bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of the Gene Family Encoding Lipases in
Candida rugosa
by Competitive Reverse Transcription-PCR
Authors: Lee Guan-Chiun , Tang Shye-Jye , Sun Kuang-Hui , Shaw Jei-Fu
Published: December 2019

Synthesis of multiple extracellular lipases in
Candida rugosa
has been demonstrated. However, it is difficult to characterize the expression spectrum of
lip
genes, since the sequences of the
lip
multigene family are very closely related. A competitive reverse transcription-PCR assay was developed to quantify the expression of
lip
genes. In agreement with the protein profile, the abundance of
lip
mRNAs was found to be (in decreasing order)
lip1
,
lip3
,
lip2
,
lip5
, and
lip4
. To analyze the effects of different culture conditions, the transcript concentrations for these mRNA species were normalized relative to the values for
gpd
, encoding glyceraldehyde-3-phosphate dehydrogenase. In relative terms,
lip1
and
lip3
were highly and constitutively expressed (about 10
5
molecules per μg of total RNA) whereas the other inducible
lip
genes, especially
lip4
, showed significant changes in mRNA expression under different culture conditions. These results indicate that differential transcriptional control of
lip
genes results in multiple forms of lipase proteins.
Construction of Environmental DNA Libraries in
Escherichia coli
and Screening for the Presence of Genes Conferring Utilization of 4-Hydroxybutyrate
Authors: Henne Anke , Daniel Rolf , Schmitz Ruth A. , Gottschalk Gerhard
Published: December 2019

Environmental DNA libraries from three different soil samples were constructed. The average insert size was 5 to 8 kb and the percentage of plasmids with inserts was approximately 80%. The recombinant
Escherichia coli
strains (approximately 930,000) were screened for 4-hydroxybutyrate utilization. Thirty-six positive
E. coli
clones were obtained during the initial screen, and five of them contained a recombinant plasmid (pAH1 to pAH5) which conferred a stable 4-hydroxybutyrate-positive phenotype. These
E. coli
clones were studied further. All five were able to grow with 4-hydroxybutyrate as sole carbon and energy source and exhibited 4-hydroxybutyrate dehydrogenase activity in crude extracts. Sequencing of pAH5 revealed a gene homologous to the
gbd
gene of
Ralstonia eutropha
, which encodes a 4-hydroxybutyrate dehydrogenase. Two other genes (
orf1
and
orf6
) conferring utilization of 4-hydroxybutyrate were identified during subcloning and sequencing of the inserts of pAH1 and pAH3. The deduced
orf1
gene product showed similarities to members of the DedA family of proteins. The sequence of the deduced
orf6
gene product harbors the fingerprint pattern of enoyl-coenzyme A hydratases/isomerases. The other sequenced inserts of the plasmids recovered from the positive clones revealed no significant similarity to any other gene or gene product whose sequence is available in the National Center for Biotechnology Information databases.
Comparison of Ribotyping, Randomly Amplified Polymorphic DNA Analysis, and Pulsed-Field Gel Electrophoresis in Typing of
Lactobacillus rhamnosus
and
L. casei
Strains
Authors: Tynkkynen Soile , Satokari Reetta , Saarela Maria , Mattila-Sandholm Tiina , Saxelin Maija
Published: December 2019

A total of 24 strains, biochemically identified as members of the
Lactobacillus casei
group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for
L. rhamnosus
and
L. casei
identified the type strain
L. rhamnosus
ATCC 7469 and the neotype strain
L. casei
ATCC 334, respectively, but did not give any signal with the recently revived species
L. zeae
, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified as
L. casei
. Our results are in accordance with the suggested new classification of the
L. casei
group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively.
Glucose Metabolism and Kinetics of Phosphorus Removal by the Fermentative Bacterium
Microlunatus phosphovorus
Authors: Santos Margarida M. , Lemos Paulo C. , Reis Maria A. M. , Santos Helena
Published: December 2019

Phosphorus and carbon metabolism in
Microlunatus phosphovorus
was investigated by using a batch reactor to study the kinetics of uptake and release of extracellular compounds, in combination with
31
P and
13
C nuclear magnetic resonance (NMR) to characterize intracellular pools and to trace the fate of carbon substrates through the anaerobic and aerobic cycles. The organism was subjected to repetitive anaerobic and aerobic cycles to induce phosphorus release and uptake in a sequencial batch reactor; an ultrafiltration membrane module was required since cell suspensions did not sediment.
M. phosphovorus
fermented glucose to acetate via an Embden-Meyerhof pathway but was unable to grow under anaerobic conditions. A remarkable time shift was observed between the uptake of glucose and excretion of acetate, resulting in an intracellular accumulation of acetate. The acetate produced was oxidized in the subsequent aerobic stage. Very high phosphorus release and uptake rates were measured, 3.34 mmol g of cell
−1
h
−1
and 1.56 mmol g of cell
−1
h
−1
, respectively, values only comparable with those determined in activated sludge. In the aerobic period, growth was strictly dependent on the availability of external phosphate. Natural abundance
13
C NMR showed the presence of reserves of glutamate and trehalose in cell suspensions. Unexpectedly, [1-
13
C]glucose was not significantly channeled to the synthesis of internal reserves in the anaerobic phase, and acetate was not during the aerobic stage, although the glutamate pool became labeled via the exchange with intermediates of the tricarboxylic acid cycle at the level of glutamate dehydrogenase. The intracellular pool of glutamate increased under anaerobic conditions and decreased during the aerobic period. The contribution of
M. phosphovorus
for phosphorus removal in wastewater treatment plants is discussed on the basis of the metabolic features disclosed by this study.
Purification and Characterization of the Soluble Methane Monooxygenase of the Type II Methanotrophic Bacterium
Methylocystis
sp. Strain WI 14
Authors: Grosse Stephan , Laramee Louise , Wendlandt Karin-Dagmar , McDonald Ian R. , Miguez Carlos B. , Kleber Hans-Peter
Published: December 2019

Methane monooxygenase (MMO) catalyzes the oxidation of methane to methanol as the first step of methane degradation. A soluble NAD(P)H-dependent methane monooxygenase (sMMO) from the type II methanotrophic bacterium WI 14 was purified to homogeneity. Sequencing of the 16S rDNA and comparison with that of other known methanotrophic bacteria confirmed that strain WI 14 is very close to the genus
Methylocystis
. The sMMO is expressed only during growth under copper limitation (<0.1 μM) and with ammonium or nitrate ions as the nitrogen source. The enzyme exhibits a low substrate specificity and is able to oxidize several alkanes and alkenes, cyclic hydrocarbons, aromatics, and halogenic aromatics. It has three components, hydroxylase, reductase and protein B, which is involved in enzyme regulation and increases sMMO activity about 10-fold. The relative molecular masses of the native components were estimated to be 229, 41, and 18 kDa, respectively. The hydroxylase contains three subunits with relative molecular masses of 57, 43, and 23 kDa, which are present in stoichiometric amounts, suggesting that the native protein has an α
2
β
2
γ
2
structure. We detected 3.6 mol of iron per mol of hydroxylase by atomic absorption spectrometry. sMMO is strongly inhibited by Hg
2+
ions (with a total loss of enzyme activity at 0.01 mM Hg
2+
) and Cu
2+
, Zn
2+
, and Ni
2+
ions (95, 80, and 40% loss of activity at 1 mM ions). The complete sMMO gene sequence has been determined. sMMO genes from strain WI 14 are clustered on the chromosome and show a high degree of homology (at both the nucleotide and amino acid levels) to the corresponding genes from
Methylosinus trichosporium
OB3b,
Methylocystis
sp. strain M, and
Methylococcus capsulatus
(Bath).
Nested Allele-Specific PCR Primers Distinguish Genetic Groups of
Uncinula necator
Authors: Délye Christophe , Ronchi Valérie , Laigret Frédéric , Corio-Costet Marie-France
Published: December 2019

Isolates of the obligately biotrophic fungus
Uncinula necator
cluster in three distinct genetic groups (groups I, II, and III). We designed PCR primers specific for these groups in order to monitor field populations of
U. necator
. We used the nucleotide sequences of the gene that encodes eburicol 14α-demethylase (
CYP51
) and of the ribosomal DNA internal transcribed spacer 1 (ITS1), ITS2, and 5.8S regions. We identified four point mutations (three in
CYP51
and one in ITS1) that distinguished groups I and II from group III based on a sample of 132 single-spore isolates originating from Europe, Tunisia, Israel, India, and Australia. We developed a nested allele-specific PCR assay in which the
CYP51
point mutations were used to detect and distinguish groups I and II from group III in crude mildewed samples from vineyards. In a preliminary study performed with samples from French vineyards in which isolates belonging to genetic groups I and III were present, we found that a shift from a population composed primarily of group I isolates to a population composed primarily of group III isolates occurred during the grapevine growing season.
Phylogenetic Affiliation and Quantification of Psychrophilic Sulfate-Reducing Isolates in Marine Arctic Sediments
Authors: Sahm Kerstin , Knoblauch Christian , Amann Rudolf
Published: December 2019

Thirteen psychrophilic sulfate-reducing isolates from two permanently cold fjords of the Arctic island Spitsbergen (Hornsund and Storfjord) were phylogenetically analyzed. They all belonged to the δ subclass of
Proteobacteria
and were widely distributed within this group, indicating that psychrophily is a polyphyletic property. A new 16S rRNA-directed oligonucleotide probe was designed against the largest coherent cluster of these isolates. The new probe, as well as a set of available probes, was applied in rRNA slot blot hybridization to investigate the composition of the sulfate-reducing bacterial community in the sediments. rRNA related to the new cluster of incompletely oxidizing, psychrophilic isolates made up 1.4 to 20.9% of eubacterial rRNA at Storfjord and 0.6 to 3.5% of eubacterial rRNA at Hornsund. This group was the second-most-abundant group of sulfate reducers at these sites. Denaturing gradient gel electrophoresis and hybridization analysis showed bands identical to those produced by our isolates. The data indicate that the psychrophilic isolates are quantitatively important in Svalbard sediments.
d
-Lactate Dehydrogenase Gene (
ldhD
) Inactivation and Resulting Metabolic Effects in the
Lactobacillus johnsonii
Strains La1 and N312
Authors: Lapierre Luciane , Germond Jacques-Edouard , Ott Andreas , Delley Michele , Mollet Beat
Published: December 2019

Lactobacillus johnsonii
La1, a probiotic bacterium with demonstrated health effects, grows in milk, where it ferments lactose to
d
- and
l
-lactate in a 60:40% ratio. The
d
-lactate dehydrogenase (D-LDH) gene (
ldhD
) of this strain was isolated, and an in vitro-truncated copy of that gene was used to inactivate the genomic copy in two strains, La1 and N312, by gene replacement. For that, an 8-bp deletion was generated within the cloned
ldhD
gene to inactivate its function. The plasmid containing the altered
ldhD
was transferred to
L. johnsonii
via conjugative comobilization with
Lactococcus lactis
carrying pAMβ1. Crossover integrations of the plasmid at the genomic
ldhD
site were selected, and appropriate resolution of the cointegrate structures resulted in mutants that had lost the plasmid and in which the original
ldhD
was replaced by the truncated copy. These mutants completely lacked D-LDH activity. Nevertheless, the lower remaining L-LDH activity of the cells was sufficient to reroute most of the accumulating pyruvate to
l
-lactate. Only a marginal increase in production of the secondary end products acetaldehyde, diacetyl, and acetoin was observed. It can be concluded that in
L. johnsonii
D- and L-LDH are present in substantial excess for their role to eliminate pyruvate and regenerate NAD
+
and that accumulated pyruvate is therefore not easily redirected in high amounts to secondary metabolic routes.
Microbial Proline 4-Hydroxylase Screening and Gene Cloning
Authors: Shibasaki Takeshi , Mori Hideo , Chiba Shigeru , Ozaki Akio
Published: December 2019

Microbial proline 4-hydroxylases, which hydroxylate free
l
-proline to
trans
-4-hydroxy-
l
-proline, were screened in order to establish an industrial system for biotransformation of
l
-proline to
trans
-4-hydroxy-
l
-proline. Enzyme activities were detected in eight strains, including strains of
Dactylosporangium
spp. and
Amycolatopsis
spp. The
Dactylosporangium
sp. strain RH1 enzyme was partially purified 3,300-fold and was estimated to be a monomer polypeptide with an apparent molecular mass of 31 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Degenerate primers based on the N-terminal amino acid sequence of the 31-kDa polypeptide were synthesized in order to amplify the corresponding 71-bp DNA fragment. A 5.5-kbp DNA fragment was isolated by using the 71-bp fragment labeled with digoxigenin as a probe for a genomic library of
Dactylosporangium
sp. strain RH1 constructed in
Escherichia coli
. One of the open reading frames found in the cloned DNA, which encoded a 272-amino-acid polypeptide (molecular mass, 29,715 daltons), was thought to be a proline 4-hydroxylase gene. The gene was expressed in
E. coli
as a fused protein with the N-terminal 34 amino acids of the β-galactosidase α-fragment. The
E. coli
recombinant exhibited proline 4-hydroxylase activity that was 13.6-fold higher than the activity in the original strain,
Dactylosporangium
sp. strain RH1. No homology was detected with other 2-oxoglutarate-dependent dioxygenases when databases were searched; however, the histidine motif conserved in 2-oxoglutarate-dependent dioxygenases was found in the gene.
Identification of the
Pseudomonas stutzeri
OX1 Toluene–
o
-Xylene Monooxygenase Regulatory Gene (
touR
) and of Its Cognate Promoter
Authors: Arenghi Fabio L. G. , Pinti Marcello , Galli Enrica , Barbieri Paola
Published: December 2019

Toluene–
o
-xylene monooxygenase is an enzymatic complex, encoded by the
touABCDEF
genes, responsible for the early stages of toluene and
o
-xylene degradation in
Pseudomonas stutzeri
OX1. In order to identify the loci involved in the transcriptional regulation of the
tou
gene cluster, deletion analysis and complementation studies were carried out with
Pseudomonas putida
PaW340 as a heterologous host harboring pFB1112, a plasmid that allowed regulated expression, inducible by toluene and
o
-xylene and their corresponding phenols, of the toluene–
o
-xylene monooxygenase. A locus encoding a positive regulator, designated
touR
, was mapped downstream from the
tou
gene cluster. TouR was found to be similar to transcriptional activators of aromatic compound catabolic pathways belonging to the NtrC family and, in particular, to DmpR (83% similarity), which controls phenol catabolism. By using a
touA
-C2,3O fusion reporter system and by primer extension analysis, a TouR cognate promoter (

P
ToMO

) was mapped, which showed the typical −24 TGGC, −12 TTGC sequences characteristic of ς
54
-dependent promoters and putative upstream activating sequences. By using the reporter system described, we found that TouR responds to mono- and dimethylphenols, but not the corresponding methylbenzenes. In this respect, the regulation of the
P. stutzeri
system differs from that of other toluene or xylene catabolic systems, in which the hydrocarbons themselves function as effectors. Northern analyses indicated low transcription levels of
tou
structural genes in the absence of inducers. Basal toluene–
o
-xylene monooxygenase activity may thus transform these compounds to phenols, which then trigger the TouR-mediated response.
Radioactive Fingerprinting of Microorganisms That Oxidize Atmospheric Methane in Different Soils
Authors: Roslev Peter , Iversen Niels
Published: December 2019

Microorganisms that oxidize atmospheric methane in soils were characterized by radioactive labelling with
14
CH
4
followed by analysis of radiolabelled phospholipid ester-linked fatty acids (
14
C-PLFAs). The radioactive fingerprinting technique was used to compare active methanotrophs in soil samples from Greenland, Denmark, the United States, and Brazil. The
14
C-PLFA fingerprints indicated that closely related methanotrophic bacteria were responsible for the oxidation of atmospheric methane in the soils. Significant amounts of labelled PLFAs produced by the unknown soil methanotrophs coeluted with a group of fatty acids that included i17:0, a17:0, and 17:1ω8c (up to 9.0% of the total
14
C-PLFAs). These PLFAs are not known to be significant constituents of methanotrophic bacteria. The major PLFAs of the soil methanotrophs (73.5 to 89.0% of the total PLFAs) coeluted with 18:1 and 18:0 fatty acids (e.g., 18:1ω9, 18:1ω7, and 18:0). The
14
C-PLFAs fingerprints of the soil methanotrophs that oxidized atmospheric methane did not change after long-term methane enrichment at 170 ppm CH
4
. The
14
C-PLFA fingerprints of the soil methanotrophs were different from the PLFA profiles of type I and type II methanotrophic bacteria described previously. Some similarity at the PLFA level was observed between the unknown soil methanotrophs and the PLFA phenotype of the type II methanotrophs. Methanotrophs in Arctic, temperate, and tropical regions assimilated between 20 and 54% of the atmospheric methane that was metabolized. The lowest relative assimilation (percent) was observed for methanotrophs in agricultural soil, whereas the highest assimilation was observed for methanotrophs in rain forest soil. The results suggest that methanotrophs with relatively high carbon conversion efficiencies and very similar PLFA compositions dominate atmospheric methane metabolism in different soils. The characteristics of the methane metabolism and the
14
C-PLFA fingerprints excluded any significant role of autotrophic ammonia oxidizers in the metabolism of atmospheric methane.
Enhanced (+)-Catechin Transglucosylating Activity of
Streptococcus mutans
GS-5 Glucosyltransferase-D due to Fructose Removal
Authors: Meulenbeld Gerwin H. , Zuilhof Han , van Veldhuizen Adelbertus , van den Heuvel Robert H. H. , Hartmans Sybe
Published: December 2019

The (+)-catechin transglucosylating activities of several glucosyltransferases (GTFs) from the genus
Streptococcus
were compared. For this purpose, a mixture of four GTFs from
Streptococcus sobrinus
SL-1 and recombinant GTF-B and GTF-D from
Streptococcus mutans
GS-5 expressed in
Escherichia coli
were studied. It was shown that after removal of α-glucosidase activity, GTF-D transglucosylated catechin with the highest efficiency. A maximal yield (expressed as the ratio of moles of glucoside formed to moles of catechin initially added) of 90% was observed with 10 mM catechin and 100 mM sucrose (

K
m

, 13 mM) in 125 mM potassium phosphate, pH 6.0, at 37°C.
1
H and
13
C nuclear magnetic resonance spectroscopy revealed the structures of two catechin glucosides, (+)-catechin-4′-
O
-α-
d
-glucopyranoside and (+)-catechin-4′,7-
O
-α-di-
d
-glucopyranoside. Fructose accumulation during glucosyl transfer from sucrose to the acceptor competitively inhibited catechin transglucosylation (

K
i

, 9.3 mM), whereas glucose did not inhibit catechin transglucosylation. The addition of yeasts was studied in order to minimize fructose inhibition by means of fructose removal. For this purpose, the yeasts
Pichia pastoris
and the mutant
Saccharomyces cerevisiae
T2-3D were selected because of their inabilities to utilize sucrose. Addition of
P. pastoris
or
S. cerevisiae
T2-3D to the standard reaction mixture resulted in a twofold increase in the duration of the maximum GTF-D transglucosylation rate. The addition of the yeasts also stimulated sucrose utilization by GTF-D.
Expression of the Isoamylase Gene of
Flavobacterium odoratum
KU in
Escherichia coli
and Identification of Essential Residues of the Enzyme by Site-Directed Mutagenesis
Authors: Abe Jun-ichi , Ushijima Chiaki , Hizukuri Susumu
Published: December 2019

The isoamylase gene from
Flavobacterium odoratum
KU was cloned into and expressed in
Escherichia coli
JM109. The promoter of the gene was successful in
E. coli
, and the enzyme produced was excreted into the culture medium, depending on the amount of the enzyme expressed. The enzyme found in the culture medium showed almost the same
M
r
, heat-inactivating constant, and N-terminal sequence as those of the enzyme accumulated in the periplasmic space. This result indicated that the enzyme accumulated in an active form at the periplasm was transported out of the cell. The primary sequence of the enzyme, which was deduced from its nucleotide sequence, showed that the mature enzyme consisted of 741 amino acid residues. By changing five possible residues to Ala independently, it was found that Asp-374, Glu-422, and Asp-497 were essential. The sequences around those residues were highly conserved in isoamylases of different origins and the glycogen operon protein X, GlgX. The comparison of the distance between these essential residues with those of various amylases suggested that the bacterial and plant isoamylase but not GlgX had a longer fourth loop than the other amylases. This longer fourth loop had a possible role in accommodating the long branched chains of native glycogens and starches.
On the Occurrence of Anoxic Microniches, Denitrification, and Sulfate Reduction in Aerated Activated Sludge
Authors: Schramm Andreas , Santegoeds Cecilia M. , Nielsen Helle K. , Ploug Helle , Wagner Michael , Pribyl Milan , Wanner Jiri , Amann Rudolf , de Beer Dirk
Published: December 2019

A combination of different methods was applied to investigate the occurrence of anaerobic processes in aerated activated sludge. Microsensor measurements (O
2
, NO
2
−
, NO
3
−
, and H
2
S) were performed on single sludge flocs to detect anoxic niches, nitrate reduction, or sulfate reduction on a microscale. Incubations of activated sludge with
15
NO
3
−
and
35
SO
4
2−
were used to determine denitrification and sulfate reduction rates on a batch scale. In four of six investigated sludges, no anoxic zones developed during aeration, and consequently denitrification rates were very low. However, in two sludges anoxia in flocs coincided with significant denitrification rates. Sulfate reduction could not be detected in any sludge in either the microsensor or the batch investigation, not even under short-term anoxic conditions. In contrast, the presence of sulfate-reducing bacteria was shown by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes and by PCR-based detection of genes coding for the dissimilatory sulfite reductase. A possible explanation for the absence of anoxia even in most of the larger flocs might be that oxygen transport is not only diffusional but enhanced by advection, i.e., facilitated by flow through pores and channels. This possibility is suggested by the irregularity of some oxygen profiles and by confocal laser scanning microscopy of the three-dimensional floc structures, which showed that flocs from the two sludges in which anoxic zones were found were apparently denser than flocs from the other sludges.
Effect of Methodology on the Tuberculocidal Activity of a Glutaraldehyde-Based Disinfectant
Authors: Dauendorffer J. N. , Laurain C. , Weber M. , Dailloux M.
Published: December 2019

Although official guidelines recommend a plate counting method for testing the susceptibility of mycobacteria to disinfectants, manufacturers usually prefer to employ the BACTEC procedure. Data showing that the BACTEC method overestimates the activity of a glutaraldehyde-based disinfectant against
Mycobacterium tuberculosis
in comparison with a conventional plate counting procedure are presented.
Perkinsus marinus
Extracellular Protease Modulates Survival of
Vibrio vulnificus
in Eastern Oyster (
Crassostrea virginica
) Hemocytes
Authors: Tall B. D. , La Peyre J. F. , Bier J. W. , Miliotis M. D. , Hanes D. E. , Kothary M. H. , Shah D. B. , Faisal M.
Published: December 2019

The in vitro effects of the
Perkinsus marinus
serine protease on the intracellular survival of
Vibrio vulnificus
in oyster hemocytes were examined by using a time-course gentamicin internalization assay. Results showed that protease-treated hemocytes were initially slower to internalize
V. vulnificus
than untreated hemocytes. After 1 h, the elimination of
V. vulnificus
by treated hemocytes was significantly suppressed compared with hemocytes infected with invasive and noninvasive controls. Our data suggest that the serine protease produced by
P. marinus
suppresses the vibriocidal activity of oyster hemocytes to effectively eliminate
V. vulnificus
, potentially leading to conditions favoring higher numbers of vibrios in oyster tissues.
Association of Bacteria and Yeasts in Hot Springs
Authors: Rikhvanov Eugene G. , Varakina Nina N. , Sozinov Dmitri Yu , Voinikov Viktor K.
Published: December 2019

The thermophilic bacterium
Bacillus
sp. strain TB-1 was isolated in association with the yeast
Debaryomyces vanriji
from hot springs at 46°C. It was shown that TB-1 excreted thiamine into the culture broth, which not only promoted
D. vanriji
growth in mixed culture but also increased the maximal temperature for yeast growth.
Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned
Authors: Zhu YanChun , O’Brien Brittany , Leach Lynn , Clarke Alexandra , Bates Marian , Adams Eleanor , Ostrowsky Belinda , Quinn Monica , Dufort Elizabeth , Southwick Karen , Erazo Richard , Haley Valerie B. , Bucher Coralie , Chaturvedi Vishnu , Limberger Ronald J. , Blog Debra , Lutterloh Emily , Chaturvedi Sudha
Published: December 2019

Candida auris
is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing
C. auris
outbreak in New York (NY) from August 2016 through 2018.
Streptococcus constellatus: a rare causative agent of pyogenic liver abscess
Authors: Dsouza Royson , Roopavathana Beulah , Chase Suchita , Nayak Sukriya
Published: December 2019

A 26-year-old man who was previously well presented to the emergency in septic shock. He had a preceding history of fever, right upper abdominal pain and jaundice. On examination, there was tenderness over the right hypochondrium and epigastrium, without features of generalised peritonitis. His blood tests were suggestive of sepsis with deranged liver function tests. CT scan of the abdomen showed multiples abscesses in various segments of the liver and a thrombus in the inferior venacava, without any other intraabdominal focus of infection. The abscess was aspirated under sonographic guidance, and the cultures grewStreptococcus constellatusspecies ofS. millerigroup (SMG). He received crystalline penicillin, based on culture sensitivity and underwent drainage of the abscess. There was a clinical improvement and he was subsequently discharged in a stable condition. On 3 months follow-up, there was a complete resolution of the liver abscess and normalisation of the liver function tests.
Physical activity, sedentary leisure-time and risk of incident type 2 diabetes: a prospective study of 512 000 Chinese adults
Authors: Bennett Derrick A , Du Huaidong , Bragg Fiona , Guo Yu , Wright Neil , Yang Ling , Bian Zheng , Chen Yiping , YU Canqing , Wang Sisi , Meng Fanwen , Lv Jun , Chen Junshi , Li Liming , Clarke Robert , Chen Zhengming
Published: December 2019

Objective

Aim to examine the independent and joint associations of physical activity (PA) and sedentary leisure-time (SLT) with risk of diabetes and assess the extent to which these associations were mediated by adiposity.

Research design and methods

The prospective China Kadoorie Biobank recruited ~512 000 adults from 10 diverse areas across China. Self-reported PA was estimated based on type, frequency and duration of specific types of PA, covering four domains (occupation, leisure, household and commuting). SLT was defined as hours per day spent watching television, reading or playing card games. Stratified Cox proportional hazards models were used to estimate adjusted HRs (aHRs) for PA and SLT associated with incident diabetes. Analyses were stratified by age-at-risk (5-year intervals), sex and region and adjusted for household income, education, alcohol consumption, smoking, fresh fruit intake, self-reported general health status, family history of diabetes and body mass index (BMI) status. Analyses of total PA, occupational and non-occupational PA and SLT were mutually adjusted for each other, as appropriate.

Results

After ~9 years of follow-up, there were 14 940 incident diabetes cases among 460 736 participants without prior diabetes or cardiovascular diseases at baseline. The mean (SD) age at baseline was 51 (10.6) years, 59% were women and 43% resided in urban areas. Overall, the mean BMI was 23.5 (3.3) kg/m2, which differed by ~0.5 kg/m2among individuals in the highest compared with the lowest PA and SLT groups. PA was inversely associated the risk of diabetes 16% (aHR: 0.84, 95% CI 0.81 to 0.88) lower in top than bottom fifth. After further adjustment for BMI this was attenuated to 0.99 (95% CI 0.98 to 1.00). SLT was positively associated with diabetes and each 1 hour per day higher usual level was associated with aHR of 1.13 (95% CI 1.09 to 1.17) for diabetes, attenuated to 1.05 (95% CI 1.01 to 1.09) after further adjustment for BMI.

Conclusions

Among Chinese adults, higher levels of PA and lower levels of SLT were associated with lower risks of diabetes with no evidence of effect modification by each other. These associations appeared to arise mainly through adiposity.
Enhancing fieldworkers’ performance management support in health research: an exploratory study on the views of field managers and fieldworkers from major research centres in Africa
Authors: Kombe Francis Kazungu , Marsh Vicki , Molyneux Sassy , Kamuya Dorcas Mwikali , Ikamba Dorothy , Kinyanjui Samson Muchina
Published: December 2019

Introduction

Fieldworkers are part of the system that promotes scientific and ethical standards in research, through data collection, consenting and supporting research, due to their insider cultural knowledge and fluency in local languages. The credibility and integrity of health research, therefore, rely on how fieldworkers adhere to institutional and research procedures and guidelines.

Objectives

This study mapped out existing practices in training, support and performance management of fieldworkers in Africa, described fieldworkers’ and their managers’ experiences, and lessons learnt. A consultative process, involving field managers from 15 international health research institutions, was used to identify appropriate ways of addressing the challenges fieldworkers face.

Methods

In phase 1, we conducted 32 telephone interviews with 20 field managers and 12 senior fieldworkers from 18 major research centres in Africa, Medical Research Council-UK and the INDEPTH Network Secretariat. In phase 2, we held a 2.5-day workshop involving 25 delegates, including 18 field managers from the institutions that were involved in phase 1 and 7 additional stakeholders from the KEMRI Wellcome Trust Research Programme (KWTRP). An earlier report from phase 1 was published inBMC MedicalEthicsin 2015. Data transcribed from the interviews and workshop proceedings were analysed thematically using NVivo V.10 software.

Results

Most institutions employed fieldworkers, usually with 12 years of formal education and residing within the geographical areas of research, to support studies. Although their roles were common, there were marked differences in the type of training, professional development schemes and fieldworkers support. Fieldworkers faced various challenges, with the potential to affect their ethical and scientific practices.

Discussion

Fieldworkers undertake vital tasks that promote data quality and ethical practice in research. There is a need for research institutions to develop a structured support system, provide fieldworkers with interpersonal skills training, and provide space for discussion, reflection and experience sharing to help fieldworkers tackle the practical and ethical challenges they face.
Czech Brain Aging Study (CBAS): prospective multicentre cohort study on risk and protective factors for dementia in the Czech Republic
Authors: Sheardova Katerina , Vyhnalek Martin , Nedelska Zuzana , Laczo Jan , Andel Ross , Marciniak Rafal , Cerman Jiri , Lerch Ondrej , Hort Jakub
Published: December 2019

Purpose

Identification of demographic, physical/physiological, lifestyle and genetic factors contributing to the onset of dementia, specifically Alzheimer disease (AD), and implementation of novel methods for early diagnosis are important to alleviate prevalence of dementia globally. The Czech Brain Aging Study (CBAS) is the first large, prospective study to address these issues in Central/Eastern Europe by enrolling non-demented adults aged 55+ years, collecting a variety of personal and biological measures and tracking cognitive function over time.

Participants

The CBAS recruitment was initiated in 2011 from memory clinics at Brno and Prague University Hospitals, and by the end of 2018, the study included 1228 participants. Annual follow-ups include collection of socioeconomic, lifestyle and personal history information, neurology, neuropsychology, laboratory, vital sign and brain MRI data. In a subset, biomarker assessment (cerebrospinal fluid (CSF) and amyloid positron emission tomography) and spatial navigation were performed. Participants were 69.7±8.1 years old and had 14.6±3.3 years of education at baseline, and 59% were women. By the end of 2018, 31% finished three and more years of follow-up; 9% converted to dementia. Apolipoprotein E status is available from 95% of the participants. The biological sample bank linked to CBAS database contained CSF, serum and DNA.

Findings to date

Overall, the findings, mainly from cross-sectional analyses, indicate that spatial navigation is a promising marker of early AD and that it can be distinguished from other cognitive functions. Specificity of several standard memory tests for early AD pathology was assessed with implications for clinical practice. The relationship of various lifestyle factors to cognition and brain atrophy was reported.

Future plans

Recruitment is ongoing with secured funding. Longitudinal data analyses are currently being conducted. Proposals for collaboration on specific data from the database or biospecimen, as well as collaborations with similar cohort studies to increase sample size, are welcome. Study details are available online (www.cbas.cz).
How well do mothers recall their own and their infants’ perinatal events? A two-district study using cross-sectional stratified random sampling in Bihar, India
Authors: Valadez Joseph James , Devkota Baburam , Jeffery Caroline , Hadden Wilbur C
Published: December 2019

Objective

Global monitoring of maternal, newborn and child health (MNCH) programmes use self-reported data subject to recall error which may lead to incorrect decisions for improving health services and wasted resources. To minimise this risk, samples of mothers of infants aged 0–2 and 3–5 months are sometimes used. We test whether a single sample of mothers of infants aged 0–5 months provides the same information.

Design

An annual MNCH household survey in two districts of Bihar, India (n=6 million).

Participants

Independent samples (n=475 each) of mothers of infants aged 0–5, 0–2 and 3–5 months.

Outcome measures

Main analyses compare responses from the samples of infants aged 0–5 and 0–2 months with Mantel-Haenszel-Cochran statistics using 51 indicators in two districts.

Results

No measurable differences are detected in 79.4% (81/102) comparisons; 20.6% (21/102) display differences for the main comparison. Subanalyses produce similar results. A difference detected for exclusive breast feeding is due to premature complementary feeding by older infants. Measurable differences are detected in 33% (8/24) of the indicators on Front Line Worker (FLW) support, 26.9% (7/26) of indicators of birth preparedness and place of birth and attendant, and 9.5% (4/42) of the indicators on neonatal and antenatal care.

Conclusions

Differences in FLW visits and compliance with their advice may be due to seasonal effects: mothers of older infants aged 3–5 months were pregnant during the dry season; mothers of infants aged 0–2 months were pregnant during the monsoons, making transportation difficult. Useful coverage estimates can be obtained by sampling mothers with infants aged 0–5 months as with two samples suggesting that mothers of young infants recall their own perinatal events and those of their children. For some indicators (eg, exclusive breast feeding), it may be necessary to adjust targets. Excessive stratification wastes resources, does not improve the quality of information and increases the burden placed on data collectors and communities which can increase non-sampling error.
Association of brain amyloidosis with the incidence and frequency of neuropsychiatric symptoms in ADNI: a multisite observational cohort study
Authors: Goukasian Naira , Hwang Kristy S. , Romero Tamineh , Grotts Jonathan , Do Triet M. , Groh Jenna R. , Bateman Daniel R. , Apostolova Liana G.
Published: December 2019

Objective

To investigate the relationship between amyloid burden and frequency of existing and incidence of new neuropsychiatric symptoms (NPS) in elderly with and without cognitive decline.

Methods

275 cognitively normal controls (NC), 100 subjective memory complaint (SMC), 559 mild cognitive impairment (MCI) and 143 Alzheimer’s disease dementia subjects from the Alzheimer’s Disease Neuroimaging Initiative received (18F)-florbetapir positron emission tomography (PET) scans. Yearly neuropsychiatric inventory (Neuropsychiatric Inventory (NPI)/NPI-Questionnaire) data were collected from the study partners at each visit. Mean standard uptake volume ratios (SUVR) normalised to whole cerebellum were obtained. Positive amyloid PET scan was defined as mean SUVR ≥1.17. Fisher’s exact test was used to compare frequency and incidence between amyloid positive and amyloid negative subjects. Survival analyses were used to estimate of neuropsychiatric symptoms (NPS) between amyloid positive and amyloid negative subjects. Survival analyses were used to estimate hazard ratios for developing the most common NPS by amyloid status.

Results

No differences in NPS frequency were seen between amyloid positive and amyloid negative NC, SMC, MCI or dementia groups. MCI subjects with amyloid pathology however tended to have greater frequency x severity (FxS) of anxiety, hallucinations, delusions, apathy, disinhibition, irritability, aberrant motor behavior, and appetite, but not agitation, depression, night-time disturbances, or elation. MCI subjects with amyloid pathology were at greater risk for developing apathy, anxiety and agitation over time. Baseline presence of agitation and apathy and new onset agitation, irritability and apathy predicted faster conversion to dementia among MCI subjects.

Conclusions

Amyloid pathology is associated with greater rate of development of new NPS in MCI. Anxiety and delusions are significant predictors of amyloid pathology. Agitation, irritability and apathy are significant predictors for conversion from MCI to dementia.
Time to recurrence after first-ever ischaemic stroke within 3 years and its risk factors in Chinese population: a prospective cohort study
Authors: Zhang Jing , Zhu Ping , Liu Bingqing , Yao Qiang , Yan Ke , Zheng Qianwen , Li Yawen , Zhang Lu , Li Mier , Wang Ju , Zhu Cairong , Zhou Muke
Published: December 2019

Objective

This study aimed to estimate the time of recurrent ischaemic stroke events among the first 3 years of follow-up after hospitalisation discharge.

Study design

A prospective cohort study.

Setting

The research was conducted in the Department of Neurology at a tertiary hospital, Chengdu of China, from January 2010 to June 2016.

Outcome measures

We estimated the restricted mean survival time (RMST) of ischaemic stroke recurrence for the first 3 years after discharge. Basic sociodemographic characteristics and major potential risk factors for recurrence were collected using a semistructured questionnaire. Regression analysis of RMST was used to identify risk factors of recurrent stroke.

Participants

Patients hospitalised with first-ever ischaemic stroke were eligible for this study. Patients with severe cognitive impairment were excluded.

Results

We included 641 surviving patients who were followed up for 3 years. Stroke recurrence occurred in 115 patients, including 16 patients who died of stroke recurrence. The cumulative risk of stroke recurrence rate was 11.51% (9.20%–14.35%) at 1 year, 16.76% (13.96%–20.05%) at 2 years and 20.07% (17.00%–23.61%) at 3 years. Modified Rankin Scale (mRS) score ≥3 thus resulted in the recurrence time loss, which was 0.22 months (p=0.008) at 6 months, 0.61 months (p=0.004) at 1 year, 1.49 months (p=0.007) at 2 years and 2.46 months (p=0.008) at 3 years. It is similar with the effects of drug adherence after stroke. The recurrence time of patients ≥75 years at 3 years was 2.02 months (p=0.220) less than that of those aged <55 years.

Conclusion

In China, the time of first recurrence varies among different patients with ischaemic stroke. The mRS and the level of drug adherence after stroke are important risk factors of stroke recurrence.
Physical activity for people with chronic kidney disease: an international survey of nephrologist practice patterns and research priorities
Authors: Taryana Airis Astiani , Krishnasamy Rathika , Bohm Clara , Palmer Suetonia C , Wiebe Natasha , Boudville Neil , MacRae Jennifer , Coombes Jeff Scott , Hawley Carmel , Isbel Nicole , Thompson Stephanie
Published: December 2019

Objectives

People with chronic kidney diseases (CKD) have identified exercise as a research priority. To inform the research agenda, we surveyed nephrologists on their practice patterns, available resources and research priorities for exercise and physical activity (PA) in CKD.

Design

Cross-sectional international survey.

Setting and participants

19-item electronic survey was administered to practising nephrologists with publicly available email addresses in Canada (n=354) and Australia and New Zealand (ANZ) and via newsletters for the Australian and New Zealand Society of Nephrology (n=598).

Outcomes

Frequency and predictors of exercise and PA counselling in practice and research priorities.

Results

189 respondents (20% response) completed the survey. Eighty-one per cent of ANZ and 42% of Canadian respondents reported that their renal programmes did not have any exercise programmes or resources. The most frequently reported barrier for exercise programme implementation was a lack of funding (77%). Ninety per cent of respondents thought regular exercise provides ‘health benefits’ for all CKD stages; 59% reported that exercise counselling was within the nephrologists’ scope of practice and 47% reported ‘frequently’ or ‘always’ counselling patients. In multivariable analysis, female gender (OR 2.31; 95% CI 1.16 to 4.58) and older age (OR 1.94 per age category increase; 95% CI 1.15 to 3.26) were associated with exercise counselling. Out of 194 research priorities, 65 (34%) were clinical outcomes (cardiovascular parameters) and 30% were patient-reported outcomes (quality of life).

Conclusions

Most nephrologists consider exercise and PA counselling as within their scope of practice and beneficial but, due to competing priorities, do not regularly counsel patients. This suggests a need for the evaluation of effective and efficient counselling strategies and a role for the routine involvement of exercise specialists in kidney care. Cardiovascular parameters and quality of life were identified as important outcomes for future exercise trials.
Developing a web-based patient decision aid for gastrostomy in motor neuron disease: a study protocol
Authors: Maunsell Rose , Bloomfield Suzanne , Erridge Clare , Foster Claire , Hardcastle Maggi , Hogden Anne , Kidd Alison , Lisiecka Dominika , McDermott Christopher J , Morrison Karen , Recio-Saucedo Alejandra , Rickenbach Louise , White Sean , Williams Peter , Wheelwright Sally J
Published: December 2019

Introduction

Motor neuron disease (MND) is a progressive, incurable disease, characterised by degeneration of the nerves in the brain and spinal cord. Due to the multisystem effects of the disease, patients are faced with many complex, time-sensitive decisions, one of which is the decision on gastrostomy feeding. There are currently no published decision aids (DAs) to support patients making this decision in the UK. This study will develop and pilot a patient DA to provide evidence-based information on gastrostomy placement and feeding that is relevant to people with MND; communicate the risks and benefits associated with each option; check understanding and clarify personal values and preferences, enabling patients to make a decision congruent with their values and appropriate for them.

Methods and analysis

A two-phase process, observing the International Patient Decision Aid Standards, will be used to develop the DA, over 24 months starting January 2019. Phase 1 will use literature reviews and stakeholder interviews and surveys to identify essential content for the DA, and explore the best way to present this. In the second phase, a prototype DA will be developed and revised using stakeholder feedback in an iterative process. Stakeholders will include individuals with MND, their carers and the healthcare professionals working with them.

Ethics and dissemination

Ethical approval for the study has been granted by West of Scotland Research Ethics Service, reference 19/WS/0078. Study findings will be disseminated through academic and non-academic publications, conference presentations, stakeholder websites and social media. A feasibility study will follow to explore the acceptability and practicality of the DA for patients, carers and HCPs in practice and to assess whether the DA shows promise of being beneficial for the intended population.