified by (surveillance) cultures of endotracheal aspirates obtained in the icus of two dutch teaching hospitals in 2007 and 2012 were retrospectively collected and analysed. an ...	2015	26385348
overcoming differences: the catalytic mechanism of metallo-β-lactamases.	metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. the worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. inhibitor design has been mostly impeded by the structural diversity of these enzymes. here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyze ...	2015	26297824
host response to the lung microbiome in chronic obstructive pulmonary disease.	the relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (copd). this article examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression.	2015	25945594
complementary lc-ms/ms-based n-glycan, n-glycopeptide, and intact n-glycoprotein profiling reveals unconventional asn71-glycosylation of human neutrophil cathepsin g.	neutrophil cathepsin g (ncg) is a central serine protease in the human innate immune system, but the importance of its n-glycosylation remains largely undescribed. to facilitate such investigations, we here use complementary lc-ms/ms-based n-glycan, n-glycopeptide, and intact glycoprotein profiling to accurately establish the micro- and macro-heterogeneity of ncg from healthy individuals. the fully occupied asn71 carried unconventional n-glycosylation consisting of truncated chitobiose core (glc ...	2015	26274980
draft genome sequence of strain atcc 33958, reported to be elizabethkingia miricola.	we report the draft genome of elizabethkingia strain atcc 33958, which has been classified as elizabethkingia miricola. similar to other elizabethkingia species, the atcc 33958 draft genome contains numerous β-lactamase genes. atcc 33958 also harbors a urease gene cluster which supports classification as e. miricola.	2015	26205869
structure-based mechanism of oleate hydratase from elizabethkingia meningoseptica.	hydratases provide access to secondary and tertiary alcohols by regio- and/or stereospecifically adding water to carbon-carbon double bonds. thereby, hydroxy groups are introduced without the need for costly cofactor recycling, and that makes this approach highly interesting on an industrial scale. here we present the first crystal structure of a recombinant oleate hydratase originating from elizabethkingia meningoseptica in the presence of flavin adenine dinucleotide (fad). a structure-based mu ...	2015	26077980
structure and functional properties of norrin mimic wnt for signalling with frizzled4, lrp5/6, and proteoglycan.	wnt signalling regulates multiple processes including angiogenesis, inflammation, and tumorigenesis. norrin (norrie disease protein) is a cystine-knot like growth factor. although unrelated to wnt, norrin activates the wnt/β-catenin pathway. signal complex formation involves frizzled4 (fz4), low-density lipoprotein receptor related protein 5/6 (lrp5/6), tetraspanin-12 and glycosaminoglycans (gags). here, we report crystallographic and small-angle x-ray scattering analyses of norrin in complex wi ...	2015	26158506
mutations in plasmalemma vesicle associated protein result in sieving protein-losing enteropathy characterized by hypoproteinemia, hypoalbuminemia, and hypertriglyceridemia.	severe intestinal diseases observed in very young children are often the result of monogenic defects. we used whole exome sequencing (wes) to examine the genetic cause in a patient with a distinct severe form of protein losing enteropathy (ple) characterized by hypoproteinemia, hypoalbuminemia, and hypertriglyceridemia.	2015	26207260
complete genome sequence of elizabethkingia meningoseptica, isolated from a t-cell non-hodgkin's lymphoma patient.	an elizabethkingia meningoseptica infection was detected at the end stage of a patient with t-cell non-hodgkin's lymphoma. the complete genome of this isolated strain, fms-007, was generated in one contig with a total size of 3,938,967 bp. a preliminary screening indicated that the genome contains drug resistance genes to aminoglycosides and β-lactams. a clustered regularly interspaced short palindromic repeats (crispr)/crispr-associated proteins (crispr/cas) system with 16 direct repeats and 15 ...	2015	26112786
characterization of the glycosylation site of human psa prompted by missense mutation using lc-ms/ms.	prostate specific antigen (psa) is currently used as a diagnostic biomarker for prostate cancer. it is a glycoprotein possessing a single glycosylation site at n69. during our previous study of psa n69 glycosylation, additional glycopeptides were observed in the psa sample that were not previously reported and did not match glycopeptides of impure glycoproteins existing in the sample. this extra glycosylation site of psa is associated with a mutation in klk3 genes. among single nucleotide polymo ...	2015	26022737
paratransgenesis: a promising new strategy for mosquito vector control.	the three main mosquito genera, anopheles, aedes and culex, transmit respectively malaria, dengue and lymphatic filariasis. current mosquito control strategies have proved unsuccessful, and there still is a substantial number of morbidity and mortality from these diseases. genetic control methods have now arisen as promising alternative strategies, based on two approaches: the replacement of a vector population by disease-refractory mosquitoes and the release of mosquitoes carrying a lethal gene ...	2015	26104575
comparative analysis of the glycosylation profiles of membrane-anchored hiv-1 envelope glycoprotein trimers and soluble gp140.	the human immunodeficiency virus type 1 (hiv-1) envelope glycoprotein (env) trimer, which consists of the gp120 and gp41 subunits, is the focus of multiple strategies for vaccine development. extensive env glycosylation provides hiv-1 with protection from the immune system, yet the glycans are also essential components of binding epitopes for numerous broadly neutralizing antibodies. recent studies have shown that when env is isolated from virions, its glycosylation profile differs significantly ...	2015	26018173
complete genome sequence and transcriptomic analysis of the novel pathogen elizabethkingia anophelis in response to oxidative stress.	elizabethkingia anophelis is an emerging pathogen that can cause life-threatening infections in neonates, severely immunocompromised and postoperative patients. the lack of genomic information on e. anophelis hinders our understanding of its mechanisms of pathogenesis. here, we report the first complete genome sequence of e. anophelis nuhp1 and assess its response to oxidative stress. elizabethkingia anophelis nuhp1 has a circular genome of 4,369,828 base pairs and 4,141 predicted coding sequenc ...	2015	26019164
pneumonia in the neutropenic cancer patient.	pneumonia is the leading cause of death among neutropenic cancer patients, particularly those with acute leukaemia. even with empiric therapy, case fatality rates of neutropenic pneumonias remain unacceptably high. however, recent advances in the management of neutropenic pneumonia offer hope for improved outcomes in the cancer setting. this review summarizes recent literature regarding the clinical presentation, microbiologic trends, diagnostic advances and therapeutic recommendations for cance ...	2015	25784246
leprous lesion presents enrichment of opportunistic pathogenic bacteria.	leprosy is a chronic infectious disease that remains a major challenge to public health in endemic countries. increasing evidence has highlighted the importance of microbiota for human general health and, as such, the study of skin microbiota is of interest. but while studies are continuously revealing the complexity of human skin microbiota, the microbiota of leprous cutaneous lesions has not yet been characterized. here we used sanger and massively parallel small sub-unit rrna (ssu) rrna gene ...	2015	25918684
breaking the allergic response by disrupting antibody glycosylation.		2015	25847971
self-cleavage of the pseudomonas aeruginosa cell-surface signaling anti-sigma factor foxr occurs through an n-o acyl rearrangement.	the fox system of pseudomonas aeruginosa is a cell-surface signaling (css) pathway employed by the bacterium to sense and respond to the presence of the heterologous siderophore ferrioxamine in the environment. this regulatory pathway controls the transcription of the foxa ferrioxamine receptor gene through the extracytoplasmic function sigma factor σ(foxi). in the absence of ferrioxamine, the activity of σ(foxi) is inhibited by the transmembrane anti-sigma factor foxr. upon binding of ferrioxam ...	2015	25809487
n-linked glycan profiling in neuroblastoma cell lines.	although mycn amplification has been associated with aggressive neuroblastoma, the molecular mechanisms that differentiate low-risk, mycn-nonamplified neuroblastoma from high-risk, mycn-amplified disease are largely unknown. genomic and proteomic studies have been limited in discerning differences in signaling pathways that account for this heterogeneity. n-linked glycosylation is a common protein modification resulting from the attachment of sugars to protein residues and is important in cell s ...	2015	25730103
multidomain human peroxidasin 1 is a highly glycosylated and stable homotrimeric high spin ferric peroxidase.	human peroxidasin 1 (hspxd01) is a multidomain heme peroxidase that uses bromide as a cofactor for the formation of sulfilimine cross-links. the latter confers critical structural reinforcement to collagen iv scaffolds. here, hspxd01 and various truncated variants lacking nonenzymatic domains were recombinantly expressed in hek cell lines. the n-glycosylation site occupancy and disulfide pattern, the oligomeric structure, and unfolding pathway are reported. the homotrimeric iron protein contains ...	2015	25713063
whole-genome sequence of chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in france.	for the first time, we report the whole-genome sequence analysis of chryseobacterium oranimense g311, a multidrug-resistant bacterium, from a cystic fibrosis patient in france, including resistance to colistin. whole-genome sequencing of c. oranimense g311 was performed using ion torrent pgm, and rast, the embl-ebi server, and the antibiotic resistance gene-annotation (arg-annot) database were used for annotation of all genes, including antibiotic resistance (ar) genes. general features of the c ...	2015	25583710
human neutrophils secrete bioactive paucimannosidic proteins from azurophilic granules into pathogen-infected sputum.	unlike plants and invertebrates, mammals reportedly lack proteins displaying asparagine (n)-linked paucimannosylation (mannose(1-3)fucose(0-1)n-acetylglucosamine(2)asn). enabled by technology advancements in system-wide biomolecular characterization, we document that protein paucimannosylation is a significant host-derived molecular signature of neutrophil-rich sputum from pathogen-infected human lungs and is negligible in pathogen-free sputum. five types of paucimannosidic n-glycans were carrie ...	2015	25645918
evidence for elizabethkingia anophelis transmission from mother to infant, hong kong.	elizabethkingia anophelis, recently discovered from mosquito gut, is an emerging bacterium associated with neonatal meningitis and nosocomial outbreaks. however, its transmission route remains unknown. we use rapid genome sequencing to investigate 3 cases of e. anophelis sepsis involving 2 neonates who had meningitis and 1 neonate's mother who had chorioamnionitis. comparative genomics revealed evidence for perinatal vertical transmission from a mother to her neonate; the 2 isolates from these p ...	2015	25625669
identification and characterization of a novel prokaryotic peptide: n-glycosidase from elizabethkingia meningoseptica.	peptide:n-glycosidase (pngase) f, the first pngase identified in prokaryotic cells, catalyzes the removal of intact asparagine-linked oligosaccharide chains from glycoproteins and/or glycopeptides. since its discovery in 1984, pngase f has remained as the sole prokaryotic pngase. recently, a novel gene encoding a protein with a predicted pngase domain was identified from a clinical isolate of elizabethkingia meningoseptica. in this study, the candidate protein was expressed in vitro and was subj ...	2015	25614628
bacteremia due to elizabethkingia meningoseptica.	elizabethkingia meningoseptica is a nonfermentative gram-negative bacillus that is ubiquitously found in hospital environments and as such, it has been associated with various nosocomial infections. immunocompromised individuals are particularly at increased risk for developing severe infections due to e. meningoseptica, including bacteremia. e. meningoseptica is resistant to multiple antimicrobials commonly used for gram-negative bacteria and conventional empirical antimicrobials targeting thos ...	2015	26793448
automated annotation and quantitation of glycans by liquid chromatography/electrospray ionization mass spectrometric analysis using the multiglycan-esi computational tool.	liquid chromatography/mass spectrometry (lc/ms) is currently considered to be a conventional glycomics analysis strategy due to the high sensitivity and ability to handle complex biological samples. interpretation of lc/ms data is a major bottleneck in high-throughput glycomics lc/ms-based analysis. the complexity of lc/ms data associated with biological samples prompts the needs to develop computational tools capable of facilitating automated data annotation and quantitation.	2015	25462374
septin dynamics are essential for exocytosis.	septins are a family of 14 cytoskeletal proteins that dynamically form hetero-oligomers and organize membrane microdomains for protein complexes. the previously reported interactions with snare proteins suggested the involvement of septins in exocytosis. however, the contradictory results of up- or down-regulation of septin-5 in various cells and mouse models or septin-4 in mice suggested either an inhibitory or a stimulatory role for these septins in exocytosis. the involvement of the ubiquitou ...	2015	25575596
discovery, primary, and crystal structures and capacitation-related properties of a prostate-derived heparin-binding protein wga16 from boar sperm.	mammalian sperm acquire fertility through a functional maturation process called capacitation, where sperm membrane molecules are drastically remodeled. in this study, we found that a wheat germ agglutinin (wga)-reactive protein on lipid rafts, named wga16, is removed from the sperm surface on capacitation. wga16 is a prostate-derived seminal plasma protein that has never been reported and is deposited on the sperm surface in the male reproductive tract. based on protein and cdna sequences for p ...	2015	25568322
recombinant α-nacetylgalactosaminidase from marine bacterium-modifying a erythrocyte antigens.	a plasmid based on pet-40b was constructed to synthesize recombinant α-n-acetylgalactosaminidase of the marine bacterium arenibacter latericius kmm 426t (α-alnagal) in escherichia coli cells. the yield of α-al- nagal attains 10 mg/ml with activity of 49.7 ± 1.3 u at 16°c, concentration of inductor 2 mm, and cultivation for 12 h. techniques such as anion exchange, metal affinity and gel filtration chromatography to purify α-alnagal were applied. α-alnagal is a homodimer with a molecular weight of ...	2015	25927009
elizabethkingia meningoseptica outbreak in intensive care unit.		2015	25722622
a nephrostomy-associated urinary tract infection caused by elizabethkingia meningoseptica.	we report a case of nephrostomy-associated urinary tract infection caused by elizabethkingia meningoseptica that occurred in a patient with retroperitoneal fibrosis. though conventional identification methods failed to detect the causative organism, it was identified on the basis of the complete sequencing of 16s rrna. four weeks of levofloxacin and minocycline administration successfully eradicated the infection. e. meningoseptica rarely causes urinary tract infections, and we believe that this ...	2015	26666619
[tracheobronchitis by elizabethkingia meningoseptica in a patient with tracheostomy].		2015	26200032
a preterm infant with intractable metabolic acidosis: a devastating presentation of chryseobacterium meningosepticum meningitis.	sepsis-related mortality and morbidity are the leading issues that neonatal intensive care units struggle with worldwide. we report a preterm infant with septic shock and intractable metabolic acidosis whose postmortem microbiologic examination revealed chryseobacterium meningosepticum meningitis. we would like to alert clinicians about this uncommon sepsis agent, and to call into question the treatment modalities for metabolic acidosis.	2015	26022592
elizabethkingia endophytica sp. nov., isolated from zea mays and emended description of elizabethkingia anopheliskämpfer et al. 2011.	a slightly yellow bacterial strain (jm-87(t)), isolated from the stem of healthy 10 day-old sweet corn (zea mays), was studied for its taxonomic allocation. the isolate revealed gram-stain-negative, rod-shaped cells. a comparison of the 16s rrna gene sequence of the isolate showed 99.1, 97.8, and 97.4% similarity to the 16s rrna gene sequences of the type strains of elizabethkingia anophelis, elizabethkingia meningoseptica and elizabethkingia miricola, respectively. the fatty acid profile of str ...	2015	25858248
biliary tract infection or colonization with elizabethkingia meningoseptica after endoscopic procedures involving the biliary tract.	this study was performed to investigate the clinical significance of detecting elizabethkingia meningoseptica in the bile.	2015	25742887
tubercular pleural effusion complicated with elizabethkingia meningoseptica infection in a diabetic male.		2015	25673621
[a case of community acquired elisabethkingia meningoseptica meningitis in an infant].		2015	25547190
lack of a type-2 glycosyltransferase in the fish pathogen flavobacterium psychrophilum determines pleiotropic changes and loss of virulence.	flavobacterium psychrophilum is an important fish pathogen, responsible for cold water disease, with a significant economic impact on salmonid farms worldwide. in spite of this, little is known about the bacterial physiology and pathogenesis mechanisms, maybe because it is difficult to manipulate, being considered a fastidious microorganism. mutants obtained using a tn4351 transposon were screened in order to identify those with alteration in colony morphology, colony spreading and extracellular ...	2015	25582708
development of real-time pcr assays for the detection of moraxella macacae associated with bloody nose syndrome in rhesus (macaca mulatta) and cynomolgus (macaca fascicularis) macaques.	moraxella macacae is a recently described bacterial pathogen that causes epistaxis or so-called bloody nose syndrome in captive macaques. the aim of this study was to develop specific molecular diagnostic assays for m. macacae and to determine their performance characteristics.	2015	26365904
tick-borne infections in human and animal population worldwide.	the abundance and activity of ectoparasites and its hosts are affected by various abiotic factors, such as climate and other organisms (predators, pathogens and competitors) presenting thus multiples forms of association (obligate to facultative, permanent to intermittent and superficial to subcutaneous) developed during long co-evolving processes. ticks are ectoparasites widespread globally and its eco epidemiology are closely related to the environmental conditions. they are obligatory hematop ...	2015	27047089
single cells within the puerto rico trench suggest hadal adaptation of microbial lineages.	hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. the microbial communities and metabolic potential in these ecosystems are largely uncharacterized. here, we present four single amplified genomes (sags) obtained from 8,219 m below the sea surface within the hadal ecosystem of the puerto rico trench (prt). these sags are derived from members of deep-sea clades, including the thaumarchaeota and sar11 clade, and two ar ...	2015	26386059
pseudomonas aeruginosa and periodontal pathogens in the oral cavity and lungs of cystic fibrosis patients: a case-control study.	cystic fibrosis (cf) is the most frequent lethal genetic disease in the caucasian population. lung destruction is the principal cause of death by chronic pseudomonas aeruginosa colonization. there is a high prevalence of oropharyngeal anaerobic bacteria in sputum of cf patients. this study was carried out due to the lack of results comparing subgingival periodontal pathogenic bacteria between the oral cavity and lungs in patients with cf in relation with p. aeruginosa presence. our first goal wa ...	2015	25854483
development of a new real-time pcr system for simultaneous detection of bacteria and fungi in pathological samples.	a novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (pcr) system. this system, designated the "multi-microbial real-time pcr", has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. all probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. the specificity and sensitivit ...	2015	26823918
development of a single-replicon minibyv vector for co-expression of heterologous proteins.	in planta production of recombinant proteins, including vaccine antigens and monoclonal antibodies, continues gaining acceptance. with the broadening range of target proteins, the need for vectors with higher performance is increasing. here, we have developed a single-replicon vector based on beet yellows virus (byv) that enables co-delivery of two target genes into the same host cell, resulting in transient expression of each target. this byv vector maintained genetic stability during systemic ...	2015	25280556
biofilm formation on the surface of polylactide during its biodegradation in different environments.	the research was aimed at determining the abundance and viability of biofilm formed on the surface of polylactide (pla) during its biodegradation in different environments. it was also aimed at isolating biofilm forming bacteria, determining their hydrolytic activity and taxonomic status. the first step was to evaluate pla biodegradability in lake water, compost and soil, using oxitop control. the next step was to assess the ability of isolated bacteria to form biofilm in the investigated enviro ...	2015	26433346
ineffective degradation of immunogenic gluten epitopes by currently available digestive enzyme supplements.	due to the high proline content of gluten molecules, gastrointestinal proteases are unable to fully degrade them leaving large proline-rich gluten fragments intact, including an immunogenic 33-mer from α-gliadin and a 26-mer from γ-gliadin. these latter peptides can trigger pro-inflammatory t cell responses resulting in tissue remodeling, malnutrition and a variety of other complications. a strict lifelong gluten-free diet is currently the only available treatment to cope with gluten intolerance ...	2015	26030273
therapeutic approaches for celiac disease.	celiac disease is a common, lifelong autoimmune disorder for which dietary control is the only accepted form of therapy. a strict gluten-free diet is burdensome to patients and can be limited in efficacy, indicating there is an unmet need for novel therapeutic approaches to supplement or supplant dietary therapy. many molecular events required for disease pathogenesis have been recently characterized and inspire most current and emerging drug-discovery efforts. genome-wide association studies (g ...	2015	26060114
identification of pseudolysin (lasb) as an aciduric gluten-degrading enzyme with high therapeutic potential for celiac disease.	immunogenic gluten proteins implicated in celiac disease (cd) largely resist degradation by human digestive enzymes. here we pursued the isolation of gluten-degrading organisms from human feces, aiming at bacteria that would digest gluten under acidic conditions, as prevails in the stomach.	2015	25895519
properties of gluten intolerance: gluten structure, evolution, pathogenicity and detoxification capabilities.	theterm gluten intolerance may refer to three types of human disorders: autoimmune celiac disease (cd), allergy to wheat and non-celiac gluten sensitivity (ncgs). gluten is a mixture of prolamin proteins present mostly in wheat, but also in barley, rye and oat. gluten can be subdivided into three major groups: s-rich, s-poor and high molecular weight proteins. prolamins within the groups possess similar structures and properties. all gluten proteins are evolutionarily connected and share the sam ...	2016	27763541
spectrum and sensitivity of bacterial keratitis isolates in auckland.	background. the bacteria isolated from severe cases of keratitis and their antibiotic sensitivity are recognised to vary geographically and over time. objectives. to identify the most commonly isolated bacteria in keratitis cases admitted over a 24-month period to a public hospital in auckland, new zealand, and to investigate in vitro sensitivity to antibiotics. methods. hospital admissions for culture-proven bacterial keratitis between january 2013 and december 2014 were identified. laboratory ...	2016	27213052
assessment of biofilm formation of e. meningoseptica, d. acidovorans, and s. maltophilia in lens cases and their growth on recovery media.	bacterial biofilm formation in contact lens cases is a risk factor in the development of both microbial and infiltrative keratitis. this investigation evaluated three emerging pathogens: stenotrophomonas maltophilia, elizabethkingia meningoseptica, and delftia acidovorans for biofilm formation and metabolic activity in lens cases. also, growth of these bacteria on different media was assessed to optimize recovery conditions.	2016	26383012
outbreak of elizabethkingia meningoseptica sepsis with meningitis in a well-baby nursery.	between march and may 2012, three neonates born at a regional maternity hospital developed elizabethkingia meningoseptica (previously chryseobacterium meningosepticum) sepsis with meningitis aged <10 days, and were treated successfully with intravenous ciprofloxacin plus vancomycin or piperacillin-tazobactam for three to six weeks. four (16.6%) of 24 environmental specimens obtained from the nursery and delivery room were positive for this organism. all of the clinical isolates and two isolates ...	2016	28077242
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.	for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...	2016	26511485
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.	for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...	2016	26511485
mechanistic and evolutionary insights from comparative enzymology of phosphomonoesterases and phosphodiesterases across the alkaline phosphatase superfamily.	naively one might have expected an early division between phosphate monoesterases and diesterases of the alkaline phosphatase (ap) superfamily. on the contrary, prior results and our structural and biochemical analyses of phosphate monoesterase pafa, from chryseobacterium meningosepticum, indicate similarities to a superfamily phosphate diesterase [xanthomonas citri nucleotide pyrophosphatase/phosphodiesterase (npp)] and distinct differences from the three metal ion ap superfamily monoesterase, ...	2016	27670607
successful management of elizabethkingia meningoseptica meningitis with intraventricular vancomycin.	elizabethkingia meningoseptica, formerly chryseobacterium meningosepticum usually causes neonatal meningitis and is a rare cause of nosocomial meningitis in adults. e. meningoseptica is resistant to most antibiotics, and the use of inactive drugs as empirical therapy may contribute to poor outcome in many patients. vancomycin, alone or in combination with rifampicin, has been successful in the treatment of meningitis in infants1. we present a case of e. meningoseptica meningitis in an adult who ...	2016	27766817
first report of bacteremia caused by elizabethkingia meningoseptica in a dog.		2016	27587896
crystal structure of the metallo-β-lactamase gob in the periplasmic dizinc form reveals an unusual metal site.	metallo-beta-lactamases (mbls) are broad-spectrum, zn(ii)-dependent lactamases able to confer resistance to virtually every β-lactam antibiotic currently available. the large diversity of active-site structures and metal content among mbls from different sources has limited the design of a pan-mbl inhibitor. gob-18 is a divergent mbl from subclass b3 that is expressed by the opportunistic gram-negative pathogen elizabethkingia meningoseptica this mbl is atypical, since several residues conserved ...	2016	27458232
elizabethkingia meningoseptica and contact lens use.	a 47-year-old man presented to our emergency department complaining of acute ocular pain and redness of his left eye. ophthalmological antecedents included use of semi-rigid contact lens and primary open-angle glaucoma. slit-lamp examination revealed a small central corneal ulcer associated with stromal inflammatory infiltrate. scraping from the corneal ulcer was positive for elizabethkingia meningoseptica. he was empirically treated with topical 0.5% levofloxacin and 0.3% gentamicin, and five w ...	2016	27349783
microbial contamination of ice machines is mediated by activated charcoal filtration systems in a city hospital.	although microbial contamination of ice machines has been reported, no previous study has addressed microbial contamination of ice produced by machines equipped with activated charcoal (ac) filters in hospitals. the aim of this study was to provide clinical data for evaluating ac filters to prevent microbial contamination of ice. we compared microbial contamination in ice samples produced by machines with (n = 20) and without an ac filter (n = 40) in shunan city shinnanyo municipal hospital. all ...	2016	27348980
diversity of culturable gram-negative bacteria isolated from irrigation water of two rice crop regions in southern brazil.	in this study, we assessed the diversity of gram-negative bacteria found in water used for irrigation of rice crops in two growing areas of southern brazil. samples were collected from the main irrigation channel and field drain area. twenty-two bacterial species were found in cachoeirinha and 28 in camaquã. in both areas, the most frequent bacterial families were enterobacteriaceae and aeromonadaceae. differences in microbial diversity were observed in both study areas. thirty-five gram-negativ ...	2016	27197729
endo-f3 glycosynthase mutants enable chemoenzymatic synthesis of core-fucosylated triantennary complex type glycopeptides and glycoproteins.	chemoenzymatic synthesis is emerging as a promising approach to the synthesis of homogeneous glycopeptides and glycoproteins highly demanded for functional glycomics studies, but its generality relies on the availability of a range of enzymes with high catalytic efficiency and well defined substrate specificity. we describe in this paper the discovery of glycosynthase mutants derived from elizabethkingia meningoseptica endoglycosidase f3 (endo-f3) of the gh18 family, which are devoid of the inhe ...	2016	26966183
infections due to elizabethkingia meningoseptica in critically injured trauma patients: a seven-year study.	elizabethkingia meningoseptica is an infrequent cause of hospital-acquired infections. the clinical and microbiological profiles of infections due to e. meningoseptica over a seven-year period at a level-i trauma centre are reported in this study. medical records of patients from whose clinical samples e. meningoseptica was isolated on more than one occasion were reviewed. a total of 21 cases were observed during the study, 16 (76.2%) of which exhibited multidrug resistance. the observed in-hosp ...	2016	26763750
correction for pradeep et al., draft genome sequence of elizabethkingia anopheles, isolated from a postoperative endophthalmitis patient.		2016	27932658
taxonogenomics and description of vaginella massiliensis gen. nov., sp. nov., strain marseille p2517(t), a new bacterial genus isolated from the human vagina.	an obligate aerobic, gram-negative, nonmotile and nonsporulating rod designated marseille p2517 was isolated from the vaginal flora. we describe its features, annotate the genome and compare it to the closest species. the 16s rrna analysis shows 93.03% sequence similarity with weeksella virosa, the phylogenetically closest species. its genome is 2 434 475 bp long and presents 38.16% g+c. on the basis of these data, it can be considered as a new genus in the flavobacteriaceae family, for which we ...	2016	28053707
taxonogenomics and description of vaginella massiliensis gen. nov., sp. nov., strain marseille p2517(t), a new bacterial genus isolated from the human vagina.	an obligate aerobic, gram-negative, nonmotile and nonsporulating rod designated marseille p2517 was isolated from the vaginal flora. we describe its features, annotate the genome and compare it to the closest species. the 16s rrna analysis shows 93.03% sequence similarity with weeksella virosa, the phylogenetically closest species. its genome is 2 434 475 bp long and presents 38.16% g+c. on the basis of these data, it can be considered as a new genus in the flavobacteriaceae family, for which we ...	2016	28053707
cp40 from corynebacterium pseudotuberculosis is an endo-β-n-acetylglucosaminidase.	c. pseudotuberculosis is an important animal pathogen that causes substantial economical loss in sheep and goat farming. zoonotic infections in humans are rare, but when they occur they are often severe and difficult to treat. one of the most studied proteins from this bacterium, the secreted protein cp40 is being developed as a promising vaccine candidate and has been characterized as a serine protease. in this study we have investigated if cp40 is an endoglycosidase rather than a protease.	2016	27821068
genome sequence of elizabethkingia meningoseptica em1, isolated from a patient with a bloodstream infection.	elizabethkingia meningoseptica em1 was isolated from a whole-blood sample from a female patient. the draft genome sequence of em1 contains 4,038,467 bp, with a g+c content of 36.37%. a preliminary genome analysis showed that em1 contains genes conferring resistance to β-lactams. the bacterium has hemolysin genes and a set of genes involved in heme uptake and heme utilization, showing its potential to cause bloodstream infections. a clustered regularly interspaced short palindromic repeat (crispr ...	2016	27789634
protein n-glycosylation and n-glycan trimming are required for postembryonic development of the pest beetle tribolium castaneum.	in holometabolous insects the transition from larva to adult requires a complete body reorganization and relies on n-glycosylated proteins. n-glycosylation is an important posttranslational modification that influences protein activity but its impact on the metamorphosis has not been studied yet. here we used the red flour beetle, tribolium castaneum, to perform a first comprehensive study on the involvement of the protein n-glycosylation pathway in metamorphosis. the transcript levels for genes ...	2016	27731363