bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lacazia loboi
gen. nov., comb. nov., the Etiologic Agent of Lobomycosis
Authors: Taborda Paulo R. , Taborda Valeria A. , McGinnis Michael R. 
Published: December 2019

ABSTRACT

The new genus
Lacazia
P. Taborda, V. Taborda, et McGinnis is proposed to accommodate
Lacazia loboi
(O. M. Fonseca et Lacaz) P. Taborda, V. Taborda, et McGinnis, the obligate pathogen that causes lobomycosis in mammals. The continued placement of that fungus in the genus
Paracoccidioides
Almeida as
Paracoccidioides loboi
is taxonomically inappropriate.
Loboa loboi
Ciferri et al. is a synonym of
Paracoccidioides brasiliensis
.
Epidemiological Study of an
Acinetobacter baumannii
Outbreak by Using a Combination of Antibiotyping and Ribotyping
Authors: Biendo M. , Laurans G. , Lefebvre J. F. , Daoudi F. , Eb F. 
Published: December 2019

ABSTRACT

From June to November 1994 (period 1) and from February to June 1995 (period 2), multiresistant
Acinetobacter baumannii
strains were isolated in intensive care units and surgical wards of the Amiens Teaching Hospital Center (Amiens, France). Eighteen isolates were obtained from 17 (1%) of 1,706 patients admitted during both of these periods, giving an incidence rate of nosocomial infection per 1,000 patient days of 0.6%. Of 17 infected patients, 9 had pneumonia, 3 had urinary tract infection, 2 had peritonitis, 1 had septicemia, 1 had a catheter infection, and 1 had pneumonia and urinary tract infection. According to typing results, four antibiotic resistance profiles were detected: a, b, c, and d; seven ribotypes were distinguished by both restriction enzymes
Eco
RI and
Sal
I (A, B, C, D, E, F, and G). By combining antibiotyping and ribotyping, we obtained eight groups of strains (groups I to VIII). Group I contained five strains (strains 4, 5, 7, 8, and 9) which had antibiogram pattern a and ribopattern A and constituted the outbreak strains. The strains of group II (strains 3, 10, 11, 13, and 14) were closely related to outbreak strain A and appeared to be variants of ribotype A (A2 [strain 3]; A4 [strain 10]; A5 [strains 11, 13, and 14]). Groups III, IV, V, VI, VII, and VIII included strains which were epidemiologically unrelated to the strains of group I and were considered nonoutbreak strains.
Nosocomial Pseudoepidemic Caused by
Bacillus cereus
Traced to Contaminated Ethyl Alcohol from a Liquor Factory
Authors: Hsueh Po-Ren , Teng Lee-Jene , Yang Pan-Chyr , Pan Hui-Lu , Ho Shen-Wu , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

From September 1990 to October 1990, 15 patients who were admitted to four different departments of the National Taiwan University Hospital, including nine patients in the emergency department, three in the hematology/oncology ward, two in the surgical intensive care unit, and one in a pediatric ward, were found to have positive blood (14 patients) or pleural effusion (1 patient) cultures for
Bacillus cereus
. After extensive surveillance cultures, 19 additional isolates of
B. cereus
were recovered from 70% ethyl alcohol that had been used as a skin disinfectant (14 isolates from different locations in the hospital) and from 95% ethyl alcohol (5 isolates from five alcohol tanks in the pharmacy department), and 10 isolates were recovered from 95% ethyl alcohol from the factory which supplied the alcohol to the hospital. In addition to these 44 isolates of
B. cereus
, 12 epidemiologically unrelated
B. cereus
isolates, one
Bacillus sphaericus
isolate from a blood specimen from a patient seen in May 1990, and two
B. sphaericus
isolates from 95% alcohol in the liquor factory were also studied for their microbiological relatedness. Among these isolates, antibiotypes were determined by using the disk diffusion method and the E test, biotypes were created with the results of the Vitek
Bacillus
Biochemical Card test, and random amplified polymorphic DNA (RAPD) patterns were generated by arbitrarily primed PCR. Two clones of the 15
B. cereus
isolates recovered from patients were identified (clone A from 2 patients and clone B from 13 patients), and all 29 isolates of
B. cereus
recovered from 70 or 95% ethyl alcohol in the hospital or in the factory belonged to clone B. The antibiotype and RAPD pattern of the
B. sphaericus
isolate from the patient were different from those of isolates from the factory. Our data show that the pseudoepidemic was caused by a clone (clone B) of
B. cereus
from contaminated 70% ethyl alcohol used in the hospital, which we successfully traced to preexisting contaminated 95% ethyl alcohol from the supplier, and by another clone (clone A) without an identifiable source.
Worldwide Evaluation of DNA Sequencing Approaches for Identification of Drug Resistance Mutations in the Human Immunodeficiency Virus Type 1 Reverse Transcriptase
Authors: Schuurman Rob , Demeter Lisa , Reichelderfer Patricia , Tijnagel Jolanda , de Groot Tom , Boucher Charles 
Published: December 2019

ABSTRACT
A panel (ENVA-1) of well-defined blinded samples containing wild-type and mutant human immunodeficiency virus type 1 (HIV-1) reverse transcriptase was analyzed by automated DNA sequencing in 23 laboratories worldwide. Drug resistance mutations at codons 41, 215, and 184 were present in the panel samples at different ratios to the wild type. The presence of mutant genotypes was determined qualitatively and quantitatively. All laboratories reported the presence of sequence heterogeneities at codons 41, 215, and 184 in one or more of the panel samples, though not all reported the correct codon genotypes. Two laboratories reported a mutant genotype in samples containing only the wild type, whereas two and three laboratories failed to detect the mutant genotypes at codons 41 and 215, respectively, in a completely mutant DNA population. Mutations present at relative concentrations of 25% of the total DNA population were successfully identified by 13 of 23, 10 of 23, and 16 of 23 labs for codons 41, 215, and 184Val, respectively. For more than 80% of those laboratories that qualitatively detected the presence of a mutation correctly, the estimated wild type/mutant ratio was less than 25% different from the input ratio in those samples containing 25 to 50% or 75% mutant input. This first multicenter study on the quality of DNA sequencing approaches for identifying HIV-1 drug resistance mutations revealed large interlaboratory differences in the quality of the results. The application of these procedures in their current state would in several cases lead to inaccurate or even incorrect diagnostic results. Therefore, proper quality control and standardization are urgently needed.
Detection by an Immunofluorescence Test of
Encephalitozoon intestinalis
Spores in Routinely Formalin-Fixed Stool Samples Stored at Room Temperature
Authors: Moura H. , Sodre F. C. , Bornay-Llinares F. J. , Leitch G. J. , Navin T. , Wahlquist S. , Bryan R. , Meseguer I. , Visvesvara G. S. 
Published: December 2019

ABSTRACT

Of the several microsporidia that infect humans,
Enterocytozoon bieneusi
is known to cause a gastrointestinal disease whereas
Encephalitozoon intestinalis
causes both a disseminated and an intestinal disease. Although several different staining techniques, including the chromotrope technique and its modifications, Uvitex 2B, and the quick-hot Gram-chromotrope procedure, detect microsporidian spores in fecal smears and other clinical samples, they do not identify the species of microsporidia. A need for an easily performed test therefore exists. We reevaluated 120 stool samples that had been found positive for microsporidia previously, using the quick-hot Gram-chromotrope technique, and segregated them into two groups on the basis of spore size. We also screened the smears by immunofluorescence microscopy, using a polyclonal rabbit anti-
E. intestinalis
serum at a dilution of 1:400. Spores in 29 (24.1%) of the 120 samples fluoresced brightly, indicating that they were
E. intestinalis
spores. No intense background or cross-reactivity with bacteria, yeasts, or other structures in the stool samples was seen. Additionally, the numbers of spores that fluoresced in seven of these samples were substantially smaller than the numbers of spores that were present in the stained smears, indicating that these samples were probably derived from patients with mixed infections of
Enterocytozoon bieneusi
and
E. intestinalis
. Because a 1:400 dilution of this serum does not react with culture-grown
Encephalitozoon hellem
,
Encephalitozoon cuniculi
, or
Vittaforma corneae
or with
Enterocytozoon bieneusi
spores in feces, we concluded that an immunofluorescence test using this serum is a good alternative for the specific identification of
E. intestinalis
infections.
Molecular Evidence of Mother-to-Infant Transmission of Hepatitis G Virus among Women without Known Risk Factors for Parenteral Infections
Authors: Menéndez Clara , Sánchez-Tapias José-María , Alonso Pedro-Luis , Giménez-Barcons Mireia , Kahigwa Elizeus , Aponte John-Jairo , Mshinda Hassan , Navia Margarita-María , Jiménez de Anta María-Teresa , Rodés Juan , Saiz Juan-Carlos 
Published: December 2019

ABSTRACT
Hepatitis G virus (HGV) RNA was detected in 18 of 133 pregnant women from Tanzania without known risk factors for HGV infection and in 7 of 18 children born to HGV RNA-positive mothers. Molecular evidence of mother-to-infant transmission was obtained only for three of seven children. HGV RNA was also detected in 4 of 42 children born to non-HGV-infected women. Thus, mechanisms other than materno-filial may play an important role in HGV transmission during early childhood.
In Vitro Amphotericin B Resistance in Clinical Isolates of
Aspergillus terreus
, with a Head-to-Head Comparison to Voriconazole
Authors: Sutton Deanna A. , Sanche Stephen E. , Revankar Sanjay G. , Fothergill Annette W. , Rinaldi Michael G. 
Published: December 2019

ABSTRACT

Amphotericin B therapy continues to be the “gold standard” in the treatment of invasive aspergillosis in the immunocompromised host. Although
Aspergillus fumigatus
and
Aspergillus flavus
constitute the major species, several reports have described invasive pulmonary or disseminated disease due to the less common
Aspergillus terreus
and dismal clinical outcomes with high-dose amphotericin B. We therefore evaluated 101 clinical isolates of
A. terreus
for their susceptibility to amphotericin B and the investigational triazole voriconazole by using the National Committee for Clinical Laboratory Standards M27-A method modified for mould testing. Forty-eight-hour MICs indicated 98 and 0% resistance to amphotericin B and voriconazole, respectively. We conclude that
A. terreus
should be added to the list of etiologic agents refractory to conventional amphotericin B therapy and suggest the potential clinical utility of voriconazole in aspergillosis due to this species.
Molecular Epidemiology of Hepatitis C Virus Infection in an Area of Hyperendemicity in Southern Italy: a Population-Based Study
Authors: Osella Alberto R. , Sonzogni Laura , Cavallini Aldo , Foti Luciana , Guerra Vito , Di Leo Alfredo , Mondelli Mario U. , Misciagna Giovanni , Silini Enrico M. 
Published: December 2019

ABSTRACT
In a cohort of subjects from Italy, anti-hepatitis C virus (HCV) and HCV RNA [HCV(+) subgroup] prevalences were 24.6 and 79.6%, respectively. HCV types 1b and 2a/c accounted for 95% of infections. Adjusted alanine aminotransferase levels were higher in males than in females and in RNA-positive subjects than in RNA-negative subjects regardless of HCV type. Genotype distribution was unrelated to demographic variables.
Evaluation of the AnaeroPack Campylo System for Growth of Microaerophilic Bacteria
Authors: Van Horn Kenneth , Tóth Clara 
Published: December 2019

ABSTRACT

Growth of microaerophilic bacteria in the AnaeroPack Campylo (Mitsubishi Gas Chemical America, Inc., New York, N.Y.) atmosphere generation system was compared to growth in the CampyPak Plus jar and CampyPak pouch (Becton-Dickinson Microbiology Systems [BDMS], Cockeysville, Md.). Growth in the AnaeroPack Campylo system was considered equivalent to or better than growth obtained in the CampyPak Plus and CampyPak pouch systems for 48 of the 50
Helicobacter pylori
strains and for all 28
Campylobacter
species tested. All of the 78 organisms tested were recovered in each system in equivalent colony counts. Two strains of
H. pylori
grown in the AnaeroPack Campylo system were observed to have colony morphology growth discrepancies when compared to growth in the two BDMS systems. Atmosphere failure with the AnaeroPack Campylo was not detected with
Campylobacter jejuni
ATCC 33291 used as a growth control. The AnaeroPack Campylo system is easy to use and supports the growth of campylobacters and
H. pylori
.
Field Evaluation of the ICT Malaria P.f/P.v Immunochromatographic Test for Detection of
Plasmodium falciparum
and
Plasmodium vivax
in Patients with a Presumptive Clinical Diagnosis of Malaria in Eastern Indonesia
Authors: Tjitra Emiliana , Suprianto Sri , Dyer Mary , Currie Bart J. , Anstey Nicholas M. 
Published: December 2019

ABSTRACT

In areas such as eastern Indonesia where both
Plasmodium falciparum
and
Plasmodium vivax
occur, rapid antigen detection tests for malaria need to be able to detect both species. We evaluated the new combined
P. falciparum-P. vivax
immunochromatographic test (ICT Malaria P.f/P.v.) in Radamata Primary Health Centre, Sumba, Indonesia, from February to May 1998 with 560 symptomatic adults and children with a presumptive clinical diagnosis of malaria. Blinded microscopy was used as the “gold standard,” with all discordant and 20% of concordant results cross-checked blindly. Only 50% of those with a presumptive clinical diagnosis of malaria were parasitemic. The ICT Malaria P.f/P.v immunochromatographic test was sensitive (95.5%) and specific (89.8%) for the diagnosis of falciparum malaria, with a positive predictive value (PPV) and a negative predictive value (NPV) of 88.1 and 96.2%, respectively. HRP2 and panmalarial antigen line intensities were associated with parasitemia density for both species. Although the specificity and NPV for the diagnosis of vivax malaria were 94.8 and 98.2%, respectively, the overall sensitivity (75%) and PPV (50%) for the diagnosis of vivax malaria were less than the desirable levels. The sensitivity for the diagnosis of
P. vivax
malaria was 96% with parasitemias of >500/μl but only 29% with parasitemias of <500/μl. Nevertheless, compared with the test with HRP2 alone, use of the combined antigen detection test would reduce the rate of undertreatment from 14.7 to 3.6% for microscopy-positive patients, and this would be at the expense of only a modest increase in the rate of overtreatment of microscopy-negative patients from 7.1 to 15.4%. Cost remains a major obstacle to widespread use in areas of endemicity.
Effects of Anticoagulant, Processing Delay, and Assay Method (Branched DNA versus Reverse Transcriptase PCR) on Measurement of Human Immunodeficiency Virus Type 1 RNA Levels in Plasma
Authors: Kirstein Lynn M. , Mellors John W. , Rinaldo Charles R. , Margolick Joseph B. , Giorgi Janis V. , Phair John P. , Dietz Edith , Gupta Phalguni , Sherlock Christopher H. , Hogg Robert , Montaner J. S. G. , Muñoz Alvaro 
Published: December 2019

ABSTRACT

We conducted two studies to determine the potential influence of delays in blood processing, type of anticoagulant, and assay method on human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma. The first was an experimental study in which heparin- and EDTA-anticoagulated blood samples were collected from 101 HIV-positive individuals and processed to plasma after delays of 2, 6, and 18 h. HIV-1 RNA levels in each sample were then measured by both branched-DNA (bDNA) and reverse transcriptase PCR (RT-PCR) assays. Compared to samples processed within 2 h, the loss (decay) of HIV-1 RNA in heparinized blood was significant (
P
< 0.05) but small after 6 h (bDNA assay, −0.12 log
10
copies/ml; RT-PCR, −0.05 log
10
copies/ml) and after 18 h (bDNA assay, −0.27 log
10
copies/ml; RT-PCR, −0.15 log
10
copies/ml). Decay in EDTA-anticoagulated blood was not significant after 6 h (bDNA assay, −0.002 log
10
copies/ml; RT-PCR, −0.02 log
10
copies/ml), but it was after 18 h (bDNA assay, −0.09 log
10
copies/ml; RT-PCR, −0.09 log
10
copies/ml). Only 4% of samples processed after 6 h lost more than 50% (≥0.3 log
10
copies/ml) of the HIV-1 RNA, regardless of the anticoagulant or the assay that was used. The second study compared HIV-1 RNA levels in samples from the Multicenter AIDS Cohort Study (MACS; samples were collected in heparin-containing tubes in 1985, had a 6-h average processing delay, and were assayed by bDNA assay) and the British Columbia Drug Treatment Program (BCDTP) (collected in EDTA- or acid citrate dextrose-containing tubes in 1996 and 1997, had a 2-h maximum processing delay, and were assayed by RT-PCR). HIV-1 RNA levels in samples from the two cohorts were not significantly different after adjusting for CD4
+
-cell count and converting bDNA assay values to those corresponding to the RT-PCR results. In summary, the decay of HIV-1 RNA measured in heparinized blood after 6 h was small (−0.05 to −0.12 log
10
copies/ml), and the minor impact of this decay on HIV-1 RNA concentrations in archived plasma samples of the MACS was confirmed by the similarity of CD4
+
-cell counts and assay-adjusted HIV-1 RNA concentrations in the MACS and BCDTP.
Recurrent Bacteremia Caused by a “
Flexispira
”-Like Organism in a Patient with X-Linked (Bruton’s) Agammaglobulinemia
Authors: Weir Susan , Cuccherini Brenda , Whitney Anne M. , Ray Marsha L. , MacGregor John P. , Steigerwalt Arnold , Daneshvar Maryam I. , Weyant Robbin , Wray Betty , Steele John , Strober Warren , Gill Vee J. 
Published: December 2019

ABSTRACT

Helicobacter
spp., except for
Helicobacter cinaedi
, have only rarely been reported in cases of septicemia. A patient with X-linked (Bruton’s) agammaglobulinemia was found to have persistent sepsis with a
Helicobacter
-like organism despite multiple courses of antibiotics. His periods of sepsis were associated with leg swelling thought to be consistent with cellulitis. The organism was fastidious and required a microaerophilic environment containing H
2
for growth. Optimal growth was observed at 35 to 37°C on sheep blood, CDC anaerobe, and Bordet-Gengou agars. Serial subcultures every 4 to 5 days were required to maintain viability. The organism was strongly urease positive and showed highest relatedness to
Helicobacter
-like organisms with the vernacular name “
Flexispira rappini
” by 16S rRNA gene sequence analysis. Genomic DNA hybridization studies, however, found 24 to 37% relatedness to “
F. rappini
” and even less to other
Helicobacter
spp. Although the organism phenotypically resembles “
Flexispira
” and
Helicobacter
, it is thought to represent a new taxon. The patient’s infection was eventually cleared with a prolonged (5-month) course of intravenous imipenem and gentamicin.
Novel Human Erythrovirus Associated with Transient Aplastic Anemia
Authors: Nguyen Quang Tri , Sifer Christophe , Schneider Véronique , Allaume Xavier , Servant Annabelle , Bernaudin Françoise , Auguste Véronique , Garbarg-Chenon Antoine 
Published: December 2019

ABSTRACT
Erythrovirus (formerly parvovirus) B19 causes a wide range of diseases in humans, including anemia due to aplastic crisis. Diagnosis of B19 infection relies on serology and the detection of viral DNA by PCR. These techniques are usually thought to detect all erythrovirus field isolates, since the B19 genome is known to undergo few genetic variations. We have detected an erythrovirus (V9) markedly different from B19 in the serum and bone marrow of a child with transient aplastic anemia. The B19 PCR assay yielded a product that hybridized only very weakly to the B19-specific probe and whose sequence diverged more from those of 24 B19 viruses (11 to 14%) than the divergence found within the B19 group (≤6.65%). Restriction enzyme analysis of the V9 genome revealed that this genetic divergence extended beyond the amplified region. Interestingly, serological tests failed to demonstrate a response characteristic of acute B19 infection. V9 could be a new erythrovirus, and new diagnostic tests are needed for its detection.
Isolation of a New Subspecies,
Bartonella vinsonii
subsp.
arupensis
, from a Cattle Rancher: Identity with Isolates Found in Conjunction with
Borrelia burgdorferi
and
Babesia microti
among Naturally Infected Mice
Authors: Welch David F. , Carroll Karen C. , Hofmeister Erik K. , Persing David H. , Robison Denise A. , Steigerwalt Arnold G. , Brenner Don J. 
Published: December 2019

ABSTRACT

Bacteremia with fever due to a novel subspecies of
Bartonella vinsonii
was found in a cattle rancher. The subspecies shared major characteristics of the genus
Bartonella
in terms of most biochemical features and cellular fatty acid profile, but it was distinguishable from other subspecies of
B. vinsonii
by good growth on heart infusion agar supplemented with X factor and by its pattern of enzymatic hydrolysis of peptide substrates. DNA relatedness studies verified that the isolate belonged to the genus
Bartonella
and that it was genotypically related to
B. vinsonii
. The highest level of relatedness was observed with recently characterized strains from naturally infected mice that were coinfected with
Borrelia burgdorferi
and
Babesia microti
. We propose the name
Bartonella vinsonii
subsp.
arupensis
subsp. nov. as the new subspecies to accommodate these human and murine isolates.
Disseminated Zygomycosis Due to
Rhizopus schipperae
after Heatstroke
Authors: Anstead Gregory M. , Sutton Deanna A. , Thompson Elizabeth H. , Weitzman Irene , Otto Randal A. , Ahuja Sunil K. 
Published: December 2019

ABSTRACT

A 21-year-old woman suffered heatstroke and developed diarrhea while trekking across south Texas. The heatstroke was complicated by seizures, rhabdomyolysis, pneumonia, renal failure, and disseminated intravascular coagulation. The patient’s stool and blood cultures grew
Campylobacter jejuni
. The patient subsequently developed paranasal and gastrointestinal zygomycosis and required surgical debridement and a prolonged course of amphotericin B. The zygomycete cultured was
Rhizopus schipperae
. This is only the second isolate of
R. schipperae
that has been described.
R. schipperae
is characterized by the production of clusters of up to 10 sporangiophores arising from simple but well-developed rhizoids. These asexual reproductive propagules are produced on Czapek Dox agar but are absent on routine mycology media, where only chlamydospores are observed. Despite multiorgan failure, bacteremia, and disseminated zygomycosis, the patient survived and had a good neurological outcome. Heatstroke has not been previously described as a risk factor for the development of disseminated zygomycosis.