Antimicrobial Agents and Chemotherapy
1098-6596
0066-4804
Mỹ
Cơ quản chủ quản: AMER SOC MICROBIOLOGY , American Society for Microbiology
Lĩnh vực:
PharmacologyPharmacology (medical)Infectious Diseases
Các bài báo tiêu biểu
<i>In Silico</i> Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing ABSTRACT
In the work presented here, we designed and developed two easy-to-use Web tools for
in silico
detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family
Enterobacteriaceae
. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant
Enterobacteriaceae
species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family
Enterobacteriaceae
in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from
www.pubmlst.org
and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of
Salmonella enterica
serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49
S
. Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.
Tập 58 Số 7 - Trang 3895-3903 - 2014
A functional classification scheme for beta-lactamases and its correlation with molecular structure
Tập 39 Số 6 - Trang 1211-1233 - 1995
Characterization of a New Metallo-β-Lactamase Gene, <i>bla</i> <sub>NDM-1</sub> , and a Novel Erythromycin Esterase Gene Carried on a Unique Genetic Structure in <i>Klebsiella pneumoniae</i> Sequence Type 14 from India ABSTRACT
A Swedish patient of Indian origin traveled to New Delhi, India, and acquired a urinary tract infection caused by a carbapenem-resistant
Klebsiella pneumoniae
strain that typed to the sequence type 14 complex. The isolate,
Klebsiella pneumoniae
05-506, was shown to possess a metallo-β-lactamase (MBL) but was negative for previously known MBL genes. Gene libraries and amplification of class 1 integrons revealed three resistance-conferring regions; the first contained
bla
CMY-4
flanked by IS
EcP1
and
blc
. The second region of 4.8 kb contained a complex class 1 integron with the gene cassettes
arr
-
2
, a new erythromycin esterase gene;
ereC
;
aadA1
; and
cmlA7
. An intact IS
CR1
element was shown to be downstream from the
qac
/
sul
genes. The third region consisted of a new MBL gene, designated
bla
NDM-1
, flanked on one side by
K. pneumoniae
DNA and a truncated IS
26
element on its other side. The last two regions lie adjacent to one another, and all three regions are found on a 180-kb region that is easily transferable to recipient strains and that confers resistance to all antibiotics except fluoroquinolones and colistin. NDM-1 shares very little identity with other MBLs, with the most similar MBLs being VIM-1/VIM-2, with which it has only 32.4% identity. As well as possessing unique residues near the active site, NDM-1 also has an additional insert between positions 162 and 166 not present in other MBLs. NDM-1 has a molecular mass of 28 kDa, is monomeric, and can hydrolyze all β-lactams except aztreonam. Compared to VIM-2, NDM-1 displays tighter binding to most cephalosporins, in particular, cefuroxime, cefotaxime, and cephalothin (cefalotin), and also to the penicillins. NDM-1 does not bind to the carbapenems as tightly as IMP-1 or VIM-2 and turns over the carbapenems at a rate similar to that of VIM-2. In addition to
K. pneumoniae
05-506,
bla
NDM-1
was found on a 140-kb plasmid in an
Escherichia coli
strain isolated from the patient's feces, inferring the possibility of in vivo conjugation. The broad resistance carried on these plasmids is a further worrying development for India, which already has high levels of antibiotic resistance.
Tập 53 Số 12 - Trang 5046-5054 - 2009
Emergence of Resistant Human Immunodeficiency Virus Type 1 in Patients Receiving Fusion Inhibitor (T-20) Monotherapy ABSTRACT
The synthetic peptide T-20 (enfuvirtide) represents the first of a new class of antiretroviral compounds to demonstrate in vivo potency by targeting a step in viral entry. T-20 inhibits a conformational change in the human immunodeficiency virus type 1 (HIV-1) transmembrane glycoprotein (gp41) that is required for fusion between HIV-1 and target cell membranes. The initial phase I clinical trial of T-20 treatment for HIV-infected patients thus provided a unique opportunity to evaluate the emergence of resistant virus in vivo to this novel class of antiretroviral agents. All four patients who received an intermediate dose of T-20 (30 mg twice daily) had an initial decline in plasma viral load over the first 10 days but a rising trend by day 14, suggestive of selection for resistant virus. Plasma virus derived from patients enrolled in all dosage groups of the phase I T-20 trial was analyzed by population sequencing before and after treatment. While no mutations were found within a highly conserved 3-amino-acid sequence (GIV) known to be critical for fusion at baseline, after 14 days of therapy, virus from one patient in the 30-mg dose group (30-1) developed a mutation in this motif, specifically an aspartic acid (D) substitution for glycine (G) at position 36. Multiple
env
clones were derived from the plasma virus of all four patients in the 30-mg dosage group. Sequence analysis of 49 clones derived from the plasma of patient 30-1 on day 14 revealed that 25 clones contained the G36D mutation, while 8 contained the V38A mutation. Dual mutations involving G36D and other residues within the HR1 domain were also identified. In 5 of the 49
env
clones, other mutations involving residues 32 (Q32R or Q32H) and 39 (Q39R) were found in combination with G36D. Cloned
env
sequences derived from the plasma virus of subject 30-3 also had single mutations in the GIV sequence (V38M and I37V) detectable following therapy with T-20. The plasma virus from subjects 30-2 and 30-4 did not contain changes within the GIV sequence. To analyze the biological resistance properties of these mutations, we developed a novel single-cycle HIV-1 entry assay using JC53BL cells which express β-galactosidase and luciferase under control of the HIV-1 long terminal repeat. Full-length
env
clones were derived from the plasma virus of patients 30-1 and 30-3 and used to generate pseudotyped virus stocks. The mean 50% inhibition concentrations (IC
50
s) for mutants G36D and V38A (patient 30-1) were 2.3 μg/ml and 11.2 μg/ml, respectively, statistically significant increases of 9.1- and 45-fold, respectively, compared with those of wild-type Env. The IC
50
for the V38 M mutation (patient 30-3) was 7.6 μg/ml, an 8-fold increase compared with that of the wild type. The I37V mutation resulted in an IC
50
3.2-fold greater than that of the wild type. Envs with double mutations (Q32R plus G36D and Q32H plus G36D) exhibited a level of resistance similar to that of G36D alone. These findings provide the first evidence for the rapid emergence of clinical resistance to a novel class of HIV-1 entry inhibitors and may be relevant to future treatment strategies involving these agents.
Tập 46 Số 6 - Trang 1896-1905 - 2002
Multiplex PCR Strategy for Rapid Identification of Structural Types and Variants of the <i>mec</i> Element in Methicillin-Resistant <i>Staphylococcus aureus</i> ABSTRACT
Full characterization of methicillin-resistant
Staphylococcus aureus
(MRSA) requires definition of not only the bacterial genetic background but also the structure of the complex and heterologous
mec
element these bacteria carry, which is associated with drug resistance determinant
mecA
. We report the development, validation, and application of a multiplex PCR strategy that allows quick presumptive characterization of the
mec
element types based on the structural features that were shown to be typical of
mec
elements carried by several MRSA clones. The strategy was validated by using a representative collection of pandemic MRSA clones in which the full structure of the associated
mec
elements was previously determined by hybridization and PCR screenings and also by DNA sequencing. The method was tested together with multilocus sequence typing and other typing methods for the characterization of 18 isolates representative of the MRSA clones recovered during a hospital outbreak in Barcelona, Spain. The multiplex PCR was shown to be rapid, robust, and capable in a single assay of identifying five structural types of the
mec
element among these strains, three major and two minor variants, each one of which has been already been seen among MRSA characterized earlier. This technique should be a useful addition to the armamentarium of molecular typing tools for the characterization of MRSA clonal types and for the rapid tentative identification of structural variants of the
mec
element.
Tập 46 Số 7 - Trang 2155-2161 - 2002
Carbapenems: Past, Present, and Future ABSTRACT In this review, we summarize the current “state of the art” of carbapenem antibiotics and their role in our antimicrobial armamentarium. Among the β-lactams currently available, carbapenems are unique because they are relatively resistant to hydrolysis by most β-lactamases, in some cases act as “slow substrates” or inhibitors of β-lactamases, and still target penicillin binding proteins. This “value-added feature” of inhibiting β-lactamases serves as a major rationale for expansion of this class of β-lactams. We describe the initial discovery and development of the carbapenem family of β-lactams. Of the early carbapenems evaluated, thienamycin demonstrated the greatest antimicrobial activity and became the parent compound for all subsequent carbapenems. To date, more than 80 compounds with mostly improved antimicrobial properties, compared to those of thienamycin, are described in the literature. We also highlight important features of the carbapenems that are presently in clinical use: imipenem-cilastatin, meropenem, ertapenem, doripenem, panipenem-betamipron, and biapenem. In closing, we emphasize some major challenges and urge the medicinal chemist to continue development of these versatile and potent compounds, as they have served us well for more than 3 decades.
Tập 55 Số 11 - Trang 4943-4960 - 2011
Delaying the Empiric Treatment of <i>Candida</i> Bloodstream Infection until Positive Blood Culture Results Are Obtained: a Potential Risk Factor for Hospital Mortality ABSTRACT
Fungal bloodstream infections are associated with significant patient mortality and health care costs. Nevertheless, the relationship between a delay of the initial empiric antifungal treatment until blood culture results are known and the clinical outcome is not well established. A retrospective cohort analysis with automated patient medical records and the pharmacy database at Barnes-Jewish Hospital was conducted. One hundred fifty-seven patients with a
Candida
bloodstream infection were identified over a 4-year period (January 2001 through December 2004). Fifty (31.8%) patients died during hospitalization. One hundred thirty-four patients had empiric antifungal treatment begun after the results of fungal cultures were known. From the time that the first blood sample for culture that was positive was drawn, 9 (5.7%) patients received antifungal treatment within 12 h, 10 (6.4%) patients received antifungal treatment between 12 and 24 h, 86 (54.8%) patients received antifungal treatment between 24 and 48 h, and 52 (33.1%) patients received antifungal treatment after 48 h. Multiple logistic regression analysis identified Acute Physiology and Chronic Health Evaluation II scores (one-point increments) (adjusted odds ratio [AOR], 1.24; 95% confidence interval [CI], 1.18 to 1.31;
P
< 0.001), prior antibiotic treatment (AOR, 4.05; 95% CI, 2.14 to 7.65;
P
= 0.028), and administration of antifungal treatment 12 h after having the first positive blood sample for culture (AOR, 2.09; 95% CI, 1.53 to 2.84;
P
= 0.018) as independent determinants of hospital mortality. Administration of empiric antifungal treatment 12 h after a positive blood sample for culture is drawn is common among patients with
Candida
bloodstream infections and is associated with greater hospital mortality. Delayed treatment of
Candida
bloodstream infections could be minimized by the development of more rapid diagnostic techniques for the identification of
Candida
bloodstream infections. Alternatively, increased use of empiric antifungal treatment in selected patients at high risk for fungal bloodstream infection could also reduce delays in treatment.
Tập 49 Số 9 - Trang 3640-3645 - 2005
Mechanisms of Antibacterial Action of Three Monoterpenes ABSTRACT
In the present paper, we report the antimicrobial efficacy of three monoterpenes [linalyl acetate, (+)menthol, and thymol] against the gram-positive bacterium
Staphylococcus aureus
and the gram-negative bacterium
Escherichia coli
. For a better understanding of their mechanisms of action, the capability of these three monoterpenes to damage biomembranes was evaluated by monitoring the release, following exposure to the compounds under study, of the water-soluble fluorescent marker carboxyfluorescein from unilamellar vesicles with different lipidic compositions (phosphatidylcholine, phosphatidylcholine/phosphatidylserine [9:1], phosphatidylcholine/stearylamine [9:1], and phosphatidylglycerol/cardiolipin [9:1]). Furthermore, the interaction of the terpenes tested with dimyristoylphosphatidylcholine multilamellar vesicles as model membranes was monitored by means of differential scanning calorimetry. Finally, the results were related to the relative lipophilicity and water solubility of the compounds examined. Taken together, our findings lead us to speculate that the antimicrobial effect of (+)menthol, thymol, and linalyl acetate may result, at least partially, from a perturbation of the lipid fraction of microorganism plasma membrane, resulting in alterations of membrane permeability and in leakage of intracellular materials. Besides being related to physicochemical characteristics of the drugs (such as lipophilicity and water solubility), this effect seems to be dependent on lipid composition and net surface charge of microbial membranes. Furthermore, the drugs might cross the cell membranes, penetrating into the interior of the cell and interacting with intracellular sites critical for antibacterial activity.
Tập 49 Số 6 - Trang 2474-2478 - 2005