bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multilocus Sequence Typing System for the EndosymbiontWolbachia pipientis
Authors: Baldo Laura , Dunning Hotopp Julie C. , Jolley Keith A. , Bordenstein Seth R. , Biber Sarah A. , Choudhury Rhitoban Ray , Hayashi Cheryl , Maiden Martin C. J. , Tettelin Hervè , Werren John H. 
Published: November 2006

ABSTRACTThe eubacterial genusWolbachiacomprises one of the most abundant groups of obligate intracellular bacteria, and it has a host range that spans the phyla Arthropoda and Nematoda. Here we developed a multilocus sequence typing (MLST) scheme as a universal genotyping tool forWolbachia.Internal fragments of five ubiquitous genes (gatB,coxA,hcpA,fbpA, andftsZ) were chosen, and primers that amplified across the majorWolbachiasupergroups found in arthropods, as well as other divergent lineages, were designed. A supplemental typing system using the hypervariable regions of theWolbachiasurface protein (WSP) was also developed. Thirty-seven strains belonging to supergroups A, B, D, and F obtained from singly infected hosts were characterized by using MLST and WSP. The number of alleles per MLST locus ranged from 25 to 31, and the average levels of genetic diversity among alleles were 6.5% to 9.2%. A total of 35 unique allelic profiles were found. The results confirmed that there is a high level of recombination in chromosomal genes. MLST was shown to be effective for detecting diversity among strains within a single host species, as well as for identifying closely related strains found in different arthropod hosts. Identical or similar allelic profiles were obtained for strains harbored by different insect species and causing distinct reproductive phenotypes. Strains with similar WSP sequences can have very different MLST allelic profiles and vice versa, indicating the importance of the MLST approach for strain identification. The MLST system provides a universal and unambiguous tool for strain typing, population genetics, and molecular evolutionary studies. The central database for storing and organizingWolbachiabacterial and host information can be accessed athttp://pubmlst.org/wolbachia/.
Genetic Analysis of Bacteriocin 43 of Vancomycin-Resistant
Enterococcus faecium
Authors: Todokoro Daisuke , Tomita Haruyoshi , Inoue Takako , Ike Yasuyoshi 
Published: November 2006

ABSTRACT

A total of 636 vancomycin-resistant
Enterococcus faecium
(VRE) isolates obtained between 1994 and 1999 from the Medical School Hospital of the University of Michigan were tested for bacteriocin production. Of the 277 (44%) bacteriocinogenic strains, 21 were active against
E. faecalis
,
E. faecium
,
E. hirae
,
E. durans
, and
Listeria monocytogenes
. Of those 21 strains, a representative bacteriocin of strain VRE82, designated bacteriocin 43, was found to be encoded on mobilizable plasmid pDT1 (6.2 kbp). Nine open reading frames (ORFs), ORF1 to ORF9, were presented on pDT1 and were oriented in the same direction. The bacteriocin 43 locus (bac43) consists of the bacteriocin gene
bacA
(ORF1) and the immunity gene
bacB
(ORF2). The deduced
bacA
product is 74 amino acids in length with a putative signal peptide of 30 amino acids at the N terminus. The
bacB
gene encodes a deduced 95-amino-acid protein without a signal sequence. The predicted mature BacA protein (44 amino acids) showed sequence homology with the membrane-active class IIa bacteriocins of lactic acid bacteria and showed 86% homology with bacteriocin 31 from
E. faecalis
YI717 and 98% homology with bacteriocin RC714. Southern analysis with a bac43 probe of each plasmid DNA from the 21 strains showed hybridization to a specific fragment corresponding to the 6.2-kbp EcoRI fragment, suggesting that the strains harbored the pDT1-like plasmid (6.2 kb) which encoded the bacteriocin 43-type bacteriocin. The bac43 determinant was not identified among non-VRE clinical isolates.
Diversity and Distribution of
Escherichia coli
Genotypes and Antibiotic Resistance Phenotypes in Feces of Humans, Cattle, and Horses
Authors: Anderson Matthew A. , Whitlock John E. , Harwood Valerie J. 
Published: November 2006

ABSTRACT

Escherichia coli
is the most completely characterized prokaryotic model organism and one of the dominant indicator organisms for food and water quality testing, yet comparatively little is known about the structure of
E. coli
populations in their various hosts. The diversities of
E. coli
populations isolated from the feces of three host species (human, cow, and horse) were compared by two subtyping methods: ribotyping (using HindIII) and antibiotic resistance analysis (ARA). The sampling effort required to obtain a representative sample differed by host species, as
E. coli
diversity was consistently greatest in horses, followed by cattle, and was lowest in humans. The diversity of antibiotic resistance patterns isolated from individuals was consistently greater than the diversity of ribotypes.
E. coli
populations in individuals sampled monthly, over a 7- to 8-month period, were highly variable in terms of both ribotypes and ARA phenotypes. In contrast,
E. coli
populations in cattle and humans were stable over an 8-h period. Following the cessation of antibiotic therapy, the
E. coli
population in the feces of one human experienced a rapid and substantial shift, from a multiply antibiotic-resistant phenotype associated with a particular ribotype to a relatively antibiotic-susceptible phenotype associated with a different ribotype. The high genetic diversity of
E. coli
populations, differences in diversity among hosts, and temporal variability all indicate complex population dynamics that influence the usefulness of
E. coli
as a water quality indicator and its use in microbial source tracking studies.
Validation of a Green Fluorescent Protein-Labeled Strain of
Vibrio vulnificus
for Use in the Evaluation of Postharvest Strategies for Handling of Raw Oysters
Authors: Drake S. L. , Elhanafi D. , Bang W. , Drake M. A. , Green D. P. , Jaykus L. A. 
Published: November 2006

ABSTRACT

In this paper we describe a biological indicator which can be used to study the behavior of
Vibrio vulnificus
, an important molluscan shellfish-associated human pathogen. A
V. vulnificus
ATCC 27562 derivative that expresses green fluorescent protein (GFP) and kanamycin resistance was constructed using conjugation. Strain validation was performed by comparing the GFP-expressing strain (
Vv-
GFP) and the wild-type strain (
Vv
-WT) with respect to growth characteristics, heat tolerance (45°C), freeze-thaw tolerance (−20
o
and −80°C), acid tolerance (pH 5.0, 4.0, and 3.5), cold storage tolerance (5°C), cold adaptation (15°C), and response to starvation. Levels of recovery were evaluated using nonselective medium (tryptic soy agar containing 2% NaCl) with and without sodium pyruvate. The indicator strain was subsequently used to evaluate the survival of
V. vulnificus
in oysters exposed to organic acids (citric and acetic acids) and various cooling regimens. In most cases,
Vv
-GFP was comparable to
Vv
-WT with respect to growth and survival upon exposure to various biological stressors; when differences between the GFP-expressing and parent strains occurred, they usually disappeared when sodium pyruvate was added to media. When
V. vulnificus
was inoculated into shellstock oysters, the counts dropped 2 log
10
after 11 to 12 days of refrigerated storage, regardless of the way in which the oysters were initially cooled. Steeper population declines after 12 days of refrigerated storage were observed for both iced and refrigerated products than for slowly cooled product and product held under conservative harvest conditions. By the end of the refrigeration storage study (22 days), the counts of
Vv
-GFP in iced and refrigerated oysters had reached the limit of detection (10
2
CFU/oyster), but slowly cooled oysters and oysters stored under conservative harvest conditions still contained approximately 10
3
and >10
4
CFU
V. vulnificus
/oyster by day 22, respectively. The
Vv
-GFP levels in the oyster meat remained stable for up to 24 h when the meat was exposed to acidic conditions at various pH values. Ease of detection and comparability to the wild-type parent make
Vv
-GFP a good candidate for use in studying the behavior of
V. vulnificus
upon exposure to sublethal stressors that might be encountered during postharvest handling of molluscan shellfish.
Isolation and Characterization of a Novel Lipase from a Metagenomic Library of Tidal Flat Sediments: Evidence for a New Family of Bacterial Lipases
Authors: Lee Mi-Hwa , Lee Choong-Hwan , Oh Tae-Kwang , Song Jae Kwang , Yoon Jung-Hoon 
Published: November 2006

ABSTRACT

We cloned
lipG
, which encoded a lipolytic enzyme, from a Korean tidal flat metagenomic library. LipG was related to six putative lipases previously identified only in bacterial genome sequences. These enzymes comprise a new family. We partially characterized LipG, providing the first experimental data for a member of this family.
Symbiotic Bacteria Associated with Stomach Discs of Human Lice
Authors: Sasaki-Fukatsu Kayoko , Koga Ryuichi , Nikoh Naruo , Yoshizawa Kazunori , Kasai Shinji , Mihara Minoru , Kobayashi Mutsuo , Tomita Takashi , Fukatsu Takema 
Published: November 2006

ABSTRACT

The symbiotic bacteria associated with the stomach disc, a large aggregate of bacteriocytes on the ventral side of the midgut, of human body and head lice were characterized. Molecular phylogenetic analysis of 16S rRNA gene sequences showed that the symbionts formed a distinct and well-defined clade in the
Gammaproteobacteria
. The sequences exhibited AT-biased nucleotide composition and accelerated molecular evolution. In situ hybridization revealed that in nymphs and adult males, the symbiont was localized in the stomach disc, while in adult females, the symbiont was not in the stomach disc but in the lateral oviducts and the posterior pole of the oocytes due to female-specific symbiont migration. We propose the designation “
Candidatus
Riesia pediculicola” for the louse symbionts.
The
SPI1
Gene, Encoding a Glycosylphosphatidylinositol-Anchored Cell Wall Protein, Plays a Prominent Role in the Development of Yeast Resistance to Lipophilic Weak-Acid Food Preservatives
Authors: Simões T. , Mira N. P. , Fernandes A. R. , Sá-Correia Isabel 
Published: November 2006

ABSTRACT

The
Saccharomyces cerevisiae SPI1
gene encodes a member of the glycosylphosphatidylinositol-anchored cell wall protein family. In this work we show results indicating that
SPI1
expression protects the yeast cell from damage caused by weak acids used as food preservatives. This is documented by a less extended period of adaptation to growth in their presence and by a less inhibited specific growth rate for a parental strain compared with a mutant with
SPI1
deleted. Maximal protection exerted by Spi1p against equivalent concentrations of the various weak acids tested was registered for the more lipophilic acids (octanoic acid, followed by benzoic acid) and was minimal for acetic acid. Weak-acid adaptation was found to involve the rapid activation of
SPI1
transcription, which is dependent on the presence of the Msn2p transcription factor. Activation of
SPI1
transcription upon acetic acid stress also requires Haa1p, whereas this recently described transcription factor has a negligible role in the adaptive response to benzoic acid. The expression of
SPI1
was found to play a prominent role in the development of yeast resistance to 1,3-β-glucanase in benzoic acid-stressed cells, while its involvement in acetic acid-induced resistance to the cell wall-lytic enzyme is slighter. The results are consistent with the notion that Spi1p expression upon weak-acid stress leads to cell wall remodeling, especially for the more lipophilic acids, decreasing cell wall porosity. Decreased cell wall porosity, in turn, reduces access to the plasma membrane, reducing membrane damage, intracellular acidification, and viability loss.
Genetic Characterization of the Phenylacetyl-Coenzyme A Oxygenase from the Aerobic Phenylacetic Acid Degradation Pathway of
Escherichia coli
Authors: Fernández Cristina , Ferrández Abel , Miñambres Baltasar , Díaz Eduardo , García José L. 
Published: November 2006

ABSTRACT

We show here that the
paaABCDE
genes of the
paa
cluster responsible for phenylacetate degradation in
Escherichia coli
W encode a five-component oxygenase that hydroxylates phenylacetyl-coenzyme A (CoA), the first intermediate of the pathway. The primary structure of the subunits of bacterial phenylacetyl-CoA oxygenases revealed that these enzymes constitute the prototype of a new and distinct group of the large bacterial diiron multicomponent oxygenase family.
Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease
Authors: Scanlan Pauline D. , Shanahan Fergus , O'Mahony Caitlin , Marchesi Julian R. 
Published: November 2006

ABSTRACT

Gut microbiota shows host-specific diversity and temporal stability and significantly contributes to maintenance of a healthy gut. However, in inflammatory bowel disease, this microbiota has been implicated as a contributory factor to the illness. This study compared bacterial dynamics in Crohn's disease patients to those in a control group using a culture-independent method to assess the temporal stability, relative diversity, and similarity of the dominant fecal microbiota,
Clostridium
spp.,
Bacteroides
spp.,
Bifidobacterium
spp., and lactic acid bacteria spp. (LAB) for all individuals. Fecal samples were collected over several time points from individuals with Crohn's disease who were in remission (
n
= 11), from Crohn's disease patients who relapsed into an active Crohn's disease state (
n
= 5), and from a control group (
n
= 18). Denaturing gradient gel electrophoresis profiles were generated for the different microbial groups by specifically targeting different regions of the 16S rRNA gene and were compared on the basis of similarity and diversity. The temporal stability of dominant species for all Crohn's disease patients was significantly lower (
P
< 0.005) than that for the control group. Analysis of group-specific profiles for
Bifidobacterium
spp. found that they were similar in all samples, while the diversity of the LAB varied significantly between the groups, but temporal stability was not significantly altered. We observed significant changes in two functionally important mutualistic groups of bacteria, viz.,
Clostridium
and
Bacteroides
spp., which may have implications for the host's gut health, since some genera are involved in production of short-chain fatty acid, e.g., butyrate.
First Detection of the Ambler Class C 1 AmpC β-Lactamase in
Citrobacter freundii
by a New, Simple Double-Disk Synergy Test
Authors: Ruppé Etienne , Bidet Philippe , Verdet Charlotte , Arlet Guillaume , Bingen Edouard 
Published: November 2006

ABSTRACT

We report on the first detection of an AmpC-type Ambler class C 1 (ACC-1) β-lactamase in
Citrobacter freundi
isolated from a patient also harboring ACC-1-producing
Escherichia coli
and
Klebsiella pneumoniae
. We propose a simple cefoxitin-based double-disk synergy test (DDST) for the specific detection of ACC-1 in members of the family
Enterobacteriaceae
, including natural AmpC producers, in association with a cloxacillin-based DDST as a first-line AmpC-type β-lactamase screening test.
Methods for Detection of
Trichomonas vaginalis
in the Male Partners of Infected Women: Implications for Control of Trichomoniasis
Authors: Hobbs Marcia M. , Lapple Dana M. , Lawing Lisa F. , Schwebke Jane R. , Cohen Myron S. , Swygard Heidi , Atashili Julius , Leone Peter A. , Miller William C. , Seña Arlene C. 
Published: November 2006

ABSTRACT

Trichomonas vaginalis
infection in men is an important cause of nongonococcal urethritis. Effective detection of the parasite in men using culture requires examination of multiple specimens. We compared culture and PCR-enzyme-linked immunosorbent assay in urethral swabs, urine, and semen for
T. vaginalis
detection in male sexual partners of women with trichomoniasis identified by wet mount and culture. Trichomonads were detected by at least one positive test in 205/280 men (73.2%) who submitted at least one specimen for culture and PCR. Whereas InPouch TV culture detected only 46/205 cases (22.5%), PCR detected 201/205 (98.0%). Urethral swab cultures from men with urethritis were more likely to be positive with shorter incubation than specimens from men without urethritis.
T. vaginalis
was detected more often in men with wet-mount-positive partners. Even with a sensitive PCR assay, reliable detection of
T. vaginalis
in male partners required multiple specimens. The majority of male sexual partners in this study were infected, emphasizing the importance of partner evaluation and treatment.
FDJS03 Isolates Causing an Outbreak of Aseptic Meningitis in China That Evolved from a Distinct Echovirus 30 Lineage Imported from Countries of the Commonwealth of Independent States
Authors: Zhao Ya Nan , Perlin David S. , Park Steven , Jiang Ren Jie , Chen Liang , Chen Yue , Gardiner Rebecca , Jiang Qing Wu 
Published: November 2006

ABSTRACT
We compared echovirus 30 strains (FDJS03) which caused an outbreak of aseptic meningitis in China in 2003 with other human enterovirus B strains. Sequencing of the complete genome of FDJS03_84, a representative strain from this outbreak, revealed a mosaic structure with a putative recombination spot within the 2B gene. It was most similar to a strain of the same serotype, E30-14125-00, in the 5′ half of the genome but was almost equidistant to all strains analyzed in most of the 3′ half of the genome. Phylogenetic relationships in the 5′-untranslated region and the VP1 gene indicated that the FDJS03 isolates were closely related to a distinct lineage of E30 which circulated in countries of the Commonwealth of Independent States during 1999 and 2000. It is most likely that the ancestor of FDJS03 isolates experienced multiple recombination events in the nonstructural protein coding region, which were partly observed in the phylogenetic analysis of the 3D region.
Usefulness of Inter-IS
1
Spacer Polymorphisms for Subtyping of
Shigella sonnei
Isolates
Authors: Chiou Chien-Shun , Wei Hsiao-Lun , Wang You-Wen , Liao Jui-Cheng , Li Chun-Chin 
Published: November 2006

ABSTRACT

Shigella sonnei
contains numerous IS
1
elements. The existence of polymorphisms in the length of the inter-IS
1
spacer is a basis for the development of a PCR-based method for the subtyping of
S. sonnei
strains. The usefulness of inter-IS
1
spacer typing (IST) was evaluated and compared with that of pulsed-field gel electrophoresis (PFGE) by characterization of
S. sonnei
isolates from epidemiologically nonrelated cases and outbreaks and of isolates that were indistinguishable by PFGE and that were collected from independent infection events. IST was less discriminatory than PFGE, with discriminatory indices of 0.96 and 0.63, respectively, but was able to compensate for the drawbacks of PFGE. PFGE exhibited a high level of discriminatory power for
S. sonnei
isolates; however, PFGE was also, at times, too discriminatory, which was a disadvantage in constructing the clonal relationships among strains circulating over a period of months or years. Furthermore, IST provided greater subtyping information for isolates indistinguishable by PFGE. The present study indicates that IST is more useful than PFGE for investigating the genetic relationships among
S. sonnei
strains circulating over a longer time span and also for discriminating certain strains which are indistinguishable by PFGE.
Emergence and Outbreaks of CTX-M β-Lactamase-Producing
Escherichia coli
and
Klebsiella pneumoniae
Strains in a Tunisian Hospital
Authors: Mamlouk Kelthoum , Boutiba-Ben Boubaker Ilhem , Gautier Valérie , Vimont Sophie , Picard Bertrand , Ben Redjeb Saida , Arlet Guillaume 
Published: November 2006

ABSTRACT

Sixty-two isolates of
Enterobacteriaceae
(35
Escherichia coli
and 27
Klebsiella pneumoniae
isolates) producing CTX-M-type β-lactamases were collected between March 2000 and June 2003 in different wards of Charles Nicolle Hospital in Tunis (Tunisia). Sequencing identified the
bla
CTX-M-15
determinant in 55 isolates and
bla
CTX-M-16
in 7 isolates. The CTX-M-15-producing strains were isolated in several wards and consisted mainly of two successive clonal groups of
E. coli
and a major clonal group of
K. pneumoniae
. The second clonal group of
E. coli
belonged to phylogenetic group B2 and harbored more virulence factors than the first clonal group. Among the 22 transconjugants or electroporants obtained with selected
E. coli
and
K. pneumoniae
CTX-M-15-producing strains, a predominant plasmid restriction pattern was obtained with 17 isolates. The four CTX-M-16-producing strains of
E. coli
yielded the same pulsed-field gel electrophoresis (PFGE) pattern, while the three CTX-M-16-producing strains of
K. pneumoniae
yielded two different PFGE patterns. All of the CTX-M-16-producing isolates were recovered in the pediatric ward and had the same plasmid restriction pattern.
The
Escherichia coli argW-dsdCXA
Genetic Island Is Highly Variable, and
E. coli
K1 Strains Commonly Possess Two Copies of
dsdCXA
Authors: Moritz Rebecca L. , Welch Rodney A. 
Published: November 2006

ABSTRACT

The genome sequences of
Escherichia coli
pathotypes reveal extensive genetic variability in the
argW-dsdCXA
island. Interestingly, the archetype
E. coli
K1 neonatal meningitis strain, strain RS218, has two copies of the
dsdCXA
genes for
d
-serine utilization at the
argW
and
leuX
islands. Because the human brain contains
d
-serine, an epidemiological study emphasizing K1 isolates surveyed the
dsdCXA
copy number and function. Forty of 41 (97.5%) independent
E. coli
K1 isolates could utilize
d
-serine. Southern blot hybridization revealed physical variability within the
argW
-
dsdC
region, even among 22
E. coli
O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two
dsdCXA
loci. Mutational analysis indicated that each of the
dsdA
genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use
d
-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic
E. coli
(DEC) collection have this activity. The genome sequence of diarrheagenic
E. coli
isolates indicates that the
csrRAKB
genes for sucrose utilization are often substituted for
dsdC
and a portion of
dsdX
present at the
argW-dsdCXA
island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus
d
-serine utilization. The ability to use
d
-serine is a trait strongly selected for among
E. coli
K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic
E. coli
pathotypes appear to have substituted sucrose for
d
-serine as a potential nutrient.