bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity of
Neisseria gonorrhoeae
Housekeeping Genes
Authors: Viscidi Raphael P. , Demma James C. 
Published: January 2003

ABSTRACT

Molecular typing of
Neisseria gonorrhoeae
strains is an important tool for epidemiological studies of gonococcal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for the development of such a method, we characterized the genetic diversity at 18 gonococcal housekeeping gene loci. Approximately 17,500 nucleotides, spanning 18 loci, were sequenced from 24 isolates. Including strain FA 1090, which has been fully sequenced, and three unique
glnA
sequences from GenBank, the number of alleles identified for the 18 loci ranged from 2 to 18, with a mean of 8.3 alleles per locus. The majority of polymorphic sites were distributed randomly along the genes, consistent with evolution of DNA sequences by point mutation. In addition, several examples of clustered mutations and insertions or deletions were detected, which most likely occurred by recombinational events. While purifying selection is the dominant force driving the evolution of these housekeeping genes, positive selection also appeared to operate on the
abcZ
and
gpdh
loci. The 25 completely characterized strains each had a unique allelic profile with as few as three loci (
pilA
,
abcZ
, and
pip
or
pgi2
). Molecular typing based on the allelic profile of housekeeping genes resolved the isolates better than either
porB
nucleotide sequencing or typing of the
opa
gene. The allelic profiles for the
pilA
,
abcZ
, and
serC
loci of paired strains from 16 sexual contacts were identical. A potential MLST for
N. gonorrhoeae
, based on ∼500- to 600-bp gene fragments of seven housekeeping gene loci, would include the
pilA
,
abcZ
,
serC
,
glnA
,
gdh
,
gnd
, and
pip
loci.
Comparison of Recovery of Blood Culture Isolates from Two BacT/ALERT FAN Aerobic Blood Culture Bottles with Recovery from One FAN Aerobic Bottle and One FAN Anaerobic Bottle
Authors: Riley Julie A. , Heiter Barbara J. , Bourbeau Paul P. 
Published: January 2003

ABSTRACT

Traditionally, a routine blood culture for adult patients consisted of paired aerobic and anaerobic bottles, but the routine use of an anaerobic blood culture bottle has been challenged in recent years. In this study, we compared the recovery of two FAN aerobic bottles with one FAN aerobic and one FAN anaerobic bottle. Each pair of bottles was collected by a separate collection procedure, and each bottle held a recommended 8- to 12-ml draw. A total of 704 clinically significant isolates were recovered from 8,620 sets (17,240 pairs), with 487 (69.2%) isolates recovered from one or both bottles in each pair of bottles, 86 isolates (12.2%) recovered only from the FAN aerobic-FAN aerobic pair, and 131 isolates (18.6%) recovered only from the FAN aerobic-FAN anaerobic pair. Significantly more total organisms (
P
= 0.002), gram-positive cocci (
P
= 0.03),
Staphylococcus aureus
(
P
= 0.05),
Enterobacteriaceae
other than
Escherichia coli
(
P
= 0.02), and anaerobes (
P
= 0.01) were recovered from the FAN aerobic-FAN anaerobic pair than from the FAN aerobic-FAN aerobic pair. A separate analysis was performed on the 618 isolates that were recovered from the FAN aerobic-FAN anaerobic pair to compare recovery by bottle type. Significantly more
S. aureus
(
P
= 0.005) and anaerobes (
P
< 0.001) were recovered from the FAN anaerobic bottle, while significantly more coagulase-negative staphylococci (
P
= 0.01),
Streptococcus pneumoniae
(
P
= 0.03), and other gram-negative bacilli (
P
= 0.004) were recovered from the FAN aerobic bottle. These results support the routine use of a FAN anaerobic bottle for use in the culture of blood with the BacT/ALERT system in our institution. These results also suggest that the decision of whether to routinely utilize an anaerobic blood culture bottle should be influenced by the overall recovery of bacteria and yeast, the recovery of specific types of bacteria or yeast, the medium type, and the blood culture system utilized by the laboratory.
Extended Virulence Genotype of Pathogenic
Escherichia coli
Isolates Carrying the
afa-8
Operon: Evidence of Similarities between Isolates from Humans and Animals with Extraintestinal Infections
Authors: Girardeau Jean Pierre , Lalioui Lila , Said A. Mohamed Ou , De Champs Christophe , Le Bouguénec Chantal 
Published: January 2003

ABSTRACT

The afimbrial AfaE-VIII adhesin is common among
Escherichia coli
isolates from calves with intestinal and/or extraintestinal infections and from humans with sepsis or pyelonephritis. The virulence genotypes of 77
Escherichia coli afa-8
isolates from farm animals and humans were compared to determine whether any trait of commonality exists between isolates of the different host species. Over half of the extraintestinal
afa-8
isolates were associated with
pap
and
f17Ac
adhesin genes and contained virulence genes (
pap
,
hly
, and
cnf1
) which are characteristic of human extraintestinal pathogenic
E. coli
(ExPEC). PapG, which occurs as three known variants (variants I to III), is encoded by the corresponding three alleles of
papG
. Among the
pap
-positive strains, new
papG
variants (
papGrs
) that differed from the isolates with genes for the three adhesin classes predominated over isolates with
papG
allele III, which in turn were more prevalent than those with allele II. The data showed the substantial prevalence of the enteroaggregative
E. coli
heat-stable enterotoxin gene (
east1
) among
afa-8
isolates. Most of the
afa-8
isolates harbored the high-pathogenicity island (HPI) present in pathogenic
Yersinia
; however, two-thirds of the HPI-positive strains shared a truncated HPI integrase gene. The presence of ExPEC-associated virulence factors (VFs) in extraintestinal isolates that carry genes typical of enteric strains and that express O antigens associated with intestinal
E. coli
is consistent with transfer of VFs and O-antigen determinants between ExPEC and enteric strains. The similarities between animal and human ExPEC strains support the hypothesis of overlapping populations, with members of certain clones or clonal groups including animal and human strains. The presence of multiple-antibiotic-resistant bovine
afa-8
strains among such clones may represent a potential public health risk.
Quality Assessment Program for Genotypic Antiretroviral Testing Improves Detection of Drug Resistance Mutations
Authors: Sayer D. C. , Land S. , Gizzarelli L. , French M. , Hales G. , Emery S. , Christiansen F. T. , Dax E. M. 
Published: January 2003

ABSTRACTGenotypic antiretroviral testing is now widely used for the management of patients who are undergoing antiretroviral therapy for human immunodeficiency virus infection. The assays are complex, and there is considerable potential for variation between laboratories. Informative and ongoing quality assessment programs (QAPs) which address all aspects of testing are required. The panel distribution of clinical material is a critical component of QAPs. We report on the results and data from a recent panel. Four cryopreserved plasma samples from treated donors were distributed to nine laboratories. Three laboratories performed testing by commercial assays, and six laboratories used in-house assays, with one laboratory reporting results from two in-house assays. There was complete concordance between results for 95.9% of the nucleotide sequence and 94.5% of the amino acid sequence. Despite this overall high level of concordance, the degree of concordance at drug resistance mutation (DRM) sites when DRMs were present was considerably less (38% of DRM sites). Consequently, only 3 of the 10 methods reported 100% of DRMs as present. This elevated discrepancy rate is almost certainly a result of variability in the identification of mixtures of nucleotides (mixtures) at any site within the sequence. In addition, laboratories differed in the number of codons in the reverse transcriptase gene that were sequenced and their ability to amplify all samples. This panel distribution demonstrated a requirement for laboratory participation in ongoing QAPs and the optimization of assays with standards that contain mixtures.
Detection and Differentiation of
Entamoeba histolytica
and
Entamoeba dispar
Isolates in Clinical Samples by PCR and Enzyme-Linked Immunosorbent Assay
Authors: Gonin Patrick , Trudel Louise 
Published: January 2003

ABSTRACT

Differential diagnosis of
Entamoeba histolytica
(pathogenic) and
Entamoeba dispar
(nonpathogenic), which are two morphologically identical species of amebae, is essential both for treatment decision and public health knowledge. The study reported here was designed to choose a reference differentiation technique. Stool samples (
n
= 95) were tested by microscopy, TechLab enzyme-linked immunosorbent assays (ELISAs), and an in-house PCR. The target for the PCR amplification was a small region (135 bp) of the SSU rRNA selected to increase the sensitivity of the test. Sixty-eight specimens tested positive by PCR: 2 for
E. histolytica
and 66 for
E. dispar
. For detection of
E. dispar
, ELISA performance was lower than that of microscopy in this reference context, while PCR was much more sensitive than microscopy. Given the low proportion of
E. histolytica
cases, test performance for this species is difficult to assess. However, for differentiation, PCR performed well on simulated samples, while ELISA gave a discordant result for one of the two samples PCR positive for
E. histolytica
during the study. This report also confirms that
E. dispar
infection is significantly higher among travelers and underlines the possibility of acquiring
E. histolytica
infection in regions that are not areas of endemicity. Because of its lower sensitivity, the interest of ELISA for
Entamoeba
detection and differentiation in stools seems questionable in nontropical regions. On the other hand, results suggest that PCR should be useful as a reference test for sensitive differentiation of both species and to contribute to physicians' decision in treatment of
E. histolytica-
or
E. dispar
-infected patients.
Comparison of LightCycler PCR, Rapid Antigen Immunoassay, and Culture for Detection of Group A Streptococci from Throat Swabs
Authors: Uhl J. R. , Adamson S. C. , Vetter E. A. , Schleck C. D. , Harmsen W. S. , Iverson L. K. , Santrach P. J. , Henry N. K. , Cockerill F. R. 
Published: January 2003

ABSTRACT

We compared the performance characteristics of a real-time PCR method, the LightCycler Strep-A assay (Roche Applied Science, Indianapolis, Ind.), to those of a rapid antigen immunoassay, the Directigen 1-2-3 Group A Strep Test kit (BD Diagnostic Systems, Sparks, Md.), and a standard culture method for detection of group A streptococci (GAS) from 384 throat swabs. The LightCycler PCR produced more positive results (
n
= 58) than either culture (
n
= 55) or the Directigen immunoassay (
n
= 31). The results of the LightCycler PCR and the Directigen method were independently compared to the results of the accepted “gold standard,” bacterial culture. The sensitivities, specificities, and positive and negative predictive values for this comparison were as follows: for the Directigen method, 55, 99, 97, and 93%, respectively; for the LightCycler PCR, 93, 98, 88, and 99%, respectively. In no case was a throat swab positive by both the LightCycler PCR and the Directigen method but negative by culture. The medical histories of patients whose throat swabs were negative by culture but positive by either the LightCycler PCR (
n
= 7) or the Directigen method (
n
= 1) were reviewed. All of these patients had signs or symptoms compatible with GAS disease, and therefore, all of these discordant positive results (along with positive results by either the Directigen method or the LightCycler PCR that agreed with the culture results) were counted as true positives for statistical analysis. For this analysis, the LightCycler PCR detected more true-positive results than the culture method (58 versus 55 swabs); however, this difference was not statistically significant (
P
= 0.5465). In contrast, statistically significantly more true-positive results occurred by culture than by the Directigen method (55 versus 31 swabs;
P
< 0.0001) and by the LightCycler PCR than by the Directigen method (58 versus 31 swabs;
P
< 0.0001). The LightCycler PCR is a suitable stand-alone method for the detection of GAS from throat swabs. Additionally, this method requires less than half the personnel time and the procedure can be completed in considerably less time (∼1 h) than our standard approach (up to 2 days) for detection of GAS in throat swabs (i.e., testing by the Directigen method with negative results verified by culture).
Evaluation of a Novel Automated Chemiluminescent Assay System for Antimicrobial Susceptibility Testing
Authors: Manome Isao , Ikedo Masanari , Saito Yoshihiko , Ishii Keiko Kumura , Kaku Mitsuo 
Published: January 2003

ABSTRACTThe newly developed Rapid Lumi Eiken/IS60 (RL/IS60) system automatically determines MICs by detecting chemiluminescence produced in the reaction of a chemiluminescent probe and oxygen metabolites from living microorganisms. The present study evaluated this system for accuracy in antimicrobial susceptibility testing. Chemiluminescence intensities after 4 h of cultivation of clinically important strains were plotted against various concentrations of antimicrobial agents, which resulted in curves reflecting the levels of susceptibility. Sixty-percent inhibitory concentrations based on the susceptibility curves agreed with MICs determined by the reference microdilution method. When the MICs of antimicrobial agents for four quality control (QC) strains (Staphylococcus aureus,Enterococcus faecalis,Escherichia coli, andPseudomonas aeruginosa) were determined by the RL/IS60 system, most (91.1%) of them were within the QC limits proposed by the National Committee for Clinical Laboratory Standards. The system was further assessed for a total of 162 clinical isolates, includingE. coli,Citrobacter freundii,Enterobacter cloacae,Klebsiella pneumoniae,Serratia marcescens,Proteus mirabilis,Morganella morganii,P. aeruginosa,Haemophilus influenzae,S. aureus, coagulase-negative staphylococci,Enterococcus faecalis,Enterococcus faecium, andStreptococcus pneumoniae. Overall, there was 90.6% agreement between the RL/IS60 system and the reference microdilution method. Our results suggest that the RL/IS60 system provides rapid and reliable MICs of a variety of antimicrobial agents for clinical isolates as well as QC strains.
Identification of a Gene Encoding Heat-Resistant Agglutinin in
Escherichia coli
as a Putative Virulence Factor in Urinary Tract Infection
Authors: Srinivasan Usha , Foxman Betsy , Marrs Carl F. 
Published: January 2003

ABSTRACT

Escherichia coli
causes the vast majority of urinary tract infections (UTI) in both ambulatory and hospital patients. Several uropathogenic virulence factors have been identified, but half of all
E. coli
isolates that cause UTI have none or only one of the known virulence factors. Thus, it is reasonable to presume that other bacterial factors may be important in UTI pathogenesis. In order to find additional uropathogenic
E. coli
genes, we used genomic subtraction to identify DNA regions present in a uropathogenic strain of
E. coli
(1128-11). Genomic subtraction yielded 40 tester-specific fragments, including a novel heat-resistant agglutinin (
hra
) gene fragment.
hra
occurred in 55% of 486 UTI strains compared to 28% of 165 rectal strains (
P
= 0.001). The
hra
gene in 1128-11 was cloned, sequenced, and found to have 91% homology to the
hra
gene from
E. coli
meningitis strain RS218. The genetic organization of genes flanking
hra
in 1128-11 is distinct from the
hra
found in
E. coli
strains J96 and RS218. In our UTI and rectal specimen collections,
hra
was positively associated with a number of known virulence genes, including pathogenicity island genes
hly
and
cnf
, which are absent in 1128-11. The presence of
hra
in 1128-11 independent of
hly/cnf
suggests multiple mechanisms by which
hra
can be acquired by pathogenic
E. coli
strains. The flanking genes suggest that in 1128-11,
hra
may be part of a novel variant of a pathogenicity island V.
Evaluation of a Human Group A Rotavirus Assay for On-Site Detection of Bovine Rotavirus
Authors: Maes Roger K. , Grooms Daniel L. , Wise Annabel G. , Han Cunqin , Ciesicki Valerie , Hanson Lora , Vickers Mary Lynne , Kanitz Charles , Holland Robert 
Published: January 2003

ABSTRACTNeonatal diarrhea induced by bovine group A rotavirus causes significant economic loss in the dairy and beef industry due to increased morbidity and mortality, treatment costs, and reduced growth rates. The objective of this study was to evaluate a human group A rotavirus assay (ImmunoCardSTAT Rotavirus [ICS-RV]) as an on-site diagnostic test for bovine rotavirus. When used with a collection of bovine diarrhea samples submitted to the Virology Section of the Diagnostic Center for Population and Animal Health at Michigan State University and compared to a bovine group A rotavirus-specific reverse transcription-PCR (RT-PCR), the ICS-RV assay had a sensitivity and specificity of 87.0 and 93.6%, respectively. A commercially available group A rotavirus enzyme-linked immunosorbent assay (ELISA) (Pathfinder; Sanofi Diagnostics, Redmond, Wash.), when used with the same fecal sample collection and compared to the same RT-PCR, had a sensitivity and specificity of 78.3 and 67.7%, respectively. Subsequently, the ICS-RV assay, RT-PCR, and a different commercially available group A rotavirus ELISA (Rotaclone; Meridian Diagnostics, Cincinnati, Ohio) were used to evaluate fecal samples collected from neonatal calves experimentally infected with bovine rotavirus. When diarrheic fecal samples that were positive for bovine rotavirus by RT-PCR were evaluated, the ICS-RV assay and the Rotaclone assay detected bovine rotavirus 85 and 95% of the time, respectively. Based on these studies, the ICS-RV assay appears to be an excellent test for detecting group A bovine rotaviruses. This assay may be useful as an on-site diagnostic test for veterinarians as an aid in the management of bovine neonatal diarrhea.
Culture-Independent Molecular Analysis of Microbial Constituents of the Healthy Human Outer Ear
Authors: Frank Daniel N. , Spiegelman George B. , Davis William , Wagner Eileen , Lyons Eric , Pace Norman R. 
Published: January 2003

ABSTRACT

Molecular-phylogenetic sequence analyses have provided a new perspective on microbial communities by allowing the detection and identification of constituent microorganisms in the absence of cultivation. In this study we used broad-specificity amplification of ribosomal DNA (rDNA) genes to survey organisms present in the human outer ear canal. Samples were obtained from 24 individuals, including members of three extended families, in order to survey the resident microbiota and to examine microbial population structures in individuals related by familial or household associations. To examine the stability of the microbial populations, one individual was sampled four times and another twice over a 14-month period. We found that a distinct set of microbial types was present in the majority of the subjects sampled. The two most prevalent rDNA sequence types that were identified in multiple individuals corresponded closely to those of
Alloiococcus otitis
and
Corynebacterium otitidis
, commonly thought to be associated exclusively with infections of the middle ear. Our results suggest, therefore, that the outer ear canal may serve as a reservoir for normally commensal microbes that can contribute to pathogenesis upon introduction into the middle ear. Alternatively, culture analyses of diseases of the middle ear may have been confounded by these contaminating commensal organisms.
Performance of the APTIMA Combo 2 Assay for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in Female Urine and Endocervical Swab Specimens
Authors: Gaydos C. A. , Quinn T. C. , Willis D. , Weissfeld A. , Hook E. W. , Martin D. H. , Ferrero D. V. , Schachter J. 
Published: January 2003

ABSTRACT

The greater sensitivity of nucleic acid amplification tests (NAATs) for
Chlamydia trachomatis
and
Neisseria gonorrhoeae
permits the use of urine and other noninvasive specimens, which can increase the reach and decrease the costs of public health screening programs aimed at controlling these infections. This study evaluated the performance of the APTIMA Combo 2 assay, a multiplex assay based on the transcription-mediated amplification reaction, for the simultaneous detection of both pathogens in endocervical swab and urine specimens from females. Combo 2 assay results were compared with patient infected status, which were available by using other commercial NAATs. Sensitivity and specificity for
C. trachomatis
were 94.2 and 97.6%, respectively, in swabs and 94.7 and 98.9%, respectively, in first-catch urine (FCU). Sensitivity and specificity for
N. gonorrhoeae
were 99.2 and 98.7%, respectively, in swabs and 91.3 and 99.3%, respectively, in FCU. The assay reliably detected both infections in coinfected patients. The Combo 2 assay can be recommended for use with endocervical swab and urine specimens from females, especially for screening tests for asymptomatic women in sexually transmitted disease surveillance programs. This Food and Drug Administration-cleared assay can be a useful tool in efforts to reduce the prevalence and incidence of
C. trachomatis
and
N. gonorrhoeae
infections in sexually active women and to prevent their costly and serious sequelae.
Validation of a Urine-Based PCR-Enzyme-Linked Immunosorbent Assay for Use in Clinical Research Settings To Detect
Trichomonas vaginalis
in Men
Authors: Kaydos-Daniels S. Cornelia , Miller William C. , Hoffman Irving , Banda Topia , Dzinyemba Willard , Martinson Francis , Cohen Myron S. , Hobbs Marcia M. 
Published: January 2003

ABSTRACT

Trichomonas vaginalis
infection is highly prevalent worldwide and is associated with urethritis, prostatitis, and urethral strictures in men. However, the natural history and importance of
T. vaginalis
in men are poorly understood, in part because of difficulties in diagnosing infection. Traditional detection methods rely on culture and wet-mount microscopy, which can be insensitive and time consuming. Urethral swabs are commonly used to detect
T. vaginalis
in men, but discomfort from specimen collection is a barrier to large studies. One thousand two hundred twenty-five Malawian men attending sexually transmitted disease and dermatology clinics were enrolled in this cross-sectional study to validate detection by urine-based PCR-enzyme-linked immunosorbent assay (ELISA) with urine and urethral swab culture as the reference standard. This assay for detection of amplified
T. vaginalis
DNA in first-catch urine (≤30 ml) performed with a sensitivity of 92.7%, a specificity of 88.6%, and an adjusted specificity of 95.2% compared to culture of urethral swabs or urine sediment. For clinical research settings in which urethral swabs are not available and culture is not feasible, the urine-based PCR-ELISA may be useful for detection of trichomoniasis in men.