bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infection of Hickman Catheter by
Pseudomonas
(formerly
Flavimonas
)
oryzihabitans
Traced to a Synthetic Bath Sponge
Authors: Marı́n Mercedes , Garcı́a de Viedma Darı́o , Martı́n-Rabadán Pablo , Rodrı́guez-Créixems Marta , Bouza Emilio 
Published: December 2019

ABSTRACT

Pseudomonas
(formerly
Flavimonas
)
oryzihabitans
is an uncommon pathogen that may cause catheter-associated infections. Although it has occasionally been isolated from the environment, the source of human infection has not previously been documented. We describe an AIDS patient who developed
Pseudomonas oryzihabitans
bacteremia due to colonization of a Hickman catheter. The patient reported having strictly followed the recommendations for catheter hygiene. The only flaw detected was the use of a synthetic bath sponge in the shower. The sponge was cultured and yielded
P. oryzihabitans
among other nonfermentative, gram-negative bacilli. To determine the prevalence of
P. oryzihabitans
in sponges, we cultured 15 samples from unrelated households. The microorganism was isolated from 3 of the 15 samples. Molecular typing by arbitrarily primed PCR (AP-PCR) was performed with the environmental and clinical isolates. Three different profiles were obtained for the six isolates analyzed from the patient's sponge. The strain from the AIDS patient was identical to one of those from his sponge and was different from all the remaining strains. The AP-PCR typing results were subsequently confirmed by pulsed-field gel electrophoresis. It can be concluded that sponges are occasionally colonized by
P. oryzihabitans
. For the first time a probable source of an indwelling catheter contamination with this bacterium has been found. Patients carrying these devices should avoid using sponge-like materials, as these are suitable environments for nonfermentative, gram-negative bacilli.
Cost-Effective and Rapid Presumptive Identification of Gram-Negative Bacilli in Routine Urine, Pus, and Stool Cultures: Evaluation of the Use of CHROMagar Orientation Medium in Conjunction with Simple Biochemical Tests
Authors: Ohkusu Kiyofumi 
Published: December 2019

ABSTRACT

The algorithm for a new identification system was designed on the basis of colony color and morphology on CHROMagar Orientation medium in conjunction with simple biochemical tests such as indole (IND), lysine decarboxylase (LDC), and ornithine decarboxylase (ODC) utilization tests with gram-negative bacilli isolated from urine samples as well as pus, stool, and other clinical specimens by the following colony characteristics, biochemical reactions, and serological results: pinkish to red, IND positive (IND
+
),
Escherichia coli
; metallic blue, IND
+
, LDC
+
, and ODC negative (ODC
−
),
Klebsiella oxytoca
; IND
+
, LDC
−
, and ODC
+
,
Citrobacter diversus
; IND
+
or IND
−
, LDC
−
, and ODC
−
,
Citrobacter freundii
; IND
−
, LDC
+
, and ODC
+
,
Enterobacter aerogenes
; IND
−
, LDC
−
, and ODC
+
,
Enterobacter cloacae
; IND
−
, LDC
+
, and ODC
−
,
Klebsiella pneumoniae
; diffuse brown and IND
+
,
Morganella morganii
; IND
−
,
Proteus mirabilis
; aqua blue,
Serratia marcescens
; bluish green and IND
+
,
Proteus vulgaris
; transparent yellow-green, serology positive,
Pseudomonas aeruginosa
; clear and serology positive,
Salmonella
sp.; other colors and reactions, the organism was identified by the full identification methods. The accuracy and cost-effectiveness of this new system were prospectively evaluated. During an 8-month period, a total of 345 specimens yielded one or more gram-negative bacilli. A total of 472 gram-negative bacillus isolates were detected on CHROMagar Orientation medium. For 466 of the isolates (98.7%), no discrepancies in the results were obtained on the basis of the identification algorithm. The cost of identification of gram-negative bacilli during this period was reduced by about 70%. The results of this trial for the differentiation of the most commonly encountered gram-negative pathogens in clinical specimens with the new algorithm were favourable in that it permitted reliable detection and presumptive identification. In addition, this rapid identification system not only significantly reduced costs but it also improved the daily work flow within the clinical microbiology laboratory.
PCR-Restriction Enzyme Analysis of a Bone Marrow Isolate from a Human Immunodeficiency Virus-Positive Patient Discloses Polyclonal Infection with Two
Mycobacterium avium
Strains
Authors: Oliveira R. S. , Sircili M. P. , Ueki S. Y. M. , Telles M. A. S. , Schnabel B. , Briones M. R. S. , Leão S. C. 
Published: December 2019

ABSTRACT

Polyclonal infection by
Mycobacterium avium
was detected by
hsp65
PCR-restriction enzyme analysis (PRA) in a bone marrow isolate from an AIDS patient. Two
M. avium
strains, differing in colony morphology, PRA
Hae
III digestion pattern, insertion element (IS)
1245
amplification, and restriction fragment length polymorphism fingerprints with IS
1245
and IS
1311
probes, were isolated.
Preliminary Evaluation of a Semisolid Agar Antifungal Susceptibility Test for Yeasts and Molds
Authors: Provine Harriet , Hadley Susan 
Published: December 2019

ABSTRACT

This report presents a semisolid agar antifungal susceptibility (SAAS) method for the rapid susceptibility screening of yeasts and molds. The reproducibility and accuracy of the SAAS method were assessed by comparing the MICs of amphotericin B and fluconazole obtained for 10 candidate quality control (QC) American Type Culture Collection yeast strains in ≥15 replicates with those found by six independent laboratories using the National Committee for Clinical Laboratory Standards (NCCLS) M27-P broth macrodilution method (M. A. Pfaller et al., J. Clin. Microbiol. 33:1104–1107, 1995). Overall, 96% of MICs for both drugs fell within 1 log
2
dilution of the modal MIC for each strain. The MICs for amphotericin B showed 99% agreement with the NCCLS proposed QC ranges within 1 log
2
dilution. Likewise, the MICs for fluconazole at ≥75% growth reduction showed 99% agreement for seven strains. Three strains,
Candida albicans
ATCC 24333 and ATCC 76615 and
Candida tropicalis
ATCC 750, showed a less sharp fluconazole endpoint at ≥75% growth reduction, but at >50% growth reduction, the agreement was 98% within 1 log
2
dilution of the proposed range. The MIC agreement within the proposed range for the suggested QC strains
Candida parapsilosis
ATCC 22019 and
Candida krusei
ATCC 6258 was 100% for fluconazole and 100% within 1 log
2
dilution of the proposed range for amphotericin B. The SAAS method demonstrated the susceptibility or resistance of 25 clinical isolates of filamentous fungi such as
Aspergillus fumigatus
to amphotericin B, itraconazole, and fluconazole, usually within 48 h. Although the results are preliminary, this SAAS method is promising as a rapid and cost-effective screen and is worthy of concerted investigation.
Detection of Extended-Spectrum β-Lactamases in Clinical Isolates of
Enterobacter cloacae
and
Enterobacter aerogenes
Authors: Tzelepi Eva , Giakkoupi Panagiota , Sofianou Danai , Loukova Veneta , Kemeroglou Anastassia , Tsakris Athanassios 
Published: December 2019

ABSTRACT

The aim of the present study was to investigate the frequency of extended-spectrum β-lactamases (ESBLs) in a consecutive collection of clinical isolates of
Enterobacter
spp. The abilities of various screening methods to detect ESBLs in enterobacters were simultaneously tested. Among the 68 consecutive isolates (56
Enterobacter cloacae
and 12
Enterobacter aerogenes
isolates) that were analyzed for β-lactamase content, 21 (25 and 58%, respectively) possessed transferable ESBLs with pIs of 8.2 and phenotypic characteristics of SHV-type enzymes, 8 (14.3%) of the
E. cloacae
isolates produced a previously nondescribed, clavulanate-susceptible ESBL that exhibited a pI of 6.9 and that conferred a ceftazidime resistance phenotype on
Escherichia coli
transconjugants, and 2
E. cloacae
isolates produced both of these enzymes. Among the total of 31 isolates that were considered ESBL producers, the Vitek ESBL detection test was positive for 2 (6.5%) strains, and the conventional double-disk synergy test (DDST) with amoxicillin-clavulanate and with expanded-spectrum cephalosporins and aztreonam was positive for 5 (16%) strains. Modifications of the DDST consisting of closer application of the disks (at 20 instead of 30 mm), the use of cefepime, and the use of both modifications increased the sensitivity of this test to 71, 61, and 90%, respectively. Of the 37 isolates for which isoelectric focusing failed to determine ESBLs, the Vitek test was false positive for 1 isolate and the various forms of DDSTs were false-positive for 3 isolates.
Evaluation of the COBAS AMPLICOR CMV MONITOR Test for Detection of Viral DNA in Specimens Taken from Patients after Liver Transplantation
Authors: Sia Irene G. , Wilson Jennie A. , Espy Mark J. , Paya Carlos V. , Smith Thomas F. 
Published: December 2019

ABSTRACT
Detection of cytomegalovirus (CMV) DNA in blood by PCR is a sensitive method for the detection of infection in patients posttransplantation. The test, however, has low specificity for the identification of overt CMV disease. Quantitative CMV PCR has been shown to overcome this shortcoming. The COBAS AMPLICOR CMV MONITOR test was evaluated by using consecutive serum and peripheral blood mononuclear cell (PBMN) samples from liver transplant patients. Twenty-five patients had CMV viremia (by shell vial cell culture assay) and/or tissue-invasive disease (by biopsy); 20 had no active infection. A total of 262 serum and 62 PBMN specimens were tested. Of 159 serum specimens from patients with overt CMV infection, the COBAS assay detected CMV DNA in 21 patients (sensitivity, 84%). Only 1 of 103 samples from patients with no evidence of active infection had detectable CMV DNA (341 copies/ml). By comparison of 62 matching serum and PBMN samples by the same assay, 12 PBMN samples were exclusively positive, whereas only 2 serum samples were exclusively positive (P < 0.05). At the time of clinical CMV infection, viral copy numbers were higher in PBMNs than serum from four of five patients. The COBAS AMPLICOR CMV MONITOR test is a sensitive and specific test for the quantitative detection of CMV DNA in blood. Clinical applications of the assay will require further validation with samples from a larger population of transplant patients.
Serologic Testing for
Trypanosoma cruzi
: Comparison of Radioimmunoprecipitation Assay with Commercially Available Indirect Immunofluorescence Assay, Indirect Hemagglutination Assay, and Enzyme-Linked Immunosorbent Assay Kits
Authors: Leiby David A. , Wendel Silvano , Takaoka Deise T. , Fachini Roberta M. , Oliveira Lea C. , Tibbals Melinda A. 
Published: December 2019

ABSTRACT

The radioimmunoprecipitation assay (RIPA) has been used as a confirmatory test in several ongoing and published studies of
Trypanosoma cruzi
in blood donors in the United States. Despite its use as a confirmatory test, few studies are available comparing RIPA to commercially available serologic test methods. Thus, we compared RIPA with two indirect hemagglutination assays (Biolab Diagnostica SA, São Paulo, Brazil; Hemagen Diagnostics, Inc., Waltham, Mass.) and four different enzyme-linked immunosorbent assays (Abbott Laboratories, Abbott Park, Ill.; Embrabio, São Paulo, Brazil; Organon Teknika, São Paulo, Brazil; and Gull Laboratories, Salt Lake City, Utah) using a panel of 220 serum specimens from Brazilian blood donors with a range of
T. cruzi
antibody titers as determined by indirect immunofluorescence assay (IFA). A titer of 1:20 was used as the baseline for seropositivity. All IFA-negative serum specimens (
n
= 19) were nonreactive on all tests. At a titer of 1:20 (
n
= 9), reactivity rates varied considerably among the tests, with only the RIPA and the Organon and Gull assays identifying reactive specimens. For specimens at a 1:40 titer (
n
= 35), most assays identified at least 32 of 35 (91%) specimens as reactive, but the Biolab assay only identified 24 (69%). At higher titers (1:80,
n
= 56; 1:160,
n
= 101) the assays were comparable, with the exception of the Biolab assay, demonstrating rates of agreement with IFA of ≥98%. Overall, when compared with several other test formats, RIPA demonstrated equivalent or superior rates of agreement with IFA-positive specimens across all titers examined. In particular, at titers of >1:40, the RIPA compared favorably with other test methods currently in use, supporting its application as a confirmatory test, particularly in a research setting.
Development of a Real-Time Quantitative Assay for Detection of Epstein-Barr Virus
Authors: Niesters Hubert G. M. , van Esser Joost , Fries Edwin , Wolthers Katja C. , Cornelissen Jan , Osterhaus Albert D. M. E. 
Published: December 2019

ABSTRACT

With the use of real-time PCR, we developed and evaluated a rapid, sensitive, specific, and reproducible method for the detection of Epstein-Barr virus (EBV) DNA in plasma samples. This method allowed us to screen plasma and serum samples over a range between 100 and 10
7
copies of DNA per ml using two sample preparation methods based on absorption. A precision study yielded an average coefficient of variation for both methods of less than 12%, with a coefficient of regression for the standard curve of a minimum of 0.98. We detected EBV DNA in 19.2% of plasma samples from immunosuppressed solid-organ transplant patients without symptoms of EBV infections with a mean load of 440 copies per ml. EBV DNA could be detected in all transplant patients diagnosed with posttransplant lymphoproliferative disorder, with a mean load of 544,570 copies per ml. No EBV DNA could be detected in healthy individuals in nonimmunosuppressed control groups and a mean of 6,400 copies per ml could be detected in patients with infectious mononucleosis. Further studies revealed that the inhibitory effect of heparinized plasma could be efficiently removed by use of an extraction method with Celite as the absorbent.
Survival of Enterococci and Staphylococci on Hospital Fabrics and Plastic
Authors: Neely Alice N. , Maley Matthew P. 
Published: December 2019

ABSTRACT

The transfer of gram-positive bacteria, particularly multiresistant
Staphylococcus aureus
(MRSA) and vancomycin-resistant enterococci (VRE), among patients is a growing concern. One critical aspect of bacterial transfer is the ability of the microorganism to survive on various common hospital surfaces. The purpose of this study was to determine the survival of 22 gram-positive bacteria (vancomycin-sensitive and -resistant enterococci and methicillin-sensitive and -resistant staphylococci) on five common hospital materials: smooth 100% cotton (clothing), 100% cotton terry (towels), 60% cotton–40% polyester blend (scrub suits and lab coats), 100% polyester (privacy drapes), and 100% polypropylene plastic (splash aprons). Swatches were inoculated with 10
4
to 10
5
CFU of a microorganism, assayed daily by placing the swatches in nutritive media, and examining for growth after 48 h. All isolates survived for at least 1 day, and some survived for more than 90 days on the various materials. Smaller inocula (10
2
) survived for shorter times but still generally for days. Antibiotic sensitivity had no consistent effect on survival. The long survival of these bacteria, including MRSA and VRE, on commonly used hospital fabrics, such as scrub suits, lab coats, and hospital privacy drapes, underscores the need for meticulous contact control procedures and careful disinfection to limit the spread of these bacteria.
Correlation of Oxacillin MIC with
mecA
Gene Carriage in Coagulase-Negative Staphylococci
Authors: Hussain Zafar , Stoakes Luba , Massey Viki , Diagre Deb , Fitzgerald Viivi , El Sayed Sameer , Lannigan Robert 
Published: December 2019

ABSTRACT

The National Committee for Clinical Laboratory Standards has recently changed the oxacillin breakpoint from ≥4 mg/liter to ≥0.5 mg/liter to detect methicillin-resistant coagulase-negative staphylococci (CoNS) because the previous breakpoint lacked sensitivity. To determine the correlation between the new oxacillin breakpoint and the presence of the
mecA
gene, 493 CoNS of 11 species were tested. The presence of the
mecA
gene was determined by PCR, and oxacillin susceptibility was determined by the agar dilution method with Mueller-Hinton agar containing 2% NaCl and oxacillin (0.125 to 4.0 mg/liter). The new breakpoint correctly classified all CoNS strains with
mecA
as methicillin resistant and strains of
Staphylococcus epidermidis
,
S. haemolyticus
, and
S. hominis
without
mecA
as methicillin susceptible. The breakpoint of ≥0.5 mg/liter was not specific for
S. cohnii
,
S. lugdunensis
,
S. saprophyticus
,
S. warneri
, and
S. xylosus
, in that it categorized 70 of 74 strains of these species without
mecA
(94.6%) as methicillin resistant. The results of this study indicate that the new oxacillin breakpoint accurately identifies strains of CoNS with
mecA
but is not specific for strains of certain species of CoNS without
mecA
.
Molecular Epidemiology of Rabies Virus Isolates from Israel and Other Middle- and Near-Eastern Countries
Authors: David D. , Yakobson B. , Smith J. S. , Stram Y. 
Published: December 2019

ABSTRACT
A total of 226 isolates of rabies virus from different areas of Israel, including three human isolates and one sample from South Lebanon were identified between 1993 and 1998 by direct immunofluorescence using monoclonal antibodies to the viral nucleoprotein (N). An epidemiological survey based on nucleotide sequence analysis of 328 bp from the C terminus of the N coding region and the noncoding region between the nucleoprotein and the phosphoprotein (NS gene) was performed. Phylogenetic analysis of the isolates from Israel showed that they were related geographically, but not according to host species. Five variants, related groups distributed among four geographical regions, were identified. In each region, rabies virus was isolated from more than one animal species. A comparison of the sequence analysis of rabies virus samples from the rest of world revealed a 2-nucleotide change that distinguished the Middle East variants from the rest.
Unusual Case of
Acanthamoeba polyphaga
and
Pseudomonas aeruginosa
Keratitis in a Contact Lens Wearer from Gauteng, South Africa
Authors: Dini L. A. , Cockinos C. , Frean J. A. , Niszl I. A. , Markus M. B. 
Published: December 2019

ABSTRACT

Acanthamoeba
species can cause a chronic, progressive ulcerative keratitis of the eye which is not responsive to the usual antimicrobial therapy and is frequently mistaken for stromal herpes keratitis. An unusual case of coinfection with
Acanthamoeba polyphaga
and
Pseudomonas aeruginosa
as causes of corneal keratitis in a contact lens wearer from Gauteng, South Africa, is reported. These two pathogens have previously been assumed to be selectively exclusive. Cysts of the isolated acanthameba tolerated an incubation temperature of 40°C, indicating a pathogenic species. This case highlights the importance of culture methods in the diagnosis of corneal infection and the choice of treatment regimen. The patient's history of careless contact lens-disinfecting habits emphasizes the need to adhere strictly to recommended methods of contact lens care.
Thyrotoxicosis Induced by Thyroid Involvement of Disseminated
Aspergillus fumigatus
Infection
Authors: Hornef Mathias W. , Schopohl Jochen , Zietz Christian , Hallfeldt Klaus K. J. , Roggenkamp Andreas , Gärtner Roland , Heesemann Jürgen 
Published: December 2019

ABSTRACT

Aspergillus fumigatus
is increasingly recognized as an important nosocomial pathogen in severely immunocompromised patients. Infection is difficult to diagnose antemortem and typically has a fatal outcome. Here we report the case of a cardiac transplant recipient with disseminated
A. fumigatus
infection which clinically presented as thyrotoxicosis due to massive involvement of the thyroid gland.
Growth Competition between
Candida dubliniensis
and
Candida albicans
under Broth and Biofilm Growing Conditions
Authors: Kirkpatrick W. R. , Lopez-Ribot J. L. , Mcatee R. K. , Patterson T. F. 
Published: December 2019

ABSTRACT

Seven isolates each of
Candida albicans
and
Candida dubliniensis
were paired (11 pairs) and examined for competitive interaction. Equal numbers of CFU of each competitor were inoculated into Sabouraud dextrose broth and incubated at 37°C with vigorous shaking under conditions favorable to either broth or biofilm growth. Surviving proportions of each competitor were calculated from the broth culture at 24 and 96 h and the biofilm culture at 96 h, with species differentiation done on CHROMagar Candida medium.
C. albicans
had a competitive advantage over
C. dubliniensis
in broth culture and under biofilm growing conditions; however, with the presence of a supporting structure for biofilm formation,
C. dubliniensis
was able to better withstand the competitive pressures from
C. albicans
.
Temperature-Sensitive Strain ofCryptococcus neoformansProducing Hyphal Elements in a Feline Nasal Granuloma
Authors: Bemis D. A. , Krahwinkel D. J. , Bowman L. A. , Mondon P. , Kwon-Chung K. J. 
Published: December 2019

ABSTRACTWe report the isolation of a temperature-sensitive, serotype A, mating type α strain ofCryptococcus neoformansfrom a case of nasal cryptococcosis in a cat. The strain grew extremely slowly at 35°C and failed to grow at 37°C in vitro. Histopathological sections of the infected tissue revealed yeast cells producing hyphae up to several hundred micrometers in length, in addition to numerous encapsulated yeast cells typical ofC. neoformans. The cultures grown on yeast extract-peptone-glucose agar at 35°C also produced some yeast cells with germ tube-like hyphal elements up to 100 μm in length.
Prevalence and Characterization of Shiga Toxin-Producing
Escherichia coli
Isolated from Cattle, Food, and Children during a One-Year Prospective Study in France
Authors: Pradel Nathalie , Livrelli Valérie , De Champs Christophe , Palcoux Jean-Bernard , Reynaud Alain , Scheutz Flemming , Sirot Jacques , Joly Bernard , Forestier Christiane 
Published: December 2019

ABSTRACT

During a 1-year survey of Shiga toxin-producing
Escherichia coli
(STEC) prevalence in central France, 2,143 samples were investigated by PCR for Shiga toxin-encoding genes. A total of 330 (70%) of 471 fecal samples collected from healthy cattle at the Clermont-Ferrand slaughterhouse, 47 (11%) of 411 beef samples, 60 (10%) of 603 cheese samples, and 19 (3%) of 658 stool specimens from hospitalized children with and without diarrhea were positive for the
stx
gene(s). A STEC strain was isolated from 34% (162 of 471) of bovine feces, 4% (16 of 411) of beef samples, 1% (5 of 603) of cheese samples, and 1.5% (10 of 658) of stool specimens. Of the 220 STEC strains isolated, 34 (15%) harbored the
stx
1
gene, 116 (53%) harbored the
stx
2
gene, and 70 (32%) carried both the
stx
1
and
stx
2
genes. However, 32 (14.5%) were not cytotoxic for Vero cells. The
eae
gene, found in 12 (5%) of the 220 strains, was significantly associated with the
stx
1
gene and with isolates from children. Sequences homologous to
ehxA
were found in 102 (46%) of the 220 strains. Thirteen serotypes, OX3:H2, O113:H21, O113:H4, OX3:H21, O6:H10, OX178:H19, O171:H2, O46:H38, O172:H21, O22:H16, O91:H10, O91:H21, and O22:H8, accounted for 102 (55%) of 186 typeable isolates, and only one strain (0.5% of the 186 STEC isolates from cattle), belonged to the O157:H7 serotype. We showed that the majority of the STEC isolates from cattle, beef, and cheese were not likely to be pathogenic for humans and that the STEC strains isolated from children in this study were probably not responsible for diarrheal disease. Finally, the strains associated with hemolytic-uremic syndrome in the same geographical area were shown to belong to particular subsets of the STEC population found in the bovine reservoir.