bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity amongEscherichia coliIsolates Carryingf18Genes from Pigs with Porcine Postweaning Diarrhea and Edema Disease
Authors: Nagy Béla , Wilson Richard A. , Whittam Thomas S. 
Published: December 2019

ABSTRACTMultilocus enzyme electrophoresis was applied to detect allelic variation and multilocus genotypes (electrophoretic types [ETs]) among 43Escherichia coliisolates from weaned pigs suffering from edema disease or from diarrhea. ETs were analyzed in relation to O serogroups and virulence genes (sta,stb,lt,stx2, andf18) by DNA hybridization. Genomic diversity was the lowest in serogroup O138, while virulence genes (stx2andf18) were the most uniform in serogroup O139. In general, the serogroups or toxin and F18 fimbria types were not related to selected ETs, suggesting that the toxin andf18fimbria genes inE. coliisolates from pigs with postweaning diarrhea or edema disease occur in a variety of chromosomal backgrounds.
Detection of Poliovirus Circulation by Environmental Surveillance in the Absence of Clinical Cases in Israel and the Palestinian Authority
Authors: Manor Y. , Handsher R. , Halmut T. , Neuman M. , Bobrov A. , Rudich H. , Vonsover A. , Shulman L. , Kew O. , Mendelson E. 
Published: December 2019

ABSTRACT
The global eradication of poliomyelitis, believed to be achievable around the year 2000, relies on strategies which include high routine immunization coverage and mass vaccination campaigns, along with continuous monitoring of wild-type virus circulation by using the laboratory-based acute flaccid paralysis (AFP) surveillance. Israel and the Palestinian Authority are located in a geographical region in which poliovirus is still endemic but have been free of poliomyelitis since 1988 as a result of intensive immunization programs and mass vaccination campaigns. To monitor the wild-type virus circulation, environmental surveillance of sewage samples collected monthly from 25 to 30 sites across the country was implemented in 1989 and AFP surveillance began in 1994. The sewage samples were processed in the laboratory with a double-selective tissue culture system, which enabled economical processing of large number of samples. Between 1989 and 1997, 2,294 samples were processed, and wild-type poliovirus was isolated from 17 of them in four clusters, termed “silent outbreaks,” in September 1990 (type 3), between May and September 1991 (type 1), between October 1994 and June 1995 (type 1), and in December 1996 (type 1). Fifteen of the 17 positive samples were collected in the Gaza Strip, 1 was collected in the West Bank, and 1 was collected in the Israeli city of Ashdod, located close to the Gaza Strip. The AFP surveillance system failed to detect the circulating wild-type viruses. These findings further emphasize the important role that environmental surveillance can play in monitoring the eradication of polioviruses.
Epidemiology of Visceral Mycoses: Analysis of Data in
Annual of the Pathological Autopsy Cases in Japan
Authors: Yamazaki Toshikazu , Kume Hikaru , Murase Setsuko , Yamashita Eriko , Arisawa Mikio 
Published: December 2019

ABSTRACT

The data on visceral mycoses that had been reported in the
Annual of the Pathological Autopsy Cases in Japan
from 1969 to 1994 by the Japanese Society of Pathology were analyzed epidemiologically. The frequency of visceral mycoses among the annual total number of pathological autopsy cases increased noticeably from 1.60% in 1969 to a peak of 4.66% in 1990. Among them, the incidences of candidiasis and aspergillosis increased the most. After 1990, however, the frequency of visceral mycoses decreased gradually. Until 1989, the predominant causative agent was
Candida
, followed in order by
Aspergillus
and
Cryptococcus
. Although the rate of candidiasis decreased by degrees from 1990, the rate of aspergillosis increased up to and then surpassed that of candidiasis in 1991. Leukemia was the major disease underlying the visceral mycoses, followed by solid cancers and other blood and hematopoietic system diseases. Severe mycotic infection has increased over the reported 25-year period, from 6.6% of the total visceral mycosis cases in 1969 to 71% in 1994. The reasons for this decrease of candidiasis combined with an increase of aspergillosis or of severe mycotic infection might be that (i) nonsevere (not disseminated) infections were excluded from the case totals, since they have become controllable by antifungal drugs such as fluconazole, but (ii) the available antifungal drugs were not efficacious against severe infections such as pulmonary aspergillosis, and (iii) the number of patients living longer in an immunocompromised state had increased because of developments in chemotherapy and progress in medical care.
Density and Molecular Epidemiology of
Aspergillus
in Air and Relationship to Outbreaks of
Aspergillus
Infection
Authors: Leenders Alexander C. A. P. , van Belkum Alex , Behrendt Myra , Luijendijk Ad , Verbrugh Henri A. 
Published: December 2019

ABSTRACT

After five patients were diagnosed with nosocomial invasive aspergillosis caused by
Aspergillus fumigatus
and
A. flavus
, a 14-month surveillance program for pathogenic and nonpathogenic fungal conidia in the air within and outside the University Hospital in Rotterdam (The Netherlands) was begun.
A. fumigatus
isolates obtained from the Department of Hematology were studied for genetic relatedness by randomly amplified polymorphic DNA (RAPD) analysis. This was repeated with
A. fumigatus
isolates contaminating culture media in the microbiology laboratory. The density of the conidia of nonpathogenic fungi in the outside air showed a seasonal variation: higher densities were measured during the summer, while lower densities were determined during the fall and winter. Hardly any variation was found in the numbers of
Aspergillus
conidia. We found decreasing numbers of conidia when comparing air from outside the hospital to that inside the hospital and when comparing open areas within the hospital to the closed department of hematology. The increase in the number of patients with invasive aspergillosis could not be explained by an increase in the number of
Aspergillus
conidia in the outside air. The short-term presence of
A. flavus
can only be explained by the presence of a point source, which was probably patient related. Genotyping
A. fumigatus
isolates from the department of hematology showed that clonally related isolates were persistently present for more than 1 year. Clinical isolates of
A. fumigatus
obtained during the outbreak period were different from these persistent clones.
A. fumigatus
isolates contaminating culture media were all genotypically identical, indicating a causative point source. Knowledge of the epidemiology of
Aspergillus
species is necessary for the development of strategies to prevent invasive aspergillosis. RAPD fingerprinting of
Aspergillus
isolates can help to determine the cause of an outbreak of invasive aspergillosis.
Survey of Extended-Spectrum β-Lactamases in Clinical Isolates of
Escherichia coli
and
Klebsiella pneumoniae
: Prevalence of TEM-52 in Korea
Authors: Pai Hyunjoo , Lyu Sen , Lee Ji Hyang , Kim Jungmin , Kwon Youngmi , Kim Jong-Won , Choe Kang Won 
Published: December 2019

ABSTRACT

Two hundred ninety isolates of
Escherichia coli
were investigated for the production of extended-spectrum β-lactamases (ESBLs). Fourteen (4.8%) of the 290 strains were found to produce ESBLs. Each of the 14 strains produced one or two ESBLs, as follows: 10 strains produced TEM-52, 1 strain produced SHV-2a, 1 strain produced SHV-12, 1 strain produced a CMY-1-like enzyme, and 1 strain expressed SHV-2a and a CMY-1-like enzyme. Another two strains for which the MICs of ceftazidime and cefoxitin were high, were probable AmpC enzyme hyperproducers. Because of the high prevalence of TEM-52 in
E. coli
isolates, we further investigated the TEM-type ESBLs produced by
Klebsiella pneumoniae
in order to observe the distribution of TEM-52 enzymes among
Enterobacteriaceae
in Korea. All TEM enzymes produced by 12 strains of
K. pneumoniae
were identified as TEM-52. To evaluate the genetic relatedness among the organisms, ribotyping of TEM-52-producing
E. coli
and
K. pneumoniae
was performed. The ribotyping profiles of the organisms showed similar but clearly different patterns. In conclusion, TEM-52 is the most prevalent TEM-type ESBL in Korea.
Nonisotopic Detection and Typing of Human Papillomavirus DNA in Genital Samples by the Line Blot Assay
Authors: Coutlée François , Gravitt Patti , Richardson Harriet , Hankins Catherine , Franco Eduardo , Lapointe Normand , Voyer Hélène ,   The Canadian Women’s HIV Study Group
Published: December 2019

ABSTRACT
The line blot assay, a gene amplification method that combines PCR with nonisotopic detection of amplified DNA, was evaluated for its ability to detect human papillomavirus (HPV) DNA in genital specimens. Processed samples were amplified with biotin-labeled primers for HPV detection (primers MY09, MY11, and HMB01) and for β-globin detection (primers PC03 and PC04). Amplified DNA products were hybridized by a reverse blot method with oligonucleotide probe mixtures fixed on a strip that allowed the identification of 27 HPV genotypes. The line blot assay was compared to a standard consensus PCR test in which HPV amplicons were detected with radiolabeled probes in a dot blot assay. Two hundred fifty-five cervicovaginal lavage specimens and cervical scrapings were tested in parallel by both PCR tests. The line blot assay consistently detected 25 copies of HPV type 18 per run. The overall positivity for the DNA of HPV types detectable by both methods was 37.7% (96 of 255 samples) by the line blot assay, whereas it was 43.5% (111 of 255 samples) by the standard consensus PCR assay. The sensitivity and specificity of the line blot assay reached 84.7% (94 of 111 samples) and 98.6% (142 of 144 samples), respectively. The agreement for HPV typing between the two PCR assays reached 83.9% (214 of 255 samples). Of the 37 samples with discrepant results, 33 (89%) were resolved by avoiding coamplification of β-globin and modifying the amplification parameters. With these modifications, the line blot assay compared favorably to an assay that used radiolabeled probes. Its convenience allows the faster analysis of samples for large-scale epidemiological studies. Also, the increased probe spectrum in this single hybridization assay permits more complete type discrimination.
Evaluation of a Nested Reverse Transcription-PCR Assay Based on the Nucleoprotein Gene for Diagnosis of Spontaneous and Experimental Bovine Respiratory Syncytial Virus Infections
Authors: Valarcher Jean-François , Bourhy Hervé , Gelfi Jacqueline , Schelcher François 
Published: December 2019

ABSTRACT
The first nested reverse transcription (RT)-PCR based on the nucleoprotein gene (n RT-PCR-N) of the bovine respiratory syncytial virus (BRSV) has been developed and optimized for the detection of BRSV in bronchoalveolar lavage fluid cells of calves. This test is characterized by a low threshold of detection (0.17 PFU/ml), which is 506 times lower than that obtained by an enzyme immunosorbent assay (EIA) test (RSV TESTPACK ABBOTT). During an experimental infection of 17 immunocompetent calves less than 3 months old, BRSV RNA could be detected up to 13 days after the onset of symptoms whereas isolation in cell culture was possible only up to 5 days. Compiling results obtained by conventional techniques (serology, antigen detection, and culture isolation) for 132 field samples collected from calves with acute respiratory signs revealed that n RT-PCR-N showed the highest diagnostic sensitivity and very good specificity. This n RT-PCR-N with its long period of detection during BRSV infection thus provides a valuable tool for diagnostic and epidemiological purposes.
Evidence of High-Frequency Genomic Reassortment of Group A Rotavirus Strains in Bangladesh: Emergence of Type G9 in 1995
Authors: Unicomb Leanne E. , Podder Goutam , Gentsch Jon R. , Woods Patricia A. , Hasan K. Zahid , Faruque A. S. G. , Albert M. John , Glass Roger I. 
Published: December 2019

ABSTRACT

We characterized 1,534 rotavirus (RV) strains collected in Bangladesh from 1992 to 1997 to assess temporal changes in G type and to study the most common G and P types using reverse transcription-PCR, oligonucleotide probe hybridization, and monoclonal antibody-based enzyme immunoassay. Results from this study combined with our previous findings from 1987 to 1991 (F. Bingnan et al., J. Clin. Microbiol. 29:862–868, 1991, and L. E. Unicomb et al., Arch. Virol. 132:201–208, 1993) (
n
= 2,515 fecal specimens) demonstrated that the distribution of the four major G types varied from year to year, types G1 to G4 constituted 51% of all strains tested (
n
= 1,364), and type G4 was the most prevalent type (22%), followed by type G2 (17%). Of 351 strains tested for both G and P types, three globally common types, type P[8], G1, type P[4], G2, and type P[8], G4, comprised 45% (
n
= 159) of the strains, although eight other strains were circulating during the study period. Mixed G and/or P types were found in 23% (
n
= 79) of the samples tested. Type G9 RVs that were genotype P[6] and P[8] with both long and short electrophoretic patterns emerged in 1995. The finding of five different genotypes among G9 strains, of which three were frequently detected, suggests that they may have an unusual propensity for reassortment that exceeds that found among the common G types. We also detected antigenic changes in serotypes G2 and G4 over time, as indicated by the loss of reactivity with standard typing monoclonal antibodies. Our data suggest that a vaccine must provide protection against type G9 RVs as well as against the four major G types because G9 strains constituted 16% (
n
= 56) of the typeable RV strains and have predominated since 1996.
Detection of an Archaic Clone of
Staphylococcus aureus
with Low-Level Resistance to Methicillin in a Pediatric Hospital in Portugal and in International Samples: Relics of a Formerly Widely Disseminated Strain?
Authors: Sá-Leão Raquel , Santos Sanches Ilda , Dias Dora , Peres Isabel , Barros Rosa M. , de Lencastre Hermínia 
Published: December 2019

ABSTRACT

Close to half of the 878 methicillin-resistant
Staphylococcus aureus
(MRSA) strains recovered between 1992 and 1997 from the pediatric hospital in Lisbon were bacteria in which antibiotic resistance was limited to β-lactam antibiotics. The other half were multidrug resistant. The coexistence of MRSA with such unequal antibiotic resistance profiles prompted us to use molecular typing techniques for the characterization of the MRSA strains. Fifty-three strains chosen randomly were typed by a combination of genotypic methods. Over 90% of the MRSA strains belonged to two clones: the most frequent one, designated the “pediatric clone,” was reminiscent of historically “early” MRSA: most isolates of this clone were only resistant to β-lactam antimicrobials and remained susceptible to macrolides, quinolones, clindamycin, spectinomycin, and tetracycline. They showed heterogeneous and low-level resistance to methicillin (MIC, 1.5 to 6 μg/ml), carried the
Cla
I-
mecA
polymorph II, were free of the transposon Tn
554
, and showed macrorestriction pattern D (clonal type II::NH::D). The second major clone was the internationally spread and multiresistant “Iberian” MRSA with homogeneous and high-level resistance to methicillin (MIC, >200 μg/ml) and clonal type I::E::A. Surprisingly, the multidrug-resistant and highly epidemic Iberian MRSA did not replace the much less resistant pediatric clone during the 6 years of surveillance. The pediatric clone was also identified among contemporary MRSA isolates from Poland, Argentina, The United States, and Colombia, and the overwhelming majority of these were also associated with pediatric settings. We propose that the pediatric MRSA strain represents a formerly widely spread archaic clone which survived in some epidemiological settings with relatively limited antimicrobial pressure.
Use of Pulsed-Field Gel Electrophoresis for Molecular Epidemiologic and Population Genetic Studies of
Mycobacterium tuberculosis
Authors: Singh Samir P. , Salamon Hugh , Lahti Carol J. , Farid-Moyer Mehran , Small Peter M. 
Published: December 2019

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) is a powerful molecular biology technique which has provided important insights into the epidemiology and population biology of many pathogens. However, few studies have used PFGE for the molecular epidemiology of
Mycobacterium tuberculosis
. A laboratory protocol was developed to determine the typeability, stability, and reproducibility of PFGE typing of
M. tuberculosis
. Formal data-analytical techniques were used to assess the genetic diversity elucidated by PFGE analyses using four separate restriction enzymes and by IS
6110
RFLP analyses, as well as to assess the concordance among these typing methods. One hundred epidemiologically characterized clinical isolates of
M. tuberculosis
were genotyped with four different PFGE enzymes (
Ase
I,
Dra
I,
Spe
I, and
Xba
I), as well as by RFLP analysis with IS
6110
. Identical patterns were found among 34 isolates known to be genetically related, suggesting that the PFGE protocol is robust and reproducible. Among 66 isolates representing population-sampled cases, heterozygosity and information content dependency estimates indicate that all five genotyping systems capture quantitatively similar levels of genetic diversity. Nevertheless, comparisons between PFGE analyses and IS
6110
typing reveals that PFGE provided more discrimination among isolates with fewer than five copies of IS
6110
and less clustering in isolates with five or more copies. The comparisons confirm the hypothesis that the resolution of IS
6110
RFLP genotyping is dependent upon the number of IS
6110
elements in the genome of isolates. The general concordance among the results obtained with four independent enzymes suggests that
M. tuberculosis
is a clonal organism. The availability of a robust genotyping technique largely independent of repetitive elements has implications for the molecular epidemiology of
M. tuberculosis
.
Distribution of aNocardia brasiliensisCatalase Gene Fragment in Members of the GeneraNocardia,Gordona, andRhodococcus
Authors: Vera-Cabrera Lucio , Johnson Wendy M. , Welsh Oliverio , Resendiz-Uresti Francisco L. , Salinas-Carmona Mario C. 
Published: December 2019

ABSTRACTAn immunodominant protein fromNocardia brasiliensis, P61, was subjected to amino-terminal and internal sequence analysis. Three sequences of 22, 17, and 38 residues, respectively, were obtained and compared with the protein database from GenBank by using the BLAST system. The sequences showed homology to some eukaryotic catalases and to a bromoperoxidase-catalase fromStreptomyces violaceus. Its identity as a catalase was confirmed by analysis of its enzymatic activity on H2O2and by a double-staining method on a nondenaturing polyacrylamide gel with 3,3′-diaminobenzidine and ferricyanide; the result showed only catalase activity, but no peroxidase. By using one of the internal amino acid sequences and a consensus catalase motif (VGNNTP), we were able to design a PCR assay that generated a 500-bp PCR product. The amplicon was analyzed, and the nucleotide sequence was compared to the GenBank database with the observation of high homology to other bacterial and eukaryotic catalases. A PCR assay based on this target sequence was performed with primers NB10 and NB11 to confirm the presence of the NB10-NB11 gene fragment in severalN. brasiliensisstrains isolated from mycetoma. The same assay was used to determine whether there were homologous sequences in several type strains from the generaNocardia,Rhodococcus,Gordona, andStreptomyces. All of theN. brasiliensisstrains presented a positive result but only some of the actinomycetes species tested were positive in the PCR assay. In order to confirm these findings, genomic DNA was subjected to Southern blot analysis. A 1.7-kbp band was observed in theN. brasiliensisstrains, and bands of different molecular weight were observed in cross-reacting actinomycetes. Sequence analysis of the amplicons of selected actinomycetes showed high homology in this catalase fragment, thus demonstrating that this protein is highly conserved in this group of bacteria.
Evaluation of the ImmunoCardSTAT! Rotavirus Assay for Detection of Group A Rotavirus in Fecal Specimens
Authors: Dennehy Penelope H. , Hartin Michele , Nelson Sara M. , Reising Shirley F. 
Published: December 2019

ABSTRACT
Rapid detection of group A rotavirus was performed by using ImmunoCardStat! Rotavirus (ICS-RV) (which uses immunogold-based, horizontal-flow membrane technology), two commercial enzyme immunoassays (Premier Rotaclone and TestPack Rotavirus), and electron microscopy. A total of 249 stool specimens collected from children with gastroenteritis between February and April 1997 were tested. After resolution of 19 of the 22 discordant results by reverse transcription-PCR for group A rotavirus, ICS-RV detected 125 positives while Rotaclone and TestPack detected 127 and 129 positives, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value were 94.0, 100, 100, and 93.4% for ICS-RV; 95.5, 100, 100, and 95.0% for Rotaclone; and 97.0, 96.5, 97.0, and 96.5% for TestPack. ICS-RV was sensitive and specific and was relatively simple to perform and interpret.
Activity of Gatifloxacin against
Haemophilus influenzae
and
Moraxella catarrhalis
, Including Susceptibility Test Development, E-Test Comparisons, and Quality Control Guidelines for
H. influenzae
Authors: Jones Ronald N. , Biedenbach Douglas J. , Erwin Meredith E. , Beach Mondell L. , Pfaller Michael A. ,   The Quality Control Study Group
Published: December 2019

ABSTRACT

In vitro antimicrobial activity and susceptibility testing interpretation criteria and quality control were studied for gatifloxacin, a new 8-methoxy fluoroquinolone, tested against
Haemophilus influenzae. Moraxella catarrhalis
(600 strains) and
H. influenzae
(1,400 strains) from the SENTRY Antimicrobial Surveillance Program in North America (Canada and the United States) were also tested against gatifloxacin and 12 other antimicrobial agents. Gatifloxacin (MIC at which 90% of the isolates are inhibited [MIC
90
], ≤0.03 μg/ml; 100.0% of strains inhibited at ≤2 μg/ml) was the most active agent tested against
H. influenzae
and was similar to four comparison fluoroquinolones (MICs, ≤0.03 to 2 μg/ml) against
M. catarrhalis
. A subset of 300 recent clinical isolates of
H. influenzae
were tested by using media (Haemophilus Test Medium agar and broth) and procedures recommended by the National Committee for Clinical Laboratory Standards (NCCLS) and with the E-test (AB BIODISK, Solna, Sweden). Gatifloxacin (MIC
50
, 0.008 μg/ml) was slightly more active than levofloxacin, and E-test results were generally elevated by 0.5 log
2
dilution step compared to reference MICs. The gatifloxacin 5-μg disk test produced zone diameters that were routinely above 30 mm for
H. influenzae
strains, corresponding to gatifloxacin MICs of 0.008 or 0.016 μg/ml. The gatifloxacin susceptibility breakpoint proposed for nonfastidious species (≤2 μg/ml; ≥18 mm) was also suggested for
H. influenzae
testing. No interpretive errors were observed. Quality control guidelines for
H. influenzae
ATCC 49247 were determined by using the NCCLS M23-T3 (1998) study design. The results from the nine-laboratory protocol suggested the following control ranges: for broth microdilution tests, 0.004 to 0.03 μg/ml; for disk diffusion testing, 33 to 41 mm. Gatifloxacin appears to be a potent anti-
Haemophilus
fluoroquinolone compound with in vitro testing interpretive criteria that will produce accurate results (disk diffusion, broth microdilution, and E-test).