bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of Penicillin-Resistant
Streptococcus pneumoniae
Isolates from Bulgaria
Authors: Setchanova Lena , Tomasz Alexander 
Published: December 2019

ABSTRACT

As part of an ongoing surveillance program of antibiotic-resistant
Streptococcus pneumoniae
in Sofia, Bulgaria, 120 penicillin-resistant strains (PRSP) (most of them recovered from children hospitalized with pneumococcal disease) were analyzed by microbiological and molecular methods. Several unique features of this collection are of particular interest. (i) Most isolates (112 of 120) were also resistant to trimethoprim-sulfamethoxazole (SXT) (97 of 120 isolates, or 80%), and over 70% (86 of 120) of the isolates were resistant to at least three antibiotics in addition to penicillin. (ii) Close to 80% of all isolates were represented by large clusters of bacteria, each with a unique serotype, antibiotype, and chromosomal macrorestriction pattern (determined by pulsed-field gel electrophoresis), as well as unique restriction fragmentation length polymorphisms of the penicillin-binding protein genes
pbp1a
,
pbp2x
, and
pbp2b
. (iii) A large proportion (45 of 120, or 38%) of the strains belonged to two internationally spread epidemic clones of
S. pneumoniae
, the first expressing capsular type 23F and the second expressing serotype 9. (iv) A unique Bulgarian cluster composed of eight serotype 19F isolates was resistant to tetracycline, SXT, cefotaxime, and extremely high levels of penicillin and erythromycin. Nevertheless, this clone did not react with either the
erm
or the
mef
DNA probes, and thus the mechanism of macrolide resistance in this group of PRSP remains to be elucidated.
Detection of the 70-Kilodalton
Histoplasma capsulatum
Antigen in Serum of Histoplasmosis Patients: Correlation between Antigenemia and Therapy during Follow-Up
Authors: Gómez B. L. , Figueroa J. I. , Hamilton A. J. , Diez S. , Rojas M. , Tobón A. , Restrepo A. , Hay R. J. 
Published: December 2019

ABSTRACT

Histoplasmosis is an important systemic fungal infection, particularly among immunocompromised individuals, who may develop a progressive disseminated form which is often fatal if it is untreated. In such patients, the detection of antibody responses for both diagnosis and follow-up may be of limited use, whereas the detection of
Histoplasma capsulatum
var.
capsulatum
antigens may provide a more practical approach. We have recently described an inhibition enzyme-linked immunosorbent assay (ELISA) for the detection in patients’ sera of a 69- to 70-kDa
H. capsulatum
var.
capsulatum
-specific antigen which appears to be useful in diagnosis. To investigate its potential for the follow-up of histoplasmosis patients during treatment, antigen titers in the sera of 16 patients presenting with different clinical forms of histoplasmosis were monitored at regular intervals for up to 80 weeks. Sera from four of five patients with the acute form of the disease showed rapid falls in antigenemia, becoming antigen negative by week 14 (range, weeks 10 to 16). Sera from four patients with disseminated histoplasmosis showed falls in antigen levels; three of them became antigen negative by week 32; the fourth patient became negative by week 48. In contrast, antigen titers in four of six AIDS patients with the disseminated form of the disease remained positive throughout follow-up. Sera from only one patient who presented with the chronic form of the disease were analyzed, and this individual’s serum became antigen negative by week 9. The inhibition ELISA is shown to be of particular use in the monitoring of non-AIDS patients with the acute and disseminated forms of the disease and may complement existing means of follow-up.
Evaluation of Two Commercial Kits and Arbitrarily Primed PCR for Identification and Differentiation of
Actinobacillus actinomycetemcomitans
,
Haemophilus aphrophilus
, and
Haemophilus paraphrophilus
Authors: Doğan Başak , Asikainen Sirkka , Jousimies-Somer Hannele 
Published: December 2019

ABSTRACT

The closely related species
Actinobacillus actinomycetemcomitans
,
Haemophilus aphrophilus
, and
Haemophilus paraphrophilus
are common findings in oral microbiota. The aims of this study were to evaluate the applicability of the Rapid NH and API ZYM kits and arbitrarily primed PCR (AP-PCR) in the identification and differentiation of the three species from each other. The material included 62 clinical isolates and three reference strains of
A. actinomycetemcomitans
representing the 5 serotypes and 18 AP-PCR genotypes.
Haemophilus
species included 12 clinical isolates and 11 reference strains of
H. aphrophilus
,
H. paraphrophilus
, and 5 other species. For the PCR amplification, the oligonucleotide 5′-CAGCACCCAC-3′ was used as a primer. Contrary to the consistent performance of API ZYM, the Rapid NH system was able to identify only 10 of 65 (15%)
A. actinomycetemcomitans
isolates, whereas all
Haemophilus
species were correctly identified. The API ZYM test differentiated
A. actinomycetemcomitans
from
H. aphrophilus
and
H. paraphrophilus
by negative β-galactosidase and α-glucosidase reactions and a positive esterase lipase reaction. However, the API ZYM test was unable to differentiate
H. aphrophilus
from
H. paraphrophilus
, it also could not differentiate
A. actinomycetemcomitans
serotypes from each other. Among the
H. aphrophilus
isolates three AP-PCR genotypes and among
H. paraphrophilus
isolates only one AP-PCR genotype, distinct from those of
A. actinomycetemcomitans
, were found. The Rapid NH test showed poor ability to identify clinical isolates of all
A. actinomycetemcomitans
serotypes. Moreover, AP-PCR genotyping proved to be a rapid method for the species differentiation of
A. actinomycetemcomitans
,
H. aphrophilus
, and
H. paraphrophilus
.
Isolation of
Legionella pneumophila
by Centrifugation of Shell Vial Cell Cultures from Multiple Liver and Lung Abscesses
Authors: La Scola Bernard , Michel Gérard , Raoult Didier 
Published: December 2019

ABSTRACT

A 7-year-old girl was admitted to the hospital with acute lymphoblastic leukemia and was treated with allogenic cord blood transplantation. At day 30 after graft, she developed a fever and multiple nodular lesions disseminated in the liver and lungs. All bacterial cultures attempted on liver and lung biopsy specimens and blood remained sterile on standard axenic media. However, inoculation of liver and lung biopsy specimens on eukaryotic cell monolayers by the centrifugation-shell vial technique (M. Marrero and D. Raoult, Am. J. Trop. Med. Hyg. 40:197–199, 1989) led to the recovery of a strain of
Legionella pneumophila
serogroup 1, identified by 16S rRNA gene amplification and sequencing and serotyping. Our findings demonstrate that the centrifugation-cell culture method, which has previously been useful for the isolation of other strictly or facultatively intracellular bacteria, can also serve as a method for the recovery of
L. pneumophila
from clinical material.
Optimal Detection and Identification of
Mycobacterium haemophilum
in Specimens from Pediatric Patients with Cervical Lymphadenopathy
Authors: Samra Zmira , Kaufmann Lea , Zeharia Avraham , Ashkenazi Shai , Amir Jacob , Bahar Judy , Reischl Udo , Naumann Ludmilla 
Published: December 2019

ABSTRACT

Acid-fast bacilli from pediatric patients with lymphadenopathy were detected in the BACTEC radiometric system and in MB Redox broth, but not on Löwenstein Jensen medium. PCR amplification identified the isolates as
Mycobacterium haemophilum
, which has special nutrition requirements (iron supplements) for growth. Suitable culture medium ensures optimal recovery of this microorganism, avoiding underdiagnosis.
hsp65
Sequencing for Identification of Rapidly Growing Mycobacteria
Authors: Ringuet H. , Akoua-Koffi C. , Honore S. , Varnerot A. , Vincent V. , Berche P. , Gaillard J. L. , Pierre-Audigier C. 
Published: December 2019

ABSTRACT

Partial sequencing of the
hsp65
gene was used for the identification of rapidly growing mycobacteria (RGM). A 441-bp fragment (A. Telenti, F. Marchesi, M. Balz, F. Bally, E. Böttger, and T. Bodmer, J. Clin. Microbiol. 31:175–178, 1993) was amplified and sequenced by an automated fluorescence-based method involving capillary electrophoresis. Type strains of 10 RGM species were first studied. Each species had a unique nucleotide sequence, distinguishing it clearly from the other species. A panel of strains from the four main RGM species responsible for human infections,
Mycobacterium abscessus
,
Mycobacterium chelonae
,
Mycobacterium fortuitum
, and
Mycobacterium peregrinum
, was also studied. There were few sequence differences within each of these species (<2% of bases were different from the type strain sequence), and they had no effect on species assignment.
hsp65
sequencing unambiguously differentiated
M. chelonae
and
M. abscessus
, two species difficult to identify by classical methods and 16S rRNA gene sequencing. The devised procedure is a rapid and reliable tool for the identification of RGM species.
Comparative Study of Susceptibilities of Germinated and Ungerminated Conidia of
Aspergillus fumigatus
to Various Antifungal Agents
Authors: Manavathu Elias K. , Cutright Jessica , Chandrasekar Pranatharthi H. 
Published: December 2019

ABSTRACT

Conidia are used as inocula for the in vitro susceptibility testing of
Aspergillus fumigatus
. Since the MIC is defined on the basis of visible mycelial growth, conidia should germinate and produce sporelings (germinated conidia) for monitoring of the growth inhibition and fungicidal activity of a drug. If a compound is capable of inhibiting germination of conidia while affecting or not affecting the growth of the organism, the MIC obtained will be the concentration of the drug required for the inhibition of conidial germination but not necessarily that required for inhibition of the growth of the organism. We investigated the susceptibility of germinated and ungerminated conidia to amphotericin B, itraconazole, voriconazole, and SCH56592. The MICs of various antifungal agents for germinated conidia were almost identical to those obtained for ungerminated conidia. In addition, both the germinated and ungerminated conidia were killed with almost equal efficiency by all of the compounds tested when exposed to the drugs for 24 h. These results suggest that either germinated or ungerminated conidia could be used as inocula for in vitro susceptibility studies of
A. fumigatus
with identical results.
Identification and Characterization of IS
2404
and IS
2606
: Two Distinct Repeated Sequences for Detection of
Mycobacterium ulcerans
by PCR
Authors: Stinear Timothy , Ross Bruce C. , Davies John K. , Marino Lui , Robins-Browne Roy M. , Oppedisano Frances , Sievers Aina , Johnson Paul D. R. 
Published: December 2019

ABSTRACT

Molecular analysis of
Mycobacterium ulcerans
has revealed two new insertion sequences (ISs), IS
2404
and IS
2606
. IS
2404
was identified by complete sequencing of a previously described repetitive DNA segment from
M. ulcerans
. This element is 1,274 bp long, contains 12-bp inverted repeats and a single open reading frame (ORF) potentially encoding a protein of 327 amino acids (aa), and apparently generates 7-bp direct repeats upon transposition. Amino acid similarity was found between the putative transposase and those encoded by ISs in other bacterial sequences from
Aeromonas salmonicida
(
As
Is
1
),
Escherichia coli
(H repeat element),
Vibrio cholerae
(
Vc
IS
1
), and
Porphyromonas gingivalis
(
PG
IS
2
). The second IS, IS
2606
, was discovered by sequence analysis of a
Hae
III fragment of
M. ulcerans
genomic DNA containing a repetitive sequence. This element is 1,404 bp long, with 12-bp inverted repeats and a single ORF potentially encoding a protein of 445 aa. Database searches revealed a high degree of amino acid identity (70%) with the putative transposase of IS
1554
from
M. tuberculosis
. Significant amino acid identity (40%) was also observed with transposases from several other microorganisms, including
Rhizobium meliloti
(IS
Rm3
),
Burkholderia cepacia
(IS
1356
),
Corynebacterium diphtheriae
, and
Yersinia pestis
. PCR screening of DNA from 45 other species of mycobacteria with primers for IS
2404
confirm that this element is found only in
M. ulcerans
. However, by PCR, IS
2606
was also found in
Mycobacterium lentiflavum
, another slow-growing member of the genus
Mycobacterium
that is apparently genetically distinct from
M. ulcerans
. Testing the sensitivity of PCR based on IS
2404
and IS
2606
primers demonstrated the ability to detect 0.1 and 1
M. ulcerans
genome equivalents, respectively. The ability to detect small numbers of cells by using two gene targets will be particularly useful for analyzing environmental samples, where there may be low concentrations of
M. ulcerans
among large numbers of other environmental mycobacteria.
Antimicrobial Susceptibilities and Plasmid Contents of
Neisseria gonorrhoeae
Isolates from Commercial Sex Workers in Dhaka, Bangladesh: Emergence of High-Level Resistance to Ciprofloxacin
Authors: Bhuiyan Bahar Uddin , Rahman Motiur , Miah Mohammed Ruhul Amin , Nahar Shamsun , Islam Nazrul , Ahmed Monira , Rahman Kazi Masihur , Albert M. John 
Published: December 2019

ABSTRACT

Commercial sex workers (CSWs) serve as the most important reservoir of sexually transmitted diseases (STD), including gonorrhea. Periodic monitoring of the antimicrobial susceptibility profile of
Neisseria gonorrhoeae
in a high-risk population provides essential clues regarding the rapidly changing pattern of antimicrobial susceptibilities. A study concerning the prevalence of gonococcal infection among CSWs was conducted in Bangladesh. The isolates were examined with regards to their antimicrobial susceptibility to, and the MICs of, penicillin, tetracycline, ciprofloxacin, cefuroxime, ceftriaxone, and spectinomycin by disk diffusion and agar dilution methods. The total plasmid profile of the isolates was also analyzed. Of the 224 CSWs, 94 (42%) were culture positive for
N. gonorrhoeae
. There was a good correlation between the results of the disk diffusion and agar dilution methods. Some 66% of the isolates were resistant to penicillin, and 34% were moderately susceptible to penicillin. Among the resistant isolates, 23.4% were penicillinase-producing
N. gonorrhoeae
(PPNG). 60.6% of the isolates were resistant and 38.3% were moderately susceptible to tetracycline, 17.5% were tetracycline-resistant
N. gonorrhoeae
, 11.7% were resistant and 26.6% had reduced susceptibility to ciprofloxacin, 2.1% were resistant and 11.7% had reduced susceptibility to cefuroxime, and 1% were resistant to ceftriaxone. All PPNG isolates contained a 3.2-MDa African type of plasmid, and a 24.2-MDa conjugative plasmid was present in 34.1% of the isolates. Since quinolones such as ciprofloxacin are recommended as the first line of therapy for gonorrhea, the emergence of significant resistance to ciprofloxacin will limit the usefulness of this drug for treatment of gonorrhea in Bangladesh.
Human Herpesvirus 8 Seroprevalence and Evaluation of Nonsexual Transmission Routes by Detection of DNA in Clinical Specimens from Human Immunodeficiency Virus-Seronegative Patients from Central and Southern Italy, with and without Kaposi’s Sarcoma
Authors: Cattani Paola , Capuano Maria , Cerimele Francesca , La Parola Ilaria Lesnoni , Santangelo Rosaria , Masini Cinzia , Cerimele Decio , Fadda Giovanni 
Published: December 2019

ABSTRACT
In order to investigate the seroprevalence of human herpesvirus 8 (HHV-8) infection in central and southern Italy, sera from human immunodeficiency virus (HIV)-seronegative subjects, with and without Kaposi’s sarcoma (KS), were analyzed by immunofluorescence assay, using BC-3, a cell line latently infected with HHV-8. High titers of antibody against HHV-8 lytic and latent antigens were detected in all 50 KS patients studied, while in 50 HIV-seronegative subjects without KS, 32 (64%) were found positive for HHV-8 antibodies. Titers in the sera of these patients were lower than those for KS patients. This data suggests that HHV-8 infection is not restricted to KS patients and that the prevalence of HHV-8 infection in the general population may be correlated with differing rates of prevalence of KS in different parts of the world. In view of these findings, possible nonsexual transmission routes were evaluated. Nested PCR was used to test for the presence of HHV-8 DNA in saliva, urine, and tonsillar swabs from KS and non-KS patients. In KS patients, 14 out of 32 tonsillar swabs (43.7%), 11 out of 24 saliva samples (45.8%), and just 2 out of 24 urine samples (8.3%) tested positive for HHV-8 DNA. In the control group, on the contrary, none of the 20 saliva and 20 urine specimens was positive for HHV-8 DNA; only 1 out of 22 tonsillar swabs gave a positive result. This data supports the hypothesis that HHV-8 infects the general population in a latent form. The reactivation of viral infection may result in salivary shedding of HHV-8, contributing to viral spread by nonsexual transmission routes.
Serological Evidence of Infection with
Ehrlichia
spp. in Red Foxes (
Vulpes vulpes
) in Switzerland
Authors: Pusterla Nicola , Deplazes Peter , Braun Ueli , Lutz Hans 
Published: December 2019

ABSTRACT

Serum samples from 1,550 red foxes in Switzerland were tested for antibodies to the agents of canine granulocytic and monocytic ehrlichiosis by an indirect immunofluorescent technique. Forty-four (2.8%) of the samples were positive for
Ehrlichia phagocytophila
, which is an antigen marker for granulocytic ehrlichiosis. In contrast, none of the samples had antibodies specific to
Ehrlichia canis
, the agent of monocytic ehrlichiosis.
Serotyping ofCryptococcus neoformansIsolates from Clinical and Environmental Sources in Spain
Authors: Baró Teresa , Torres-Rodríguez Josep M. , Morera Yolanda , Alía Concepción , López Olga , Méndez Raul 
Published: December 2019

ABSTRACTWe determined biovars and serotypes of 154 isolates ofCryptococcus neoformansfrom clinical and environmental sources from different areas of Spain. All clinical isolates belonged toC. neoformansvar.neoformans. Serotypes showed an irregular distribution.C. neoformansvar.gattiiserotype B was isolated from necropsy specimens from goats with pulmonary disease.
rpoB
Mutations in Multidrug-Resistant Strains of
Mycobacterium tuberculosis
Isolated in Italy
Authors: Pozzi G. , Meloni M. , Iona E. , Orrù G. , Thoresen O. F. , Ricci M. L. , Oggioni M. R. , Fattorini L. , Orefici G. 
Published: December 2019

ABSTRACT

Mutations of
rpoB
associated with rifampin resistance were studied in 37 multidrug-resistant (MDR) clinical strains of
Mycobacterium tuberculosis
isolated in Italy. At least one mutated codon was found in each MDR strain. It was always a single-base substitution leading to an amino acid change. Nine different
rpoB
alleles, three of which had not been reported before, were found. The relative frequencies of specific mutations in this sample were different from those previously reported from different geographical areas, since 22 strains (59.5%) carried the mutated codon TTG in position 531 (Ser→Leu) and 11 (29.7%) had GAC in position 526 (His→Asp).
Specificity of IS
6110
-Based DNA Fingerprinting and Diagnostic Techniques for
Mycobacterium tuberculosis
Complex
Authors: Githui Willie A. , Wilson Stuart M. , Drobniewski Francis A. 
Published: December 2019

ABSTRACT

Restriction fragment length polymorphism and hybridization of DNA extracted from
Mycobacterium tuberculosis
, nontuberculous mycobacteria, and nonmycobacterial species with a probe derived from IS
6110
confirmed that IS
6110
was specific to
M. tuberculosis
complex. In addition, DNA amplification with IS
6110
-specific primers yielded a 181-bp fragment only in DNA from
M. tuberculosis
complex isolates.
Detection of Cell Wall Mannoprotein Mp1p in Culture Supernatants of
Penicillium marneffei
and in Sera of Penicilliosis Patients
Authors: Cao Liang , Chan King-Man , Chen Daliang , Vanittanakom Nongnuch , Lee Cindy , Chan Che-Man , Sirisanthana Thira , Tsang Dominic N. C. , Yuen Kwok-Yung 
Published: December 2019

ABSTRACT

Mannoproteins are important and abundant structural components of fungal cell walls. The
MP1
gene encodes a cell wall mannoprotein of the pathogenic fungus
Penicillium marneffei
. In the present study, we show that Mp1p is secreted into the cell culture supernatant at a level that can be detected by Western blotting. A sensitive enzyme-linked immunosorbent assay (ELISA) developed with antibodies against Mp1p was capable of detecting this protein from the cell culture supernatant of
P. marneffei
at 10
4
cells/ml. The anti-Mp1p antibody is specific since it fails to react with any protein-form lysates of
Candida albicans
,
Histoplasma capsulatum
, or
Cryptococcus neoformans
by Western blotting. In addition, this Mp1p antigen-based ELISA is also specific for
P. marneffei
since the cell culture supernatants of the other three fungi gave negative results. Finally, a clinical evaluation of sera from penicilliosis patients indicates that 17 of 26 (65%) patients are Mp1p antigen test positive. Furthermore, a Mp1p antibody test was performed with these serum specimens. The combined antibody and antigen tests for
P. marneffei
carry a sensitive of 88% (23 of 26), with a positive predictive value of 100% and a negative predictive value of 96%. The specificities of the tests are high since none of the 85 control sera was positive by either test.
Molecular Epidemiology of Tuberculosis in Malaysia
Authors: Dale Jeremy W. , Nor Rohana Mat , Ramayah Soshila , Tang Thean Hock , Zainuddin Zainul F. 
Published: December 2019

ABSTRACT

Molecular typing with IS
6110
was applied to
Mycobacterium tuberculosis
isolates from all parts of Malaysia. The degree of clustering increased with patient age, suggesting that reactivation may contribute to clustering. Identical banding patterns were also obtained for isolates from widely separate regions. Therefore, the use of clustering as a measure of recent transmission must be treated with caution. Strains related to the Beijing family were common in Peninsular Malaysia but were less common in Sabah and Sarawak, while a distinct group of strains comprised nearly 40% of isolates from East Malaysia but such strains were rare in Peninsular Malaysia. Single-copy strains, common in South and Southeastern Asia, constituted nearly 20% of isolates from the peninsula but were virtually absent in East Malaysia. The marked geographical difference in the prevailing strains indicates not only a restricted dissemination of
M. tuberculosis
but also a considerable degree of stability in the banding patterns.
Recurrent “
Flexispira rappini
” Bacteremia in an Adult Patient Undergoing Hemodialysis: Case Report
Authors: Sorlin P. , Vandamme P. , Nortier J. , Hoste B. , Rossi C. , Pavlof S. , Struelens M. J. 
Published: December 2019

ABSTRACT

A blood culture from a 65-year-old febrile man undergoing hemodialysis revealed, 5 days after inoculation, an unusual gram-negative fusiform rod with darting motility. During another episode of fever 21 days later, this
Campylobacter
-like organism was again recovered from three blood cultures and subcultured under an H
2
-enriched microaerobic atmosphere. The organism was catalase negative and oxidase positive and hydrolyzed urea rapidly. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of whole-cell proteins was indistinguishable from that of “
Flexispira rappini
” LMG 8738 described by Archer et al. in 1988 (J. R. Archer, S. Romero, A. E. Ritchier, M. E. Hamacher, B. M. Steiner, J. H. Bryner, and R. F. Schell, J. Clin. Microbiol. 26:101–105, 1988). The analysis of the 16S ribosomal DNA sequence revealed a similarity of 99.3% between the two strains. The patient recovered completely after a 4-week course of meropenem therapy. This is the first reported case of a recurrent “
F. rappini
” bacteremia in an adult patient, which confirms that this organism may be an invasive pathogen in immunocompromised patients, like other newly described
Helicobacter
species.