bluuebunny/crossref_metadata_2025 huggingface dataset:
Asymmetrical Interactions betweenWolbachiaandSpiroplasmaEndosymbionts Coexisting in the Same Insect Host
Authors: Goto Shunsuke , Anbutsu Hisashi , Fukatsu Takema
Published: July 2006

We investigated the interactions between the endosymbiontsWolbachia pipientisstrainwMel andSpiroplasmasp. strain NSRO coinfecting the host insectDrosophila melanogaster. By making use of antibiotic therapy, temperature stress, and hemolymph microinjection, we established the following strains in the same host genetic background: the SW strain, infected with bothSpiroplasmaandWolbachia; the S strain, infected withSpiroplasmaonly; and the W strain, infected withWolbachiaonly. The infection dynamics of the symbionts in these strains were monitored by quantitative PCR during host development. The infection densities ofSpiroplasmaexhibited no significant differences between the SW and S strains throughout the developmental course. In contrast, the infection densities ofWolbachiawere significantly lower in the SW strain than in the W strain at the pupal and young adult stages. These results indicated that the interactions between the coinfecting symbionts were asymmetrical, i.e.,Spiroplasmaorganisms negatively affected the population ofWolbachiaorganisms, whileWolbachiaorganisms did not influence the population ofSpiroplasmaorganisms. In the host body, the symbionts exhibited their own tissue tropisms: among the tissues examined,Spiroplasmawas the most abundant in the ovaries, whileWolbachiashowed the highest density in Malpighian tubules. Strikingly, basically noWolbachiaorganisms were detected in hemolymph, the principal location ofSpiroplasma. These results suggest that different host tissues act as distinct microhabitats for the symbionts and that the lytic process in host metamorphosis might be involved in the asymmetrical interactions between the coinfecting symbionts.
Isolation and Characterization of
Listeria monocytogenes
Isolates from Ready-To-Eat Foods in Florida
Authors: Shen Yuelian , Liu Yan , Zhang Yifan , Cripe Jennifer , Conway William , Meng Jianghong , Hall Grace , Bhagwat Arvind A.
Published: July 2006

Of 3,063 ready-to-eat food samples tested, 91 (2.97%) were positive for
Listeria monocytogenes
, and lineage 1 strains outnumbered lineage 2 strains 57 to 34. Seventy-one isolates (78%) exhibited multiple antibiotic resistance, and an
L. monocytogenes
-specific bacteriophage cocktail lysed 65 of 91 (71%) isolates. Determining phage, acid, and antibiotic susceptibility phenotypes enabled us to identify differences among strains which were otherwise indistinguishable by conventional methods.
A Functional
mobA
Gene for Molybdopterin Cytosine Dinucleotide Cofactor Biosynthesis Is Required for Activity and Holoenzyme Assembly of the Heterotrimeric Nicotine Dehydrogenases of
Arthrobacter nicotinovorans
Authors: Sachelaru Paula , Schiltz Emile , Brandsch Roderich
Published: July 2006

Two
Arthrobacter nicotinovorans
molybdenum enzymes hydroxylate the pyridine ring of nicotine. Molybdopterin cytosine dinucleotide (MCD) was determined to be a cofactor of these enzymes. A
mobA
gene responsible for the formation of MCD could be identified and its function shown to be required for assembly of the heterotrimeric molybdenum enzymes.
Changes in the Spoilage-Related Microbiota of Beef during Refrigerated Storage under Different Packaging Conditions
Authors: Ercolini Danilo , Russo Federica , Torrieri Elena , Masi Paolo , Villani Francesco
Published: July 2006

The microbial spoilage of beef was monitored during storage at 5°C under three different conditions of modified-atmosphere packaging (MAP): (i) air (MAP1), (ii) 60% O
2
and 40% CO
2
(MAP2), and (iii) 20% O
2
and 40% CO
2
(MAP3).
Pseudomonas
,
Enterobacteriaceae
,
Brochothrix thermosphacta
, and lactic acid bacteria were monitored by viable counts and PCR-denaturing gradient gel electrophoresis (DGGE) analysis during 14 days of storage. Moreover, headspace gas composition, weight loss, and beef color change were also determined at each sampling time. Overall, MAP2 was shown to have the best protective effect, keeping the microbial loads and color change to acceptable levels in the first 7 days of refrigerated storage. The microbial colonies from the plate counts of each microbial group were identified by PCR-DGGE of the variable V6-V8 region of the 16S rRNA gene. Thirteen different genera and at least 17 different species were identified after sequencing of DGGE fragments that showed a wide diversity of spoilage-related bacteria taking turns during beef storage in the function of the packaging conditions. The countable species for each spoilage-related microbial group were different according to packaging conditions and times of storage. In fact, the DGGE profiles displayed significant changes during time and depending on the initial atmosphere used. The spoilage occurred between 7 and 14 days of storage, and the microbial species found in the spoiled meat varied according to the packaging conditions.
Rahnella aquatilis
,
Rahnella
spp.,
Pseudomonas
spp., and
Carnobacterium divergens
were identified as acting during beef storage in air (MAP1).
Pseudomonas
spp. and
Lactobacillus sakei
were found in beef stored under MAP conditions with high oxygen content (MAP2), while
Rahnella
spp. and
L. sakei
were the main species found during storage using MAP3. The identification of the spoilage-related microbiota by molecular methods can help in the effective establishment of storage conditions for fresh meat.
Citrate Inhibition-Resistant Form of 6-Phosphofructo-1-Kinase fromAspergillus niger
Authors: Mlakar Tina , Legiša Matic
Published: July 2006

Two forms ofAspergillus niger6-phosphofructo-1-kinase (PFK1) have been described recently, the 85-kDa native enzyme and 49-kDa shorter fragment that is formed from the former by posttranslational modification. So far, kinetic characteristics have never been determined on the enzyme purified to near homogeneity. For the first time, kinetic parameters were determined for individual enzymes with respect to citrate inhibition. The native 85-kDa enzyme was found to be moderately inhibited by citrate, with theKivalue determined to be 1.5 mM, in the system with 5 mM Mg2+ions, while increasing magnesium concentrations relieved the negative effect of citrate. An identical inhibition coefficient was determined also in the presence of ammonium ions, although ammonium acted as a strong activator of enzyme activity. On the other hand, the shorter fragment of PFK1 proved to be completely resistant to inhibition by citrate. Allosteric citrate binding sites were most probably lost after the truncation of the C-terminal part of the native protein, in which region some binding sites for inhibitor are known to be located. At near physiological conditions, characterized by low fructose-6-phosphate concentrations, a much higher efficiency of the shorter fragment was observed during an in vitro experiment. Since the enzyme became more susceptible to the positive control by specific ligands, while the negative control was lost after posttranslational modification, the shorter PFK1 fragment seems to be the enzyme most responsible for generating undisturbed metabolic flow through glycolysis inA. nigercells.
Caenorhabditis elegans
Senses Bacterial Autoinducers
Authors: Beale Elmus , Li Guigen , Tan Man-Wah , Rumbaugh Kendra P.
Published: July 2006

Pseudomonas aeruginosa
uses virulence factors controlled by quorum sensing (QS) to kill
Caenorhabditis elegans
. Here we show that
C. elegans
is attracted to the acylated homoserine lactones (AHSLs) that mediate QS in
P. aeruginosa
. Our data also indicate that
C. elegans
can distinguish AHSLs and may use them to mediate aversive or attractive learning.
Saccharomyces cerevisiae
-Based Molecular Tool Kit for Manipulation of Genes from Gram-Negative Bacteria
Authors: Shanks Robert M. Q. , Caiazza Nicky C. , Hinsa Shannon M. , Toutain Christine M. , O'Toole George A.
Published: July 2006

A tool kit of vectors was designed to manipulate and express genes from a wide range of gram-negative species by using in vivo recombination.
Saccharomyces cerevisiae
can use its native recombination proteins to combine several amplicons in a single transformation step with high efficiency. We show that this technology is particularly useful for vector design. Shuttle, suicide, and expression vectors useful in a diverse group of bacteria are described and utilized. This report describes the use of these vectors to mutate
clpX
and
clpP
of the opportunistic pathogen
Pseudomonas aeruginosa
and to explore their roles in biofilm formation and surface motility. Complementation of the rhamnolipid biosynthetic gene
rhlB
is also described. Expression vectors are used for controlled expression of genes in two pseudomonad species. To demonstrate the facility of building complicated constructs with this technique, the recombination of four PCR-generated amplicons in a single step at >80% efficiency into one of these vectors is shown. These tools can be used for genetic studies of pseudomonads and many other gram-negative bacteria.
Colonization Dynamics of Altered Schaedler Flora Is Influenced by Gender, Aging, and
Helicobacter hepaticus
Infection in the Intestines of Swiss Webster Mice
Authors: Ge Zhongming , Feng Yang , Taylor Nancy S. , Ohtani Masahiro , Polz Martin F. , Schauer David B. , Fox James G.
Published: July 2006

The distribution and colonization levels of the altered Schaedler flora (ASF) in their natural hosts are poorly understood. Intestinal colonization levels of the eight ASF strains in outbred Swiss Webster mice with or without
Helicobacter hepaticus
infection were characterized by real-time quantitative PCR. All ASF strains were detected in the cecum and colon, but some strains displayed significant variation in colonization levels with host age, gender, and
H. hepaticus
infection status.
Functional Heterogeneity of RpoS in Stress Tolerance of Enterohemorrhagic
Escherichia coli
Strains
Authors: Bhagwat Arvind A. , Tan Jasmine , Sharma Manan , Kothary Mahendra , Low Sharon , Tall Ben D. , Bhagwat Medha
Published: July 2006

The stationary-phase sigma factor (RpoS) regulates many cellular responses to environmental stress conditions such as heat, acid, and alkali shocks. On the other hand, mutations at the
rpoS
locus have frequently been detected among pathogenic as well as commensal strains of
Escherichia coli
. The objective of this study was to perform a functional analysis of the RpoS-mediated stress responses of enterohemorrhagic
E. coli
strains from food-borne outbreaks.
E. coli
strains belonging to serotypes O157:H7, O111:H11, and O26:H11 exhibited polymorphisms for two phenotypes widely used to monitor
rpoS
mutations, heat tolerance and glycogen synthesis, as well as for two others, alkali tolerance and adherence to Caco-2 cells. However, these strains synthesized the oxidative acid resistance system through an
rpoS
-dependent pathway. During the transition from mildly acidic growth conditions (pH 5.5) to alkaline stress (pH 10.2), cell survival was dependent on
rpoS
functionality. Some strains were able to overcome negative regulation by RpoS and induced higher β-galactosidase activity without compromising their acid resistance. There were no major differences in the DNA sequences in the
rpoS
coding regions among the tested strains. The heterogeneity of
rpoS
-dependent phenotypes observed for stress-related phenotypes was also evident in the Caco-2 cell adherence assay. Wild-type O157:H7 strains with native
rpoS
were less adherent than
rpoS
-complemented counterpart strains, suggesting that
rpoS
functionality is needed. These results show that some pathogenic
E. coli
strains can maintain their acid tolerance capability while compromising other RpoS-dependent stress responses. Such adaptation processes may have significant impact on a pathogen's survival in food processing environments, as well in the host's stomach and intestine.
Survival of Yogurt Bacteria in the Human Gut
Authors: Elli Marina , Callegari Maria Luisa , Ferrari Susanna , Bessi Elena , Cattivelli Daniela , Soldi Sara , Morelli Lorenzo , Goupil Feuillerat Nathalie , Antoine Jean-Michel
Published: July 2006

Whether
Lactobacillus delbrueckii
subsp.
bulgaricus
and
Streptococcus thermophilus
can be recovered after passage through the human gut was tested by feeding 20 healthy volunteers commercial yogurt. Yogurt bacteria were found in human feces, suggesting that they can survive transit in the gastrointestinal tract.
Effects ofGPD1Overexpression inSaccharomyces cerevisiaeCommercial Wine Yeast Strains LackingALD6Genes
Authors: Cambon Brigitte , Monteil Virginie , Remize Fabienne , Camarasa Carole , Dequin Sylvie
Published: July 2006

The utilization ofSaccharomyces cerevisiaestrains overproducing glycerol and with a reduced ethanol yield is a potentially valuable strategy for producing wine with decreased ethanol content. However, glycerol overproduction is accompanied by acetate accumulation. In this study, we evaluated the effects of the overexpression ofGPD1, coding for glycerol-3-phosphate dehydrogenase, in three commercial wine yeast strains in which the two copies ofALD6encoding the NADP+-dependent Mg2+-activated cytosolic acetaldehyde dehydrogenase have been deleted. Under wine fermentation conditions, the engineered industrial strains exhibit fermentation performance and growth properties similar to those of the wild type. Acetate was produced at concentrations similar to that of the wild-type strains, whereas sugar was efficiently diverted to glycerol. The ethanol yield of theGPD1 ald6industrial strains was 15 to 20% lower than that in the controls. However, these strains accumulated acetoin at considerable levels due to inefficient reduction to 2,3-butanediol. Due to the low taste and odor thresholds of acetoin and its negative sensorial impact on wine, novel engineering strategies will be required for a proper adjustment of the metabolites at the acetaldehyde branch point.
Phenotypic Properties and Microbial Diversity of Methanogenic Granules from a Full-Scale Upflow Anaerobic Sludge Bed Reactor Treating Brewery Wastewater
Authors: Díaz Emiliano E. , Stams Alfons J. M. , Amils Ricardo , Sanz José L.
Published: July 2006

Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH), and scanning and transmission electron microscopy. We propose here that the different types of granules reflect the different stages in the life cycle of granules. Young granules were small, black, and compact and harbored active cells. Gray granules were the most abundant granules. These granules have a multilayer structure with channels and void areas. The core was composed of dead or starving cells with low activity. The brown granules, which were the largest granules, showed a loose and amorphous structure with big channels that resulted in fractured zones and corresponded to the older granules.Firmicutes(as determined by FISH) andNitrospiraandDeferribacteres(as determined by cloning and sequencing) were the predominantBacteria. Remarkably,Firmicutescould not be detected in the brown granules. The methanogenicArchaeaidentified wereMethanosaeta concilii(70 to 90% by FISH and cloning),Methanosarcina mazei, andMethanospirillumspp. The phenotypic appearance of the granules reflected the physiological condition of the granules. This may be valuable to easily select appropriate seed sludges to start up other reactors.
Effects of Low-Shear Modeled Microgravity on Cell Function, Gene Expression, and Phenotype in
Saccharomyces cerevisiae
Authors: Purevdorj-Gage B. , Sheehan K. B. , Hyman L. E.
Published: July 2006

Only limited information is available concerning the effects of low-shear modeled microgravity (LSMMG) on cell function and morphology. We examined the behavior of
Saccharomyces cerevisiae
grown in a high-aspect-ratio vessel, which simulates the low-shear and microgravity conditions encountered in spaceflight. With the exception of a shortened lag phase (90 min less than controls;
P
< 0.05), yeast cells grown under LSMMG conditions did not differ in growth rate, size, shape, or viability from the controls but did differ in the establishment of polarity as exhibited by aberrant (random) budding compared to the usual bipolar pattern of controls. The aberrant budding was accompanied by an increased tendency of cells to clump, as indicated by aggregates containing five or more cells. We also found significant changes (greater than or equal to twofold) in the expression of genes associated with the establishment of polarity (
BUD5
), bipolar budding (
RAX1
,
RAX2
, and
BUD25
), and cell separation (
DSE1
,
DSE2
, and
EGT2
). Thus, low-shear environments may significantly alter yeast gene expression and phenotype as well as evolutionary conserved cellular functions such as polarization. The results provide a paradigm for understanding polarity-dependent cell responses to microgravity ranging from pathogenesis in fungi to the immune response in mammals.
The Cell Lysis Activity of the
Streptococcus agalactiae
Bacteriophage B30 Endolysin Relies on the Cysteine, Histidine-Dependent Amidohydrolase/Peptidase Domain
Authors: Donovan David M. , Foster-Frey Juli , Dong Shengli , Rousseau Geneviève M. , Moineau Sylvain , Pritchard David G.
Published: July 2006

The
Streptococcus agalactiae
bacteriophage B30 endolysin contains three domains: cysteine, histidine-dependent amidohydrolase/peptidase (CHAP), Acm glycosidase, and the SH3b cell wall binding domain. Truncations and point mutations indicated that the Acm domain requires the SH3b domain for activity, while the CHAP domain is responsible for nearly all the cell lysis activity.
Persisting Immune Responses Indicating Long-Term Protection after Booster Dose with Meningococcal Group B Outer Membrane Vesicle Vaccine
Authors: Feiring Berit , Fuglesang Jan , Oster Philipp , Næss Lisbeth M. , Helland Oddveig S. , Tilman Sandrine , Rosenqvist Einar , Bergsaker Marianne A. R. , Nøkleby Hanne , Aaberge Ingeborg S.
Published: July 2006

MenBvac is an outer membrane vesicle vaccine against systemic meningococcal disease caused by serogroup B
Neisseria meningitidis
. In this placebo-controlled double-blind study including 374 healthy adolescents, the safety and immunogenicity of a schedule of three primary doses 6 weeks apart followed by a fourth dose a year later were evaluated. Antibody responses to the vaccine strain and heterologous strains (non-vaccine-type strains) and the persistence of these antibodies were measured by the serum bactericidal assay (SBA) and enzyme-linked immunosorbent assay up to 1 year after the last dose. The proportion of subjects with SBA titers of ≥4 against the vaccine strain increased from 3% prevaccination to 65% after the third dose. Ten months later, this proportion had declined to 28%. The fourth dose induced a booster response demonstrated by 93% of subjects achieving a titer of ≥4. One year after the booster dose, 64% still showed SBA titers of ≥4. Cross-reacting antibodies were induced against all heterologous strains tested, although the magnitude of SBA titers differed widely between the different strains. All four doses of MenBvac were safe. Both MenBvac and the placebo had reactogenicity profiles of mild to moderate local and systemic reactions. Pain, the most common reaction, was reported with similar frequencies in both groups. No serious adverse events occurred in the MenBvac group. This study confirmed the good immunogenicity of the primary course of MenBvac and demonstrated prolonged persistence and increased cross-reactivity of functional antibodies elicited by a booster dose.
Factors Associated with Immunoglobulin G Subclass Polarization in Naturally Acquired Antibodies to
Plasmodium falciparum
Merozoite Surface Proteins: a Cross-Sectional Survey in Brazilian Amazonia
Authors: Scopel Kézia K. G. , Fontes Cor J. F. , Ferreira Marcelo U. , Braga Érika M.
Published: July 2006

We investigated immunoglobulin G (IgG) subclass antibody responses to
Plasmodium falciparum
merozoite surface protein 1 (MSP-1) and MSP-2 in 112 malaria-exposed subjects in Brazil. IgG3 polarization was primarily epitope driven, being little affected by cumulative or current exposure to malaria and not affected by a subject's age and Fcγ receptor IIA genotype.
Rapid Genetic Grouping of Factor H-Binding Protein (Genome-Derived Neisserial Antigen 1870), a Promising Group B Meningococcal Vaccine Candidate
Authors: Beernink Peter T. , Leipus Arunas , Granoff Dan M.
Published: July 2006

The most important antigen component of a promising multicomponent group B meningococcal recombinant protein vaccine is based on genome-derived neisserial antigen 1870, which recently was renamed factor H-binding protein (FHBP) to reflect one of its critical functions as a complement regulatory protein.
Neisseria meningitidis
strains can be subdivided into three FHBP variant groups based on divergence of FHBP amino acid sequences. Within each variant group, amino acid sequences are >90% conserved. To develop an FHBP-based group B vaccine, it is important to know the distribution of FHBP variant 1, 2, and 3 strains in different geographic regions, since antibodies against FHBP are bactericidal against strains within the homologous group but show minimal activity against strains from other groups. We have devised a high-throughput, quantitative PCR-based method that allows rapid and precise assignment of FHBP genes into each of the three major variant lineages. Among 48 group B isolates from patients hospitalized in California in 2003 to 2004, 83%, 13%, and 4%, respectively, had variant 1, 2, and 3 genes. Thus, a vaccine based on the variant 1 protein has the potential to prevent the majority of cases of group B disease. The quantitative PCR-based method will be useful for determining and monitoring the prevalence of meningococcal isolates with genes encoding different FHBP variant proteins. The technique also is suitable for monitoring variation of genes encoding other protein antigens targeted for vaccination.
Comparison of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Typing for Characterization of
Salmonella enterica
Serotype Newport Isolates
Authors: Harbottle H. , White D. G. , McDermott P. F. , Walker R. D. , Zhao S.
Published: July 2006

In the United States, multidrug-resistant phenotypes of
Salmonella enterica
serotype Newport (commonly referred to as MDR-AmpC) have emerged in animals and humans and have become a major public health problem. Although pulsed-field gel electrophoresis (PFGE) is the current “gold standard” typing method for
Salmonella
, multilocus sequence typing (MLST) may be more relevant to investigations exploring evolutionary and population biology relationships. In this study, 81
Salmonella enterica
serotype Newport isolates from humans, food animals, and retail foods were examined for antimicrobial susceptibility and characterized using PFGE and MLST of seven genes,
aroC
,
dnaN
,
hemD
,
hisD
,
purE
,
sucA
, and
thrA
. Forty-nine percent of the isolates were resistant to nine or more of the tested antimicrobials.
Salmonella
isolates displayed resistance most often to sulfamethoxazole (57%), streptomycin (56%), tetracycline (56%), ampicillin (52%), and ceftiofur (49%) and, to a lesser extent, to kanamycin (19%), trimethoprim-sulfamethoxazole (17%), and gentamicin (11%). A total of 43 PFGE patterns were generated using XbaI, indicating a genetically diverse population. The largest PFGE cluster contained isolates from clinically ill swine, cattle, and humans. MLST resulted in 12 sequence types (STs), with one type encompassing 62% of the strains. Ten new sequence types and one novel allele type were identified. Furthermore, MLST typing showed that strains closely related by PFGE clustered in major STs, whereas more distantly related strains were separated into two clusters by PFGE. The results of this study demonstrated that the MLST scheme employed here clustered
S. enterica
serovar Newport isolates in distinct molecular populations, and strain discrimination was enhanced by combining PFGE, antimicrobial susceptibility, and MLST results.
Classifying
spa
Types in Complexes Improves Interpretation of Typing Results for Methicillin-Resistant
Staphylococcus aureus
Authors: Ruppitsch Werner , Indra Alexander , Stöger Anna , Mayer Barbara , Stadlbauer Silke , Wewalka Günther , Allerberger Franz
Published: July 2006

A total of 382 isolates of methicillin-resistant
Staphylococcus aureus
originating from three Austrian regions and one adjacent Italian region (Vienna, Lower Austria, North Tyrol, and South Tyrol) were typed by DNA sequence analysis of the variable repeat region of the protein A gene (
spa
typing). The strain collection consisted of arbitrarily chosen isolates originating from clinical specimens taken in the years 2003 to 2005 at 17 hospitals. The most common
spa
types found were t001 (28.8% of all isolates), t190 (27.0%), t008 (14.1%), and t041 (11.3%). The 42 remaining
spa
types accounted for ≤2.4% each. The dominating
spa
types varied between the different regions. As short sequence DNA repeat units are unstable entities, the 46
spa
types were classified into seven
spa
complexes with respect to short sequence repeat unit composition and organization. Such classification into complexes can provide additional information for the hospital epidemiologist, empowering one to differentiate the introduction of a new strain from mere variation of endemic
spa
types.
Real-Time PCR Assays for Hepatitis C Virus (HCV) RNA Quantitation Are Adequate for Clinical Management of Patients with Chronic HCV Infection
Authors: Halfon Philippe , Bourlière Marc , Pénaranda Guillaume , Khiri Hacène , Ouzan Denis
Published: July 2006

Because of the use of viral kinetics during polyethylene glycol (PEG)-interferon-ribavirin therapy and the development of specific new anti-hepatitis C virus (anti-HCV) drugs, assessment of the efficacy of anti-HCV drugs needs to be based not on end-point PCR assays but on real-time PCR. The aim of this study was to determine if the two available commercial real-time PCR assays, the Abbott RealTime HCV assay and the Roche Cobas TaqMan HCV assay, can become the standard for HCV RNA quantification. We investigated the prognostic relevance of HCV RNA viral loads at baseline, week 4, and week 12 to a rapid and early virological response to antiviral therapy by using the two assays. Of 59 naïve patients chronically infected by HCV (41 infected with genotype 1) who were treated with ribavirin plus PEG-interferon alfa-2b for 48 weeks, 24 patients (41%) showed a sustained virological response (SVR). With the two assays, viral loads were highly correlated, irrespective of genotype (
R
2
= 0.94 for all cases). No difference in diagnostic value was found between the Abbott and Roche assays at week 4, with respective negative predictive values (NPVs) of 84% and 78% and positive predictive values (PPVs) of 62% and 56% (not significant), and at week 12, the respective NPVs were 91% and 90% and PPVs were 44% and 46% (not significant). At week 12, 83% (20/24) and 96% (23/24) of patients with SVR tested negative for HCV RNA by the Abbott and Roche assays, respectively (the difference is not significant). In conclusion, the high sensitivities and large dynamic ranges of the Abbott and Roche assays show that a single real-time quantitative PCR assay is fully adequate for clinical and therapeutic management of HCV.
High Prevalence of Multiple Human Herpesviruses in Saliva from Human Immunodeficiency Virus-Infected Persons in the Era of Highly Active Antiretroviral Therapy
Authors: Miller Craig S. , Berger Joseph R. , Mootoor Yunanan , Avdiushko Sergei A. , Zhu Hua , Kryscio Richard J.
Published: July 2006

Human immunodeficiency virus (HIV) infection is associated with an increased risk for human herpesviruses (HHVs) and their related diseases. Methods for limiting the transmission of HHVs require a better understanding of the prevalence and infectiousness of oral HHVs in HIV-infected patients. We performed quantitative PCR to investigate the prevalence, quantity, risk, and correlates of salivary HHVs from 58 HIV-seropositive individuals in a case control study. HHVs were significantly more prevalent in the salivas of HIV-seropositive persons than in those of the controls (odds ratios [ORs], 4.2 to 26.2;
P
≤ 0.008). In HIV-infected patients, Epstein-Barr virus (EBV), human herpesvirus 8 (HHV-8), cytomegalovirus (CMV), and herpes simplex virus type 1 (HSV-1) were detected in 90%, 57%, 31% and 16% of samples, respectively, compared with 48%, 24%, 2%, and 2%, respectively, of samples from controls. Multiple HHVs were observed in 71% of HIV-seropositive persons and only 16% of controls (OR, 13.0; 95% confidence interval, 5.29 to 32.56). HIV-positive patients had significantly higher EBV loads than HIV-negative persons (
P
< 0.0001). HIV-infected patients with CD4 counts above 200 cells/μl had increased probability for having HHV-8 in saliva (
P
= 0.009) compared with patients whose counts were less than 200. In contrast, HSV-1, EBV, and CMV were detected more often when CD4 counts were low. High salivary HHV loads were detected for those (
n
= 7) with oral lesions. These findings suggest that saliva is a potential risk factor for the acquisition of multiple HHVs, and several host factors may function to accelerate HHV reactivation or replication in patients with HIV infection.
Lamivudine Resistance of Hepatitis B Virus Masked by Coemergence of Mutations in Probe Region of the COBAS AMPLICOR Assay
Authors: Lindh Magnus , Hannoun Charles , Malmström Sebastian , Lindberg Johan , Norkrans Gunnar
Published: July 2006

The COBAS AMPLICOR hepatitis B virus assay targets a conserved region of the genome and is widely used to monitor treatment of hepatitis B in order to identify emerging resistance. However, the assay failed to recognize increasing viremia levels when YMDD mutations were paralleled by mutations in the segment targeted by the COBAS AMPLICOR probe.
Candida guilliermondii
Fungemia in Patients with Hematologic Malignancies
Authors: Girmenia Corrado , Pizzarelli Giampaolo , Cristini Francesco , Barchiesi Francesco , Spreghini Elisabetta , Scalise Giorgio , Martino Pietro
Published: July 2006

The microbiological, clinical, and epidemiological features of most non-
Candida albicans Candida
species are well known, but much less is known about species such as
Candida guilliermondii
, an uncommon pathogen causing a variety of deep-seated infections in immunocompromised hosts. To characterize
C. guilliermondii
fungemia in patients with hematological malignancies and its susceptibility to antifungal drugs, all cases of
C. guilliermondii
fungemia diagnosed in our department between 1983 and 2005 were retrospectively analyzed and the literature was reviewed.
C. guilliermondii
caused 29/243 (11.7%) candidemia episodes diagnosed during the study period. Central venous catheters were the documented sources of candidemia in 19/29 episodes (65.5%), and invasive tissue infections were documented in 2 (6.9%). In the remaining eight, the catheter was not removed and the source of the fungemia remained obscure. Seven episodes ended in death, but only one could be attributed to invasive
C. guilliermondii
infection. Molecular typing data reveal no evidence of common infection sources. Isolates displayed high rates of in vitro susceptibility to amphotericin B (100%), voriconazole (95%), and fluconazole (90%) and lower rates of in vitro susceptibility to flucytosine (86%), itraconazole (76%), and caspofungin (33%). Our literature review confirms that
C. guilliermondii
is a significantly more frequent cause of candidemia among cancer patients compared with the general hospital population. It accounted for <1% of the total number of
Candida
bloodstream isolates reported in the articles we reviewed, with higher rates in Europe (1.4%) and Asia (1.8%) compared with North America (0.3%).
Cluster of Cases of Human
Rickettsia felis
Infection from Southern Europe (Spain) Diagnosed by PCR
Authors: Oteo José A. , Portillo Aránzazu , Santibáñez Sonia , Blanco José R. , Pérez-Martínez Laura , Ibarra Valvanera
Published: July 2006

The first cluster of cases of human
Rickettsia felis
infection in Spain diagnosed by PCR is reported.
Assignment of
Staphylococcus
Isolates to Groups by
spa
Typing, SmaI Macrorestriction Analysis, and Multilocus Sequence Typing
Authors: Strommenger B. , Kettlitz C. , Weniger T. , Harmsen D. , Friedrich A. W. , Witte W.
Published: July 2006

The implementation of the new clustering algorithm
B
ased
U
pon
R
epeat
P
attern (BURP) into the Ridom StaphType software tool enables clustering based on
spa
typing data for
Staphylococcus aureus
. We compared clustering results obtained by
spa
typing/BURP to those obtained by currently well-established methods, i.e., SmaI macrorestriction analysis and multilocus sequence typing/eBURST. A total of 99 clinical
S. aureus
strains, including MRSA and representing major clonal lineages associated with important kinds of infections which have been prevalent in Germany and Central Europe during the last 10 years, were used for comparison. SmaI macrorestriction analysis revealed the highest discriminatory power, and clustering results for all three methods resulted in concordance values ranging from 96.8% between the two sequence-based methods to 93.4% between
spa
typing/BURP and SmaI macrorestriction/cluster analysis. The results of this study indicate that
spa
typing, together with BURP clustering, is a useful tool in
S. aureus
epidemiology, especially because of ease of use and the advantages of unambiguous sequence analysis as well as reproducibility and exchange of typing data.
Evaluation of the Genotype MTBDR Assay for Rapid Detection of Rifampin and Isoniazid Resistance in
Mycobacterium tuberculosis
Isolates
Authors: Cavusoglu Cengiz , Turhan Ajda , Akinci Pinar , Soyler Ilknur
Published: July 2006

A novel PCR-based reverse hybridization method Genotype MTBDR assay (Hain Lifescience GmbH, Nehren, Germany) was evaluated for rapid detection of rifampin (RIF) and isoniazid (INH) resistance in Turkish
Mycobacterium tuberculosis
isolates. The Genotype MTBDR assay is designed to detect mutations within the 81-bp hotspot region of
rpoB
and mutations at
katG
codon 315. A total of 41 RIF-resistant
M. tuberculosis
isolates with
rpoB
mutations that were previously tested by the INNO-LiPA Rif.TB kit and also characterized by DNA sequencing were included in the study. Thirty-seven of these isolates were also resistant to INH. RIF resistance was correctly identified in 39 of 41 isolates (95.1%) with the Genotype MTBDR assay probes specific for these mutations. One isolate with a Gln-490-His mutation and another one with a CGG insertion between codons 514 and 515 were identified as RIF sensitive by the Genotype MTBDR assay. While the INNO-LiPA Rif.TB kit was able to determine the CGG insertion between codons 514 and 515, the Gln-490-His mutation outside the 81-bp hotspot region was not detected by the INNO-LiPA Rif.TB kit. These isolates had MICs of ≥32 μg/ml for RIF. The Genotype MTBDR assay also correctly identified 27 of 37 INH-resistant isolates (73%) with mutations in
katG
codon 315. In conclusion, the Genotype MTBDR assay may be useful for the rapid diagnosis of the most common mutations found in multidrug-resistant
M. tuberculosis
strains. However, the test results should always be confirmed with phenotypic methods.
Evaluation of the TB-Biochip Oligonucleotide Microarray System for Rapid Detection of Rifampin Resistance in
Mycobacterium tuberculosis
Authors: Caoili Janice C. , Mayorova Angelina , Sikes David , Hickman Laura , Plikaytis Bonnie B. , Shinnick Thomas M.
Published: July 2006

The TB-Biochip oligonucleotide microarray system is a rapid system to detect mutations associated with rifampin (RIF) resistance in mycobacteria. After optimizing the system with 29 laboratory-generated rifampin-resistant mutants of
Mycobacterium tuberculosis
, we evaluated the performance of this test using 75 clinical isolates of
Mycobacterium tuberculosis
. With this small sample set, the TB-Biochip system displayed a sensitivity of 80% and a specificity of 100% relative to conventional drug susceptibility testing results for RIF resistance. For these samples (∼50% tested positive), the positive predictive value was 100% and the negative predictive value was 85%. Four of the seven observed discrepancies were attributed to rare and new mutations not represented in the microarray, while three of the strains with discrepant results did not carry mutations in the RIF resistance-determining region. The results of this study confirm the utility of the system for rapid detection of RIF resistance and suggest approaches to increasing its sensitivity.
Sepsis Caused byVeillonella parvulaInfection in a 17-Year-Old Patient with X-Linked Agammaglobulinemia (Bruton's Disease)
Authors: Strach Magdalena , Siedlar Maciej , Kowalczyk Danuta , Zembala Marek , Grodzicki Tomasz
Published: July 2006

A case of a male, 17-year-old, X-linked agammaglobulinemia patient with bacteremia caused byVeillonella parvula, without a defined primary site of infection, is presented. The report demonstrates thatV. parvulashould not be regarded as a nonpathogenic microorganism, at least not in patients with certain forms of immunodeficiency disease.
Canine Strangles Case Reveals a New Host Susceptible to Infection with
Streptococcus equi
Authors: Ladlow Jane , Scase Timothy , Waller Andrew
Published: July 2006

We report the first documented case of canine strangles due to infection with
Streptococcus equi
in a dog with enlarged lymph nodes. Genetic typing, via sequencing of 12 housekeeping genes and the SeM gene, demonstrated the isolate to be a member of a common equine strain type circulating in the United Kingdom.
Nonrandom Distribution of
Burkholderia pseudomallei
Clones in Relation to Geographical Location and Virulence
Authors: Vesaratchavest Mongkol , Tumapa Sarinna , Day Nicholas P. J. , Wuthiekanun Vanaporn , Chierakul Wirongrong , Holden Matthew T. G. , White Nicholas J. , Currie Bart J. , Spratt Brian G. , Feil Edward J. , Peacock Sharon J.
Published: July 2006

Burkholderia pseudomallei
is a soil-dwelling saprophyte and the causative agent of melioidosis, a life-threatening human infection. Most cases are reported from northeast Thailand and northern Australia. Using multilocus sequence typing (MLST), we have compared (i) soil and invasive isolates from northeast Thailand and (ii) invasive isolates from Thailand and Australia. A total of 266 Thai
B. pseudomallei
isolates were characterized (83 soil and 183 invasive). These corresponded to 123 sequence types (STs), the most abundant being ST70 (
n
= 21), ST167 (
n
= 15), ST54 (
n
= 12), and ST58 (
n
= 11). Two clusters of related STs (clonal complexes) were identified; the larger clonal complex (CC48) did not conform to a simple pattern of radial expansion from an assumed ancestor, while a second (CC70) corresponded to a simple radial expansion from ST70. Despite the large number of STs, overall nucleotide diversity was low. Of the Thai isolates, those isolated from patients with melioidosis were overrepresented in the 10 largest clones (
P
< 0.0001). There was a significant difference in the classification index between environmental and disease isolates (
P
< 0.001), confirming that genotypes were not distributed randomly between the two samples. MLST profiles for 158 isolates from Australia (mainly disease associated) contained a number of STs (96) similar to that seen with the Thai invasive isolates, but no ST was found in both populations. There were also differences in diversity and allele frequency distribution between the two populations. This analysis reveals strong genetic differentiation on the basis of geographical isolation and a significant differentiation on the basis of virulence potential.
Diagnosis of Streptococcal Pharyngitis by Detection of
Streptococcus pyogenes
in Posterior Pharyngeal versus Oral Cavity Specimens
Authors: Fox James W. , Marcon Mario J. , Bonsu Bema K.
Published: July 2006

Carbohydrate antigen detection, nucleic acid probe detection, and bacterial culture are commonly used to confirm group A streptococcus (GAS) pharyngitis. Compared to standard throat swab specimens, the sensitivities of these tests with mouth specimens are poor. When testing for GAS pharyngitis, the throat remains the optimum site for sampling.
Voriconazole Susceptibilities of Dermatophyte Isolates Obtained from a Worldwide Tinea Capitis Clinical Trial
Authors: Ghannoum M. , Isham N. , Sheehan D.
Published: July 2006

In this study, the voriconazole susceptibilities of dermatophyte isolates obtained from a worldwide tinea capitis trial were compared to their susceptibilities to fluconazole and griseofulvin. The MIC ranges of voriconazole, fluconazole, and griseofulvin, were 0.002 to 0.06 μg/ml, 0.25 to 32 μg/ml, and 0.125 to 2.0 μg/ml, respectively.
Effect of Storage Temperature on Survival of
Chlamydia trachomatis
after Lyophilization
Authors: Eley Adrian , Geary Ian , Bahador Abbas , Hakimi Hamid
Published: July 2006

Lyophilized preparations of
Chlamydia trachomatis
were made to investigate how well they would survive storage at four relevant incubation temperatures for 1 week and 1 month. Good viability was maintained by storage at either 4°C or 20°C for 1 week. If the ambient temperature is not too high, short-term transportation of
C. trachomatis
is achievable through lyophilization.
Molecular Characterization of Nontypeable Group B Streptococcus
Authors: Ramaswamy Srinivas V. , Ferrieri Patricia , Flores Aurea E. , Paoletti Lawrence C.
Published: July 2006

Traditionally, the capsular polysaccharide (CPS) antigen has been used to distinguish between the nine known serotypes of group B streptococcus (GBS) by classical antibody-antigen reactions. In this study, we used PCR for all CPSs and selected protein antigens, multilocus sequencing typing (MLST), and pulsed-field gel electrophoresis (PFGE) to molecularly characterize 92 clinical isolates identified as nontypeable (NT) by CPS-specific antibody-antigen reactivity. The PCR and MLST were performed on blinded, randomly numbered isolates. All isolates contained the
cfb
gene coding for CAMP factor. While most (56.5%) contained a single CPS-specific gene, 40 isolates contained either two or three CPS-specific genes. Type V CPS-specific gene was present in 66% of the isolates, and all serotypes except types IV, VII, and VIII were represented. Most (44.5%) of the isolates contained a single protein antigen gene (
bca
,
bac
,
rib
,
alp1
, or
alp3
), and the remaining isolates had multiple protein antigen genes. Of the 61 isolates that had the V CPS-specific gene, 48 (78.6%) had the
alp3
gene. PFGE analysis classified the isolates into 21 profile groups, while MLST analysis divided the isolates into 16 sequence types. Forty-two (69%) of 61 isolates with the V CPS-specific gene were in PFGE profile group 4; 41 of these 42 were sequence type 1 by MLST. These data shed new light on the antigenic complexity of NT GBS isolates, information that can be valuable in the formulation of an effective GBS vaccine.
Clearance ofCellulosimicrobium cellulansBacteremia in a Child without Central Venous Catheter Removal
Authors: Rowlinson Marie-Claire , Bruckner David A. , Hinnebusch Claudia , Nielsen Karin , Deville Jaime G.
Published: July 2006

Cellulosimicrobium cellulans(formerly known asOerskovia xanthineolytica) rarely causes human infection. Infections have been reported in immunocompromised hosts or in patients with foreign bodies, such as catheters, where treatment has generally involved removal of the foreign body. We report on a case in which the organism was isolated in multiple blood cultures from a 13-year-old male. After initial therapy failed, treatment with vancomycin and rifampin resulted in infection clearance without removal of the central venous catheter.
Prevalence of Inducible Clindamycin Resistance among Community- and Hospital-Associated
Staphylococcus aureus
Isolates
Authors: Patel Mukesh , Waites Ken B. , Moser Stephen A. , Cloud Gretchen A. , Hoesley Craig J.
Published: July 2006

Methicillin-resistant
Staphylococcus aureus
(MRSA) infections have become common among both hospitalized and nonhospitalized patients. Optimal outpatient therapy for MRSA infections has yet to be determined, but this matter is complicated by the possibility of inducible macrolide-lincosamide-streptogramin B resistance (MLSBi). We studied the prevalence of MLSBi in community- and hospital-associated
S. aureus
isolates and the prevalence of community-associated MRSA (CA-MRSA) and identified clinical predictors of CA-MRSA and MLSBi. Among 402
S. aureus
isolates, the overall prevalence of MLSBi was 52%, with 50% of MRSA and 60% of methicillin-susceptible
S. aureus
isolates exhibiting MLSBi. CA-MRSA represented 14% of all isolates and had a lower prevalence of MLSBi than hospital-associated MRSA (33% versus 55%). The presence of skin or soft-tissue infection was predictive for CA-MRSA, and the presence of a comorbidity was predictive for MLSBi. Due to the low prevalence of MLSBi among CA-MRSA isolates, clindamycin remains a useful option for outpatient therapy.
Characterization and Comparison of Galactomannan Enzyme Immunoassay and Quantitative Real-Time PCR Assay for Detection of
Aspergillus fumigatus
in Bronchoalveolar Lavage Fluid from Experimental Invasive Pulmonary Aspergillosis
Authors: Francesconi Andrea , Kasai Miki , Petraitiene Ruta , Petraitis Vidmantas , Kelaher Amy M. , Schaufele Robert , Hope William W. , Shea Yvonne R. , Bacher John , Walsh Thomas J.
Published: July 2006

Bronchoalveolar lavage (BAL) is widely used for evaluation of patients with suspected invasive pulmonary aspergillosis (IPA). However, the diagnostic yield of BAL for detection of IPA by culture and direct examination is limited. Earlier diagnosis may be facilitated by assays that can detect
Aspergillus
galactomannan antigen or DNA in BAL fluid. We therefore characterized and compared the diagnostic yields of a galactomannan enzyme immunoassay (GM EIA), quantitative real-time PCR (qPCR), and quantitative cultures in experiments using BAL fluid from neutropenic rabbits with experimentally induced IPA defined as microbiologically and histologically evident invasion. The qPCR assay targeted the rRNA gene complex of
Aspergillus fumigatus
. The GM EIA and qPCR assay were characterized by receiver operator curve analysis. With an optimal cutoff of 0.75, the GM EIA had a sensitivity and specificity of 100% in untreated controls. A decline in sensitivity (92%) was observed when antifungal therapy (AFT) was administered. The optimal cutoff for qPCR was a crossover of 36 cycles, with sensitivity and specificity of 80% and 100%, respectively. The sensitivity of qPCR also decreased with AFT to 50%. Quantitative culture of BAL had a sensitivity of 46% and a specificity of 100%. The sensitivity of quantitative culture decreased with AFT to 16%. The GM EIA and qPCR assay had greater sensitivity than culture in detection of
A. fumigatus
in BAL fluid in experimentally induced IPA (
P
± 0.04). Use of the GM EIA and qPCR assay in conjunction with culture-based diagnostic methods applied to BAL fluid could facilitate accurate diagnosis and more-timely initiation of specific therapy.
OPTICAL NONLINEARITY OF A TRIPHENYLMETHANE DYE AS STUDIED BY Z-SCAN AND SELF-DIFFRACTION TECHNIQUES
Authors: SUNDARI R. MADHANA , PALANISAMY P. K.
Published: July 2006

The optical nonlinearity of an organic dye from a triphenylmethane group is measured using the Z-scan technique. The sample under study is found to exhibit the negative nature of nonlinearity, which is mainly due to the thermally induced refractive index change. Since this thermally induced refractive index change can lead to self-diffraction, the self-diffraction properties of the sample is studied by using thin films of a dye-sensitized gelatin. A He-Ne laser (633 nm) is used for both the Z-scan and self-diffraction studies. In the self-diffraction studies, it is also found that the different diffracted orders exhibit varying phase differences.