bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of Resistance Associated with Integrons, the Extended-Spectrum β-Lactamase SHV-5 Gene, and a Multidrug Efflux Pump of
Klebsiella pneumoniae
Causing a Nosocomial Outbreak
Authors: Gruteke Paul , Goessens Wil , van Gils Jan , Peerbooms Paul , Lemmens-den Toom Nicole , van Santen-Verheuvel Marga , van Belkum Alex , Verbrugh Henri 
Published: March 2003

ABSTRACT

Multiresistant
Klebsiella pneumoniae
caused a nosocomial outbreak. Resistance patterns of the presumed outbreak isolates varied among and within patients. In order to control the outbreak, screening for extended-spectrum β-lactamase (ESBL)-producing
K. pneumoniae
was commenced. A number of susceptible
K. pneumoniae
strains were stored to serve as controls in genetic strain typing. Typing by pulsed-field gel electrophoresis proved the clonality of the strains in the recognized outbreak patients. Typing of the control strains by pulsed-field gel electrophoresis showed that at least one patient had been missed by the ESBL screening procedure. Further genetic typing confirmed the presence of the SHV-5 ESBL gene in all but one of the outbreak strains. Variable presence of integrons that carried the aminoglycoside resistance genes
aadB
and
aadA2
was found. A
gyrA
mutation in codon 83 was present in all outbreak strains tested, despite considerable differences in ciprofloxacin MICs. The MICs of ciprofloxacin and the chemically unrelated drug cefoxitin were correlated (
r
= 0.86,
P
< 0.01) and were compatible with the overexpression of an efflux pump in a subset of the outbreak strains. We conclude that outbreak strains that express an ESBL gene only at a low level may pass unnoticed in a screening procedure, when the laboratory is unaware of variable ESBL expression. In this particular outbreak, screening for strains for which ciprofloxacin MICs were ≥0.25 μg/ml would in retrospect have been the most sensitive method for detection of the
K. pneumoniae
outbreak strain.
Identification of a Mutation Associated with Erythromycin Resistance in
Bordetella pertussis
: Implications for Surveillance of Antimicrobial Resistance
Authors: Bartkus J. M. , Juni B. A. , Ehresmann K. , Miller C. A. , Sanden G. N. , Cassiday P. K. , Saubolle M. , Lee B. , Long J. , Harrison, A. R. , Besser J. M. 
Published: March 2003

ABSTRACT

Erythromycin treatment failures and in vitro resistance of
Bordetella pertussis
have been reported on several occasions in the past few years, but the mechanism of resistance has not been described. One potential mechanism, genetic modification of the erythromycin-binding site on the 23S rRNA of the 50S ribosomal subunit, has been observed in other bacteria. To explore this possibility, we amplified the portion of the 23S rRNA gene encoding the central loop of domain V. DNA sequencing and restriction fragment length polymorphism of the PCR products showed that each of the four erythromycin-resistant
B. pertussis
strains tested contained an A-to-G transition mutation at position 2058 (
Escherichia coli
numbering) of the 23S rRNA gene. The mutation was not found in seven erythromycin-susceptible isolates tested. Two of the resistant isolates were heterozygous, containing at least one mutant copy and one wild-type copy of the 23S rRNA gene. These results indicate that erythromycin resistance in these strains is likely due to a mutation of the erythromycin-binding site in the 23S rRNA gene. Identification of the resistance mechanism will facilitate development of molecular susceptibility testing methods that can be used directly on clinical specimens in the absence of an isolate.
Genotypes at the Internal Transcribed Spacers of the Nuclear rRNA Operon of
Pneumocystis jiroveci
in Nonimmunosuppressed Infants without Severe Pneumonia
Authors: Totet Anne , Pautard Jean-Claude , Raccurt Christian , Roux Patricia , Nevez Gilles 
Published: March 2003

ABSTRACT

The frequency of
Pneumocystis jiroveci
(human-derived
Pneumocystis
) in immunocompetent infants developing acute respiratory syndromes has recently been evaluated and has been shown to be close to 25%. Until now, there have been no data on the genomic characteristics of the fungus in these patients, while molecular typing of
P. jiroveci
organisms was mostly performed with samples from immunosuppressed patients with pneumocystosis (
Pneumocystis
carinii
pneumonia [PCP]). The present report describes the genotypes of
P. jiroveci
organisms in 26 nonimmunosuppressed infants developing a mild
Pneumocystis
infection contemporaneously with an episode of bronchioloalveolitis. The typing was based on sequence analysis of internal transcribed spacers (ITSs) 1 and 2 of the rRNA operon, followed by the use of two typing scores. By use of the first score, 11
P. jiroveci
ITS types were identified: 10 were previously reported in immunosuppressed patients with PCP, while 1 was newly described. By use of the second score, 13 types were identified, of which 2 were newly described. The most frequent type was identified as type B
1
a
3
(first score), which corresponds to type Eg (second score). Mixed infections were diagnosed in three infants. The occurrence of such diversity of
P. jiroveci
ITS types, an identical main type, and mixed infections has previously been reported in immunosuppressed patients with PCP. Thus, the
P. jiroveci
ITS genotypes detected in immunocompetent infants and immunosuppressed patients developing different forms of
Pneumocystis
infection share characteristics, suggesting that both groups of individuals make up a common human reservoir for the fungus. Finally, the frequency of
P. jiroveci
in nonimmunosuppressed infants with acute respiratory syndromes and the genotyping results provide evidence that this infant population is an important reservoir for the fungus.
Longitudinal Analysis of
Prototheca zopfii
-Specific Immune Responses: Correlation with Disease Progression and Carriage in Dairy Cows
Authors: Roesler Uwe , Hensel Andreas 
Published: March 2003

ABSTRACT

In order to characterize the humoral and cellular immune responses to bovine mammary protothecosis, serum and whey samples obtained from 72 dairy cows assigned to four different clinical stages of infection were examined for specific antibodies by indirect enzyme-linked immunosorbent assay techniques. Milk samples were analyzed for the total numbers of excreted algal cells and somatic cells. After characterization of the course of immune induction in bovine protothecal mastitis, a long-term sentinel study was performed in an affected herd in order to investigate disease progression. A total of 61 dairy cows with protothecal mastitis were examined for shedding of algae cells and for local immune responses three times in 6-month intervals. During acute and chronic stages of protothecosis, significantly elevated specific antibody activities in sera were detected. A strong correlation of whey immunoglobulin A (IgA) and whey IgG1 antibody activity with the total counts of somatic cells in milk was observed, whereas only a weak correlation of whey IgA and whey IgG1 concentrations to the number of algal cells excreted with the milk was seen. Our results from the sentinel long-term study of infected cows revealed that 70.5% of the persistently infected animals were continuously shedding the pathogen. About 4.9% of the animals showed an intermittent shedding, whereas 18% of the cows were tested culturally negative throughout the study. It can be assumed that
Prototheca zopfii
mastitis in dairy cows is maintained on the herd level by subclinically infected alga-shedding cows.
Detection by PCR and Isolation Assays of the Anaerobic Intestinal Spirochete
Brachyspira aalborgi
from the Feces of Captive Nonhuman Primates
Authors: Munshi M. Arif , Taylor Nyree M. , Mikosza Andrew S. J. , Spencer Peter B. S. , Hampson David J. 
Published: March 2003

ABSTRACT

The purpose of this study was to investigate the presence of the anaerobic intestinal spirochetes
Brachyspira aalborgi
and
Brachyspira pilosicoli
in the feces of captive nonhuman primates (
n
= 35) from 19 species housed at the Zoological Gardens, Perth, Western Australia. Both spirochete species are known to infect human beings. DNA was extracted from freshly collected feces with a commercially available QIAamp DNA stool minikit and subjected to PCR protocols amplifying portions of the 16S rRNA genes of the two spirochete species. The feces were also subjected to selective culture for the spirochetes. Subsequently, feces from 62 other captive animals or birds representing 39 species at the zoo were examined by PCR to determine whether they were reservoirs of infection. Six fecal samples from individuals from four primate species (two vervet monkeys, two Tonkean macaques, one Japanese macaque, and one hamadryas baboon) tested positive in the
B. aalborgi
PCR.
B. aalborgi
was not detected by PCR in any of the other animal or bird species tested, and
B. pilosicoli
was not detected in the primates or any of the other animals or birds.
B. aalborgi
was isolated from both PCR-positive vervet monkeys. This is the first time that
B. aalborgi
has been isolated from nonhuman primates and the first time that it has been isolated from the feces of any species.
Molecular Epidemiology of
Pseudomonas aeruginosa
Colonization in a Burn Unit: Persistence of a Multidrug-Resistant Clone and a Silver Sulfadiazine-Resistant Clone
Authors: Pirnay Jean-Paul , De Vos Daniel , Cochez Christel , Bilocq Florence , Pirson Jean , Struelens Marc , Duinslaeger Luc , Cornelis Pierre , Zizi Martin , Vanderkelen Alain 
Published: March 2003

ABSTRACT

To study the epidemiology of
Pseudomonas aeruginosa
colonization in a 32-bed burn wound center (BWC), 321 clinical and 45 environmental
P. aeruginosa
isolates were collected by prospective surveillance culture over a 1-year period and analyzed by serotyping, drug susceptibility testing, and amplified fragment length polymorphism (AFLP) analysis. Among 441 patients treated at the center, 70 (16%) were colonized with
P. aeruginosa
, including 12 (17%) patients who were colonized on admission and 58 (83%) patients who acquired the organism during their stay. Of the 48 distinct AFLP genotypes found, 21 were found exclusively in the environment, 15 were isolated from individual patients only, and 12 were responsible for the colonization of 57 patients, of which 2 were also isolated from the environment, but secondary to patient carriage. Polyclonal
P. aeruginosa
colonization with strains of two to four genotypes, often with different antibiotic susceptibility patterns, was observed in 19 patients (27%). Two predominant genotypes were responsible for recurrent outbreaks and the colonization of 42 patients (60% of all colonized patients). The strain with one of those genotypes appeared to be endemic to the BWC and developed multidrug resistance (MDR) at the end of the study period, whereas the strain with the other genotype was antibiotic susceptible but resistant to silver sulfadiazine (SSD
r
). The MDR strain was found at a higher frequency in sputum samples than the SSD
r
strain, which showed a higher prevalence in burn wound samples, suggesting that anatomic habitat selection was associated with adaptive resistance to antimicrobial drugs. Repeated and thorough surveys of the hospital environment failed to detect a primary reservoir for any of those genotypes. Cross-acquisition, resulting from insufficient compliance with infection control measures, was the major route of colonization in our BWC. In addition to the AFLP pattern and serotype, analysis of the nucleotide sequences of three (lipo)protein genes (
oprI
,
oprL
, and
oprD
) and the pyoverdine type revealed that all predominant strains except the SSD
r
strain belonged to recently identified clonal complexes. These successful clones are widespread in nature and therefore predominate in the patient population, in whom variants accumulate drug resistance mechanisms that allow their transmission and persistence in the BWC.
Community-Acquired Poliovirus Infection in Children with Primary Immunodeficiencies in Tunisia
Authors: Triki Hinda , Barbouche Mohamed Ridha , Bahri Olfa , Bejaoui Mohamed , Dellagi Koussay 
Published: March 2003

ABSTRACT
The global polio eradication program recommends the use of massive vaccination campaigns with live vaccine through National Immunization Days (NIDs) to displace the wild virus from the community. Immunodeficient patients may be indirectly infected and become chronic excretors and potential reservoirs of polioviruses, a concern for the posteradication era. This prospective study aimed to assess the risk of community-acquired infection of immunodeficient patients following NIDs, the dynamics of viral excretion and the genetic variation of excreted viruses. Sixteen children with various primary immunodeficiencies, who did not receive the vaccine during the campaign, were investigated. Stool samples were collected weekly, shortly after the NIDs, during at least 3 months, and were processed for viral isolation. Isolates were characterized by three intratypic differentiation methods and partial sequencing of the VP1/2A region. Polioviruses were detected in 4 out of 16 patients (serotype 1 in 3 patients and serotype 3 in 1 patient). Sequencing revealed more than 99% homology with homotypic Sabin strains, suggesting recent infection. Duration of viral excretion ranged from 1 to 7 weeks. Nine out of eleven isolates from the three poliovirus serotype 1-infected patients disclosed a non-Sabin-like phenotype by enzyme-linked immunosorbent assay and had recurrent mutations within or close to the neutralizing antigenic sites. In summary, the risk of secondary infection in immunodeficient patients is within the range previously reported for the general population. Although none of the four infected patients developed prolonged viral excretion, particular viral variants were selected and may be of epidemiological significance.
Bacillus anthracis
Virulence in Guinea Pigs Vaccinated with Anthrax Vaccine Adsorbed Is Linked to Plasmid Quantities and Clonality
Authors: Coker Pamala R. , Smith Kimothy L. , Fellows Patricia F. , Rybachuck Galena , Kousoulas Konstantin G. , Hugh-Jones Martin E. 
Published: March 2003

ABSTRACT

Bacillus anthracis
is a bacterial pathogen of great importance, both historically and in the present. This study presents data collected from several investigations and indicates that
B. anthracis
virulence is associated with the clonality and virulence of plasmids pXO1 and pXO2. Guinea pigs vaccinated with Anthrax Vaccine Adsorbed were challenged with 20
B. anthracis
isolates representative of worldwide genetic diversity. These same isolates were characterized with respect to plasmid copy number by using a novel method of quantitative PCR developed for rapid and efficient detection of
B. anthracis
from environmental samples. We found that the copy numbers for both pXO1 and pXO2 differed from those in previously published reports. By combining the data on survival, plasmid copy numbers, and clonality, we developed a model predicting virulence. This model was validated by using a randomly chosen set of 12 additional
B. anthracis
isolates. Results from this study will be helpful in future efforts to elucidate the basis for variation in the virulence of this important pathogen.
Five-Test Simple Scheme for Species-Level Identification of Clinically Significant Coagulase-Negative Staphylococci
Authors: De Paulis Adriana N. , Predari Silvia C. , Chazarreta Carlos D. , Santoianni Jorge E. 
Published: March 2003

ABSTRACT

A working scheme developed in our laboratory for identification (by species group and species) of coagulase-negative staphylococci (CNS) was evaluated with 201 consecutive isolates and then validated by using the reference method of Kloos and Schleifer (W. E. Kloos and K. H. Schleifer, J. Clin. Microbiol.
1:
82-88, 1975). This five-test simple scheme (referred to here as the simple scheme) combines the novobiocin susceptibility test with tests for urease, pyrrolidonyl arylamidase, ornithine decarboxylase, and aerobic acid from mannose. The addition of one or two tests within a particular species group could then positively identify the isolate. Two commercial systems, Staph-Zym (Rosco) and API-Staph (bioMérieux), along with results obtained by using Rosco diagnostic tablets (nongrowth tests), were also compared with the reference method. One isolate could not be identified even by the reference method. Of the remaining 200 strains, 191 (95.5%) strains were correctly identified with Staph-Zym and 171 strains (85.5%) were correctly identified with API-Staph. The most frequent clinical CNS species isolated were
Staphylococcus epidermidis
(50.5%),
S. haemolyticus
(18.5%),
S. saprophyticus
subsp.
saprophyticus
(16.0%),
S. lugdunensis
(6.0%), and
S. warneri
(2.5%). The simple scheme validated with the reference method has demonstrated an excellent correlation in the identification of the three most frequent species isolated:
S. epidermidis
,
S. haemolyticus
, and
S. saprophyticus
subsp.
saprophyticus
. With the simple scheme, identification of CNS was possible within 24 h after the enzymatic tests were used, whereas up to 72 h is necessary for the growth tests. This methodology would be very useful in any clinical microbiology laboratory for the presumptive identification of CNS species groups and species.
Characterization of Monkey Enteropathogenic
Escherichia coli
(EPEC) and Human Typical and Atypical EPEC Serotype Isolates from Neotropical Nonhuman Primates
Authors: Carvalho Vania M. , Gyles Carlton L. , Ziebell Kim , Ribeiro Marcela A. , Catão-Dias José L. , Sinhorini Idércio L. , Otman Jamile , Keller Rogéria , Trabulsi Luiz R. , Pestana de Castro Antônio F. 
Published: March 2003

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) has been associated with infantile diarrhea and mortality in humans in developing countries. While diarrhea is also a major problem among primates kept in captivity, the role of
E. coli
is unclear. This study was designed to characterize diarrheagenic
E. coli
recovered from the feces of 56 New World nonhuman primates, primarily marmosets (
Callithrix
spp.). Seventeen of the 56 primates had signs of diarrhea and/or enteritis.
E. coli
recovered from feces from these animals was tested by PCR for genes encoding virulence factors of diarrheagenic
E. coli
and for patterns of adherence to HeLa cells. In addition, isolates were characterized by the fluorescence actin staining test and by their ability to induce attaching and effacing lesions. PCR for the
eae
gene was positive in 10 of the 39 (27%) apparently healthy animals and in 8 of the 17 (47%) animals with diarrhea and/or enteritis. Colonies of
eae
+
E. coli
were serotyped and examined by PCR for genes encoding EPEC virulence markers. The
eae
+
E. coli
isolates recovered from both healthy and sick nonhuman primates demonstrated virulence-associated attributes similar to those of EPEC strains implicated in human disease and are designated monkey EPEC. The results presented here indicate that EPEC may be a significant pathogen for nonhuman primates, deserving further investigation. The similarities between the affected animals investigated in this study and human EPEC infections suggest that marmosets may represent an important model for EPEC in humans.
Susceptibility Testing with the Manual Mycobacteria Growth Indicator Tube (MGIT) and the MGIT 960 System Provides Rapid and Reliable Verification of Multidrug-Resistant Tuberculosis
Authors: Ådjers-Koskela Kati , Katila Marja-Leena 
Published: March 2003

ABSTRACT

The objective of the study was to compare the manual Mycobacteria Growth Indicator Tube (MGIT) method and the BACTEC MGIT 960 system to the BACTEC 460 method for susceptibility testing of
Mycobacterium tuberculosis
. The evaluation was based on testing of 36
M. tuberculosis
strains with various susceptibilities to isoniazid (INH), rifampin (RMP), ethambutol (EMB), and streptomycin (SM). In addition, five of the strains generating discrepant results in testing for EMB were analyzed for heteroresistance. For INH, the susceptibility test results obtained by the MGIT 960 and the manual MGIT systems agreed with the BACTEC 460 results in 94 and 97% of the cases, respectively. The results of susceptibility to RMP were all in agreement. For SM, 78 and 72% of the results obtained by the MGIT 960 and the manual MGIT systems, respectively, agreed with the BACTEC 460 results. In contrast, less than 80% of the results for susceptibility to EMB obtained by the two MGIT methods agreed with the BACTEC 460 results. All five strains analyzed for EMB heteroresistance were found to consist of resistant and susceptible subpopulations. The average turnaround times were 6.4 days for the MGIT 960 system, 6.5 for the manual MGIT system, and 8.7 days for the BACTEC 460 method. Both MGIT methods can be regarded as accurate and rapid alternatives to the BACTEC 460 method for detection of strains resistant to INH and RMP. However, more studies are needed for solving the problems associated with susceptibility testing to EMB and SM.
Clinical Implications of
Mycobacterium kansasii
Species Heterogeneity: Swiss National Survey
Authors: Taillard Caroline , Greub Gilbert , Weber Rainer , Pfyffer Gaby E. , Bodmer Thomas , Zimmerli Stefan , Frei Reno , Bassetti Stefano , Rohner Peter , Piffaretti Jean-Claude , Bernasconi Enos , Bille Jacques , Telenti Amalio , Prod'hom Guy 
Published: March 2003

ABSTRACT

Several subtypes of
Mycobacterium kansasii
have been described, but their respective pathogenic roles are not clear. This study investigated the distribution of subtypes and the pathogenicity of
M. kansasii
strains (
n
= 191) isolated in Switzerland between 1991 and 1997. Demographic, clinical, and microbiological information was recorded from clinical files. Patients were classified as having an infection according to the criteria of the American Thoracic Society. Subtypes were defined by PCR-restriction enzyme analysis of the
hsp65
gene. Subtype 1 comprised 67% of the isolates (
n
= 128), while subtypes 2 and 3 comprised 21% (
n
= 40) and 8% (
n
= 15), respectively. Other subtypes (subtypes 4 and 6 and a new subtype, 7) were recovered from only 4% of patients (
n
= 8).
M. kansasii
subtype 1 was considered pathogenic in 81% of patients, while
M. kansasii
subtype 2 was considered pathogenic in 67% of patients and other subtypes were considered pathogenic in 6% of patients. The majority of patients with
M. kansasii
subtype 2 were immunocompromised due to the use of corticosteroids (21% of patients) or coinfection with HIV (62.5% of patients). Subtyping
M. kansasii
may improve clinical management by distinguishing pathogenic from nonpathogenic subtypes.
Changes in the Human Immunodeficiency Virus p7-p1-p6
gag
Gene in Drug-Naive and Pretreated Patients
Authors: Gallego Oscar , de Mendoza Carmen , Corral Angélica , Soriano Vincent 
Published: March 2003

ABSTRACT

Resistance to antiretroviral agents often results from mutations within the human immunodeficiency virus (HIV)
pol
gene. Moreover, insertions within the p6
gag-pol
region have recently been found to be involved with resistance to nucleoside analogs. Overall, we found that 21% of 156 specimens collected from HIV-infected individuals (17.6% from 74 drug-naive patients and 24.4% from 82 pretreated patients) harbored these insertions. Insertions around the KQE (Lys-Gln-Glu) motif were found in 12.2% of the pretreated patients but in none of the drug-naive subjects (
P
= 0.002). In contrast, insertions around the PTAP (Prol-Thre-Ala-Prol) motif were seen at similar rates (∼15%) among drug-naive and pretreated patients, which supports the idea that they may be natural polymorphisms.