bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Rotavirus Strains in a Danish Population: High Frequency of Mixed Infections and Diversity within the VP4 Gene of P[8] Strains
Authors: Fischer T. K. , Eugen-Olsen J. , Pedersen A. G. , Mølbak K. , Böttiger B. , Rostgaard K. , Nielsen N. M. 
Published: March 2005

ABSTRACTWe characterized the G and P types from 162 rotavirus-positive stool specimens collected from 162 persons in Denmark (134 children and 28 adults) with acute diarrhea in 1998, 2000, and 2002. Samples were obtained during outpatient consultations (73%) and from hospitalized patients (27%). Although more than 20 different G-P combinations were identified, only 52% represented the globally most common types G1P[8], G2P[4], and G4P[8]. The G9 genotype, which is emerging worldwide, was identified in 12% of all samples. Twenty-one percent of the samples were of mixed genotypic origin, which is the highest frequency reported in any European population. The standard reverse transcription-PCR methods initially failed to identify a considerable fraction of the rotavirus P strains due to mutations at the VP4 primer-binding sites of P[8] strains. The application of a degenerate P[8] primer resulted in typing of most VP4 strains. There was considerable year-to-year variation among the circulating G-P types, and whereas G1P[8] was predominant in 1998 (42% of samples) and 2002 (26%), G2P[4] was the strain that was most frequently detected in 2000 (26% of samples). Our findings might implicate challenges for rotavirus vaccine implementation in a European population and underscore the importance of extensive strain surveillance prior to, during, and after introduction of any vaccine candidate.
Role of Real-Time Molecular Typing in the Surveillance of
Campylobacter
Enteritis and Comparison of Pulsed-Field Gel Electrophoresis Profiles from Chicken and Human Isolates
Authors: Michaud Sophie , Ménard Suzanne , Arbeit Robert D. 
Published: March 2005

ABSTRACT

The goal of the present study was to assess the contribution of real-time molecular typing, used alone or with clinical surveillance, to the prompt identification of clusters of
Campylobacter
enteritis. Potential poultry sources were sought by comparing the pulsed-field gel electrophoresis genotypes of human and fresh whole retail chicken isolates collected during the same study period. Among 183 human isolates, 82 (45%) had unique genotypes, 72 (39%) represented 26 clusters of 2 to 7 isolates each, and 29 (16%) represented three clusters of 8 to 11 isolates each. Molecular typing was useful for the confirmation of outbreaks suspected on the basis of epidemiological surveillance, but for most small clusters, no epidemiological link could be established. Thus, the added value of real-time molecular typing is questionable, since the numerous small clusters identified were of unclear public health significance. Among 177 chickens, 41 (23%) yielded campylobacter isolates; of these, 19 (46%) had genotypes similar to those of 41 (22%) human isolates. However, a temporal association was demonstrated in only a minority of cases, and most genotypes were present only in a single species, suggesting that sources other than chickens are important in human campylobacteriosis. Further investigation with samples from water and other possible environmental sources is needed to define the most efficient strategy for the application of molecular typing and identification of the source(s) of sporadic cases of campylobacteriosis.
Prevalence of Norovirus among Visitors from the United States to Mexico and Guatemala Who Experience Traveler's Diarrhea
Authors: Chapin Amy R. , Carpenter Colleen M. , Dudley William C. , Gibson Lucy C. , Pratdesaba Rafael , Torres Olga , Sanchez Domingo , Belkind-Gerson Jaime , Nyquist Irene , Kärnell Anders , Gustafsson Bjorn , Halpern Jane L. , Bourgeois A. Louis , Schwab Kellogg J. 
Published: March 2005

ABSTRACT

Traveler's diarrhea (TD) is the most common infectious illness acquired by visitors to developing nations. The purpose of this study was to utilize molecular diagnostic techniques to determine the prevalence of norovirus (NoV) in TD occurring among visitors from the United States to Guatemala and Mexico. Stool samples (
n
= 54) were collected from 34 TD cases and analyzed for NoV by reverse transcription-PCR and oligoprobe confirmation. The overall prevalence of NoV was 65%. Interestingly, all NoV-positive stool samples were identified as genogroup I NoVs, and time spent at travel destinations was found to be an important factor in determining the frequency of infection (
P
= 0.003). Eleven NoV-positive stool samples also tested positive for enterotoxigenic
Escherichia coli
, indicating that dual infections with this leading bacterial cause of TD were very common. Results of this study suggest that NoV infection is a frequent occurrence among travelers to Mexico and Guatemala who experience episodes of TD. In addition, the simple molecular detection method utilized here will serve to facilitate more in-depth epidemiological studies of this emergent viral pathogen in travelers and other at-risk populations.
Molecular Subtyping and Characterization of Bovine and HumanStreptococcus agalactiaeIsolates
Authors: Sukhnanand Sharinne , Dogan Belgin , Ayodele Maranatha O. , Zadoks Ruth N. , Craver Mary Patricia J. , Dumas Nellie B. , Schukken Ynte H. , Boor Kathryn J. , Wiedmann Martin 
Published: March 2005

ABSTRACTStreptococcus agalactiaecauses severe invasive disease in humans and mastitis in cattle. Temporally matched bovine milk isolates and clinical human invasive isolates (52 each) collected in New York State over 18 months were characterized by molecular subtyping and phenotypic methods to probe the interspecies transmission potential of this species. EcoRI ribotyping differentiated 17 ribotypes, and DNA sequencing of the housekeeping genesodAand the putative virulence genehylBdifferentiated 7 and 17 allelic types, respectively. Human and bovine isolates were not randomly distributed between ribotypes orhylBandsodAclusters. The combined analysis of all subtyping data allowed the differentiation of 39 clonal groups; 26 groups contained only bovine isolates, and 2 groups contained both human and bovine isolates. The EcoRI ribotype diversity among bovine isolates (Simpson's numerical index of discrimination [mean ± standard deviation], 0.90 ± 0.05) being significantly higher than that among human isolates (0.42 ± 0.15) further supports that these isolates represent distinct populations. Eight human isolates, but no bovine isolates, showed an IS1548 transposon insertion inhylB, which encodes a hyaluronidase. Based on data for 43 representative isolates, human isolates, on average, showed lower hyaluronidase activities than bovine isolates. Isolates with the IS1548 insertion inhylBshowed no hyaluronidase activity. Human and bovine isolates did not differ in their abilities to invade HeLa human epithelial cells. Our data show that (i) EcoRI ribotyping, combined withhylBandsodAsequencing, provides a discriminatory subtype analysis ofS. agalactiae; (ii) most human invasive and bovineS. agalactiaeisolates represent distinct subtypes, suggesting limited interspecies transmission; and (iii) hyaluronidase activity is not required for all human infections.
Molecular Characterization of an Epidemic Clone of Panantibiotic-ResistantPseudomonas aeruginosa
Authors: Deplano A. , Denis O. , Poirel L. , Hocquet D. , Nonhoff C. , Byl B. , Nordmann P. , Vincent J. L. , Struelens M. J. 
Published: March 2005

ABSTRACTWe describe the molecular characterization of a multiresistantPseudomonas aeruginosaclone causing an outbreak in the intensive care unit (ICU) of a tertiary-care university hospital. Analysis included antimicrobial susceptibility profile, O-serotyping, pulsed-field gel electrophoresis, and amplified fragment length polymorphism. Resistance mechanisms were characterized, including production of naturally occurring and acquired β-lactamases, porin expression, and efflux pump systems. Eighteen patients were colonized or infected with multiresistantP. aeruginosa. MultiresistantP. aeruginosawas panresistant to penicillins, cephalosporins, carbapenems, aminoglycosides, and fluoroquinolones and remained susceptible only to colistin. Sixteen isolates (89%) belonged to serotype O:11, pulsed-field gel electrophoresis type A1, and amplified fragment length polymorphism type A. Resistance characterization of this epidemic clone showed an overexpression of the chromosomal cephalosporinase AmpC combined with decreased expression of porin OprD and the absence of metallo-β-lactamase or extended-spectrum beta-lactamase. An upregulation of the MexXY efflux system due to anagrZmutation in themexZrepressor was detected. This epidemic clone was restricted to the ICU and was not found elsewhere in hospital. Contamination of the ICU environment and the hands of an ICU nurse with this clone suggests possible hand-borne transmission. Implementation of contact precautions effectively controlled transmission of the epidemic clone. This study illustrates the ability of multiresistantP. aeruginosato cause an outbreak with significant morbidity and mortality and underscores the need to identify clonal outbreaks, which require targeted infection control measures.
Analysis of
Salmonella enterica
Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Authors: Kubota K. , Barrett T. J. , Ackers M. L. , Brachman P. S. , Mintz E. D. 
Published: March 2005

ABSTRACT

Typhoid fever is a significant cause of morbidity and mortality worldwide, causing an estimated 16 million cases and 600,000 deaths annually. Although overall rates of the disease have dramatically decreased in the United States, the number of travel-related infections has increased in recent decades. Drug resistance among
Salmonella enterica
serotype Typhi strains has emerged worldwide, making antimicrobial susceptibility testing an important function in public health laboratories. Pulsed-field gel electrophoresis (PFGE) subtyping of food-borne and waterborne pathogens has proven to be a valuable tool for the detection of outbreaks and laboratory-based surveillance. This retrospective study examined the distribution of PFGE patterns of
S. enterica
serotype Typhi isolates from patients with a history of international travel. Isolates were collected as part of a passive laboratory-based antimicrobial susceptibility surveillance study. Isolates were PFGE subtyped by using the restriction enzyme XbaI to restrict the total genomic DNA. Isolates indistinguishable with XbaI were further characterized using the restriction enzyme BlnI. A total of 139 isolates were typed, representing travel to 31 countries. Restriction fragment patterns consisted of 14 to 18 fragments ranging in size from 580 to 40 kbp. Seventy-nine unique PFGE patterns were generated using XbaI. Isolates from the same geographic region did not necessarily have similar PFGE patterns. Of the 139 isolates, 46 (33%) were resistant to more than one antimicrobial agent (multidrug resistant [MDR]). Twenty-seven (59%) of 46 MDR isolates had indistinguishable PFGE patterns with both XbaI and BlnI. It appears that MDR
S. enterica
serotype Typhi has emerged as a predominant clone in Southeast Asia and the Indian subcontinent.
CHROMagar Candida as the Sole Primary Medium for Isolation of Yeasts and as a Source Medium for the Rapid-Assimilation-of-Trehalose Test
Authors: Murray Melissa P. , Zinchuk Riva , Larone Davise H. 
Published: March 2005

ABSTRACT

The chromogenic medium BBL CHROMagar Candida (CAC) was evaluated as a sole primary medium for the isolation of yeasts from clinical specimens in which yeasts are the primary concern. Additionally, the reliability of the rapid-assimilation-of-trehalose (RAT) test in yielding correct results with isolates taken from CAC was assessed. A total of 270 throat, urine, and genital (TUG) specimens were streaked onto CAC, Sabouraud dextrose agar (SDA), inhibitory mold agar (IMA), and Mycosel (MYC). A total of 69 blood culture broths that were smear positive for yeast were streaked onto CAC and SDA. A 1-h RAT test (NCCLS M35-A) was performed simultaneously on isolates from CAC and SDA. A total of 112 TUG specimens yielded yeast colonies (CAC, 111 colonies; IMA, 105; SDA, 103; MYC, 91). The 69 blood culture yeasts grew on both CAC and SDA. Mixed cultures of yeasts were detected on 11 CAC plates but were unrecognized on other media. Colonies suspected of being
C. glabrata
on 32 CAC plates were all RAT test positive and confirmed to be
C. glabrata
; of 59 colonies with various characteristics of color and morphology on CAC, none were RAT positive, and all were conventionally identified as yeasts other than
C. glabrata
(sensitivity and specificity, 100%). The same isolates from SDA tested for RAT produced six false negatives and no false positives (sensitivity, 81%; specificity, 100%). The results show that CAC can be used as the sole primary medium for recovery of yeasts from clinical specimens. Additionally, isolates grown on CAC yield excellent results with the RAT test utilized in this study.
Detection of Human Picornaviruses by Multiplex Reverse Transcription-PCR and Liquid Hybridization
Authors: Jokela Pia , Joki-Korpela Päivi , Maaronen Marita , Glumoff Virpi , Hyypiä Timo 
Published: March 2005

ABSTRACT
A qualitative multiplex reverse transcription (RT)-PCR and liquid hybridization assay for the detection of human enteroviruses, rhinoviruses, parechoviruses, and Aichi virus was developed. Furthermore, a separate assay for the recognition of hepatitis A virus was established to complement the test pattern so that all human picornaviruses were covered. The amplicons, which represented the 5′ untranslated regions of the viral RNA genomes, were identified in liquid hybridization reactions with genus-specific digoxigenin-labeled oligonucleotide probes. The sensitivity of the multiplex RT-PCR and liquid hybridization assay was 10 to 100 picornavirus genome equivalents for representatives of each picornavirus genus. The hepatitis A virus assay exhibited a sensitivity of 10 genome copies. Both the uniplex and the multiplex tests were highly specific for the target viruses. Twenty-three clinical samples, including cerebrospinal fluid, serum, and nasopharyngeal swab specimens, were used for clinical evaluation of the multiplex RT-PCR assay. The results obtained were consistent with the results of routine virus diagnostic assays. Furthermore, the assay was used to screen 68 stool specimens for the presence of parechoviruses and Aichi virus. One sample was found to contain parechovirus RNA, whereas no Aichi virus was detected. The assay described here can be applied for the efficient identification of human enteroviruses and rhinoviruses in clinical specimens and simultaneously enables the collection of information on the epidemiology and clinical outcomes of infections caused by the currently poorly known human parechoviruses and Aichi virus.
Characterization of Virulence Plasmids and Serotyping of
Rhodococcus equi
Isolates from Submaxillary Lymph Nodes of Pigs in Hungary
Authors: Makrai László , Takayama Saki , Dénes Béla , Hajtós István , Sasaki Yukako , Kakuda Tsutomu , Tsubaki Shiro , Major Andrea , Fodor László , Varga János , Takai Shinji 
Published: March 2005

ABSTRACT

The plasmid types and serotypes of 164
Rhodococcus equi
strains obtained from submaxillary lymph nodes of swine from different piggeries in 28 villages and towns located throughout the country were examined. The strains were tested by PCR for the presence of 15- to 17-kDa virulence-associated protein antigen (VapA) and 20-kDa virulence-associated protein antigen (VapB) genes. Plasmid DNAs were isolated and analyzed by digestion with restriction endonucleases to estimate size and compare their polymorphism characteristics. None of the 164 isolates contained the
vapA
gene, and 44 (26.8%) isolates were positive for the
vapB
gene, showing a product of the expected 827-bp size in the PCR amplification. The 44 isolates of intermediate virulence contained virulence plasmids that were identified as types 1 (3 isolates), 4 (1 isolate), 5 (36 isolates), 6 (1 isolate), and 7 (2 isolates) and as a new variant (1 isolate). On the basis of restriction digestion patterns of plasmid DNAs, we tentatively designated the variant as type 17. Use of the serotyping method of Prescott showed that 110 (67.1%) out of the 164 isolates were typeable and that serotype 2 predominated (83 isolates [50.6%]), followed by serotype 1 (26 strains [15.9%]). Only one isolate belonged to serotype 3. A total of 54 (32.9%) isolates were untypeable in Prescott's system. The prevalence of
R. equi
strains of intermediate virulence among the isolates that came from the submaxillary lymph nodes of swine in Hungary was lower than that seen with isolates obtained elsewhere.
Trends in Drug Resistance, Serotypes, and Molecular Types of
Streptococcus pneumoniae
Colonizing Preschool-Age Children Attending Day Care Centers in Lisbon, Portugal: a Summary of 4 Years of Annual Surveillance
Authors: Nunes S. , Sá-Leão R. , Carriço J. , Alves C. R. , Mato R. , Avô A. Brito , Saldanha J. , Almeida J. S. , Sanches I. Santos , de Lencastre H. 
Published: March 2005

ABSTRACT

Of the nasopharyngeal cultures recovered from 942 day care center (DCC) attendees in Lisbon, Portugal, 591 (62%) yielded
Streptococcus pneumoniae
during a surveillance performed in February and March of 1999. Forty percent of the isolates were resistant to one or more antimicrobial agents. In particular, 2% were penicillin resistant and 20% had intermediate penicillin resistance. Multidrug resistance to macrolides, lincosamides, and tetracycline was the most frequent antibiotype (17% of all isolates). Serotyping and molecular typing by pulsed-field gel electrophoresis were performed for 202 out of 237 drug-resistant pneumococci (DRPn). The most frequent serotypes were 6B (26%), 14 (22%), 19F (16%), 23F (10%), and nontypeable (12%). The majority (67%) of the DRPn strains were representatives of nine international clones included in the Pneumococcal Molecular Epidemiology Network; eight of them had been detected in previous studies. Fourteen novel clones were identified, corresponding to 26% of the DRPn strains. The remaining 7% of the strains were local clones detected in our previous studies. Comparison with studies conducted since 1996 in Portuguese DCCs identified several trends: (i) the rate of DRPn frequency has fluctuated between 40 and 50%; (ii) the serotypes most frequently recovered have remained the same; (iii) nontypeable strains appear to be increasing in frequency; and (iv) a clone of serotype 33F emerged in 1999. Together, our observations highlight that the nasopharynxes of children in DCCs are a melting pot of successful DRPn clones that are important to study and monitor if we aim to gain a better understanding on the epidemiology of this pathogen.
Sequence Analysis of the
msp4
Gene of
Anaplasma phagocytophilum
Strains
Authors: de la Fuente José , Massung Robert F. , Wong Susan J. , Chu Frederick K. , Lutz Hans , Meli Marina , von Loewenich Friederike D. , Grzeszczuk Anna , Torina Alessandra , Caracappa Santo , Mangold Atilio J. , Naranjo Victoria , Stuen Snorre , Kocan Katherine M. 
Published: March 2005

ABSTRACT

The causative agent of human granulocytic ehrlichiosis was recently reclassified as
Anaplasma phagocytophilum
, unifying previously described bacteria that cause disease in humans, horses, dogs, and ruminants. For the characterization of genetic heterogeneity in this species, the homologue of
Anaplasma marginale
major surface protein 4 gene (
msp4
) was identified, and the coding region was PCR amplified and sequenced from a variety of sources, including 50 samples from the United States, Germany, Poland, Norway, Italy, and Switzerland and 4 samples of
A. phagocytophilum
-like organisms obtained from white-tailed deer in the United States. Sequence variation between strains of
A. phagocytophilum
(90 to 100% identity at the nucleotide level and 92 to 100% similarity at the protein level) was higher than in
A. marginale
. Phylogenetic analyses of
msp4
sequences did not provide phylogeographic information but did differentiate strains of
A. phagocytophilum
obtained from ruminants from those obtained from humans, dogs, and horses. The sequence analysis of the recently discovered
A. phagocytophilum msp2
gene corroborated these results. The results reported here suggest that although
A. phagocytophilum
-like organisms from white-tailed deer may be closely related to
A. phagocytophilum
, they could be more diverse. These results suggest that
A. phagocytophilum
strains from ruminants could share some common characteristics, including reservoirs and pathogenicity, which may be different from strains that infect humans.
Epidemiology of Human Sporotrichosis Investigated by Amplified Fragment Length Polymorphism
Authors: Neyra Edgar , Fonteyne Pierre-Alain , Swinne Danielle , Fauche Frederic , Bustamante Beatriz , Nolard Nicole 
Published: March 2005

ABSTRACT

Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity of Peruvian strains of
Sporothrix schenckii
and to compare them to a panel of non-Peruvian strains. AFLP analysis suggests that the Peruvian strains can be divided into two homogeneous clusters with no reference to geographical origin or the clinical form of sporotrichosis. The strains from abroad present heterogeneous profiles, with the Bolivian strain and the Colombian strains related to one of the Peruvian population. Sequencing of internal transcribed spacer 2, used to examine the relationships over a longer distance, confirmed the division of Peruvian strains into two populations that can be identified on the basis of a single but specific sequence divergence. This paper introduces automated AFLP analysis as a valuable tool for further investigation of the epidemiology and ecology of
S. schenckii
.
Predominance ofafr2andralFimbrial Genes Related to Those Encoding the K88 and CS31A Fimbrial Adhesins in EnteropathogenicEscherichia coliIsolates from Rabbits with Postweaning Diarrhea in Central Europe
Authors: Dow Mohamed A. , Tóth István , Alexa Pavel , Davies Michael , Malik Anna , Oswald Eric , Nagy Béla 
Published: March 2005

ABSTRACTPCR tests designed in these studies identified three rabbit adhesive factor genes among 43 enteropathogenicE. coli(EPEC) strains:afr1(2 strains), the F4(K88)/CS31A-relatedafr2(10 strains), andral(15 strains). Several EPEC strains (i.e., O153:H7 and O157:H2) lacked these genes but did adhere to HeLa cells and produced attaching and effacing lesions in rabbits.
Confirming Positive Results of Nucleic Acid Amplification Tests (NAATs) for
Chlamydia trachomatis
: All NAATs Are Not Created Equal
Authors: Schachter J. , Hook E. W. , Martin D. H. , Willis D. , Fine P. , Fuller D. , Jordan J. , Janda W. M. , Chernesky M. 
Published: March 2005

ABSTRACT

The Centers for Disease Control and Prevention recommended confirming positive screening tests for
Chlamydia trachomatis
when positive predictive values are <90%. It is accepted that less sensitive tests (i.e., culture and immunoassays) should not be used to confirm the results of more sensitive nucleic acid amplification tests (NAATs). We show that the same principle applies when NAATs are used for confirmation.
Serotype G9 Rotavirus Infections in Adults in Sweden
Authors: Rubilar-Abreu Elba , Hedlund Kjell-Olof , Svensson Lennart , Mittelholzer Christian 
Published: March 2005

ABSTRACTRotavirus is a major cause of acute gastroenteritis. By examining 1,517 stool samples collected in 2001 and 2002 from Swedish adults with acute diarrhea, rotavirus was found in 3.2%, with the emerging G9P[8] serotype being the one most commonly identified (42.9%). This is the first documentation of G9 infections in adults in Europe.