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1.  Adverse outcomes associated with contact precautions: A review of the literature 
Background
Contact Precautions (CP) are a standard method for preventing patient-to-patient transmission of multiple drug-resistant organisms (MDROs) in hospital settings. With the ongoing worldwide concern for MDROs including methicillin-resistant Staphylococcus aureus (MRSA) and broadened use of active surveillance programs, an increasing number of patients are being placed on CP. Whereas few would argue that CP are an important tool in infection control, many reports and small studies have observed worse noninfectious outcomes in patients on CP. However, no review of this literature exists.
Methods
We systematically reviewed the literature describing adverse outcomes associated with CP. We identified 15 studies published between 1989 and 2008 relating to adverse outcomes from CP. Nine were higher quality based on standardized collection of data and/or inclusion of control groups.
Results
Four main adverse outcomes related to CP were identified in this review. These included less patient-health care worker contact, changes in systems of care that produce delays and more noninfectious adverse events, increased symptoms of depression and anxiety, and decreased patient satisfaction with care.
Conclusion
Although CP are recommended by the Centers for Disease Control and Prevention as an intervention to control spread of MDROs, our review of the literature demonstrates that this approach has unintended consequences that are potentially deleterious to the patient. Measures to ameliorate these deleterious consequences of CP are urgently needed.
doi:10.1016/j.ajic.2008.04.257
PMCID: PMC3557494  PMID: 19249637
2.  Rationale for Reading Fluconazole MICs at 24 Hours Rather than 48 Hours When Testing Candida spp. by the CLSI M27-A2 Standard Method▿  
Antimicrobial Agents and Chemotherapy  2008;52(11):4175-4177.
We investigated if CLSI M27-A2 Candida species breakpoints for fluconazole MIC are valid when read at 24 h. Analysis of a data set showed good correlation between 48- and 24-h MICs, as well as similar outcomes and pharmacodynamic efficacy parameters, except for isolates in the susceptible dose-dependent category, such as Candida glabrata.
doi:10.1128/AAC.00420-08
PMCID: PMC2573146  PMID: 18809944
3.  In Vitro Activity of Ceftaroline against Clinical Isolates of Streptococcus pneumoniae Recovered in 43 U.S. Medical Centers during 2010-2011 
The in vitro activity of ceftaroline, a recently introduced parenteral cephalosporin, was assessed versus 1,750 isolates of Streptococcus pneumoniae recovered from patients with a variety of pneumococcal infections in 43 U.S. medical centers during 2010-2011. Using a breakpoint of ≤0.5 μg/ml for susceptibility, all of the isolates were found to be susceptible to ceftaroline. Ceftaroline MICs were consistently 16-fold lower than ceftriaxone MICs. Among the isolates characterized in this investigation, 38.9% were found to be nonsusceptible to penicillin (oral penicillin breakpoints) and 9.1% were nonsusceptible to ceftriaxone (nonmeningitis breakpoints).
doi:10.1128/AAC.00582-12
PMCID: PMC3370772  PMID: 22491687
4.  Activities of E1210 and Comparator Agents Tested by CLSI and EUCAST Broth Microdilution Methods against Fusarium and Scedosporium Species Identified Using Molecular Methods 
Fusarium (n = 67) and Scedosporium (n = 63) clinical isolates were tested by two reference broth microdilution (BMD) methods against a novel broad-spectrum (active against both yeasts and molds) antifungal, E1210, and comparator agents. E1210 inhibits the inositol acylation step in glycophosphatidylinositol (GPI) biosynthesis, resulting in defects in fungal cell wall biosynthesis. Five species complex organisms/species of Fusarium (4 isolates unspeciated) and 28 Scedosporium apiospermum, 7 Scedosporium aurantiacum, and 28 Scedosporium prolificans species were identified by molecular techniques. Comparator antifungal agents included anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B. E1210 was highly active against all of the tested isolates, with minimum effective concentration (MEC)/MIC90 values (μg/ml) for E1210, anidulafungin, caspofungin, itraconazole, posaconazole, voriconazole, and amphotericin B, respectively, for Fusarium of 0.12, >16, >16, >8, >8, 8, and 4 μg/ml. E1210 was very potent against the Scedosporium spp. tested. The E1210 MEC90 was 0.12 μg/ml for S. apiospermum, but 1 to >8 μg/ml for other tested agents. Against S. aurantiacum, the MEC50 for E1210 was 0.06 μg/ml versus 0.5 to >8 μg/ml for the comparators. Against S. prolificans, the MEC90 for E1210 was only 0.12 μg/ml, compared to >4 μg/ml for amphotericin B and >8 μg/ml for itraconazole, posaconazole, and voriconazole. Both CLSI and EUCAST methods were highly concordant for E1210 and all comparator agents. The essential agreement (EA; ±2 doubling dilutions) was >93% for all comparisons, with the exception of posaconazole and F. oxysporum species complex (SC) (60%), posaconazole and S. aurantiacum (85.7%), and voriconazole and S. aurantiacum (85.7%). In conclusion, E1210 exhibited very potent and broad-spectrum antifungal activity against azole- and amphotericin B-resistant strains of Fusarium spp. and Scedosporium spp. Furthermore, in vitro susceptibility testing of E1210 against isolates of Fusarium and Scedosporium may be accomplished using either of the CLSI or EUCAST BMD methods, each producing very similar results.
doi:10.1128/AAC.05414-11
PMCID: PMC3256086  PMID: 22083469
5.  Detection of Staphylococcus aureus Isolates with Heterogeneous Intermediate-Level Resistance to Vancomycin in the United States▿  
Journal of Clinical Microbiology  2011;49(12):4203-4207.
The prevalence of heterogeneous intermediate-level resistance to vancomycin (hVISA) in Staphylococcus aureus was assessed by screening a large collection of recent isolates. Susceptibility testing by the Clinical and Laboratory Standards Institute broth microdilution method and the Etest GRD (glycopeptide resistance detection) method (bioMérieux) was performed on 4,210 clinically significant S. aureus isolates obtained in 2009 from 43 U.S. centers. Isolates with Etest GRD-positive results for hVISA were evaluated further by repeat GRD testing and population analysis profiling–area under the curve (PAP-AUC) analysis. No VISA (vancomycin MIC, 4 to 8 μg/ml) or vancomycin-resistant (MIC ≥ 16 μg/ml) strains were detected. The Etest GRD screen for hVISA was initially positive for 68 isolates (1.6%; all by teicoplanin MIC ≥ 8 μg/ml at 24 or 48 h). Among those 68 isolates, 45 were reproducibly GRD positive. PAP-AUC testing confirmed only 11 isolates as hVISA (all had reproducible GRD-positive results). The 11 hVISA isolates were from nine medical centers and appeared genetically diverse (ten different PFGE types). The rates of resistance (including intermediate) for hVISA were as follows: oxacillin, 82%; erythromycin, 82%; clindamycin, 73%; levofloxacin, 73%; trimethoprim-sulfamethoxazole, 9%; and daptomycin, 9%. All hVISA isolates were susceptible to linezolid, tigecycline, and ceftaroline. Our data suggest that the overall prevalence of hVISA in the United States is low (0.3%). The hVISA isolates represented 10.5% of isolates with vancomycin MICs of 2 μg/ml and 0.1% of isolates with vancomycin MICs of 1 μg/ml. The positive predictive value of GRD Etest for hVISA was 16.2% for initial screen positive and 24.4% for reproducibly positive results.
doi:10.1128/JCM.01152-11
PMCID: PMC3232953  PMID: 21976769
6.  Daptomycin exposure precedes infection and/or colonization with daptomycin non-susceptible enterococcus 
Background
Daptomycin non-susceptible enterococci (DNSE) are emerging as an important cause of healthcare-associated infection, however little is known about the epidemiology of DNSE. At the University of Iowa Hospitals and Clinics (UIHC) an increase in the frequency of patients infected and/or colonized with DNSE has occurred. The goals of this study were to evaluate potential factors associated with the development of DNSE colonization and/or infection and to compare the characteristics of patients with prior daptomycin exposure to those without prior daptomycin exposure.
Methods
The study is a retrospective case-series involving all patients with DNSE infection and/or colonization at UIHC, a 734-bed academic referral center, from June 1, 2005 to June 1, 2011.
Results
The majority of patients with DNSE colonization and/or infection had prior daptomycin exposure (15 of 25; 60%), a concomitant gastrointestinal process (19 of 25; 76%), or were immunosuppressed (21 of 25; 84%). DNSE infection was confirmed in 17 of 25 (68%) patients, including 9 patients with bacteremia. Twelve of 17 (71%) patients with DNSE infection had prior daptomycin exposure, including 7 of 9 (78%) patients with bacteremia. Compared to patients without prior daptomycin exposure, patients with prior daptomycin exposure were less likely to harbor E. faecalis (0% vs. 33%; p = 0.019). A high proportion of patients (10 of 25; 40%) died during their hospitalizations. Most enterococcal isolates were E. faecium (86%), and were vancomycin-resistant (72%). Molecular typing revealed a diverse population of DNSE.
Conclusions
Prior daptomycin exposure, immunosuppression, and/or a concomitant gastrointestinal process, may be associated with the development of DNSE. PFGE revealed a diverse population of DNSE, which along with both increasing numbers of DNSE detected yearly and increasing annual rates of daptomycin usage, suggests the emergence of DNSE under antimicrobial pressure.
doi:10.1186/2047-2994-1-19
PMCID: PMC3436660  PMID: 22958379
Enterococcus; Daptomycin; Resistance; Non-Susceptible; DNSE
7.  Triazole and Echinocandin MIC Distributions with Epidemiological Cutoff Values for Differentiation of Wild-Type Strains from Non-Wild-Type Strains of Six Uncommon Species of Candida▿  
Journal of Clinical Microbiology  2011;49(11):3800-3804.
When clinical susceptibility breakpoints (CBPs) are absent, establishing wild-type (WT) MIC distributions and epidemiological cutoff values (ECVs) provides a sensitive means for detecting emerging resistance. We determined species-specific ECVs for anidulafungin (ANF), caspofungin (CSF), micafungin (MCF), fluconazole (FLC), posaconazole (PSC), and voriconazole (VRC) for six rarer Candida species (819 strains) using isolates obtained from the ARTEMIS Program and the SENTRY Antimicrobial Surveillance Program, all tested by a reference broth microdilution method. The calculated ECVs, expressed in μg/ml (and the percentages of isolates that had MICs less than or equal to the ECVs), for ANF, CSF, MCF, FLC, PSC, and VRC, respectively, were 0.12 (95.2), 0.12 (97.8), 0.12 (100.0), 0.5 (95.7), 0.12 (98.6), and 0.03 (100.0) for Candida dubliniensis; 4 (100.0), 2 (96.0), 2 (99.1), 8 (95.0), 0.5 (97.5), and 0.25 (98.0) for C. guilliermondii; 0.25 (98.9), 0.03 (98.0), 0.12 (97.5), 1 (99.1), 0.25 (99.1), and 0.015 (100.0) for C. kefyr; 2 (100.0), 1 (99.6), 0.5 (96.6), 2 (96.1), 0.25 (98.6), and 0.03 (96.6) for C. lusitaniae; and 2 (100.0), 0.5 (100.0), 1 (100.0), 2 (98.0), 0.25 (97.1), and 0.06 (98.0) for C. orthopsilosis, but for C. pelliculosa, ECVs could be determined only for CSF (0.12 [94.4]), FLC (4 [98.2]), PSC (2 [98.2]), and VRC (0.25 [98.2]). In the absence of species-specific CBP values, these WT MIC distributions and ECVs will be useful for monitoring the emergence of reduced susceptibility to the triazole and echinocandin antifungals.
doi:10.1128/JCM.05047-11
PMCID: PMC3209078  PMID: 21900519
8.  Activity of Ceftaroline and Epidemiologic Trends in Staphylococcus aureus Isolates Collected from 43 Medical Centers in the United States in 2009▿ 
A Staphylococcus aureus surveillance program was initiated in the United States to examine the in vitro activity of ceftaroline and epidemiologic trends. Susceptibility testing by Clinical and Laboratory Standards Institute broth microdilution was performed on 4,210 clinically significant isolates collected in 2009 from 43 medical centers. All isolates were screened for mecA by PCR and evaluated by pulsed-field gel electrophoresis. Methicillin-resistant S. aureus (MRSA) were analyzed for Panton-Valentine leukocidin (PVL) genes and the staphylococcal cassette chromosome mec (SCCmec) type. All isolates had ceftaroline MICs of ≤2 μg/ml with an MIC50 of 0.5 and an MIC90 of 1 μg/ml. The overall resistance rates, expressed as the percentages of isolates that were intermediate and resistant (or nonsusceptible), were as follows: ceftaroline, 1.0%; clindamycin, 30.2% (17.4% MIC ≥ 4 μg/ml; 12.8% inducible); daptomycin, 0.2%; erythromycin, 65.5%; levofloxacin, 39.9%; linezolid, 0.02%; oxacillin, 53.4%; tetracycline, 4.4%; tigecycline, 0%; trimethoprim-sulfamethoxazole, 1.6%; vancomycin, 0%; and high-level mupirocin, 2.2%. The mecA PCR was positive for 53.4% of the isolates. The ceftaroline MIC90s were 0.25 μg/ml for methicillin-susceptible S. aureus and 1 μg/ml for MRSA. Among the 2,247 MRSA isolates, 51% were USA300 (96.9% PVL positive, 99.7% SCCmec type IV) and 17% were USA100 (93.4% SCCmec type II). The resistance rates for the 1,137 USA300 MRSA isolates were as follows: erythromycin, 90.9%; levofloxacin, 49.1%; clindamycin, 7.6% (6.2% MIC ≥ 4 μg/ml; 1.4% inducible); tetracycline, 3.3%; trimethoprim-sulfamethoxazole, 0.8%; high-level mupirocin, 2.7%; daptomycin, 0.4%; and ceftaroline and linezolid, 0%. USA300 is the dominant clone causing MRSA infections in the United States. Ceftaroline demonstrated potent in vitro activity against recent S. aureus clinical isolates, including MRSA, daptomycin-nonsusceptible, and linezolid-resistant strains.
doi:10.1128/AAC.00315-11
PMCID: PMC3165333  PMID: 21709080
9.  Azole Resistance in Aspergillus fumigatus Isolates from the ARTEMIS Global Surveillance Study Is Primarily Due to the TR/L98H Mutation in the cyp51A Gene▿ 
We surveyed 497 isolates of Aspergillus fumigatus collected from 2008 to 2009 as part of the ARTEMIS global surveillance study for elevated MIC values to itraconazole, voriconazole, and posaconazole. Sequencing of the cyp51A gene revealed that 8/29 isolates with elevated MIC values to one or more triazoles, all originating in China, contained the TR/L98H mutation associated with resistant European isolates of A. fumigatus. This is the first time the TR/L98H mutation has been identified outside Europe.
doi:10.1128/AAC.00185-11
PMCID: PMC3165364  PMID: 21690285
10.  Clinical Microbiology and Infection Prevention 
Journal of Clinical Microbiology  2011;49(9_Supplement):S57-S60.
doi:10.1128/JCM.00690-11
PMCID: PMC3185842
11.  Prevalence and Genetic Relatedness of Methicillin-Susceptible Staphylococcus aureus Isolates Detected by the Xpert MRSA Nasal Assay ▿  
Journal of Clinical Microbiology  2011;49(8):2996-2999.
Methicillin-susceptible Staphylococcus aureus (MSSA) isolates lacking mecA yet testing positive on the Xpert MRSA assay were recovered from culture for 7.7% of 248 Xpert-positive nasal samples. These “false-positive” Xpert results may be attributed to staphylococcal cassette chromosome (SCC) elements without the mecA gene. Pulsed-field gel electrophoresis (PFGE) analysis revealed a diverse population of MSSA strains.
doi:10.1128/JCM.00046-11
PMCID: PMC3147776  PMID: 21677066
12.  Multicenter Comparison of the Vitek 2 Antifungal Susceptibility Test with the CLSI Broth Microdilution Reference Method for Testing Caspofungin, Micafungin, and Posaconazole against Candida spp.▿ 
Journal of Clinical Microbiology  2011;49(5):1765-1771.
The performance of the automated Vitek 2 (bioMérieux, Inc., Marcy l'Etoile, France) antifungal susceptibility system was compared to that of broth microdilution (BMD) for the determination of MICs of various antifungal drugs. A total of 112 challenge strains and 755 clinical isolates of Candida spp. were tested against caspofungin and micafungin. An additional 452 clinical isolates of Candida albicans were tested against posaconazole. Reference BMD MIC endpoints were established after 24 h of incubation for caspofungin and micafungin and after 48 h of incubation for posaconazole. Essential agreements (EAs) between the Vitek 2 and BMD methods for caspofungin and micafungin were 99.5% and 98.6%, respectively. EA between the Vitek 2 and BMD methods was 95.6% for posaconazole. The overall categorical agreements (CAs) between the Vitek 2 system and BMD were 99.8% for caspofungin, 98.2% for micafungin, and 98.1% for posaconazole. The Vitek 2 system reliably determined caspofungin and micafungin MICs among Candida spp. and posaconazole MICs among C. albicans isolates and demonstrated excellent quantitative and qualitative agreement with the reference BMD method.
doi:10.1128/JCM.02517-10
PMCID: PMC3122687  PMID: 21430096
13.  Multilaboratory Testing of Two-Drug Combinations of Antifungals against Candida albicans, Candida glabrata, and Candida parapsilosis▿  
There are few multilaboratory studies of antifungal combination testing to suggest a format for use in clinical laboratories. In the present study, eight laboratories tested quality control (QC) strain Candida parapsilosis ATCC 22019 and clinical isolates Candida albicans 20533.043, C. albicans 20464.007, Candida glabrata 20205.075, and C. parapsilosis 20580.070. The clinical isolates had relatively high azole and echinocandin MICs. A modified CLSI M27-A3 protocol was used, with 96-well custom-made plates containing checkerboard pairwise combinations of amphotericin B (AMB), anidulafungin (AND), caspofungin (CSP), micafungin (MCF), posaconazole (PSC), and voriconazole (VRC). The endpoints were scored visually and on a spectrophotometer or enzyme-linked immunosorbent assay (ELISA) reader for 50% growth reduction (50% inhibitory concentration [IC50]). Combination IC50s were used to calculate summation fractional inhibitory concentration indices (FICIs) (ΣFIC) based on the Lowe additivity formula. The results revealed that the IC50s of all drug combinations were lower or equal to the IC50 of individual drugs in the combination. A majority of the ΣFIC values were indifferent (ΣFIC = 0.51 to 2.0), but no antagonism was observed (ΣFIC ≥ 4). Synergistic combinations (ΣFIC ≤ 0.5) were found for AMB-PSC against C. glabrata and for AMB-AND and AMB-CSP against C. parapsilosis by both visual and spectrophotometric readings. Additional synergistic interactions were revealed by either of the two endpoints for AMB-AND, AMB-CSP, AMB-MCF, AMB-PSC, AMB-VRC, AND-PSC, CSP-MCF, and CSP-PSC. The percent agreements among participating laboratories ranged from 37.5% (lowest) for AND-CSP and POS-VOR to 87.5% (highest) for AMB-MCF and AND-CSP. Median ΣFIC values showed a wide dispersion, and interlaboratory agreements were less than 85% in most instances. Additional studies are needed to improve the interlaboratory reproducibility of antifungal combination testing.
doi:10.1128/AAC.01510-09
PMCID: PMC3067183  PMID: 21282457
14.  Methicillin-Resistant Staphylococcus aureus in Pork Production Shower Facilities ▿  
As methicillin-resistant Staphylococcus aureus (MRSA) has been found in pigs, we sought to determine if MRSA is present in pork production shower facilities. In two production systems tested, 3% and 26% of shower samples were positive for MRSA. spa types identified included t034, t189, t753, and t1746.
doi:10.1128/AEM.01128-10
PMCID: PMC3020538  PMID: 21097587
15.  Low Prevalence of fks1 Hot Spot 1 Mutations in a Worldwide Collection of Candida Strains▿  
We evaluated the prevalence of fks1 hot spot (HS) 1 mutations among 133 Candida strains from six species displaying various caspofungin MIC values (from ≤0.008 to >8 μg/ml). Only 4 (2.9%) strains displayed FKS1 HS1 amino acid substitutions: 1 C. albicans (F641Y) among 32 isolates tested (3.1%), 1 C. glabrata (S645P) among 34 isolates tested (2.9%), and 2 C. tropicalis (F641S) among 12 isolates tested (16.7%). The 4 isolates displaying FKS1 HS1 alterations showed elevated caspofungin MIC results (1 to >8 μg/ml) but lower anidulafungin and micafungin MIC values (0.12 to 4 μg/ml and 0.25 to 4 μg/ml, respectively) in some instances within the wild-type MIC population, as determined using the epidemiologic cutoff values (ECV). Candida krusei, C. parapsilosis, and C. guilliermondii isolates tested showed no FKS1 HS1 alterations regardless of echinocandin MIC result. We additionally analyzed 8 C. albicans and 7 C. glabrata strains for mutations on other HS regions of fks1 and fks2. Three C. glabrata strains showed alterations on FKS2 HS1 (two S645P and one L644W). In general, strains displaying S645P alteration showed higher echinocandin MIC values than strains harboring other mutations. Overall, Candida spp. strains showing caspofungin MIC values within the ECV did not display fks HS mutations. In contrast, strains showing alterations in this region displayed anidulafungin and/or micafungin MIC values within the wild-type population, suggesting that caspofungin could be the most sensitive agent for detection of these resistance mutations. Furthermore, results from this large, geographically diverse Candida spp. collection demonstrated that fks1 HS1 mutations remain uncommon among isolates with various echinocandin MIC levels.
doi:10.1128/AAC.01711-09
PMCID: PMC2876398  PMID: 20368396
16.  Screening of a Large Global Aspergillus fumigatus Species Complex Collection by Using a Species-Specific Microsphere-Based Luminex Assay ▿  
Journal of Clinical Microbiology  2009;47(12):4171-4172.
A microsphere-based Luminex assay was developed and validated for rapid identification of Aspergillus fumigatus from the other species within the A. fumigatus species complex (section Fumigati). This molecular tool was then employed to screen 499 clinical A. fumigatus species complex isolates collected from multiple medical centers throughout the world with results demonstrating the exclusive presence of A. fumigatus.
doi:10.1128/JCM.01415-09
PMCID: PMC2786642  PMID: 19794043
17.  Characterization of blaKPC-containing Klebsiella pneumoniae isolates detected in different institutions in the Eastern USA 
Background
The emergence of blaKPC-containing Klebsiella pneumoniae (KPC-Kp) isolates is attracting significant attention. Outbreaks in the Eastern USA have created serious treatment and infection control problems. A comparative multi-institutional analysis of these strains has not yet been performed.
Methods
We analysed 42 KPC-Kp recovered during 2006–07 from five institutions located in the Eastern USA. Antimicrobial susceptibility tests, analytical isoelectric focusing (aIEF), PCR and sequencing of bla genes, PFGE and rep-PCR were performed.
Results
By in vitro testing, KPC-Kp isolates were highly resistant to all non-carbapenem β-lactams (MIC90s ≥ 128 mg/L). Among carbapenems, MIC50/90s were 4/64 mg/L for imipenem and meropenem, 4/32 mg/L for doripenem and 8/128 for ertapenem. Combinations of clavulanate or tazobactam with a carbapenem or cefepime did not significantly lower the MIC values. Genetic analysis revealed that the isolates possessed the following bla genes: blaKPC-2 (59.5%), blaKPC-3 (40.5%), blaTEM-1 (90.5%), blaSHV-11 (95.2%) and blaSHV-12 (50.0%). aIEF of crude β-lactamase extracts from these strains supported our findings, showing β-lactamases at pIs of 5.4, 7.6 and 8.2. The mean number of β-lactamases was 3.5 (range 3–5). PFGE demonstrated that 32 (76.2%) isolates were clonally related (type A). Type A KPC-Kp isolates (20 blaKPC-2 and 12 blaKPC-3) were detected in each of the five institutions. rep-PCR showed patterns consistent with PFGE.
Conclusions
We demonstrated the complex β-lactamase background of KPC-Kp isolates that are emerging in multiple centres in the Eastern USA. The prevalence of a single dominant clone suggests that interstate transmission has occurred.
doi:10.1093/jac/dkn547
PMCID: PMC2640158  PMID: 19155227
carbapenemases; ESBLs; Enterobacteriaceae; PFGE; rep-PCR
18.  Identification of Candida nivariensis and Candida bracarensis in a Large Global Collection of Candida glabrata Isolates: Comparison to the Literature▿  
Journal of Clinical Microbiology  2009;47(4):1216-1217.
We analyzed 1,598 Candida glabrata isolates for the presence of the cryptic species Candida nivariensis and Candida bracarensis. Both species were very rare in this collection (0.2% prevalence), despite the number of isolates analyzed and the global distribution of the isolates. We saw no associated antifungal resistance in C. nivariensis.
doi:10.1128/JCM.02315-08
PMCID: PMC2668319  PMID: 19193845
19.  Strain-Relatedness of Methicillin-Resistant Staphylococcus aureus Isolates Recovered from Patients with Repeated Infection 
Invasive disease following methicillin-resistant Staphylococcus aureus (MRSA) detection is common, regardless of whether initial detection involves colonization or infection. We assessed the genetic relatedness of isolates obtained ≥2 weeks apart representing either repeated infections or colonization-infection sets to determine if infections are likely to be caused by previously harbored strains. We found that MRSA infection following initial colonization or infection is caused by the same strain in most cases, suggesting that a single successful attempt at decolonization may prevent the majority of later infection.
doi:10.1086/529381
PMCID: PMC2723744  PMID: 18444862
20.  Identification and Susceptibility Profile of Candida fermentati from a Worldwide Collection of Candida guilliermondii Clinical Isolates▿  
Journal of Clinical Microbiology  2008;47(1):242-244.
Candida fermentati isolates make up a small percentage of the clinical isolates of the Candida guilliermondii complex and have a global distribution pattern. With the exception that the MICs of micafungin were significantly lower, the calculated average MICs for C. fermentati were not significantly different from those for C. guilliermondii.
doi:10.1128/JCM.01889-08
PMCID: PMC2620835  PMID: 19036938
21.  Molecular Phylogenetic Analysis of a Geographically and Temporally Matched Set of Candida albicans Isolates from Humans and Nonmigratory Wildlife in Central Illinois ▿  
Eukaryotic Cell  2008;7(9):1475-1486.
This study explored whether wildlife species serve as the reservoir for human Candida albicans strains in a given geographic area. C. albicans isolates were collected from nonmigratory wildlife admitted to the University of Illinois Wildlife Medical Clinic. A geographically and temporally matched set of C. albicans oral isolates was collected from healthy human volunteers. Multilocus sequence typing was used to assign strains to genetic clades. Clade 1 isolates, particularly diploid sequence type 69 (DST 69), were most common in humans. Clade 1 strains were less frequently recovered from wildlife, while clade 8 strains, particularly DST 90, were overrepresented in the wildlife collection. All instances where a wildlife and human isolate shared the same DST occurred within clade 1. Clade distributions between human and wildlife isolates were significantly different, demonstrating population isolation between the groups. These differences may indicate limited strain transfer between groups or differential selection of C. albicans isolates in humans and wildlife. Wildlife strains had an amphotericin B MIC significantly lower than that of human isolates; strains with increased susceptibility were from several clades. C. albicans isolates were collected from domestic animals to provide comparisons with human and wildlife data sets. C. albicans isolation from canine and feline oral and anal swabs was infrequent; companion animal isolates were closely related to clade 1 human isolates. Collectively, the data suggest a greater likelihood of C. albicans transfer from humans to animals than from animals to humans. The nontransient human population may maintain the connection between geography and the C. albicans genetic groups recovered from humans.
doi:10.1128/EC.00162-08
PMCID: PMC2547061  PMID: 18621922
22.  Geographic Distribution and Antifungal Susceptibility of the Newly Described Species Candida orthopsilosis and Candida metapsilosis in Comparison to the Closely Related Species Candida parapsilosis▿  
Journal of Clinical Microbiology  2008;46(8):2659-2664.
Candida orthopsilosis and Candida metapsilosis are recently described species, having previously been grouped with the more prevalent species Candida parapsilosis. Current literature contains very little data pertaining to the distributions and antifungal susceptibilities of these Candida species. We determined the species and antifungal susceptibilities of 1,929 invasive clinical isolates from the ARTEMIS antifungal surveillance program collected between 2001 and 2006 and identified as C. parapsilosis using Vitek and conventional methods. Of the 1,929 isolates of presumed C. parapsilosis tested, 117 (6.1%) were identified as C. orthopsilosis and 34 (1.8%) as C. metapsilosis. The percentage of presumed C. parapsilosis isolates found to be C. orthopsilosis varied greatly by region, with the highest percentage (10.9%) from South America and the lowest (0.7%) from Africa. The MIC distributions of the C. orthopsilosis and C. metapsilosis isolates were statistically significantly lower than those of C. parapsilosis for all drugs except fluconazole, for which they were significantly higher (P < 0.001 for all). No C. orthopsilosis or C. metapsilosis isolates were fluconazole resistant, and all were susceptible to caspofungin, anidulafungin, and micafungin.
doi:10.1128/JCM.00803-08
PMCID: PMC2519489  PMID: 18562582
23.  Analysis of ALS5 and ALS6 allelic variability in a geographically diverse collection of Candida albicans isolates 
Fungal genetics and biology : FG & B  2007;44(12):1298-1309.
The Candida albicans ALS (agglutinin-like sequence) gene family encodes eight cell-surface glycoproteins, some of which function in adhesion to host surfaces. ALS genes have a central tandem-repeat-encoding domain comprised entirely of head-to-tail copies of a conserved 108-bp sequence. The number of copies of the tandemly repeated sequence varies between C. albicans strains and often between alleles within the same strain. Because ALS alleles can encode different-sized proteins that may have different functional characteristics, defining the range of allelic variability is important. Genomic DNA from C. albicans strains representing the major genetic clades was PCR-amplified to determine the number of tandemly repeated sequence copies within the ALS5 and ALS6 central domain. ALS5 alleles had 2 to 10 tandem repeat sequence copies (mean = 4.82 copies) while ALS6 alleles had 2 to 8 copies (mean = 4.00 copies). Despite this variability, tandem repeat copy number was stable in C. albicans strains passaged for 3000 generations. Prevalent alleles and allelic distributions varied among the clades for ALS5 and ALS6. Overall, ALS6 exhibited less variability than ALS5. ALS5 deletions can occur naturally in C. albicans via direct repeats flanking the ALS5 locus. Deletion of both ALS5 alleles was associated particularly with clades III and SA. ALS5 exhibited allelic polymorphisms in the coding region 5’ of the tandem repeats; some alleles resembled ALS1, suggesting recombination between these contiguous loci. Natural deletion of ALS5 and the sequence variation within its coding region suggest relaxed selective pressure on this locus, and that Als5p function may be dispensable in C. albicans or redundant within the Als family.
doi:10.1016/j.fgb.2007.05.004
PMCID: PMC2175174  PMID: 17625934
24.  Lodderomyces elongisporus Masquerading as Candida parapsilosis as a Cause of Bloodstream Infections▿  
Journal of Clinical Microbiology  2007;46(1):374-376.
Ten yeast bloodstream isolates identified as Candida parapsilosis by conventional methods grew as turquoise blue colonies on Chromagar media. Subsequent sequence analysis showed that these isolates were the species Lodderomyces elongisporus. To our knowledge, this is the first published report of L. elongisporus as a cause of human disease.
doi:10.1128/JCM.01790-07
PMCID: PMC2224306  PMID: 17959765
25.  Antimicrobial Resistance among Gram-Negative Bacilli Causing Infections in Intensive Care Unit Patients in the United States between 1993 and 2004▿  
Journal of Clinical Microbiology  2007;45(10):3352-3359.
During the 12-year period from 1993 to 2004, antimicrobial susceptibility profiles of 74,394 gram-negative bacillus isolates recovered from intensive care unit (ICU) patients in United States hospitals were determined by participating hospitals and collected in a central location. MICs for 12 different agents were determined using a standardized broth microdilution method. The 11 organisms most frequently isolated were Pseudomonas aeruginosa (22.2%), Escherichia coli (18.8%), Klebsiella pneumoniae (14.2%), Enterobacter cloacae (9.1%), Acinetobacter spp. (6.2%), Serratia marcescens (5.5%), Enterobacter aerogenes (4.4%), Stenotrophomonas maltophilia (4.3%), Proteus mirabilis (4.0%), Klebsiella oxytoca (2.7%), and Citrobacter freundii (2.0%). Specimen sources included the lower respiratory tract (52.1%), urine (17.3%), and blood (14.2%). Rates of resistance to many of the antibiotics tested remained stable during the 12-year study period. Carbapenems were the most active drugs tested against most of the bacterial species. E. coli and P. mirabilis remained susceptible to most of the drugs tested. Mean rates of resistance to 9 of the 12 drugs tested increased with Acinetobacter spp. Rates of resistance to ciprofloxacin increased over the study period for most species. Ceftazidime was the only agent to which a number of species (Acinetobacter spp., C. freundii, E. aerogenes, K. pneumoniae, P. aeruginosa, and S. marcescens) became more susceptible. The prevalence of multidrug resistance, defined as resistance to at least one extended-spectrum cephalosporin, one aminoglycoside, and ciprofloxacin, increased substantially among ICU isolates of Acinetobacter spp., P. aeruginosa, K. pneumoniae, and E. cloacae.
doi:10.1128/JCM.01284-07
PMCID: PMC2045364  PMID: 17715376

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