bluuebunny/crossref_metadata_2025 huggingface dataset:
The
Bacillus subtilis
Nucleotidyltransferase Is a tRNA CCA-Adding Enzyme
Authors: Raynal Lelia C. , Krisch Henry M. , Carpousis Agamemnon J.
Published: March 2020

There has been increased interest in bacterial polyadenylation with the recent demonstration that 3′ poly(A) tails are involved in RNA degradation. Poly(A) polymerase I (PAP I) of
Escherichia coli
is a member of the nucleotidyltransferase (Ntr) family that includes the functionally related tRNA CCA-adding enzymes. Thirty members of the Ntr family were detected in a search of the current database of eubacterial genomic sequences. Gram-negative organisms from the β and γ subdivisions of the purple bacteria have two genes encoding putative Ntr proteins, and it was possible to predict their activities as either PAP or CCA adding by sequence comparisons with the
E. coli
homologues. Prediction of the functions of proteins encoded by the genes from more distantly related bacteria was not reliable. The
Bacillus subtilis papS
gene encodes a protein that was predicted to have PAP activity. We have overexpressed and characterized this protein, demonstrating that it is a tRNA nucleotidyltransferase. We suggest that the
papS
gene should be renamed
cca
, following the notation for its
E. coli
counterpart. The available evidence indicates that
cca
is the only gene encoding an Ntr protein, despite previous suggestions that
B. subtilis
has a PAP similar to
E. coli
PAP I. Thus, the activity involved in RNA 3′ polyadenylation in the gram-positive bacteria apparently resides in an enzyme distinct from its counterpart in gram-negative bacteria.
Identification of Conserved, RpoS-Dependent Stationary-Phase Genes of
Escherichia coli
Authors: Schellhorn Herb E. , Audia Jonathon P. , Wei Linda I. C. , Chang Lily
Published: March 2020

During entry into stationary phase, many free-living, gram-negative bacteria express genes that impart cellular resistance to environmental stresses, such as oxidative stress and osmotic stress. Many genes that are required for stationary-phase adaptation are controlled by RpoS, a conserved alternative sigma factor, whose expression is, in turn, controlled by many factors. To better understand the numbers and types of genes dependent upon RpoS, we employed a genetic screen to isolate more than 100 independent RpoS-dependent gene fusions from a bank of several thousand mutants harboring random, independent promoter-
lacZ
operon fusion mutations. Dependence on RpoS varied from 2-fold to over 100-fold. The expression of all fusion mutations was normal in an
rpoS/rpoS
+
merodiploid (
rpoS
background transformed with an
rpoS
-containing plasmid). Surprisingly, the expression of many RpoS-dependent genes was growth phase dependent, albeit at lower levels, even in an
rpoS
background, suggesting that other growth-phase-dependent regulatory mechanisms, in addition to RpoS, may control postexponential gene expression. These results are consistent with the idea that many growth-phase-regulated functions in
Escherichia coli
do not require RpoS for expression. The identities of the 10 most highly RpoS-dependent fusions identified in this study were determined by DNA sequence analysis. Three of the mutations mapped to
otsA
,
katE
,
ecnB
, and
osmY
—genes that have been previously shown by others to be highly RpoS dependent. The six remaining highly-RpoS-dependent fusion mutations were located in other genes, namely,
gabP
,
yhiUV
,
o371
,
o381
,
f186
, and
o215.
Combined Physical and Genetic Map of the
Pseudomonas putida
KT2440 Chromosome
Authors: Ramos-Díaz M. Angeles , Ramos Juan L.
Published: March 2020

A combined physical and genetic map of the
Pseudomonas putida
KT2440 genome was constructed from data obtained by pulsed-field gel electrophoresis techniques (PFGE) and Southern hybridization. Circular genome size was estimated at 6.0 Mb by adding the sizes of 19
Swa
I, 9
Pme
I, 6
Pac
I, and 6 I-
Ceu
I fragments. A complete physical map was achieved by combining the results of (i) analysis of PFGE of the DNA fragments resulting from digestion of the whole genome with
Pme
I,
Swa
I, I-
Ceu
I, and
Pac
I as well as double digestion with combinations of these enzymes and (ii) Southern hybridization analysis of the whole wild-type genome digested with different enzymes and hybridized against a series of probes obtained as cloned genes from different pseudomonads of rRNA group I and
Escherichia coli
, as
P. putida
DNA obtained by PCR amplification based on sequences deposited at the GenBank database, and by labeling of macrorestriction fragments of the
P. putida
genome eluted from agarose gels. As an alternative, 10 random mini-Tn
5
-Km mutants of
P. putida
KT2440 were used as a source of DNA, and the band carrying the mini-Tn
5
in each mutant was identified after PFGE of a series of complete chromosomal digestions and hybridization with the kanamycin resistance gene of the mini-Tn
5
as a probe. We established a circular genome map with an average resolution of 160 kb. Among the 63 genes located on the genetic map were key markers such as
oriC
, 6
rrn
loci (
rnnA
to -
F
),
recA
,
ftsZ
,
rpoS
,
rpoD
,
rpoN
, and
gyrB
; auxotrophic markers; and catabolic genes for the metabolism of aromatic compounds. The genetic map of
P. putida
KT2440 was compared to those of
Pseudomonas aeruginosa
PAO1 and
Pseudomonas fluorescens
SBW25. The chromosomal backbone revealed some similarity in gene clustering among the three pseudomonads but differences in physical organization, probably as a result of intraspecific rearrangements.
A Two-Component Signal Transduction System Essential for Growth of
Bacillus subtilis
: Implications for Anti-Infective Therapy
Authors: Fabret Céline , Hoch James A.
Published: March 2020

A two-component signal transduction system encoded by the
yycF
and
yycG
genes is part of an operon containing three genes,
yycH
,
yycI
, and
yycJ
, with no known function and a gene,
yycK
, coding for an HtrA-like protease. This operon was transcribed during growth, and its transcription shut down as the cells approached stationary phase. This decreased transcription was not Spo0A dependent. The HtrA protease gene was separately controlled during sporulation from a ς
G
promoter. Studies using insertional inactivation plasmids revealed that neither
yycF
nor
yycG
could be inactivated, whereas the other genes were inactivated without loss of viability. A temperature-sensitive YycF response regulator mutant was isolated and shown to have an H215P mutation in a putative DNA-binding domain which is closely related to the OmpR family of response regulators. At the nonpermissive temperature, cultures of the mutant strain stopped growth within 30 min, and this was followed by a decrease in optical density. Microscopically, many of the cells appeared to retain their structure while being empty of their contents. The essential processes regulated by this two-component system remain unknown. A search of the genome databases revealed YycF, YycG, and YycJ homologues encoded by three linked genes in
Streptococcus pyogenes
. The high level of identity of these proteins (71% for YycF) suggests that this system may play a similar role in gram-positive pathogens.
Sequence Analysis of Tn
10
Insertion Sites in a Collection of
Escherichia coli
Strains Used for Genetic Mapping and Strain Construction
Authors: Nichols Brian P. , Shafiq Obaid , Meiners Victoria
Published: March 2020

The chromosomal insertion sites of Tn
10
-containing
Escherichia coli
strains were amplified by inverse PCR, and the nucleotide sequences of the junctions were determined. In 95 strains analyzed, 88 unique Tn
10
positions were determined and matched to the
E. coli
chromosome sequence. Two gaps in insertion site positions were noted, one including the terminus of DNA replication and another bounded by recombination hot spots
RhsA
and
RhsB
.
Identification and Characterization of the
Myxococcus xanthus argE
Gene
Authors: Harris Baruch Z. , Singer Mitchell
Published: March 2020

The chromosomal acetylornithine deacetylase (
argE
) gene of
Myxococcus xanthus
was identified via homology to acetylornithine deacetylases from other bacterial species. A mutant carrying a disruption in
argE
was unable to grow on minimal media lacking supplemental arginine and formed fruiting bodies and spores in response to arginine starvation at high cell density.
mraY
Is an Essential Gene for Cell Growth in
Escherichia coli
Authors: Boyle David S. , Donachie William D.
Published: March 2020

The synthesis of the murein precursor lipid I is performed by MraY. We have shown that
mraY
is an essential gene for cell growth. Cells depleted of MraY first swell and then lyse. The expression of
mraY
DNA in vitro produces a 40-kDa polypeptide detectable by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Comparison of Three Commercial Rapid Identification Systems for the Unusual Gram-Positive Cocci
Dolosigranulum pigrum
,
Ignavigranum ruoffiae
, and
Facklamia
Species
Authors: LaClaire Leslye L. , Facklam Richard R.
Published: March 2020

We evaluated three rapid identification systems—The Biomerieux rapid ID 32 STREP (ID32), the BBL Crystal rapid gram-positive identification (Crystal), and the Remel IDS RapID STR (IDS) systems—for their ability to identify 7 strains of
Alloiococcus otitidis
, 27 strains of
Dolosigranulum pigrum
, 3 strains of
Ignavigranum ruoffiae
, and 18 strains of 4 different
Facklamia
species. Since none of these six species of gram-positive cocci are included in the identification databases for these systems, the correct identification for the strains tested should be “unacceptable ID” for the ID32 and Crystal systems or “no choice” for the IDS system. The ID32 system identified all 27 strains of
D. pigrum
, 6 of 18
Facklamia
species, and 2 of 3 cultures of
I. ruoffiae
as “unacceptable ID.” The Crystal system identified 10 of 27
D. pigrum
, 2 of 18
Facklamia
species, and 2 of 3
I. ruoffiae
strains as “unacceptable ID.” The IDS system identified only 1 culture of
D. pigrum
as “no choice,” but it also identified 2 cultures of
D. pigrum
as a “questionable microcode” and 19 cultures of
D. pigrum
as an “inadequate ID,
E. faecalis
90%,
S. intermedius
9%.” A total of 2 of the 18 cultures of
Facklamia
and all 3 of the
I. ruoffiae
cultures were correctly identified as “no choice.” The most common misidentifications of
Facklamia
species by the ID32 and IDS systems were as various
Streptococcus
species and as
Gemella
species. In the Crystal system, the most common erroneous identification was
Micrococcus luteus
. These data indicate the need for the commercial manufacturers of these products to update their databases to include newly described species of gram-positive cocci.
Evaluation of a New System, VITEK 2, for Identification and Antimicrobial Susceptibility Testing of Enterococci
Authors: Garcia-Garrote Fernando , Cercenado Emilia , Bouza Emilio
Published: March 2020

We evaluated the new automated VITEK 2 system (bioMérieux) for the identification and antimicrobial susceptibility testing of enterococci. The results obtained with the VITEK 2 system were compared to those obtained by reference methods: standard identification by the scheme of Facklam and Sahm [R. R. Facklam and D. F. Sahm, p. 308–314,
in
P. R. Murray et al., ed.,
Manual of Clinical Microbiology
, 6th ed., 1995] and with the API 20 STREP system and, for antimicrobial susceptibility testing, broth microdilution and agar dilution methods by the procedures of the National Committee for Clinical Laboratory Standards. The presence of
vanA
and
vanB
genes was determined by PCR. A total of 150 clinical isolates were studied, corresponding to 60
Enterococcus faecalis
, 55
Enterococcus faecium
, 26
Enterococcus gallinarum
, 5
Enterococcus avium
, 2
Enterococcus durans
, and 2
Enterococcus raffinosus
isolates. Among those isolates, 131 (87%) were correctly identified to the species level with the VITEK 2 system. Approximately half of the misidentifications were for
E. faecium
with low-level resistance to vancomycin, identified as
E. gallinarum
or
E. casseliflavus
; however, a motility test solved the discrepancies and increased the agreement to 94%. Among the strains studied, 66% were vancomycin resistant (57 VanA, 16 VanB, and 26 VanC strains), 23% were ampicillin resistant (MICs, ≥16 μg/ml), 31% were high-level gentamicin resistant, and 45% were high-level streptomycin resistant. Percentages of agreement for susceptibility and resistance to ampicillin, vancomycin, and teicoplanin and for high-level gentamicin resistance and high-level streptomycin resistance were 93, 95, 97, 97, and 96%, respectively. The accuracy of identification and antimicrobial susceptibility testing of enterococci with the VITEK 2 system, together with the significant reduction in handling time, will have a positive impact on the work flow of the clinical microbiology laboratory.
Genetic Diversity of
Borrelia burgdorferi
Sensu Lato in Ticks from Mainland Portugal
Authors: De Michelis Simona , Sewell Henna-Sisko , Collares-Pereira Margarida , Santos-Reis Margarida , Schouls Leo M. , Benes Vladimir , Holmes Edward C. , Kurtenbach Klaus
Published: March 2020

To date
Borrelia lusitaniae
is the only genospecies of
Borrelia burgdorferi
sensu lato isolated from
Ixodes ricinus
ticks collected in Portugal and Tunisia. This suggests that the genospecies diversity of
B. burgdorferi
sensu lato decreases toward the southwestern margin of its Old World subtropical range. In order to further explore the genetic diversity of
B. burgdorferi
sensu lato from this region, 55
I. ricinus
and 27
Hyalomma marginatum
questing adults, collected during the spring of 1998 from a sylvatic habitat south of Lisbon, Portugal, were analyzed. Infection prevalences of 75% in
I. ricinus
ticks and 7% in
H. marginatum
ticks were detected by a nested PCR that targets the
rrf
(5S)-
rrl
(23S) spacer of
B. burgdorferi
sensu lato. Restriction fragment length polymorphism (RFLP) analysis of the
I. ricinus
-derived amplicons showed that the sequences in the majority of samples were similar to those of
B. lusitaniae
type strains (76% for strain PotiB1, 5% for strain PotiB3). Two novel RFLP patterns were obtained from 12% of the samples. The remaining 7% of samples gave mixed RFLP patterns. Phylogenetic analysis of
rrf-rrl
spacer sequences revealed a diverse population of
B. lusitaniae
in questing adult
I. ricinus
ticks (the sequences did not cluster with those of any other genospecies). This population consisted of 10 distinct sequence types, suggesting that multiple strains of
B. lusitaniae
were present in the local
I. ricinus
population. We hypothesize that
B. lusitaniae
has a narrow ecological niche that involves host species restricted to the Mediterranean Basin.
Frequency of Low-Level Bacteremia in Children from Birth to Fifteen Years of Age
Authors: Kellogg James A. , Manzella John P. , Bankert David A.
Published: March 2020

A single blood culture inoculated with a small volume of blood is still frequently being used for the diagnosis of bacteremia in children because of the continued belief by many that bacteria are usually found in high concentrations in the blood of pediatric patients with sepsis. To determine the importance of both blood volume cultured and the number of culture devices required for the reliable detection of pathogens in our pediatric population, blood from children from birth to 15 years of age and with suspected bacteremia at York Hospital (a 500-bed community hospital) was inoculated into at least a Pediatric Isolator (Wampole Laboratories; 1.5 ml of blood) or a standard Isolator (10 ml of blood) and a bottle of ESP anaerobic broth (Trek Diagnostic Systems; 0.5 to 10 ml of blood). The use of a second Isolator and additional aerobic and anaerobic bottles and the total blood volume recommended for cultures (2 to 60 ml) depended on the weight and total blood volume of each patient. One hundred forty-seven pathogens were recovered from the blood of 137 (3.6%) of 3,829 children for whom culturing was done. Of 121 septic episodes for which the concentration of pathogens in the blood could be determined using Isolators, 73 (60.3%) represented low-level bacteremia (≤10 CFU/ml of blood), including 28 pathogens (23.1%) which were detected at concentrations of only ≤1.0 CFU/ml. Of 144 septic episodes for which two or more culture devices (Isolators and/or bottles) were inoculated, 85 (59%) were associated with false-negative results from one or more of the culture devices. Of the 128 children for whom antibiotic therapy records were complete, therapy was either started or changed for 88 (68.8%) following notification of positive blood cultures. Low-level bacteremia was common in our pediatric population, requiring the culturing of up to 4 or 4.5% of a patient's total blood volume for the reliable detection of pathogens and appropriate, timely changes in empiric therapy.
Cloning and Sequencing of a Part of the Heat Shock Protein 65 Gene (
hsp65
) of “
Tropheryma whippelii
” and Its Use for Detection of “
T. whippelii
” in Clinical Specimens by PCR
Authors: Morgenegg Silvia , Dutly Fabrizio , Altwegg Martin
Published: March 2020

Using broad-spectrum primers, we have amplified, cloned, and sequenced a 620-bp fragment of the “
Tropheryma whippelii
” heat shock protein 65 gene (
hsp65
) from the heart valve of a patient with Whipple's endocarditis. The deduced amino acid sequence shows high similarity to those from actinobacteria, confirming that “
T. whippelii
” is indeed a member of this phylum. Based on the nucleotide sequence, we have developed a “
T. whippelii
”-specific seminested PCR. Seventeen patients shown to be positive by 16S ribosomal DNA (rDNA) PCR and/or internal transcribed spacer (ITS) PCR were also positive by
hsp65
PCR. All 33 control specimens from patients without Whipple's disease and negative for “
T. whippelii
” by both seminested 16S rDNA and ITS PCR remained negative. All amplicons digested with
Xho
I revealed an identical restriction pattern. Eight of the 17
hsp65
amplicons representing all three previously described ITS types were sequenced. Three of the amplicons showed slight differences, but none of the mutations detected affected the amino acid sequence of the corresponding protein. We conclude that the
hsp65
gene is a suitable target for the specific detection of “
T. whippelii
.” Its product represents a putative antigen for a future serodiagnostic assay.
Comparative Evaluation of PASCO and National Committee for Clinical Laboratory Standards M27-A Broth Microdilution Methods for Antifungal Drug Susceptibility Testing of Yeasts
Authors: Arthington-Skaggs Beth A. , Motley Milwood , Warnock David W. , Morrison Christine J.
Published: March 2020

The PASCO antifungal susceptibility test system, developed in collaboration with a commercial company, is a broth microdilution assay which is faster and easier to use than the reference broth microdilution test performed according to the National Committee for Clinical Laboratory Standards (NCCLS) document M27-A guidelines. Advantages of the PASCO system include the system's inclusion of quality-controlled, premade antifungal panels containing 10, twofold serial dilutions of drugs and a one-step inoculation system whereby all wells are simultaneously inoculated in a single step. For the prototype panel, we chose eight antifungal agents for in vitro testing (amphotericin B, flucytosine, fluconazole, ketoconazole, itraconazole, clotrimazole, miconazole, and terconazole) and compared the results with those of the NCCLS method for testing 74 yeast isolates (14
Candida albicans
, 10
Candida glabrata
, 10
Candida tropicalis
, 10
Candida krusei
, 10
Candida dubliniensis
, 10
Candida parapsilosis
, and 10
Cryptococcus neoformans
isolates). The overall agreements between the methods were 91% for fluconazole, 89% for amphotericin B and ketoconazole, 85% for itraconazole, 80% for flucytosine, 77% for terconazole, 66% for miconazole, and 53% for clotrimazole. In contrast to the M27-A reference method, the PASCO method classified as resistant seven itraconazole-susceptible isolates (9%), two fluconazole-susceptible isolates (3%), and three flucytosine-susceptible isolates (4%), representing 12 major errors. In addition, it classified two fluconazole-resistant isolates (3%) and one flucytosine-resistant isolate (1%) as susceptible, representing three very major errors. Overall, the agreement between the methods was greater than or equal to 80% for four of the seven species tested (
C. dubliniensis
,
C. glabrata
,
C. krusei
, and
C. neoformans
). The lowest agreement between methods was observed for miconazole and clotrimazole and for
C. krusei
isolates tested against terconazole. When the data for miconazole and clotrimazole were removed from the analysis, agreement was ≥80% for all seven species tested. Therefore, the PASCO method is a suitable alternative procedure for the testing of the antifungal susceptibilities of the medically important
Candida
spp. and
C. neoformans
against a range of antifungal agents with the exceptions only of miconazole and clotrimazole and of terconazole against
C. krusei
isolates.
Recovery of
Bordetella holmesii
from Patients with Pertussis-Like Symptoms: Use of Pulsed-Field Gel Electrophoresis To Characterize Circulating Strains
Authors: Mazengia Eyob , Silva Ellen A. , Peppe Joseph A. , Timperi Ralph , George Harvey
Published: March 2020

A 4-year retrospective study showing that we isolated
Bordetella holmesii
, but not
Bordetella pertussis
, from patients with pertussis-like symptoms was performed. From 1995 through 1998, we isolated
B. holmesii
from 32 nasopharyngeal specimens that had been submitted from patients suspected of having pertussis. Previously,
B. holmesii
had been associated mainly with septicemia and was not thought to be associated with respiratory illness. A study was undertaken to describe the characteristics of the
B. holmesii
isolates recovered and why we were successful in detecting the organism in nasopharyngeal specimens.
B. holmesii
isolates were characterized for drug sensitivities and for genetic relatedness by pulsed-field gel electrophoresis (PFGE). These isolates, an additional strain of
B. holmesii
isolated from a blood culture and previously confirmed by the Centers for Disease Control and Prevention, Atlanta, Ga., and 14 other clinical isolates of
Bordetella
spp., including 4 of
B. bronchiseptica
, 5 of
B. parapertussis
, and 5 of
B. pertussis
, were studied. They were all separately inoculated on three Bordet Gengou (BG) selective media containing either 0.625 μg of oxacillin per ml, 40 μg of cephalexin per ml, or 2.5 μg of methicillin per ml, on BG agar with no antibiotic (control), and on charcoal agar (CA) with and without 40 μg of cephalexin per ml. We found that cephalexin, the antibiotic commonly incorporated in both CA and BG agar for the recovery of
Bordetella
spp., is inhibitory to the growth of
B. holmesii
. In addition, the genotypic analysis of the 32
B. holmesii
isolates by PFGE following restriction with
Xba
I and
Spe
I identified the dominant strains circulating during the study period.
Mass Spectrometric Identification of Mtb81, a Novel Serological Marker for Tuberculosis
Authors: Hendrickson Ronald C. , Douglass John F. , Reynolds Lisa D. , McNeill Patricia D. , Carter Darrick , Reed Steven G. , Houghton Raymond L.
Published: March 2020

We have used serological proteome analysis in conjunction with tandem mass spectrometry to identify and sequence a novel protein, Mtb81, which may be useful for the diagnosis of tuberculosis (TB), especially for patients coinfected with human immunodeficiency virus (HIV). Recombinant Mtb81 was tested by an enzyme-linked immunosorbent assay to detect antibodies in 25 of 27 TB patients (92%) seropositive for HIV as well as in 38 of 67 individuals (57%) who were TB positive alone. No reactivity was observed in 11 of 11 individuals (100%) who were HIV seropositive alone. In addition, neither sera from purified protein derivative (PPD)-negative (0 of 29) nor sera from healthy (0 of 45) blood donors tested positive with Mtb81. Only 2 of 57 of PPD-positive individuals tested positive with Mtb81. Sera from individuals with smear-positive TB and seropositive for HIV but who had tested negative for TB in the 38-kDa antigen immunodiagnostic assay were also tested for reactivity against Mtb81, as were sera from individuals with lung cancer and pneumonia. Mtb81 reacted with 26 of 37 HIV
+
TB
+
sera (70%) in this group, compared to 2 of 37 (5%) that reacted with the 38-kDa antigen. Together, these results demonstrate that Mtb81 may be a promising complementary antigen for the serodiagnosis of TB.
Epidemiologic Subtyping of
Escherichia coli
Serogroup O157 Strains Isolated in Ontario by Phage Typing and Pulsed-Field Gel Electrophoresis
Authors: Preston Martin A. , Johnson Wendy , Khakhria Rasik , Borczyk Alexander
Published: March 2020

Phage typing and DNA macrorestriction fragment analysis by pulsed-field gel electrophoresis (PFGE) were evaluated for use in the epidemiological subtyping of
Escherichia coli
serogroup O157 strains isolated in Ontario, Canada. Among 30 strains isolated from patients with sporadic cases of infection, 22 distinct
Xba
I macrorestriction patterns were identified and 17 strains exhibited unique PFGE patterns. In contrast, phage typing identified only seven different phage types and 17 strains belonged to the same phage type. A total of 25 phage type-macrorestriction pattern combinations were identified among the strains from patients with sporadic cases of infection. PFGE subtyping differentiated between unrelated strains that exhibited the same phage type, and in one group of strains, phage typing differentiated between strains of the same PFGE subtype. Both typing procedures correctly identified outbreak-related isolates as belonging to the same type in four separate outbreaks. Each outbreak strain was characterized by a distinct macrorestriction pattern, while phage typing subdivided the outbreak strains into only three different types. A small percentage of outbreak-related isolates had PFGE patterns that differed slightly (one or two DNA fragment differences) from that of the outbreak strain. On the other hand, each isolate from the same outbreak belonged to the same phage type as that of the outbreak strain. We conclude that phage typing and PFGE fingerprinting represent complementary procedures for the subtyping of
E. coli
serogroup O157 and that the combined use of these procedures provides optimal discrimination.
Correlation between In Vitro and In Vivo Antifungal Activities in Experimental Fluconazole-Resistant Oropharyngeal and Esophageal Candidiasis
Authors: Walsh Thomas J. , Gonzalez Corina E. , Piscitelli Steven , Bacher John D. , Peter Joanne , Torres Richard , Shetti Daiva , Katsov Victoria , Kligys Kristina , Lyman Caron A.
Published: March 2020

Oropharyngeal and esophageal candidiasis (OPEC) is a frequent opportunistic mycosis in immunocompromised patients. Azole-resistant OPEC is a refractory form of this infection occurring particularly in human immunodeficiency virus (HIV)-infected patients. The procedures developed by the Antifungal Subcommittee of the National Committee for Clinical Laboratory Standards (NCCLS) are an important advance in standardization of in vitro antifungal susceptibility methodology. In order to further understand the relationship between NCCLS methodology and antifungal therapeutic response, we studied the potential correlation between in vitro susceptibility to fluconazole and in vivo response in a rabbit model of fluconazole-resistant OPEC. MICs of fluconazole were determined by NCCLS methods. Three fluconazole-susceptible (FS) (MIC, ≤0.125 μg/ml) and three fluconazole-resistant (FR) (MIC, ≥64 μg/ml) isolates of
Candida albicans
from prospectively monitored HIV-infected children with OPEC were studied. FR isolates were recovered from children with severe OPEC refractory to fluconazole, and FS isolates were recovered from those with mucosal candidiasis responsive to fluconazole. Fluconazole at 2 mg/kg of body weight/day was administered to infected animals for 7 days. The concentrations of fluconazole in plasma were maintained above the MICs for FS isolates throughout the dosing interval. Fluconazole concentrations in the esophagus were greater than or equal to those in plasma. Rabbits infected with FS isolates and treated with fluconazole had significant reductions in oral mucosal quantitative cultures (
P
< 0.001) and tissue burden of
C. albicans
in tongue, soft palate, and esophagus (
P
< 0.001). In comparison, rabbits infected with FR isolates were unresponsive to fluconazole and had no reduction in oral mucosal quantitative cultures or tissue burden of
C. albicans
versus untreated controls. We conclude that there is a strong correlation between in vitro fluconazole susceptibility by NCCLS methods and in vivo response to fluconazole therapy of OPEC due to
C. albicans
.
Phaeoisaria clematidis
as a Cause of Keratomycosis
Authors: Guarro Josep , Vieira Luiz A. , De Freitas Denise , Gené Josepa , Zaror Luis , Hofling-Lima Ana Luisa , Fischman Olga , Zorat-Yu Cecilia , Figueras M. José
Published: March 2020

We report the first case of human infection by
Phaeoisaria clematidis
. This fungus caused a corneal ulcer in a Brazilian man who had previously suffered an eye injury. Diagnosis was established by positive direct examination and repeated cultures. The isolate was clearly resistant in vitro to the six antifungal agents tested.
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome
Authors: Taylor Bryn C. , Lejzerowicz Franck , Poirel Marion , Shaffer Justin P. , Jiang Lingjing , Aksenov Alexander , Litwin Nicole , Humphrey Gregory , Martino Cameron , Miller-Montgomery Sandrine , Dorrestein Pieter C. , Veiga Patrick , Song Se Jin , McDonald Daniel , Derrien Muriel , Knight Rob
Published: March 2020

Public interest in the effects of fermented food on the human gut microbiome is high, but limited studies have explored the association between fermented food consumption and the gut microbiome in large cohorts. Here, we used a combination of omics-based analyses to study the relationship between the microbiome and fermented food consumption in thousands of people using both cross-sectional and longitudinal data. We found that fermented food consumers have subtle differences in their gut microbiota structure, which is enriched in conjugated linoleic acid, thought to be beneficial. The results suggest that further studies of specific kinds of fermented food and their impacts on the microbiome and health will be useful.
Detrital zircon records of late Paleoproterozoic to early Neoproterozoic northern North China Craton drainage reorganization: Implications for supercontinent cycles
Authors: Liu Chaohui , Zhao Guochun , Liu Fulai , Shi Jianrong , Ji Lei
Published: March 2020

Statherian through Tonian strata of the Langshan–Zha’ertai–Bayan Obo–Huade rift zone (LZBH) at the northern margin of the North China Craton provide an excellent record of changes in sediment provenance related to the supercontinent dispersal and amalgamation. During the late Paleoproterozoic to early Neoproterozoic, the LZBH developed over the Yinshan Block and was flanked by the Khondalite Belt to the south, the Trans–North China Orogen and Yanliao rift zone to the east, ultimately preserving a >7000-m-sequence of fluvial, marginal marine, and offshore marine sediments. In order to decipher the influence of these tectonic features on sediment delivery to the area, we evaluated 4955 U-Pb and 1616 Lu-Hf analyses from 66 samples across the entire LZBH, of which 1002 U-Pb and 271 Lu-Hf analyses from 12 samples are newly reported herein. The detrital zircon results indicate three stratigraphic intervals with internally consistent age peaks: (1) Changcheng to lower Jixian system (Statherian–lower Calymmian), (2) upper Jixian system (upper Calymmian), and (3) Qingbaikou system (Tonian). Statistical analysis of the detrital zircon results reveals two distinct changes in sediment provenance. The first transition, between the lower and upper Calymmian, reflects a provenance change from the basement of the Yinshan Block and the Khondalite Belt to a mixed signature, indicating derivation from both basement and Statherian rift-related magmatic products. Such a transition implies establishment of east–west drainage systems traversing the Paleoproterozoic Trans–North China Orogen caused by continued rifting since Statherian and pre-magmatic uplift during breakup of the North China Craton from the Columbia supercontinent. The second transition is indicated by the presence of Mesoproterozoic detrital zircons with juvenile Hf isotopic features since Tonian time and the up-section and northward increase of Mesoproterozoic detrital zircons. Their provenance is interpreted to be the Fennoscandian shield by a pancontinental drainage system related to aggregation of the Rodinia supercontinent. Thus, the detrital zircon spectra in the LZBH document the transition from initial unroofing of local uplifted basement of the Yinshan Block and Khondalite Belt to the distant Yanliao rift zone, then to the more distant Fennoscandian shield.
Indwelling pleural catheter for outpatient management of tuberculous empyema
Authors: Iqbal Muhammad Ambreen , Gavin Joseph , Wilkinson Alex
Published: March 2020

The use of indwelling pleural catheters (IPC) is well established in the treatment of malignant pleural effusions. They allow symptom management with intermittent drainage without requiring overnight admission to hospital. However, little is known about their effectiveness in the treatment of pleural infections. Here, we present a case where an IPC is used in the therapeutic management of tuberculous empyema. The IPC enabled outpatient treatment, allowed the patient to return to work and reduced the cost of treatment and the risk of hospital-acquired complications.
Serum cell-free DNA and progression of diabetic kidney disease: a prospective study
Authors: Li Xuan , Hu RenZhi , Luo Ting , Peng Chuan , Gong Lilin , Hu Jinbo , Yang Shumin , Li Qifu
Published: March 2020

Aims

Cell-free DNA (cfDNA) is associated with diabetes and cardiovascular diseases. Our study was to evaluate whether serum cfDNA could predict the progression of diabetic kidney disease (DKD).

Methods

In this prospective study, a total of 160 patients with DKD were enrolled, and the kidney function was followed up by measurement of estimated glomerular filtration rate (eGFR) and urinary albumin–creatinine ratio (UACR) for three consecutive years. At baseline, concentrations of serum cfDNA were measured. DKD progression was defined as two-continuous decrease in eGFR and changes of UACR from less than 300 mg/g at baseline to higher than 300 mg/g at last follow-up. Regression models were used to analyze associations of serum cfDNA with the DKD progression.

Results

In total, 131 patients finished all the follow-up visits. At the end of the study, 64 patients showed decreased eGFR and 29 patients had changes of UACR from less than 300 mg/g at baseline to higher than 300 mg/g at follow-up. At baseline, the progression group had higher serum cfDNA levels than the non-progression group (960.49 (816.53, 1073.65) ng/mL vs 824.51 (701.34, 987.06) ng/mL, p=0.014). Serum cfDNA levels were significantly negatively associated with the 1.5-year eGFR change (r=−0.219 p=0.009) and 3-year eGFR change (r=−0.181, p=0.043). Multivariate logistic analyses showed that after adjustment of age, gender, body mass index, fast plasma glucose, smoking, triglycerides, total cholesterol, duration of diabetes, systolic blood pressure, diabetic retinopathy, eGFR, high sensitivity C-reactive protein, angiotensin receptor blocker/ACE inhibitor usage, with the increase of one SD of serum cfDNA levels, the risk of DKD progression increased by 2.4 times (OR, 2.46; 95% CI 1.84 to 4.89).

Conclusion

Serum cfDNA is closely associated with DKD, and it might be a predictor of DKD progression in patients with type 2 diabetes.
Is the continued existence of diseases of poverty an indictment of our current humanitarian ethos?
Authors: Aldridge Rachel
Published: March 2020

The continued existence of diseases of poverty is one of the great medical moral dilemmas of the 21st century. That this group of largely either preventable or treatable diseases still plagues a great many of the world’s poorest citizens is a challenging problem to address. This paper examines diseases of poverty not by looking at the pathogenic diseases themselves but by looking at the ‘diseases’ of society that lead to the prevalence of such morbidity. ‘Diseases’ such as lack of infrastructure, lack of nutrition, lack of education, lack of funding and lack of socioeconomic stability. By addressing each of these, in turn, this paper looks to stimulate thought on how society can approach and prevent diseases of poverty in the future.
Complex programme evaluation of a ‘new care model’ vanguard: a shared commitment to quality improvement in an integrated health and care context
Authors: Fowler Davis Sally , Hinde Sebastian , Ariss Steven
Published: March 2020

NHS vanguards, under-pressure to perform, required better contracting and data management arrangements with evaluation teams, to ensure that integrated service outcomes could be reported effectively. This communication reflects the experience of evaluating an NHS vanguard and suggests how academic teams can improve capacity for complex programme evaluation of rapid improvements in integrated services. This should be based on a shared commitment to data collection and management. Also, robust knowledge exchange processes can enable systems change and sustainability. The identifying features of the particular site have been withheld.
Supporting antidepressant discontinuation: the development and optimisation of a digital intervention for patients in UK primary care using a theory, evidence and person-based approach
Authors: Bowers Hannah M , Kendrick Tony , Glowacka Marta , Williams Samantha , Leydon Geraldine , May Carl , Dowrick Chris , Moncrieff Joanna , Laine Rebecca , Nestoriuc Yvonne , Andersson Gerhard , Geraghty Adam W A
Published: March 2020

Objectives

We aimed to develop a digital intervention to support antidepressant discontinuation in UK primary care that is scalable, accessible, safe and feasible. In this paper, we describe the development using a theory, evidence and person-based approach.

Design

Intervention development using a theory, evidence and person-based approach.

Setting

Primary Care in the South of England.

Participants

Fifteen participants with a range of antidepressant experience took part in ‘think aloud’ interviews for intervention optimisation.

Intervention

Our digital intervention prototype (called ‘ADvisor’) was developed on the basis of a planning phase consisting of qualitative and quantitative reviews, an in-depth qualitative study, the development of guiding principles and a theory-based behavioural analysis. Our optimisation phase consisted of ‘think aloud’ interviews where the intervention was iteratively refined.

Results

The qualitative systematic review and in-depth qualitative study highlighted the centrality of fear of depression relapse as a key barrier to discontinuation. The quantitative systematic review showed that psychologically informed approaches such as cognitive–behavioural therapy were associated with greater rates of discontinuation than simple advice to reduce. Following a behavioural diagnosis based on the behaviour change wheel, social cognitive theory provided a theoretical basis for the intervention. The intervention was optimised on the basis of think aloud interviews, where participants suggested they like the flexibility of the system and found it reassuring. Changes were made to the tone of the material and the structure was adjusted based on this qualitative feedback.

Conclusions

‘ADvisor’ is a theory, evidence and person-based digital intervention designed to support antidepressant discontinuation. The intervention was perceived as helpful and reassuring in optimisation interviews. Trials are now needed to determine the feasibility, clinical and cost-effectiveness of this approach.
Analysis of team-sport wheelchair falls during the Rio 2016 Summer Paralympic Games: a video-based cross-sectional observational study
Authors: Sasadai Junpei , Maeda Noriaki , Shimizu Reia , Kobayashi Takumi , Sakai Shogo , Komiya Makoto , Urabe Yukio
Published: March 2020

Objectives

To present the fall characteristics of athletes playing wheelchair rugby (WR) and wheelchair basketball (WB) using official videos from the Rio 2016 Paralympic Games and compare the key fall characteristics among the team wheelchair sports event.

Methods

Eighteen WR and 10 WB game videos for men (MWB) and women (WWB), including 8 teams per sport, were obtained from the official International Paralympic Committee of the Rio 2016 Paralympic Games. The videos were analysed to assess the number of falls, playing time of fall, playing phase, contact with other athletes, the direction of the fall and the body part first in contact with the floor during the fall.

Results

In total, 359 falls (96 for WR, 172 for MWB and 91 for WWB) occurred with a mean of 5.3, 17.2 and 9.1 falls per match, respectively (p<0.05). Significant differences among the three sports were detected in the playing time (p=0.011), presence of contact (p=0.037), direction (p<0.001) and body part first in contact with the floor (p<0.001). For WR, the falls were primarily lateral and caused by contact, occurring in the second half of the match. WB falls tended to be in the first half for women and the second half for men. Most falls were contact falls in the forward direction.

Conclusion

By observing the situational details, we described that a number of falls due to contact occurred during these team sports events, especially MWB. In addition, each sport exhibited characteristics attributable to differences in gender, degree of impairment and game rules. The directions of the falls and characteristics of the affected body parts indicate differences in impairments depending on the sport. A fall to the side or back may indicate a risk of injury.
Length of stay in long-term care facilities: a comparison of residents in six European countries. Results of the PACE cross-sectional study
Authors: Collingridge Moore Danni , Payne Sheila , Keegan Thomas , Van den Block Lieve , Deliens Luc , Gambassi Giovanni , Heikkila Rauha , Kijowska Viola , Pasman H Roeline , Pivodic Lara , Froggatt Katherine
Published: March 2020

Objectives

This paper aims to investigate resident, facility and country characteristics associated with length of stay in long-term care facilities (LTCFs) across six European countries.

Setting

Data from a cross-sectional study of deceased residents, conducted in LTCFs in Belgium, England, Finland, Italy, the Netherlands and Poland.

Participants

All residents aged 65 years and older at admission who died in a 3-month period residing in a proportional random sample of LTCFs were included.

Primary and secondary outcome measures

The primary outcome was length of stay in days, calculated from date of admission and date of death. Resident, facility and country characteristics were included in a proportional hazards model.

Results

The proportion of deaths within 1 year of admission was 42% (range 32%–63%). Older age at admission (HR 1.04, 95% CI 1.03 to 1.06), being married/in a civil partnership at time of death (HR 1.47, 95% CI 1.13 to 1.89), having cancer at time of death (HR 1.60, 95% CI 1.22 to 2.10) and admission from a hospital (HR 1.84, 95% CI 1.43 to 2.37) or another LTCF (HR 1.81, 95% CI 1.37 to 2.40) were associated with shorter lengths of stay across all countries. Being female (HR 0.72, 95% CI 0.57 to 0.90) was associated with longer lengths of stay.

Conclusions

Length of stay varied significantly between countries. Factors prior to LTCF admission, in particular the availability of resources that allow an older adult to remain living in the community, appear to influence length of stay. Further research is needed to explore the availability of long-term care in the community prior to admission and its influence on the trajectories of LTCF residents in Europe.
Quality of life in long-term survivors of advanced melanoma treated with checkpoint inhibitors
Authors: Mamoor Maha , Postow Michael A , Lavery Jessica A , Baxi Shrujal S , Khan Niloufer , Mao Jun J , Rogak Lauren J , Sidlow Robert , Thom Bridgette , Wolchok Jedd A , Korenstein Deborah
Published: March 2020

Background

Immune checkpoint inhibitors (CIs) have revolutionized treatment of advanced melanoma, leading to an emerging population of long-term survivors. Survivors’ quality of life (QOL) and symptom burden are poorly understood. We set out to evaluate symptom burden and QOL in patients with advanced melanoma alive more than 1 year after initiating CI therapy.

Methods

Cross-sectional surveys, accompanied by chart review of patients with advanced melanoma treated with CIs at Memorial Sloan Kettering Cancer Center, completed therapy, and were alive >1 year after treatment initiation. Surveys were administered between February and August 2018. Surveys included: European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30, EuroQOL, items from Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events and Fatigue Severity Scale.

Results

We included 90 patients. The most common CI regimens were ipilimumab plus nivolumab (53%) and pembrolizumab (41%); most patients (71%) were not treated in clinical trials. Median time from CI therapy initiation was 40 months and from last dose was 28 months. Fatigue was reported by 28%, with higher fatigue scores in women than men; 12% reported difficulty sleeping. Aching joints (17%) and muscles (12%) were fairly common. Level of functioning was generally high. Overall QOL was excellent though 40% reported ‘some or moderate’ problems with anxiety/depression and 31% with pain/discomfort.

Conclusions

After CI therapy, long-surviving advanced melanoma patients commonly report fatigue but otherwise have moderate symptom burden and good QOL. Ensuring appropriate symptom management will optimize clinical outcomes for these patients.
Understanding medical civil-military relationships within the humanitarian-development-peace ‘triple nexus’: a typology to enable effective discourse
Authors: Horne Simon , Boland S
Published: March 2020

The interface between humanitarianism, development and peacebuilding is increasingly congested. Western foreign policies have shifted towards pro-active stabilisation agendae and so Civil-Military Relationships (CMRel) will inevitably be more frequent. Debate is hampered by lack of a common language or clear, mutually understood operational contexts to define such relationships. Often it may be easier to simply assume that military co-operation attempts are solely to ‘win hearts and minds’, rather than attempt to navigate the morass of different acronyms. In healthcare, such relationships are common and more complex - partly as health is seen as both an easy entry point for diplomacy and so is a priority for militaries, and because health is so critical to apolitical humanitarian responses. This paper identifies the characteristics of commonly described kinds of CMRel, and then derives a typology that describe them in functional groups as they apply to healthcare-related contexts (although it is likely to be far more widely applicable). Three broad classifications are described, and then mapped against 6 axes; the underlying military and civilian motivations, the level of the engagement (strategic to tactical), the relative stability of the geographical area, and finally the alignment between the civilian and military interests. A visual representation shows where different types may co-exist, and where they are likely to be more problematic. The model predicts two key areas where friction is likely; tactical interactions in highly unstable areas and in lower threat areas where independent military activity may undermine ongoing civilian programmes. The former is well described, supporting the typology. The latter is not and represents an ideal area for future study. In short, we describe an in-depth typology mapping the Civil-Military space in humanitarian and development contexts with a focus on healthcare, defining operational spaces and the identifying of areas of synergy and friction.