bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryptosporidium parvum
Infections in Bergen, Norway, during an Extensive Outbreak of Waterborne Giardiasis in Autumn and Winter 2004
Authors: Robertson L. J. , Forberg T. , Hermansen L. , Gjerde B. K. , Alvsvåg J. O. , Langeland N.
Published: March 2006

During a large waterborne giardiasis outbreak in Norway, many diarrheic patients were found to have
Cryptosporidium
infections. Gene sequencing identified these infections as
Cryptosporidium parvum
infections, although they were not identical. Whether these infections were due to a simultaneous outbreak of waterborne cryptosporidiosis or reflected background levels not normally detected is discussed.
Selective Biodegradation of S and N Heterocycles by a Recombinant
Rhodococcus erythropolis
Strain Containing Carbazole Dioxygenase
Authors: Yu Bo , Xu Ping , Zhu Shanshan , Cai Xiaofeng , Wang Ying , Li Li , Li Fuli , Liu Xiaoyong , Ma Cuiqing
Published: March 2006

The carbazole dioxygenase genes were introduced into a dibenzothiophene degrader. The recombinant
Rhodococcus erythropolis
SN8 was capable of efficiently degrading dibenzothiophene and carbazole simultaneously. SN8 could also degrade various alkylated derivatives of carbazole and dibenzothiophene in FS4800 crude oil by just a one-step bioprocess.
Diverse and Unique Picocyanobacteria in Chesapeake Bay, Revealed by 16S-23S rRNA Internal Transcribed Spacer Sequences
Authors: Chen Feng , Wang Kui , Kan Jinjun , Suzuki Marcelino T. , Wommack K. Eric
Published: March 2006

rRNA internal transcribed spacer phylogeny showed that Chesapeake Bay is populated with diverse
Synechococcus
strains, including members of the poorly studied marine cluster B. Marine cluster B prevailed in the upper bay, while marine cluster A was common in the lower bay. Interestingly, marine cluster B
Synechococcus
included phycocyanin- and phycoerythrin-rich strains.
Analysis of the Clonal Relationship of Shiga Toxin-Producing
Escherichia coli
Serogroup O165:H25 Isolated from Cattle
Authors: Geue Lutz , Selhorst Thomas , Schnick Christina , Mintel Birgit , Conraths Franz J.
Published: March 2006

Variations in time and space of a clonal group of
Escherichia coli
O165:H25 on a cattle farm were monitored. The virulence marker pattern (
stx
genes,
eae
gene,
hly
EHEC
gene,
katP
gene,
espP
gene,
efa
gene) suggests that
E. coli
O165:H25 of bovine origin may represent a risk for human infection.
Casein-Derived Antimicrobial Peptides Generated by
Lactobacillus acidophilus
DPC6026
Authors: Hayes M. , Ross R. P. , Fitzgerald G. F. , Hill C. , Stanton C.
Published: March 2006

Three peptides produced by a
Lactobacillus acidophilus
DPC6026 fermentation of sodium caseinate and showing antibacterial activity against pathogenic strains
Enterobacter sakazakii
ATCC 12868 and
Escherichia coli
DPC5063 were characterized. These peptides were all generated from bovine α
s1
-casein and identified as IKHQGLPQE, VLNENLLR, and SDIPNPIGSENSEK. These peptides may have bioprotective applicability and potential use in milk-based formula, which has been linked to
E. sakazakii
infection in neonates.
Analysis of Feces Samples Collected from a Wild-Bird Garden Feeding Station in Scotland for the Presence of Verocytotoxin-Producing
Escherichia coli
O157
Authors: Foster Geoffrey , Evans Judith , Knight Hazel I. , Smith Alastair W. , Gunn George J. , Allison Lesley J. , Synge Barti A. , Pennycott Tom W.
Published: March 2006

Composite wild bird feces collected at regular intervals from a garden feeding station in southwest Scotland over a 3-year period were examined for verocytotoxin-producing
Escherichia coli
O157. One sample was positive for
Escherichia coli
O157. The isolate belonged to phage type 21/28 and possessed
vtx
2
,
eaeA
, and enterohemorrhagic
E. coli hlyA
genes.
Complementation of the
Lactococcus lactis
Secretion Machinery with
Bacillus subtilis
SecDF Improves Secretion of Staphylococcal Nuclease
Authors: Nouaille S. , Morello E. , Cortez-Peres N. , Le Loir Y. , Commissaire J. , Gratadoux J. J. , Poumerol E. , Gruss A. , Langella P.
Published: March 2006

Unlike
Bacillus subtilis
and
Escherichia coli
, the gram-positive lactic acid bacterium
Lactococcus lactis
does not possess the SecDF protein, a component of the secretion (Sec) machinery involved in late secretion stages and required for the high-capacity protein secretion in
B. subtilis
. In this study, we complemented the
L. lactis
Sec machinery with SecDF from
B. subtilis
and evaluated the effect on the secretion of two forms of staphylococcal nuclease, NucB and NucT, which are efficiently and poorly secreted, respectively. The
B. subtilis
SecDF-encoding gene was tested in
L. lactis
at different levels. Increased quantities of the precursor and mature forms were observed only at low levels of SecDF and at high NucT production levels. This SecDF secretion enhancement was observed at the optimal growth temperature (30°C) and was even greater at 15°C. Furthermore, the introduction of
B. subtilis
SecDF into
L. lactis
was shown to have a positive effect on a secreted form of
Brucella abortus
L7/L12 antigen.
Conversion of
Sphingobium chlorophenolicum
ATCC 39723 to a Hexachlorobenzene Degrader by Metabolic Engineering
Authors: Yan Da-Zhong , Liu Hong , Zhou Ning-Yi
Published: March 2006

The gene cassette (
camA
+
camB
+
camC
) encoding a cytochrome P-450
cam
variant was integrated into the nonessential gene
pcpM
of the pentachlorophenol degrader
Sphingobium chlorophenolicum
ATCC 39723 by homologous recombination. The recombinant strain could degrade hexachlorobenzene at a rate of 0.67 nmol · mg (dry weight)
−1
· h
−1
, and intermediate pentachlorophenol was also identified.
Prophagic DNA Fragments in
Streptococcus agalactiae
Strains and Association with Neonatal Meningitis
Authors: van der Mee-Marquet Nathalie , Domelier Anne-Sophie , Mereghetti Laurent , Lanotte Philippe , Rosenau Agnès , van Leeuwen Willem , Quentin Roland
Published: March 2006

We identified—by randomly amplified polymorphic DNA (RAPD) analysis at the population level followed by DNA differential display, cloning, and sequencing—three prophage DNA fragments (F5, F7, and F10) in
Streptococcus agalactiae
that displayed significant sequence similarity to the DNA of
S. agalactiae
and
Streptococcus pyogenes
. The F5 sequence aligned with a prophagic gene encoding the large subunit of a terminase, F7 aligned with a phage-associated cell wall hydrolase and a phage-associated lysin, and F10 aligned with a transcriptional regulator (
ArpU
family) and a phage-associated endonuclease. We first determined the prevalence of F5, F7, and F10 by PCR in a collection of 109 strains isolated in the 1980s and divided into two populations: one with a high risk of causing meningitis (HR group) and the other with a lower risk of causing meningitis (LR group). These fragments were significantly more prevalent in the HR group than in the LR group (
P
< 0.001). Our findings suggest that lysogeny has increased the ability of some
S. agalactiae
strains to invade the neonatal brain endothelium. We then determined the prevalence of F5, F7, and F10 by PCR in a collection of 40 strains recently isolated from neonatal meningitis cases for comparison with the cerebrospinal fluid (CSF) strains isolated in the 1980s. The prevalence of the three prophage DNA fragments was similar in these two populations isolated 15 years apart. We suggest that the prophage DNA fragments identified have remained stable in many CSF
S. agalactiae
strains, possibly due to their importance in virulence or fitness.
Use of Flocked Swabs and a Universal Transport Medium To Enhance Molecular Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
Authors: Chernesky Max , Castriciano Santina , Jang Dan , Smieja Marek
Published: March 2006

The use of new flocked swabs, compared to kit swabs, enhanced the ability of three commercial nucleic acid amplification tests to detect low levels of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
nucleic acids when the organisms were diluted in a universal transport medium as mocked specimens.
Comparison of Testing Methods for Detection of Decreased Linezolid Susceptibility Due to G2576T Mutation of the 23S rRNA Gene in
Enterococcus faecium
and
Enterococcus faecalis
Authors: Qi Chao , Zheng Xiaotian , Obias Arlene , Scheetz Marc H. , Malczynski Michael , Warren John R.
Published: March 2006

E-test, Vitek 2, MicroScan, agar dilution, and disk diffusion were compared for detection of decreased linezolid susceptibility due to 23S rRNA gene G2576T mutation among 32 clinical
Enterococcus
strains initially reported as intermediate or resistant by E-test alone or Vitek 2 confirmed by E-test. Agar and broth dilution methods were in concordance with PCR detection of the mutation, and disk diffusion was somewhat less sensitive but equally specific.
Accuracy of Three Automated Systems (MicroScan WalkAway, VITEK, and VITEK 2) for Susceptibility Testing of
Pseudomonas aeruginosa
against Five Broad-Spectrum Beta-Lactam Agents
Authors: Sader Helio S. , Fritsche Thomas R. , Jones Ronald N.
Published: March 2006

One hundred recent clinical
Pseudomonas aeruginosa
isolates were used to assess the quantitative (MIC) and qualitative (susceptibility category) accuracies of the MicroScan WalkAway, VITEK, and VITEK 2 automated susceptibility test systems when five-broad spectrum β-lactams, aztreonam, cefepime, ceftazidime, imipenem, and piperacillin-tazobactam, were tested. Isolates were selected so that the MICs for the isolates overrepresented the MICs near the breakpoints to assess precisely the agreement between the results obtained with the automated systems and the results obtained by the reference tests. The categorical and MIC results from the automated systems were compared to the consensus result of three reference methods: broth microdilution, agar dilution, and disk diffusion. The consensus categorical testing (susceptibility and resistance) rates were 47 and 27%, respectively, for aztreonam; 59 and 14%, respectively, for cefepime; 44 and 43%, respectively, for ceftazidime; 71 and 19%, respectively, for imipenem; and 50 and 50%, respectively, for piperacillin-tazobactam. All systems tested exhibited a high, unacceptable level of very major (false-susceptible) errors for piperacillin-tazobactam (19 to 27%). Major (false-resistant) error rates were generally acceptable (0 to 3%), but minor error rates were elevated (8 to 32%) for cefepime (VITEK 2 and VITEK) and for aztreonam (all three systems), leading to consistent trends toward false resistance. Manufacturer reevaluation of these automated systems for the testing of selected β-lactams with current clinical isolates of
P. aeruginosa
that exhibit contemporary resistance mechanisms would be prudent to minimize the potential for serious reporting errors.
Application of UL144 Molecular Typing To Determine Epidemiology of Cytomegalovirus Infections in Preterm Infants
Authors: Stranska R. , Schuurman R. , Toet M. , Verboon-Maciolek M. , de Vries L. S. , van Loon A. M.
Published: March 2006

Sequence analysis of the UL144 gene of human cytomegalovirus (CMV) was used to investigate the epidemiology of CMV infections in preterm infants. Nosocomial transmission of CMV from congenitally infected infant to preterm twins was excluded based on distinct molecular profiles of CMV strains. Indistinguishable molecular profiles between strains from the mother and the infant indicated postnatal acquisition of CMV through breastfeeding.
Detection of Human Bocavirus in Japanese Children with Lower Respiratory Tract Infections
Authors: Ma Xiaoming , Endo Rika , Ishiguro Nobuhisa , Ebihara Takashi , Ishiko Hiroaki , Ariga Tadashi , Kikuta Hideaki
Published: March 2006

Human bocavirus (HBoV), a newly cloned human virus of the genus
Bocavirus
, was detected by PCR from nasopharyngeal swab samples (8 of 318; 5.7%) collected from children with lower respiratory tract infections. HBoV may be one of the causative agents of lower respiratory tract infections in young children.
Distribution of the Serine-Aspartate Repeat Protein-Encoding
sdr
Genes among Nasal-Carriage and Invasive
Staphylococcus aureus
Strains
Authors: Sabat Artur , Melles Damian C. , Martirosian Gayane , Grundmann Hajo , van Belkum Alex , Hryniewicz Waleria
Published: March 2006

The
sdr
locus was found in all 497 investigated
Staphylococcus aureus
strains, although in 29 strains it contained only the
sdrC
gene (
sdrD
negative,
sdrE
negative). The
sdrC
-positive,
sdrD
-negative,
sdrE
-negative gene profile was exclusive to methicillin-sensitive
S. aureus
(MSSA) strains (Fisher's exact test;
P
= 0.0005) and was not found in the strains collected from bone infections (
P
= 0.0019). We also found a strong association between the presence of the
sdrD
gene and methicillin-resistant
S. aureus
strains (
P
< 0.0001). Our findings suggest that MSSA strains with the newly uncovered
sdrC
-positive,
sdrD
-negative,
sdrE
-negative gene profile have a substantially decreased potential to establish bone infection.
Evaluation of a Rapid Gram Stain Interpretation Method for Diagnosis of Bacterial Vaginosis
Authors: Hilmarsdóttir I. , Hauksdóttir G. S. , Jóhannesdóttir J. D. , Daníelsdóttir T. , Thorsteinsdóttir H. , Ólafsson J. H.
Published: March 2006

A simple Gram stain evaluation for the diagnosis of bacterial vaginosis was assessed in comparison to Nugent's method. The sensitivity (90%), specificity (94%), positive and negative predictive values (90% and 94%), and good interobserver agreement obtained indicate that the test method can be performed reliably in the routine clinical microbiology laboratory.
Novel Multiplex PCR Assay for Detection of the Staphylococcal Virulence Marker Panton-Valentine Leukocidin Genes and Simultaneous Discrimination of Methicillin-Susceptible from -Resistant Staphylococci
Authors: McClure Jo-Ann , Conly John M. , Lau Vicky , Elsayed Sameer , Louie Thomas , Hutchins Wendy , Zhang Kunyan
Published: March 2006

We developed a new multiplex PCR assay for detection of Panton-Valentine leukocidin virulence genes and simultaneous discrimination of methicillin-susceptible from -resistant staphylococci. This assay is simple, rapid, and accurate and offers the potential for prompt detection of newly emerging community-associated methicillin-resistant
Staphylococcus aureus
.
Effective Detection of Toxigenic
Clostridium difficile
by a Two-Step Algorithm Including Tests for Antigen and Cytotoxin
Authors: Ticehurst John R. , Aird Deborah Z. , Dam Lisa M. , Borek Anita P. , Hargrove John T. , Carroll Karen C.
Published: March 2006

We evaluated a two-step algorithm for detecting toxigenic
Clostridium difficile
: an enzyme immunoassay for glutamate dehydrogenase antigen (Ag-EIA) and then, for antigen-positive specimens, a concurrent cell culture cytotoxicity neutralization assay (CCNA). Antigen-negative results were ≥99% predictive of CCNA negativity. Because the Ag-EIA reduced cell culture workload by ≈75 to 80% and two-step testing was complete in ≤3 days, we decided that this algorithm would be effective. Over 6 months, our laboratories' expenses were US$143,000 less than if CCNA alone had been performed on all 5,887 specimens.
Comparative Prevalence of Virulence Factors in
Escherichia coli
Causing Urinary Tract Infection in Male Infants with and without Bacteremia
Authors: Bonacorsi Stéphane , Houdouin Véronique , Mariani-Kurkdjian Patricia , Mahjoub-Messai Farah , Bingen Edouard
Published: March 2006

Escherichia coli
isolates causing urinary tract infection in 83 male infants younger than 90 days with and without bacteremia were compared for phylogenetic groups and the presence of 10 virulence factors. Our result suggest that the absence of both hemolysin and antigen K1 may be used as a negative predictive factor for bacteremia.
Molecular Identification of
Tritrichomonas foetus
-Like Organisms as Coinfecting Agents of Human
Pneumocystis
Pneumonia
Authors: Duboucher Christophe , Caby Stéphanie , Dufernez Fabienne , Chabé Magali , Gantois Nausicaa , Delgado-Viscogliosi Pilar , Billy Christophe , Barré Eric , Torabi Edith , Capron Monique , Pierce Raymond J. , Dei-Cas Eduardo , Viscogliosi Eric
Published: March 2006

Trichomonads closely related to the bovid parasite
Tritrichomonas foetus
were identified in the bronchoalveolar lavage sample from a patient with AIDS in association with
Pneumocystis
pneumonia. This human case of
T. foetus
-like infection emphasizes the zoonotic potential of trichomonads, although the existence of a human-host-adapted
T. foetus
strain cannot be excluded.
Usefulness of Eschar PCR for Diagnosis of Scrub Typhus
Authors: Lee Seung-Hyun , Kim Dong-Min , Cho Young Shin , Yoon Sung Ho , Shim Soo Kyoung
Published: March 2006

We report here on the case of a child who was infected with scrub typhus, and we made the diagnosis according to the serology and by performing PCRs on the child's eschar. The patient was treated with azithromycin, and he did not experience any complications. Performing nested PCR on the eschar might be both a rapid diagnostic test for scrub typhus in the early acute stage and a differential test as to whether or not a scab is a scrub typhus eschar.
Treatment Failure Due to Emergence of Resistance to Carbapenem during Therapy for
Shewanella algae
Bacteremia
Authors: Kim Dong-Min , Kang Cheol-In , Lee Chang Seop , Kim Hong-Bin , Kim Eui-Chong , Kim Nam Joong , Oh Myoung-don , Choe Kang-Won
Published: March 2006

We describe a case of bacteremia due to imipenem-susceptible
Shewanella algae
. Despite treatment with imipenem, the patient developed a spinal epidural abscess, from which imipenem-resistant
S. algae
was isolated. The development of resistance should be monitored when
S. algae
infection is treated with imipenem, even though the strain is initially susceptible to imipenem.
Use of DNA Sequencing Analysis To Confirm Fungemia Due to
Trichosporon dermatis
in a Pediatric Patient
Authors: Gunn Shelly R. , Reveles Xavier T. , Hamlington Jeanette D. , Sadkowski Lee C. , Johnson-Pais Teresa L. , Jorgensen James H.
Published: March 2006

This is the first reported case of human disease caused by
Tricosporon dermatis
, an organism recently transferred to the genus
Trichosporon
from
Cryptococcus
and now confirmed to be a human pathogen.
Post-Kala-Azar Dermal Leishmaniasis Due to
Leishmania infantum
in a Human Immunodeficiency Virus Type 1-Infected Patient
Authors: Stark D. , Pett S. , Marriott D. , Harkness J.
Published: March 2006

We report the first case of post-kala-azar dermal leishmaniasis due to
Leishmania infantum
in a human immunodeficiency virus type 1-infected patient in Australia. Molecular characterization of the isolate was performed using PCR restriction fragment length polymorphism targeting both repetitive sequences from
Leishmania
nuclear DNA and repetitive kinetoplast DNA minicircles for species differentiation.
Use of Enzyme-Linked Immunospot Assay with
Mycobacterium tuberculosis
- Specific Peptides for Diagnosis of Recent Infection with
M. tuberculosis
after Accidental Laboratory Exposure
Authors: Leyten Eliane M. S. , Mulder Bert , Prins Corine , Weldingh Karin , Andersen Peter , Ottenhoff Tom H. M. , van Dissel Jaap T. , Arend Sandra M.
Published: March 2006

This report of an accidental exposure to
Mycobacterium tuberculosis
in a microbiological laboratory illustrates the value of gamma interferon enzyme-linked immunospot assay using peptides of ESAT-6, CFP-10, TB37.6, and TB7.7 for the diagnosis of latent infection. In particular, positive responses to peptides 2 to 6 of TB37.6 were observed exclusively in recently infected persons.
Phylogenetic, Virological, and Clinical Characteristics of Genotype C Hepatitis B Virus with TCC at Codon 15 of the Precore Region
Authors: Chan Henry Lik-Yuen , Tse Chi-Hang , Ng Eddie Yuen-Tok , Leung Kwong-Sak , Lee Kin-Hong , Tsui Stephen Kwok-Wing , Sung Joseph Jao-Yiu
Published: March 2006

Hepatitis B virus (HBV) with T-1856 of the precore region is always associated with C-1858 (i.e., TCC at nucleotides 1856 to 1858), and it is reported only in genotype C HBV isolates. We aimed to investigate the phylogenetic, virological, and clinical characteristics of HBV isolates bearing TCC at nucleotides 1856 to 1858. We have previously reported on the presence of two major subgroups in genotype C HBV, namely, HBV genotype Cs (Southeast Asia) and HBV genotype Ce (Far East). We have designed a novel 5′ nuclease technology based on the nucleotide polymorphism (C or A) at nucleotide 2733 to differentiate the two genotype C HBV subgroups. The mutations at the basal core promoter and precore regions were analyzed by direct sequencing. Among 214 genotype C HBV-infected patients, 31% had TCC, 37% had CCC, 3% had CTC, and 29% had CCT at nucleotides 1856 to 1858. All except one HBV strain with TCC at nucleotides 1856 to 1858 belonged to subgroup Cs, which has been reported only in Hong Kong; Guangzhou, China; and Vietnam. HBV with TCC at nucleotides 1856 to 1858 was associated with the G1898A mutation (64%). Patients infected with HBV harboring TCC had more liver cirrhosis than those infected with HBV harboring CCC (18% versus 5%;
P
= 0.008), and more of the patients infected with HBV harboring TCC were positive for HBeAg (58% versus 36%;
P
= 0.01) and had higher median alanine aminotransferase levels (65 IU/liter versus 49 IU/liter;
P
= 0.006); but similar proportions of patients infected with HBV harboring TCC and those infected with HBV harboring CCT had liver cirrhosis (18% versus 13%;
P
= 0.43). In summary, we report that HBV with TCC at nucleotides 1856 to 1858 of the precore region might represent a specific HBV strain associated with more aggressive liver disease than other genotype C HBV strains.
Multicenter Laboratory Validation of the BACTEC MGIT 960 Technique for Testing Susceptibilities of
Mycobacterium tuberculosis
to Classical Second-Line Drugs and Newer Antimicrobials
Authors: Rüsch-Gerdes Sabine , Pfyffer Gaby E. , Casal Manuel , Chadwick Maureen , Siddiqi Salman
Published: March 2006

The BACTEC MGIT 960 system, a fully automated, nonradiometric, noninvasive system for detection and drug susceptibility testing of mycobacteria, was evaluated for the ability to test susceptibilities to second-line drugs. In this study, which was carried out in three phases (phase I, mostly susceptible strains; phase II, mostly resistant strains; phase III, final testing of the optimal drug concentrations found in phases I and II), we established the critical concentrations for seven drugs to be tested in the BACTEC MGIT 960 system compared to the BACTEC 460TB system. The critical concentrations for the seven drugs used in the MGIT 960 system are as follows: amikacin, 1.0 μg/ml; capreomycin, 2.5 μg/ml; ethionamide, 5.0 μg/ml; protionamide, 2.5 μg/ml; ofloxacin, 2.0 μg/ml; rifabutin, 0.5 μg/ml; linezolid, 1.0 μg/ml. Our results demonstrate that the BACTEC MGIT 960 system is an accurate method for rapid testing of the susceptibilities of
Mycobacterium tuberculosis
to second-line drugs.
Sensitivities of Antigen Detection and PCR Assays Greatly Increased Compared to That of the Standard Culture Method for Screening for Group B Streptococcus Carriage in Pregnant Women
Authors: Rallu Fabien , Barriga Peter , Scrivo Carole , Martel-Laferrière Valérie , Laferrière Céline
Published: March 2006

Group B streptococcus (GBS) is a major cause of serious infections in neonates. The 2002 revised guidelines of the Centers for Disease Control and Prevention (CDC) for the prevention of perinatal GBS disease recommend that all pregnant women be screened for GBS carriage at between 35 and 37 weeks of gestation and that intrapartum antibiotic prophylaxis be given to carriers. We studied the performances of four different GBS detection assays in the context of antenatal screening. Between May and August 2004, the 605 vaginorectal swab specimens received at our bacteriology laboratory for GBS antenatal detection were tested by the four assays. The standard culture method was done according to the CDC recommendations. The three experimental assays performed with the growth from the selective enrichment (LIM) broth (Todd-Hewitt broth with 15 μg/ml nalidixic acid and 10 μg/ml colistin) after overnight incubation were a GBS antigen detection assay (PathoDx) and two PCR assays (for
cfb
and
scpB
). The most accurate assay was the
scpB
PCR (sensitivity, 99.6%; specificity, 100%), followed by the
cfb
PCR (sensitivity, 75.3%; specificity, 100%), GBS antigen detection (sensitivity, 57.3%; specificity, 99.5%), and standard culture (sensitivity, 42.3%; specificity, 100%). The GBS antigen detection assay was found to be more sensitive than the standard culture method, and moreover, the assay has a low cost and is easy to perform in all obstetrical centers which have access to the most basic of diagnostic microbiology services. We believe that antigen detection on incubated LIM broth should replace the standard culture method for screening for GBS carriage at 35 to 37 weeks of gestation. The impact of the greater sensitivities of PCR assays on the diminution of neonatal GBS infections remains to be demonstrated.
Comparison of Conventional PCR with Real-Time PCR and Branched DNA-Based Assays for Hepatitis C Virus RNA Quantification and Clinical Significance for Genotypes 1 to 5
Authors: Sarrazin Christoph , Gärtner Barbara C. , Sizmann Dorothea , Babiel Rainer , Mihm Ulrike , Hofmann Wolf Peter , von Wagner Michael , Zeuzem Stefan
Published: March 2006

The key parameter for diagnosis and management of hepatitis C virus (HCV) infection is HCV RNA. Standardization of HCV RNA assays to IU is mainly based on genotype 1 panels. Little is known about the variability of commercially available HCV RNA assays for quantification of different genotypes. Two real-time reverse transcription (RT)-PCR assays (COBAS TaqMan HCV Test for use with the High-Pure System [HPS/CTM] and COBAS Ampliprep/COBAS TaqMan HCV Test [CAP/CTM]), one standard RT-PCR assay (COBAS Amplicor HCV Monitor 2.0 [CAM]), and one signal amplification assay (Versant Quantitative 3.0 [branched DNA {bDNA}]) were compared for quantification of genotypes 1 to 5 (n= 108). Using CAM as a reference assay for genotype 1-infected patients, the mean interassay differences compared with CAP/CTM, HPS/CTM, and bDNA were 0.16, −0.13, and −0.48 log10IU/ml HCV RNA, respectively. Comparison of CAM with CAP/CTM, HPS/CTM, and bDNA for the remaining genotypes showed the following results, respectively: 2a/c, −0.24, −0.78, and −0.49; 2b, −0.21, −0.18, and −0.64; 3a, 0.13, −1.04, and −0.55; 4, −0.52, −1.51, and −0.05; and 5, −0.28, −1.00, and −0.24 log IU/ml HCV RNA. A correct decision for treatment discontinuation in genotype 1 patients at week 12 was possible only when the same assay was used at baseline and week 12. Comparison of CAM with the CAP/CTM assay showed equal quantifications of genotype 1, 2, 3, and 5 samples, while genotype 4 samples were slightly underestimated. For the HPS/CTM assay, a significant underestimation of the HCV RNA concentrations of genotypes 2a/c, 3, 4, and 5 was observed. For the bDNA assay, a constant lower quantification of genotypes 1 to 3 was detected.
Prevalence and Spread of Enterohepatic
Helicobacter
Species in Mice Reared in a Specific-Pathogen-Free Animal Facility
Authors: Bohr U. R. M. , Selgrad M. , Ochmann C. , Backert S. , König W. , Fenske A. , Wex T. , Malfertheiner P.
Published: March 2006

Infections with enterohepatic
Helicobacter
species (EHS) can change the results of animal experiments. However, there is little information about the prevalence of EHS in noncommercial animal facilities. The aim of this study was to investigate the prevalence and the spread of EHS in specific-pathogen-free (SPF) mice. Fecal samples of 40 mouse lines were analyzed for members of the family
Helicobacteraceae
using a group-specific PCR targeting the 16S rRNA gene. Additional experiments were carried out to evaluate the spread of EHS among mice harbored in different caging systems.
Helicobacter
species were detected in 87.5% of the mouse lines tested. Five different
Helicobacter
species were identified:
H. ganmani
,
H. hepaticus
,
H. typhlonicus
, and the putative
Helicobacter
species represented by the isolates hamster B and MIT 98-5357.
Helicobacter
infection did not spread between animals in neighboring cages when individually ventilated cages were used; in contrast, when the mice were reared in open-air cages, EHS were found to spread from cage to cage. However, the spread was prevented by adding polycarbonate filter tops to the cages. When
Helicobacter-
negative and infected mice shared the same cage, transmission of the infection occurred in 100% within 2 weeks. Furthermore, we found that mice from commercial breeding facilities may carry undetected
Helicobacter
infections. Taken together, we show that infection with EHS may frequently occur and spread easily in mice reared under SPF conditions despite extensive safety precautions. Moreover, there is a high prevalence of rather uncommon
Helicobacter
species that may be a consequence of the current routine procedures used for health screening of SPF mice.
A Successful, Diverse Disease-Associated Lineage of Nontypeable Pneumococci That Has Lost the Capsular Biosynthesis Locus
Authors: Hanage W. P. , Kaijalainen T. , Saukkoriipi A. , Rickcord J. L. , Spratt B. G.
Published: March 2006

Streptococcus pneumoniae
strains which fail to produce a polysaccharide capsule are commonly isolated from carriage and disease contexts. Here we use a multilocus approach to distinguish genuine nontypeable pneumococci from closely related nontypeable streptococcal isolates in a data set of 121 untypeable pneumococci from nasopharyngeal swabs and middle ear fluid of Finnish children and demonstrate that 70 of these belong to a pneumococcal lineage which has lost its capsular locus. Strains of this relatively old lineage include sequence types 344, 448, and 449. Comparison with the multilocus sequence typing database shows that strains of this lineage have spread intercontinentally and have been isolated from carriage, mucosal, and invasive disease. Furthermore we note a particular association of this nontypeable lineage with outbreaks of conjunctivitis. The diversification and geographic spread of this lineage suggest that loss of capsule is not inconsistent with long-term persistence and raise questions about the capsule's role in pneumococcal transmission.
In Vitro Susceptibilities of
Candida
spp. to Caspofungin: Four Years of Global Surveillance
Authors: Pfaller M. A. , Boyken L. , Hollis R. J. , Messer S. A. , Tendolkar S. , Diekema D. J.
Published: March 2006

Caspofungin is being used increasingly as therapy for invasive candidiasis. Prospective sentinel surveillance for emergence of in vitro resistance to caspofungin among invasive
Candida
spp. isolates is indicated. We determined the in vitro activity of caspofungin against 8,197 invasive (bloodstream or sterile-site) unique patient isolates of
Candida
collected from 91 medical centers worldwide from 1 January 2001 to 31 December 2004. We performed antifungal susceptibility testing according to the Clinical and Laboratory Standards Institute (CLSI, formerly NCCLS) M27-A2 method and used a 24-h prominent inhibition endpoint for determination of the MIC. Of 8,197 invasive
Candida
spp. isolates, species distribution was as follows: 54%
Candida albicans
, 14%
C. glabrata
, 14%
C. parapsilosis
, 11%
C. tropicalis
, 3%
C. krusei
, and 4% other
Candida
spp. Overall, caspofungin was very active against
Candida
(MIC
50
/MIC
90
, 0.03/0.25 μg/ml; 98.2% were inhibited at a MIC of ≤0.5 μg/ml and 99.7% were inhibited at a MIC of ≤1 μg/ml). Results by species (expressed as MIC
50
/MIC
90
and the percentage inhibited at ≤1 μg/ml) were as follows:
C. albicans
, 0.03/0.06, 99.9;
C. glabrata
, 0.03/0.06, 99.9;
C. parapsilosis
, 0.5/0.5, 99.0;
C. tropicalis
, 0.03/0.06, 99.7;
C. krusei
, 0.12/0.5, 99.0; and
C. guilliermondii
, 0.5/1, 94.4. Of the 25 isolates with caspofungin MICs of >1 μg/ml, 12 isolates were
C. parapsilosis
, 6 isolates were
C. guilliermondii
, 2 isolates were
C. rugosa
, and 1 isolate each was
C. albicans
,
C. glabrata
,
C. krusei
,
C. lusitaniae
, and
C. tropicalis
. There was no significant change in caspofungin activity over the 4-year study period. Likewise, there was no difference in activity by geographic region. Caspofungin has excellent in vitro activity against invasive clinical isolates of
Candida
from centers worldwide. Our prospective sentinel surveillance reveals no evidence of emerging caspofungin resistance among invasive clinical isolates of
Candida
.
Peptide Mimotopes Selected from a Random Peptide Library for Diagnosis of Epstein-Barr Virus Infection
Authors: Casey Joanne L. , Coley Andrew M. , Street Graham , Parisi Kathy , Devine Peter L. , Foley Michael
Published: March 2006

Epstein-Barr virus (EBV) is a ubiquitous, worldwide infectious agent that causes infectious mononucleosis, affecting >90% of the world's population. Currently, enzyme-linked immunosorbent assay, mostly with purified preparations of EBV cell extracts to capture immunoglobulin M (IgM) antibodies in patients' serum, is used for primary diagnosis. Our objective was to determine whether a small set of peptides could contain sufficient immunogenic information to replace solid-phase antigens in EBV diagnostics. Using monoclonal antibodies, we selected four peptides that mimic different epitopes of EBV from a phage-displayed random peptide library. To assess their diagnostic value, we screened a panel of 62 individual EBV IgM sera for their reactivities with the peptides alone. For all peptides, there was a clear distinction between the EBV-positive and the EBV-negative samples, resulting in 100% specificity. The sensitivities were 88%, 85%, 71%, and 54% for peptides F1, A3, gp125, and A2, respectively. Any combination of peptides increased the sensitivity, indicating that individual peptides react with different subsets of antibodies. Furthermore, when the F1 and the gp125 peptides were coupled to bovine serum albumin and screened against 216 serum samples, there were dramatic improvements in sensitivities (95% and 92%, respectively) and little cross-reactivity with the other peptides encountered during acute viral infections, including rheumatoid factor. This study shows the potential for the use of peptide mimotopes as alternatives to the complex antigens used in current serodiagnostics for EBV infection.
Single-Nucleotide Repeat Analysis for Subtyping
Bacillus anthracis
Isolates
Authors: Stratilo Chad W. , Lewis Christopher T. , Bryden Louis , Mulvey Michael R. , Bader Doug
Published: March 2006

Single-nucleotide repeats (SNRs) are variable-number tandem repeats that display very high mutation rates. In an outbreak situation, the use of a marker system that exploits regions with very high mutation rates, such as SNRs, allows the differentiation of isolates with extremely low levels of genetic diversity. This report describes the identification and analysis of SNR loci of
Bacillus anthracis
. SNR loci were selected in silico, and the loci with the highest diversity were used to design and test locus-specific primers against a number of
B. anthracis
strains with the same multilocus variable-number tandem repeat analysis (MLVA) genotype. SNR markers that allowed strains with the same MLVA genotype to be differentiated from each other were identified. The resulting SNR marker system can be used as a molecular epidemiological tool in a natural outbreak or bioterrorism event, offering the best chance of distinguishing very closely related isolates.
Multiple Viral Infections and Genomic Divergence among Noroviruses during an Outbreak of Acute Gastroenteritis
Authors: Sasaki Yukiko , Kai Akemi , Hayashi Yukinao , Shinkai Takayuki , Noguchi Yayoi , Hasegawa Michiya , Sadamasu Kenji , Mori Kohji , Tabei Yukiko , Nagashima Mami , Morozumi Satoshi , Yamamoto Tomoko
Published: March 2006

An epidemic outbreak of both norovirus (NV) and astrovirus (ASV) occurred on a research ship surveying Tokyo Bay, causing acute gastroenteritis in 26 of its 37 crew members. The presence of viral pathogens in fecal specimens was analyzed, and noroviruses were identified by reverse transcription-PCR in 18 (48.6%) of these specimens. In addition, astroviruses were identified in 14 (37.8%) of the fecal samples from the affected crew members, and multiple viral infections of both NV and ASV were observed in 6 cases. The genogrouping of the NV-positive samples was then examined by dot blot hybridization, and it was determined that all of the isolates were from genogroup II (GII). No bacterial pathogens were subsequently isolated from fecal specimens. Furthermore, a variety of NV strains were identified by sequencing and single-stranded conformational polymorphism (SSCP) analyses of PCR products from the fecal samples. One recombinant NV isolate, Minato/14, was identified as a recombinant NV strain of GII/6 and GII/1. The other NV isolates from this outbreak were classified into three NV genotypes (GII/1 [Minato/10], GII/4 [Minato/33], and GII/5 [Minato/6]). Furthermore, ASVs in positive samples were determined to belong to serotypes 1 and 2 by sequencing analysis. Our findings thus indicate that coinfections with NV and ASV, including a number of NV genotypes, persisted during an outbreak of gastroenteritis in a closed environment.
Genetic Identification of the Main Opportunistic Mucorales by PCR-Restriction Fragment Length Polymorphism
Authors: Machouart M. , Larché J. , Burton K. , Collomb J. , Maurer P. , Cintrat A. , Biava M. F. , Greciano S. , Kuijpers A. F. A. , Contet-Audonneau N. , de Hoog G. S. , Gérard A. , Fortier B.
Published: March 2006

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera
Absidia
,
Mucor
,
Rhizopus
, and
Rhizomucor
, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis.
Correlation of MIC with Outcome for
Candida
Species Tested against Voriconazole: Analysis and Proposal for Interpretive Breakpoints
Authors: Pfaller M. A. , Diekema D. J. , Rex J. H. , Espinel-Ingroff A. , Johnson E. M. , Andes D. , Chaturvedi V. , Ghannoum M. A , Odds F. C. , Rinaldi M. G. , Sheehan D. J. , Troke P. , Walsh T. J. , Warnock D. W.
Published: March 2006

Developing interpretive breakpoints for any given organism-drug combination requires integration of the MIC distribution, pharmacokinetic and pharmacodynamic parameters, and the relationship between the in vitro activity and outcome from both in vivo and clinical studies. Using data generated by standardized broth microdilution and disk diffusion test methods, the Antifungal Susceptibility Subcommittee of the Clinical and Laboratory Standards Institute has now proposed interpretive breakpoints for voriconazole and
Candida
species. The MIC distribution for voriconazole was determined using a collection of 8,702 clinical isolates. The overall MIC
90
was 0.25 μg/ml and 99% of the isolates were inhibited at ≤1 μg/ml of voriconazole. Similar results were obtained for 1,681
Candida
isolates (16 species) from the phase III clinical trials. Analysis of the available data for 249 patients from six phase III voriconazole clinical trials demonstrated a statistically significant correlation (
P
= 0.021) between MIC and investigator end-of-treatment assessment of outcome. Consistent with parallel pharmacodynamic analyses, these data support the following MIC breakpoints for voriconazole and
Candida
species: susceptible (S), ≤1 μg/ml; susceptible dose dependent (SDD), 2 μg/ml; and resistant (R), ≥4 μg/ml. The corresponding disk test breakpoints are as follows: S, ≥17 mm; SDD, 14 to 16 mm; and R, ≤13 mm.
Chronic Colonization with
Pandoraea apista
in Cystic Fibrosis Patients Determined by Repetitive-Element-Sequence PCR
Authors: Atkinson R. M. , LiPuma J. J. , Rosenbluth D. B. , Dunne W. M.
Published: March 2006

Pandoraea apista
is recovered with increasing frequency from the lungs of patients with cystic fibrosis (CF) and may represent an emerging pathogen (I. M. Jorgensen et al., Pediatr. Pulmonol. 36:439-446, 2003). We identified two CF patients from our hospital whose sputum specimens were culture positive for
P. apista
over the course of several years. Repetitive-element-sequence PCR was employed to determine whether sequential isolates that were recovered from these patients represented a single clone and whether each patient had been chronically colonized with the same strain. Banding patterns generated with ERIC primers, REP primers, and BOX primers showed that individual patient isolates had a high degree of similarity (>97%) and were considered identical. However, only the banding patterns from the ERIC primers and BOX primers were able to show that the strains from patients I and II were unique (similarity indices of 79.8% and 70.0%, respectively). We concluded that all strains of
P. apista
from patient I were identical, as were all strains from patient II, establishing chronic colonization. Only two of the three methods employed indicate that the strains from the two patients are distinct. This implied that the organism was not transferred from one patient to the other, suggesting that the choice of methodology could generate misleading results when examining person-to-person transmission regarding this organism.
Detection of New Methicillin-Resistant
Staphylococcus aureus
Clones Containing the Toxic Shock Syndrome Toxin 1 Gene Responsible for Hospital- and Community-Acquired Infections in France
Authors: Durand Geraldine , Bes Michèle , Meugnier Helene , Enright Mark C. , Forey Françoise , Liassine Nadia , Wenger Aline , Kikuchi Ken , Lina Gerard , Vandenesch François , Etienne Jerome
Published: March 2006

Methicillin-resistant
Staphylococcus aureus
(MRSA) clones harboring the toxic shock syndrome toxin 1 (
tst
) gene have been detected in France and in Switzerland since 2002. During a passive survey conducted between 2002 and 2003, we collected 103
tst-
positive
S. aureus
isolates from 42 towns in France, of which 27 were resistant to methicillin. The
tst-
positive MRSA belonged to two clones: a major clone comprising 25 isolates of sequence type (ST) 5 and
agr
group 2 and a minor clone comprising two isolates of ST30 and
agr3
. The
tst
-positive MRSA clones were associated with both hospital-acquired (12 cases) and community-acquired (8 cases) infections. The MRSA clones were mainly isolated from children (overall median age, 3 years). They caused a variety of clinical syndromes, including toxic shock syndrome and suppurative infections. Both clones were found to harbor a type IV staphylococcal chromosomal cassette
mec
(SCC
mec
) and to have similar antibiotic resistance profiles (usually resistant to oxacillin, kanamycin, and tobramycin and with intermediate resistance to fusidic acid). The origin of these clones is unclear. The
tst
-positive
agr2
MRSA clone has the same sequence type (ST5) of two pandemic nosocomial MRSA clones, namely, the Pediatric clone and the New York/Japan clone. These findings suggest that all these clones are phylogenetically related. The pulsotype of the
tst
-positive MRSA clones differed from that of methicillin-sensitive
S. aureus
(MSSA) clones by a single band involving the SCC
mec
element. These findings suggest that the
tst
-positive MRSA clones may have emerged from their respective MSSA counterparts.
Use of Various Common Isolation Media To Evaluate the New VITEK 2 Colorimetric GN Card for Identification of
Burkholderia pseudomallei
Authors: Lowe Peter , Haswell Helen , Lewis Kirsty
Published: March 2006

The use of automated systems in the modern microbiology laboratory is becoming commonplace as the pressure of cost containment impacts on staff resources. With increased international travel and threats of bioterrorism, recognition and accurate identification of organisms such as
Burkholderia pseudomallei
is important. In areas where this organism is endemic, identification is not usually problematic. This study evaluates the performance of the new VITEK 2 colorimetric GN card for the identification of this organism. A total of 103 previously identified clinical isolates were tested with the new card with isolates taken from MacConkey agar, Columbia horse blood agar, Columbia sheep blood agar, and Trypticase soy agar in order to determine identification performance and to see if there was any variability in results due to the agar. Columbia horse blood agar produced the highest rates of identification (81%), followed by Trypticase soy agar (78%), Columbia sheep blood agar (75%), and MacConkey agar (63%). There was considerable variability in some of the reactions obtained. Seven isolates failed to identify from any of the agars used. This study highlights issues with the identification of this organism with the new VITEK 2 GN card. Enhancements of the algorithm parameters for the GN card are warranted and are in progress. Laboratory personnel need to be aware of the current limitations with this GN card and the software (version 4.02 or older for the VITEK 2 60/XL and version 1.02 or older for VITEK 2 Compact) and rely on clinical history, a high index of suspicion, and basic microbiology tests to confirm the identification of this organism.
Simultaneous Detection and Identification of
Candida
,
Aspergillus
, and
Cryptococcus
Species by Reverse Line Blot Hybridization
Authors: Playford E. Geoffrey , Kong Fanrong , Sun Ying , Wang Hui , Halliday Catriona , Sorrell Tania C.
Published: March 2006

We report on a reverse line blot (RLB) assay, utilizing fungal species-specific oligonucleotide probes to hybridize with internal transcribed spacer 2 region sequences amplified using a nested panfungal PCR. Reference and clinical strains of 16
Candida
species (116 strains),
Cryptococcus neoformans
(five strains of
Cryptococcus neoformans
var.
neoformans
, five strains of
Cryptococcus neoformans
var.
grubii
, and six strains of
Cryptococcus gatti
), and five
Aspergillus
species (68 strains) were all correctly identified by the RLB assay. Additional fungal species (16 species and 26 strains) not represented on the assay did not exhibit cross-hybridization with the oligonucleotide probes. In simulated clinical specimens, the sensitivity of the assay for
Candida
spp. and
Aspergillus
spp. was 10
0.5
cells/ml and 10
2
conidia/ml, respectively. This assay allows sensitive and specific simultaneous detection and identification of a broad range of fungal pathogens.