bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of Multidrug-Resistant Isolates of
Mycobacterium tuberculosis
from Patients in North India
Authors: Siddiqi Noman , Shamim Mohammed , Hussain Seema , Choudhary Rakesh Kumar , Ahmed Niyaz , Prachee  , Banerjee Sharmistha , Savithri G. R. , Alam Mahfooz , Pathak Niteen , Amin Amol , Hanief Mohammed , Katoch V. M. , Sharma S. K. , Hasnain Seyed E. 
Published: July 2002

ABSTRACT

The World Health Organization has identified India as a major hot-spot region for
Mycobacterium tuberculosis
infection. We have characterized the sequences of the loci associated with multidrug resistance in 126 clinical isolates of
M. tuberculosis
from India to identify the respective mutations. The loci selected were
rpoB
(rifampin),
katG
and the ribosomal binding site of
inhA
(isoniazid),
gyrA
and
gyrB
(ofloxacin), and
rpsL
and
rrs
(streptomycin). We found known as well as novel mutations at these loci. Few of the mutations at the
rpoB
locus could be correlated with the drug resistance levels exhibited by the
M. tuberculosis
isolates and occurred with frequencies different from those reported earlier. Missense mutations at codons 526 to 531 seemed to be crucial in conferring a high degree of resistance to rifampin. We identified a common Arg463Leu substitution in the
katG
locus and certain novel insertions and deletions. Mutations were also mapped in the ribosomal binding site of the
inhA
gene. A Ser95Thr substitution in the
gyrA
locus was the most common mutation observed in ofloxacin-resistant isolates. A few isolates showed other mutations in this locus. Seven streptomycin-resistant isolates had a silent mutation at the lysine residue at position 121. While certain mutations are widely present, pointing to the magnitude of the polymorphisms at these loci, others are not common, suggesting diversity in the multidrug-resistant
M. tuberculosis
strains prevalent in this region. Our results additionally have implications for the development of methods for multidrug resistance detection and are also relevant in the shaping of future clinical treatment regimens and drug design strategies.
Topoisomerase II and IV QuinoloneResistance-Determining Regions in
Stenotrophomonas maltophilia
Clinical Isolates with Different Levels of QuinoloneSusceptibility
Authors: Valdezate Sylvia , Vindel Ana , Echeita Aurora , Baquero Fernando , Cantó Rafael 
Published: July 2002

ABSTRACT

The quinolone resistance-determining regions
(QRDRs) of topoisomerase II and IV genes from
Stenotrophomonas
maltophilia
ATCC 13637 were sequenced and compared with the
corresponding regions of 32 unrelated
S. maltophilia
clinical
strains for which ciprofloxacin MICs ranged from 0.1 to 64 μg/ml. GyrA
(Leu-55 to Gln-155,
Escherichia coli
numbering), GyrB (Met-391 to
Phe-513), ParC (Ile-34 to Arg-124), and ParE (Leu-396 to Leu-567) fragments
from strain ATCC 13637 showed high degrees of identity to the corresponding
regions from the phytopathogen
Xylella fastidiosa
, with the
degrees of identity ranging from 85.0 to 93.5%. Lower degrees of identity
to the corresponding regions from
Pseudomonas aeruginosa
(70.9 to
88.6%) and
E. coli
(73.0 to 88.6%) were observed. Amino acid
changes were present in GyrA fragments from 9 of the 32 strains at
positions 70, 85, 90, 103, 112, 113, 119, and 124; but there was no
consistent relation to higher ciprofloxacin MICs. The absence of changes at
positions 83 and 87, commonly involved in quinolone resistance in
gram-negative bacteria, was unexpected. The GyrB sequences were identical
in all strains, and only one strain (ciprofloxacin MIC, 16 μg/ml)
showed a ParC amino acid change (Ser-80→Arg). In contrast, a high
frequency (16 of 32 strains) of amino acid replacements was present in
ParE. The frequencies of alterations at positions 437, 465, 477, and 485
were higher (
P
< 0.05) in strains from cystic fibrosis
patients, but these changes were not linked with high ciprofloxacin MICs.
An efflux phenotype, screened by the detection of decreases of at least
twofold doubling dilutions of the ciprofloxacin MIC in the presence of
carbonyl cyanide
m
-chlorophenylhydrazone (0.5 μg/ml) or
reserpine (10 μg/ml), was suspected in seven strains. These results
suggest that topoisomerases II and IV may not be the primary targets
involved in quinolone resistance in
S.
maltophilia.
Pharmacokinetics, Excretion, and Mass Balance of Liposomal Amphotericin B (AmBisome) and Amphotericin B Deoxycholate in Humans
Authors: Bekersky Ihor , Fielding Robert M. , Dressler Dawna E. , Lee Jean W. , Buell Donald N. , Walsh Thomas J. 
Published: July 2002

ABSTRACT

The pharmacokinetics, excretion, and mass balance of liposomal amphotericin B (AmBisome) (liposomal AMB) and the conventional formulation, AMB deoxycholate (AMB-DOC), were compared in a phase IV, open-label, parallel study in healthy volunteers. After a single 2-h infusion of 2 mg of liposomal AMB/kg of body weight or 0.6 mg of AMB-DOC/kg, plasma, urine, and feces were collected for 168 h. The concentrations of AMB were determined by liquid chromatography tandem mass spectrometry (plasma, urine, feces) or high-performance liquid chromatography (HPLC) (plasma). Infusion-related side effects similar to those reported in patients, including nausea and back pain, were observed in both groups. Both formulations had triphasic plasma profiles with long terminal half-lives (liposomal AMB, 152 ± 116 h; AMB-DOC, 127 ± 30 h), but plasma concentrations were higher (
P
< 0.01) after administration of liposomal AMB (maximum concentration of drug in serum [
C
max
], 22.9 ± 10 μg/ml) than those of AMB-DOC (
C
max
, 1.4 ± 0.2 μg/ml). Liposomal AMB had a central compartment volume close to that of plasma (50 ± 19 ml/kg) and a volume of distribution at steady state (
V
ss
) (774 ± 550 ml/kg) smaller than the
V
ss
of AMB-DOC (1,807 ± 239 ml/kg) (
P
< 0.01). Total clearances were similar (approximately 10 ml hr
−1
kg
−1
), but renal and fecal clearances of liposomal AMB were 10-fold lower than those of AMB-DOC (
P
< 0.01). Two-thirds of the AMB-DOC was excreted unchanged in the urine (20.6%) and feces (42.5%) with >90% accounted for in mass balance calculations at 1 week, suggesting that metabolism plays at most a minor role in AMB elimination. In contrast, <10% of the liposomal AMB was excreted unchanged. No metabolites were observed by HPLC or mass spectrometry. In comparison to AMB-DOC, liposomal AMB produced higher plasma exposures and lower volumes of distribution and markedly decreased the excretion of unchanged drug in urine and feces. Thus, liposomal AMB significantly alters the excretion and mass balance of AMB. The ability of liposomes to sequester drugs in circulating liposomes and within deep tissue compartments may account for these differences.
Cloning and Expression of Class A β-Lactamase Gene
blaA
BPS
in
Burkholderia pseudomallei
Authors: Cheung Terence K. M. , Ho P. L. , Woo Patrick C. Y. , Yuen K. Y. , Chau P. Y. 
Published: July 2002

ABSTRACT

The β-lactamase gene
blaA
BPS
in
Burkholderia pseudomallei
was cloned and expressed in
Escherichia coli
. BPS-1 is a cephalosporinase with an isoelectric point of 7.7. Sequence analysis of BPS-1 revealed conserved motifs typical of class A β-lactamases and a relationship to the PenA (in
B. cepacia
) and BlaI (in
Yersinia enterocolitica
) lineages.
Interactions between Biocide Cationic Agents and Bacterial Biofilms
Authors: Campanac C. , Pineau L. , Payard A. , Baziard-Mouysset G. , Roques C. 
Published: July 2002

ABSTRACT

The resistance of bacterial biofilms to physical and chemical agents is attributed in the literature to various interconnected processes. The limitation of mass transfer alters the growth rate, and physiological changes in the bacteria in the film also appear. The present work describes an approach to determination of the mechanisms involved in the resistance of bacteria to quaternary ammonium compounds (benzalkonium chloride) according to the C-chain lengths of those compounds. For
Pseudomonas aeruginosa
CIP A 22, the level of resistance of the bacteria in the biofilm relative to that of planktonic bacteria increased with the C-chain length. For cells within the biofilm, the exopolysaccharide induced a characteristic increase in surface hydrophilicity. However, this hydrophilicity was eliminated by simple resuspension and washing. The sensitivity to quaternary ammonium compounds was restored to over 90%.
Staphylococcus aureus
CIP 53 154 had a very high level of resistance when it was in the biofilm form. A characteristic of bacteria from the biofilm was a reduction in the percent hydrophobicity, but the essential point is that this hydrophobicity was retained after the biofilm bacteria were resuspended and washed. The recovery of sensitivity was thus only partial. These results indicate that the factors involved in biofilm resistance to quaternary ammonium compounds vary according to the bacterial modifications induced by the formation of a biofilm. In the case of
P. aeruginosa
, we have underlined the involvement of the exopolysaccharide and particularly the three-dimensional structure (water channels). In the case of
S. aureus
, the role of the three-dimensional structure is limited and drastic physiological changes in the biofilm cells are more highly implicated in resistance.
Cytological Effects of Cellulases in the Parasitism of
Phytophthora parasitica
by
Pythium oligandrum
Authors: Picard Karine , Tirilly Yves , Benhamou Nicole 
Published: July 2002

ABSTRACT

The ubiquitous oomycete
Pythium oligandrum
is a potential biocontrol agent for use against a wide range of pathogenic fungi and an inducer of plant disease resistance. The ability of
P. oligandrum
to compete with root pathogens for saprophytic colonization of substrates may be critical for pathogen increase in soil, but other mechanisms, including antibiosis and enzyme production, also may play a role in the antagonistic process. We used transmission electron microscopy and gold cytochemistry to analyze the intercellular interaction between
P. oligandrum
and
Phytophthora parasitica
. Growth of
P. oligandrum
towards
Phytophthora
cells correlated with changes in the host, including retraction of the plasma membrane and cytoplasmic disorganization. These changes were associated with the deposition onto the inner host cell surface of a cellulose-enriched material.
P. oligandrum
hyphae could penetrate the thickened host cell wall and the cellulose-enriched material, suggesting that large amounts of cellulolytic enzymes were produced. Labeling of cellulose with gold-complexed exoglucanase showed that the integrity of the cellulose was greatly affected both along the channel of fungal penetration and also at a distance from it. We measured cellulolytic activity of
P. oligandrum
in substrate-free liquid medium. The enzymes present were almost as effective as those from
Trichoderma viride
in degrading both carboxymethyl cellulose and
Phytophthora
wall-bound cellulose.
P. oligandrum
and its cellulolytic enzymes may be useful for biological control of oomycete pathogens, including
Phytophthora
and
Pythium
spp., which are frequently encountered in field and greenhouse production.
Oxygen-Dependent Growth of the Sulfate-Reducing Bacterium
Desulfovibrio oxyclinae
in Coculture with
Marinobacter
sp. Strain MB in an Aerated Sulfate-Depleted Chemostat
Authors: Sigalevich Pavel , Cohen Yehuda 
Published: July 2002

ABSTRACT

A chemostat coculture of the sulfate-reducing bacterium
Desulfovibrio oxyclinae
and the facultatively aerobic heterotroph
Marinobacter
sp. strain MB was grown for 1 week under anaerobic conditions at a dilution rate of 0.05 h
−1
. It was then exposed to an oxygen flux of 223 μmol min
−1
by gassing the growth vessel with 5% O
2
. Sulfate reduction persisted under these conditions, though the amount of sulfate reduced decreased by 45% compared to the amount reduced during the initial anaerobic mode. After 1 week of growth under these conditions, sulfate was excluded from the incoming medium. The sulfate concentration in the growth vessel decreased exponentially from 4.1 mM to 2.5 μM. The coculture consumed oxygen effectively, and no residual oxygen was detected during either growth mode in which oxygen was supplied. The proportion of
D. oxyclinae
cells in the coculture as determined by in situ hybridization decreased from 86% under anaerobic conditions to 70% in the microaerobic sulfate-reducing mode and 34% in the microaerobic sulfate-depleted mode. As determined by the most-probable-number (MPN) method, the numbers of viable
D. oxyclinae
cells during the two microaerobic growth modes decreased compared to the numbers during the anaerobic growth mode. However, there was no significant difference between the MPN values for the two modes when oxygen was supplied. The patterns of consumption of electron donors and acceptors suggested that when oxygen was supplied in the absence of sulfate and thiosulfate,
D. oxyclinae
performed incomplete aerobic oxidation of lactate to acetate. This is the first observation of oxygen-dependent growth of a sulfate-reducing bacterium in the absence of either sulfate or thiosulfate. Cells harvested during the microaerobic sulfate-depleted stage and exposed to sulfate and thiosulfate in a respiration chamber were capable of anaerobic sulfate and thiosulfate reduction.
A Homologue of the Tryptophan-Rich Sensory Protein TspO and FixL Regulate a Novel Nutrient Deprivation-Induced
Sinorhizobium meliloti
Locus
Authors: Davey Mary Ellen , de Bruijn Frans J. 
Published: July 2002

ABSTRACT

A nutrient deprivation-induced locus in
Sinorhizobium meliloti
strain 1021 was identified by use of a Tn
5-luxAB
reporter gene transposon. The tagged locus is comprised of two open reading frames (ORFs) designated
ndiA
and
ndiB
for nutrient deprivation-induced genes A and B. Comparison of the deduced amino acid sequences of both
ndiA
and
ndiB
to the protein databases failed to reveal similarity to any known genes. The expression of the
ndi
locus was found to be induced by carbon and nitrogen deprivation, osmotic stress, and oxygen limitation and during entry into stationary phase. To identify regulatory components involved in the control of
ndi
gene expression, a second round of mutagenesis was performed on the primary
ndiB
::Tn
5-luxAB
-tagged strain (C22) with transposon Tn
1721
. A double-mutant strain was obtained that lacked
ndi
locus transcriptional activity under all of the inducing conditions tested. The Tn
1721
-tagged gene showed a high degree of similarity to tryptophan-rich sensory protein TspO from
Rhodobacter sphaeroides
, as well as to mitochondrial benzodiazepine receptor pK18 from mammals. Induction of the
ndi
::Tn
5-luxAB
reporter gene fusion was restored under all inducing conditions by introducing the
tspO
coding region, from either
S. meliloti
or
R. sphaeroides
, in
trans
. Furthermore, it was found that, in addition to
tspO
,
fixL
, which encodes the sensor protein of an oxygen-sensing two-component system, is required for full expression of the
ndi
locus, but only under low oxygen tension.
Expression of Outer Membrane Proteins in
Escherichia coli
Growing at Acid pH
Authors: Sato Mikiko , Machida Kazuhiro , Arikado Eri , Saito Hiromi , Kakegawa Tomohito , Kobayashi Hiroshi 
Published: July 2002

ABSTRACT

It is generally accepted for
Escherichia coli
that (i) the level of OmpC increases with increased osmolarity when cells are growing in neutral and alkaline media, whereas the level of OmpF decreases at high osmolarity, and that (ii) the two-component system composed of OmpR (regulator) and EnvZ (sensor) regulates porin expression. In this study, we found that OmpC was expressed at low osmolarity in medium of pH below 6 and that the expression was repressed when medium osmolarity was increased. In contrast, the expression of
ompF
at acidic pH was essentially the same as that at alkaline pH. Neither OmpC nor OmpF was detectable in an
ompR
mutant at both acid and alkaline pH values. However, OmpC and OmpF were well expressed at acid pH in a mutant
envZ
strain, and their expression was regulated by medium osmolarity. Thus, it appears that
E. coli
has a different mechanism for porin expression at acid pH. A mutant deficient in
ompR
grew slower than its parent strain in low-osmolarity medium at acid pH (below 5.5). The same growth diminution was observed when
ompC
and
ompF
were deleted, suggesting that both OmpF and OmpC are required for optimal growth under hypoosmosis at acid pH.
Increase in Bacterial Community Diversity in Subsurface Aquifers Receiving Livestock Wastewater Input
Authors: Cho Jang-Cheon , Kim Sang-Jong 
Published: July 2002

ABSTRACT

Despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. In this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16S rDNA sequences. The similarity coefficients of restriction fragment length polymorphism (RFLP) patterns of the cloned 16S ribosomal DNAs showed that the bacterial communities in livestock wastewater samples were more closely related to those in contaminated aquifer samples. In addition, calculations of community diversity clearly showed that bacterial communities in the livestock wastewater and the contaminated aquifer were much more diverse than those in the uncontaminated aquifer. Thus, the increase in bacterial-community diversity in the contaminated aquifer was assumed to be due to the infiltration of livestock wastewater, containing high concentrations of diverse microbial flora, into the aquifer. Phylogenetic analysis of the sequences from a subset of the RFLP patterns showed that the
Cytophaga-Flexibacter-Bacteroides
and low-G+C gram-positive groups originating from livestock wastewater were responsible for the change in the bacterial community in groundwater. This was evidenced by the occurrence of rumen-related sequences not only in the livestock wastewater samples but also in the contaminated-groundwater samples. Rumen-related sequences, therefore, can be used as indicator sequences for fecal contamination of groundwater, particularly from livestock.
Evaluation of F-Specific RNA Bacteriophage as a Candidate Human Enteric Virus Indicator for Bivalve Molluscan Shellfish
Authors: Doré William J. , Henshilwood Kathleen , Lees David N. 
Published: July 2002

ABSTRACT

Escherichia coli
is a widely utilized indicator of the sanitary quality of bivalve molluscan shellfish sold for human consumption. However, it is now well documented that shellfish that meet the
E. coli
standards for human consumption may contain human enteric viruses that cause gastroenteritis and hepatitis. In this study we investigated using F-specific RNA bacteriophage (FRNA bacteriophage) to indicate the likely presence of such viruses in shellfish sold for consumption. FRNA bacteriophage and
E. coli
levels were determined over a 2-year period for oysters (
Crassostrea gigas
) harvested from four commercial sites chosen to represent various degrees of sewage pollution. Three sites were classified as category B sites under the relevant European Community (EC) Directive (91/492), which required purification (depuration) of oysters from these sites before sale. One site was classified as a category A site, and oysters from this site could be sold directly without further processing. Samples were tested at the point of sale following commercial processing and packaging. All of the shellfish complied with the mandatory EC
E. coli
standard (less than 230 per 100 g of shellfish flesh), and the levels of contamination for more than 90% of the shellfish were at or below the level of sensitivity of the assay (20
E. coli
MPN per 100 g), which indicated good quality based on this criterion. In contrast, FRNA bacteriophage were frequently detected at levels that exceeded 1,000 PFU per 100 g. High levels of FRNA bacteriophage contamination were strongly associated with harvest area fecal pollution and with shellfish-associated disease outbreaks. Interestingly, FRNA bacteriophage contamination exhibited a marked seasonal trend that was consistent with the trend of oyster-associated gastroenteritis in the United Kingdom. The correlation between FRNA bacteriophage contamination and health risk was investigated further by using a reverse transcription-PCR assay for Norwalk-like virus (NLV). NLV contamination of oysters was detected only at the most polluted site and also exhibited a seasonal trend that was consistent with the trend of FRNA bacteriophage contamination and with the incidence of disease. The results of this study suggest that FRNA bacteriophage could be used as viral indicators for market-ready oysters.
Characterization and Cloning of the Genes Encoding Enterocin 1071A and Enterocin 1071B, Two Antimicrobial Peptides Produced by
Enterococcus faecalis
BFE 1071
Authors: Balla E. , Dicks L. M. T. , Du Toit M. , Van Der Merwe M. J. , Holzapfel W. H. 
Published: July 2002

ABSTRACT

The pH-neutral cell supernatant of
Enterococcus faecalis
BFE 1071, isolated from the feces of minipigs in Göttingen, inhibited the growth of
Enterococcus
spp. and a few other gram-positive bacteria. Ammonium sulfate precipitation and cation-exchange chromatography of the cell supernatant, followed by mass spectrometry analysis, yielded two bacteriocin-like peptides of similar molecular mass: enterocin 1071A (4.285 kDa) and enterocin 1071B (3.899 kDa). Both peptides are always isolated together. The peptides are heat resistant (100°C, 60 min; 50% of activity remained after 15 min at 121°C), remain active after 30 min of incubation at pH 3 to 12, and are sensitive to treatment with proteolytic enzymes. Curing experiments indicated that the genes encoding enterocins 1071A and 1071B are located on a 50-kbp plasmid (pEF1071). Conjugation of plasmid pEF1071 to
E. faecalis
strains FA2-2 and OGX1 resulted in the expression of two active peptides with sizes identical to those of enterocins 1071A and 1071B. Sequencing of a DNA insert of 9 to 10 kbp revealed two open reading frames,
ent
1071A and
ent
1071B, which coded for 39- and 34-amino-acid peptides, respectively. The deduced amino acid sequence of the mature Ent1071A and Ent1071B peptides showed 64 and 61% homology with the α and β peptides of lactococcin G, respectively. This is the first report of two new antimicrobial peptides representative of a fourth type of
E. faecalis
bacteriocin.