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1.  Multilocus Sequence Typing for Candida albicans Isolates from Candidemic Patients: Comparison with Southern Blot Hybridization and Pulsed-field Gel Electrophoresis Analysis 
Background
We evaluated the efficacy of multilocus sequence typing (MLST) for assessing the genetic relationship among Candida albicans isolates from patients with candidemia in a hospital setting.
Methods
A total of 45 C. albicans isolates from 21 patients with candidemia were analyzed. The MLST results were compared with results obtained by Southern blot hybridization (C1 fingerprinting) and pulsed-field gel electrophoresis (PFGE). PFGE analysis included karyotyping and restriction endonuclease analysis of genomic DNAs using BssHII (REAG-B) and SfiI (REAG-S).
Results
The 45 isolates yielded 20 unique diploid sequence types (DSTs) by MLST, as well as 12 karyotypes, 15 REAG-B patterns, 13 REAG-S patterns, and 14 C1 fingerprinting types. Microevolution among intra-individual isolates was detected in 6, 5, 3, 5, and 7 sets of isolates by MLST (1 or 2 allelic differences), REAG-B, REAG-S, C1 fingerprinting, and a combination of all methods, respectively. Among 20 DSTs, 17 were unique, and 3 were found in more than 1 patient. The results of 2 DSTs obtained from 9 patient isolates were in agreement with REAG and C1 fingerprinting patterns. However, the remaining DST, which was shared by 2 patient isolates, showed 2 different PFGE and C1 fingerprinting patterns. In addition, 3 sets of isolates from different patients, which differed in only 1 or 2 alleles by MLST, also exhibited different PFGE or C1 fingerprinting patterns.
Conclusions
MLST is highly discriminating among C. albicans isolates, but it may have some limitations in typing isolates from different patients, which may necessitate additional analysis using other techniques.
doi:10.3343/kjlm.2011.31.2.107
PMCID: PMC3115997  PMID: 21474986
Candia albicans; Multilocus sequence typing; Pulsed-field gel electrophoresis; Southern hybridization; Genotyping
2.  Microevolution of Candida albicans Strains during Catheter-Related Candidemia 
Journal of Clinical Microbiology  2004;42(9):4025-4031.
We examined microevolution in a series of Candida albicans strains isolated from patients with catheter-related candidemia. Sixty-one isolates (29 from blood, 18 from catheters, 10 from urine, and 4 from other sites) were obtained from 15 patients who were admitted to the same hospital over a 3-year period. Isolates were analyzed by using Southern hybridization with the C1 fragment of Ca3 as a probe (C1 fingerprinting) and pulsed-field gel electrophoresis (PFGE). PFGE typing consisted of electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA (REAG) by using SfiI (REAG-S) and BssHII (REAG-B). When catheter isolates were compared with blood isolates from the same patient, catheter isolates from 5 of 14 patients (36%) exhibited minor band differences (microevolution) relative to blood isolates in either C1 fingerprinting (n = 4), REAG-S (n = 3), or REAG-B (n = 5) profiles, although they had identical EK patterns. However, the other sequential isolates from each patient, which had identical EK patterns, showed the same REAG and C1 fingerprinting patterns. Both fingerprinting methods revealed that two distinct genotypes were shared by isolates from seven patients in a neonatal intensive care unit, suggesting two nosocomial clusters. Except for two catheter isolates from the index patients of each cluster, no consecutive isolates collected from each of the two clusters showed any microevolution during the 2- or 7-month cluster periods. The findings suggest that in catheter-related candidemia, some C. albicans strains undergo microevolution during catheter colonization.
doi:10.1128/JCM.42.9.4025-4031.2004
PMCID: PMC516333  PMID: 15364985
3.  Investigation of the sequence of colonization and candidemia in nonneutropenic patients. 
Journal of Clinical Microbiology  1994;32(4):975-980.
Among neutropenic patients with hematologic malignancies, candidemia has been shown to arise typically from autoinfection after colonization. In patients without neutropenia, we examined the similarities of strains colonizing or infecting various body sites and those subsequently causing Candida bloodstream infections. Strain similarity was examined by karyotyping and restriction endonuclease analysis of genomic DNA (REAG) by using two restriction enzymes (SfiI and BssHII). The banding patterns of 42 isolates from 19 patients were independently evaluated in a blinded fashion by three observers. The interobserver reliability measured with a generalized kappa statistic was 0.59 for karyotyping, 0.84 for REAG with SfiI, and 0.88 for REAG with BssHII (P < 0.001 for each). REAG classified the initial colonizing or infecting isolate and subsequent blood isolates as identical in 16 patients (84%). The mean duration of colonization or infection prior to a positive blood culture was 5 and 23 days in patients infected with related and unrelated isolates, respectively (P = 0.14; 95% confidence interval = -14.5 to 50.5). Karyotyping results matched the REAG results for isolates from 14 of the 19 patients (74%). In patients infected with identical isolates, the initial isolate was most frequently recovered from the urine (n = 5) or vascular catheter tips (n = 4). In the five subjects with organisms showing disparate results between the methods, karyotyping revealed different banding patterns, whereas REAG suggested that the isolates were identical. Candida colonization or infection with an identical strain frequently precedes bloodstream infection in nonneutropenic patients. Future studies should evaluate whether patients at high risk for candidemia and who have vascular catheter or urine samples that are positive for a Candida on culture should be treated empirically.
Images
PMCID: PMC267165  PMID: 8027353
4.  Genetic Relationships between Respiratory Pathogens Isolated from Dental Plaque and Bronchoalveolar Lavage Fluid from Patients in the Intensive Care Unit Undergoing Mechanical Ventilation 
Background
Ventilator-associated pneumonia (VAP) is a leading cause of morbidity and mortality in patients hospitalized in intensive care units. Recent studies suggest that dental plaque biofilms serve as a reservoir for respiratory pathogens. The goal of this study was to determine the genetic relationship between strains of respiratory pathogens first isolated from the oral cavity and later isolated from bronchoalveolar lavage fluid from the same patient undergoing mechanical ventilation with suspected VAP.
Methods
Plaque and tracheal secretion samples were obtained on the day of hospital admission and every other day thereafter until discharge from the intensive care unit from 100 patients who underwent mechanical ventilation. Bronchoalveolar lavage was performed for 30 patients with suspected VAP. Pulse-field gel electrophoresis and multilocus sequence typing were used to determine the genetic relatedness of strains obtained from oral, tracheal, and bronchoalveolar lavage samples.
Results
Isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter species, and enteric species recovered from plaque from most patients were indistinguishable from isolates recovered from bronchoalveolar lavage fluid (i.e., had >95% similarity of pulse-field gel electrophoresis patterns). Nearly one-half of the Pseudomonas strains showed identical genetic profiles between patients, which suggested a common environmental source of infection.
Conclusions
Respiratory pathogens isolated from the lung are often genetically indistinguishable from strains of the same species isolated from the oral cavity in patients who receive mechanical ventilation who are admitted to the hospital from the community. Thus, dental plaque serves as an important reservoir for respiratory pathogens in patients who undergo mechanical ventilation.
Trial registration
ClinicalTrials.gov identifier: NCT00123123
doi:10.1086/593193
PMCID: PMC3582026  PMID: 18991508
5.  Investigation of Candida albicans transmission in a surgical intensive care unit cluster by using genomic DNA typing methods. 
Journal of Clinical Microbiology  1995;33(3):576-580.
An apparent outbreak of serious Candida albicans infections (n = 6) occurred in a surgical intensive care unit over a 4-week period. Four patients developed C. albicans bloodstream infections. An additional patient developed catheter-related C. albicans infection; the sixth patient developed an infection of cerebrospinal fluid. C. albicans was isolated from the hands of five health care workers (17%) and the throat of one health care worker (3%) during the outbreak investigation. Karyotyping and restriction endonuclease analysis of genomic DNA with BssHII of 23 C. albicans isolates from patients and the 6 health care worker isolates revealed 9 and 12 different patterns, respectively. Three of six patients appeared to be infected with the same C. albicans strain (two bloodstream infections and one cerebrospinal fluid infection). The hands of a health care worker were colonized with strain that appeared identical to an isolate from a patient prior to infection of the patient. However, restriction endonuclease analysis with SfiI found differences among the isolates determined to be identical by the other two methods. Karyotyping alone does not appear to be sufficient to differentiate between outbreak and control isolates. Restriction endonuclease analysis typing may be a more sensitive method than karyotyping alone in the investigation of a cluster of C. albicans infections. Furthermore, the use of more than one restriction enzyme may be necessary for optimal strain discrimination in restriction endonuclease analysis of genomic DNA.
PMCID: PMC227993  PMID: 7751360
6.  Physical and genetic map of Streptococcus thermophilus A054. 
Journal of Bacteriology  1994;176(24):7413-7422.
The three restriction endonucleases SfiI, BssHII, and SmaI were found to generate fragments with suitable size distributions for mapping the genome of Streptococcus thermophilus A054. A total of 5, 8, and 24 fragments were produced with SfiI, BssHII, and SmaI, respectively. An average genome size of 1,824 kb was determined by summing the total fragment sizes obtained by digestions with these three enzymes. Partial and multiple digestions of genomic DNA in conjunction with Southern hybridization were used to map SfiI, BssHII, and SmaI fragments. All restriction fragments were arranged in a unique circular chromosome. Southern hybridization analysis with specific probes allowed 23 genetic markers to be located on the restriction map. Among them, six rrn loci were precisely located. The area of the chromosome containing the ribosomal operons was further detailed by mapping some of the ApaI and SgrAI sites. Comparison of macrorestriction patterns from three clones derived from strain A054 revealed two variable regions in the chromosome. One was associated with the tandem rrnD and rrnE loci, and the other was mapped in the region of the lactose operon.
Images
PMCID: PMC197195  PMID: 8002562
7.  Construction of an SfiI macrorestriction map of the Candida albicans genome. 
Journal of Bacteriology  1993;175(20):6637-6651.
The opportunistic fungal pathogen, Candida albicans, is diploid as usually isolated and has no apparent sexual cycle. Genetic analysis has therefore been very difficult. Molecular genetics has yielded important information in the past few years, but it too is hampered by the lack of a good genetic map. Using the well-characterized strain 1006 and strain WO-1, which undergoes the white-opaque phenotypic transition, we have developed a genomic restriction map of C. albicans with the enzyme SfiI. There are approximately 34 SfiI restriction sites in the C. albicans genome. Restriction fragments were separated by pulsed-field electrophoresis and were assigned to chromosomes by hybridization of complete and partial digests with known chromosome-specific probes as well as by digestion of isolated chromosomes. Telomeric fragments were identified by hybridization with a telomere-specific probe (C. Sadhu, M.J. McEachern, E.P. Rustchenko-Bulgac, J. Schmid, D.R. Soll, and J.B. Hicks, J. Bacteriol. 173:842-850, 1991). WO-1 differs from 1006 in that it has undergone three reciprocal chromosomal translocations. Analysis of the translocation products indicates that each translocation has occurred at or near an SfiI site; thus, the SfiI fragments from the two strains are similar or identical. The tendency for translocation to occur at or near SfiI sites may be related to the repeated sequence RPS 1, which contains four such sites and could provide homology for ectopic pairing and crossing over. The genome size of both strains is about 16 to 17 megabases, in good agreement with previous determinations.
Images
PMCID: PMC206775  PMID: 8407841
8.  Changes in Karyotype and Azole Susceptibility of Sequential Bloodstream Isolates from Patients with Candida glabrata Candidemia▿  
Journal of Clinical Microbiology  2007;45(8):2385-2391.
We examined the changes in genotypes and azole susceptibilities among sequential bloodstream isolates of Candida glabrata during the course of fungemia and the relationship of these changes to antifungal therapy. Forty-one isolates were obtained from 15 patients (9 patients who received antifungal therapy and 6 patients who did not) over periods of up to 36 days. The isolates were analyzed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and tested for antifungal susceptibility to fluconazole, itraconazole, and voriconazole. PFGE typing consisted of electrophoretic karyotyping and restriction endonuclease analysis of genomic DNA by use of NotI (REAG-N). The 41 isolates yielded 23 different karyotypes and 11 different REAG-N patterns but only 3 MLST types. The sequential strains from each patient had identical or similar REAG-N patterns. However, they had two or three different karyotypes in 6 (40%) of 15 patients. The isolates from these six patients exhibited the same or similar azole susceptibilities, and five patients did not receive antifungal therapy. Development of acquired azole resistance in sequential isolates was detected for only one patient. For this patient, an isolate of the same genotype obtained after azole therapy showed three- or fourfold increases in the MICs of all three azole antifungals and exhibited increased expression of the CgCDR1 efflux pump. This study shows that karyotypic changes can develop rapidly among sequential bloodstream strains of C. glabrata from the same patient without antifungal therapy. In addition, we confirmed that C. glabrata could acquire azole resistance during the course of fungemia in association with azole therapy.
doi:10.1128/JCM.00381-07
PMCID: PMC1951250  PMID: 17581937
9.  Investigation of a Cluster of Candida albicans Invasive Candidiasis in a Neonatal Intensive Care Unit by Pulsed-Field Gel Electrophoresis 
The Scientific World Journal  2012;2012:138989.
Nosocomial invasive candidiasis (IC) has emerged as a major problem in neonatal intensive care units (NICUs). We investigated herein the temporal clustering of six cases of neonatal IC due to Candida albicans in an NICU. Eighteen isolates obtained from the six neonates and two isolates from two health care workers (HCWs) working at the same unit and suffering from fingers' onychomycosis were genotyped by electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA by using Sfi I (PFGE-Sfi I). PFGE-Sfi I was more effective in discriminating between temporally related isolates. It showed that (i) both HCWs had specific strains excluding them as a source of infections in neonates. (ii) Isolates collected from three neonates were identical providing evidence of their clonal origin and the occurrence of a horizontal transmission of C. albicans in the unit. (iii) The three remaining neonates had specific strains confirming that the IC cases were coincidental. (iv) Microevolution occurred in one catheter-related candidemia case. Our results illustrate the relevance of the molecular approach to investigate suspected outbreaks in hospital surveys and the effectiveness of PFGE-Sfi I for typing of epidemiologically related C. albicans isolates.
doi:10.1100/2012/138989
PMCID: PMC3322649  PMID: 22547975
10.  SSD1 Is Integral to Host Defense Peptide Resistance in Candida albicans▿  
Eukaryotic Cell  2008;7(8):1318-1327.
Candida albicans is usually a harmless human commensal. Because inflammatory responses are not normally induced by colonization, antimicrobial peptides are likely integral to first-line host defense against invasive candidiasis. Thus, C. albicans must have mechanisms to tolerate or circumvent molecular effectors of innate immunity and thereby colonize human tissues. Prior studies demonstrated that an antimicrobial peptide-resistant strain of C. albicans, 36082R, is hypervirulent in animal models versus its susceptible counterpart (36082S). The current study aimed to identify a genetic basis for antimicrobial peptide resistance in C. albicans. Screening of a C. albicans genomic library identified SSD1 as capable of conferring peptide resistance to a susceptible surrogate, Saccharomyces cerevisiae. Sequencing confirmed that the predicted translation products of 36082S and 36082R SSD1 genes were identical. However, Northern analyses corroborated that SSD1 is expressed at higher levels in 36082R than in 36082S. In isogenic backgrounds, ssd1Δ/ssd1Δ null mutants were significantly more susceptible to antimicrobial peptides than parental strains but had equivalent susceptibilities to nonpeptide stressors. Moreover, SSD1 complementation of ssd1Δ/ssd1Δ mutants restored parental antimicrobial peptide resistance phenotypes, and overexpression of SSD1 conferred enhanced peptide resistance. Consistent with these in vitro findings, ssd1 null mutants were significantly less virulent in a murine model of disseminated candidiasis than were their parental or complemented strains. Collectively, these results indicate that SSD1 is integral to C. albicans resistance to host defense peptides, a phenotype that appears to enhance the virulence of this organism in vivo.
doi:10.1128/EC.00402-07
PMCID: PMC2519774  PMID: 18515753
11.  Candida albicans Airway Exposure Primes the Lung Innate Immune Response against Pseudomonas aeruginosa Infection through Innate Lymphoid Cell Recruitment and Interleukin-22-Associated Mucosal Response 
Infection and Immunity  2014;82(1):306-315.
Pseudomonas aeruginosa and Candida albicans are two pathogens frequently encountered in the intensive care unit microbial community. We have demonstrated that C. albicans airway exposure protected against P. aeruginosa-induced lung injury. The goal of the present study was to characterize the cellular and molecular mechanisms associated with C. albicans-induced protection. Airway exposure by C. albicans led to the recruitment and activation of natural killer cells, innate lymphoid cells (ILCs), macrophages, and dendritic cells. This recruitment was associated with the secretion of interleukin-22 (IL-22), whose neutralization abolished C. albicans-induced protection. We identified, by flow cytometry, ILCs as the only cellular source of IL-22. Depletion of ILCs by anti-CD90.2 antibodies was associated with a decreased IL-22 secretion and impaired survival after P. aeruginosa challenge. Our results demonstrate that the production of IL-22, mainly by ILCs, is a major and inducible step in protection against P. aeruginosa-induced lung injury. This cytokine may represent a clinical target in Pseudomonas aeruginosa-induced lung injury.
doi:10.1128/IAI.01085-13
PMCID: PMC3911865  PMID: 24166952
12.  NATURAL HISTORY OF DENTAL PLAQUE ACCUMULATION IN MECHANICALLY VENTILATED ADULTS: A DESCRIPTIVE CORRELATIONAL STUDY 
Summary
Objective
The purpose of this study was to describe the pattern of dental plaque accumulation in mechanically ventilated adults. Accumulation of dental plaque and bacterial colonization of the oropharynx is associated with a number of systemic diseases including ventilator associated pneumonia.
Research Methodology/Design
Data were collected from mechanically ventilated critically ill adults (n=137), enrolled within 24 hours of intubation. Dental plaque, counts of decayed, missing and filled teeth and systemic antibiotic use was assessed on study days 1, 3, 5 and 7. Dental plaque averages per study day, tooth type and tooth location were analyzed.
Setting
Medical Respiratory, Surgical Trauma and Neuroscience ICU’s of a large tertiary care center in the southeast United States.
Results
Plaque: All surfaces > 60% plaque coverage from day 1 to day 7; Molars and Premolars contained greatest plaque average >70%. Systemic antibiotic use on day 1 had no significant effect on plaque accumulation on day 3 (p=0.73).
Conclusions
Patients arrive in critical care units with preexisting oral hygiene issues. Dental plaque tends to accumulate in the posterior teeth (molars and premolars) that may be hard for nurses to visualize and reach; this problem may be exacerbated by endotracheal tubes and other equipment. Knowing accumulation trends of plaque will guide the development of effective oral care protocols.
doi:10.1016/j.iccn.2011.08.005
PMCID: PMC3234113  PMID: 22014582
Dental plaque; mechanical ventilation; oral health; oral care
13.  Tracheobronchial Mycosis in a Retrospective Case-Series Study of Five Status Asthmaticus Patients 
The aetiology of status asthmaticus (SA), a complication of severe asthma, is unknown. Fungal exposure, as measured by fungal atopy, is a major risk factor for developing asthma, but the relationship of fungi in SA per se has not previously been reported. In this five patient retrospective case series study, lower respiratory tract cultures were performed on bronchoalveolar lavage or tracheal aspirate fluid, comparing standard clinical laboratory cultures with a specialized technique in which respiratory mucus was removed prior to culture. We show mucolytic treatment allows increased detection of fungal growth, especially yeast, from the lower airways of all SA patients. We also demonstrate that the yeast Candida albicans inhalation readily induces asthma-like disease in mice. Our observations suggest, SA may represent a fungal infectious process, and supports additional prospective studies utilizing anti-fungal therapy to supplement conventional therapy, broad-spectrum antibiotics and high-dose glucocorticoids, which can promote fungal overgrowth.
doi:10.1016/j.clim.2012.11.005
PMCID: PMC3569972  PMID: 23280490
status asthmaticus; tracheobronchial; candidiasis; asthma; allergic
14.  Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs. 
Nucleic Acids Research  1997;25(20):3991-3994.
BssHII restriction endonuclease cleaves 5'-GCGCGC-3' on double-stranded DNA between the first and second bases to generate a four base 5'overhang. BssHII restriction endonuclease was purified from the native Bacillus stearothermophilus H3 cells and its N-terminal amino acid sequence was determined. Degenerate PCR primers were used to amplify the first 20 codons of the BssHII restriction endonuclease gene. The BssHII restriction endonuclease gene (bssHIIR) and the cognate BssHII methyltransferase gene (bssHIIM) were cloned in Escherichia coli by amplification of Bacillus stearothermophilus genomic DNA using PCR and inverse PCR. BssHII methyltransferase (M.BssHII) contains all 10 conserved cytosine-5 methyltransferase motifs, but motifs IX and X precede motifs I-VIII. Thus, the conserved motifs of M. BssHII are circularly permuted relative to the motif organizations of other cytosine-5 methyltransferases. M.BssHII and the non-cognate multi-specific phiBssHII methyltransferase, M.phiBss HII [Schumann,J. et al . (1995) Gene, 157, 103-104] share 34% identity in amino acid sequences from motifs I-VIII, and 40% identity in motifs IX-X. A conserved arginine is located upstream of a TV dipeptide in the N-terminus of M.BssHII that may be responsible for the recognition of the guanine 5' of the target cytosine. The BssHII restriction endonuclease gene was expressed in E.coli via a T7 expression vector.
PMCID: PMC147014  PMID: 9321648
15.  Overabundance of rare-cutting restriction endonuclease sites in the human genome. 
Nucleic Acids Research  1987;15(3):1173-1184.
A human chromosome 3-specific cosmid library was constructed from a somatic cell hybrid containing human chromosome 3 as its only human component. This library was screened to identify 230 human recombinants which contained an average insert size of 37 kilobases. DNA prepared from 54 of these cosmids, representing 2000 kilobases of human DNA, was then tested for restriction endonuclease sites for EcoRI, HindIII, KpnI, XhoI, and DraI, as well as those of the rare-cutting restriction endonucleases NotI, SfiI, NruI, MluI, SacII, and BssHII. Sites for the latter enzymes were much more abundant than would be expected from theoretical calculations, reflecting non-random clustering of these sites. This has important implications for the use of these enzymes in the construction of physical maps of chromosomes. Some individual cosmids contained large numbers of rare sites, offering an alternative means of physically mapping chromosomes based upon identifying clusters of rare restriction sites. These clusters appear to be spaced an average of 1000 kb apart.
PMCID: PMC340516  PMID: 3029699
16.  Analysis of Legionella pneumophila Serogroup 1 Isolates by Pulsed-Field Gel Electrophoresis 
Journal of Clinical Microbiology  1999;37(1):251-254.
At a hospital in Halifax, Nova Scotia, Canada, three strains of Legionella pneumophila were detectable based on plasmid content, while the isolates collected at another hospital in Halifax had no plasmids. Genomic DNA was digested with BssHII, SalI, and SpeI and subjected to pulsed-field gel electrophoresis (PFGE). We found no relationship between plasmid profile and PFGE pattern.
PMCID: PMC84227  PMID: 9854106
17.  Molecular epidemiology of Candida albicans colonization and fungemia in very low birthweight infants 
Objective:
This study investigated the relationship between colonization and fungemia.
Design:
This was a prospective study involving surveillance cultures of the nares, base of umbilicus, point of entry of umbilical catheter and parenteral fluids. Blood cultures were done when sepsis was suspected. All Candida albicans isolates were typed using restriction enzyme analysis of DNA.
Setting:
Patients were from the neonatal intensive care unit of a tertiary care hospital.
Population Studied:
Twenty-nine very low birthweight infants.
Main Results:
Eleven babies were colonized with C albicans and five of these babies developed fungemia, including five of seven who were colonized at the point of entry of the umbilical catheter. Three different strains of C albicans caused fungemia. In four of the five patients, initial catheter entry site isolates were identical to the subsequent blood isolates. Occasionally, infants were colonized with more than one strain of C albicans.
Conclusions:
Preceding colonization with C albicans and, in particular, colonization at the site of entry of umbilical vascular catheters are risk factors for subsequent development of C albicans fungemia. Fungemic and colonizing isolates are usually identical to one another by DNA typing.
PMCID: PMC3250777  PMID: 22346467
Candida albicans; Colonization; DNA typing; Fungemia; Molecular epidemiology; Neonates
18.  A genome-wide transcriptional analysis of morphology determination in Candida albicans 
Molecular Biology of the Cell  2013;24(3):246-260.
Morphology determination is critical for virulence of the human fungal pathogen Candida albicans. A genome-wide transcriptional analysis shows that genes associated with specifying the C. albicans pseudohyphal morphology represent a subset of hyphal genes and reveals fundamental differences between forward and reverse morphological transitions.
Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship among global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated with hyphae and are generally expressed at lower levels. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition involves not only down-regulation of known hyphal-specific, genes but also differential expression of additional genes that have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide expression patterns important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.
doi:10.1091/mbc.E12-01-0065
PMCID: PMC3564527  PMID: 23242994
19.  Genotypic Characterization of Vibrio vulnificus Clinical Isolates in Korea 
Objectives
Vibrio vunificus is known to cause septicemia and severe wound infections in patients with chronic liver diseases or an immuno-compromised condition. We carried out the molecular characterization of V. vulnificus isolates from human Vibrio septicemia cases based on pulsed-field gel electrophoresis (PFGE) using NotI and SfiI.
Methods and Results
PFGE was used to characterize a total of 78 strains from clinical cases after NotI or SfiI digestion. The geographical distribution of PFGE patterns for the strains from the southern part of Korea, a high-risk region for Vibrio septicemia, indicated that the isolates from southeastern Korea showed a comparatively higher degree of homology than those from southwestern Korea.
Conclusions
We report the genetic distribution of V. vulnficus isolated from Vibrio septicemia cases during 2000–2004 in Korea. This method has potential use as a subspecies-typing tool for V. vulnificus strains isolated from distant geographic regions.
doi:10.1016/j.phrp.2011.04.008
PMCID: PMC3766911  PMID: 24159444
molecular typing; PFGE; Vibrio vulnificus
20.  Use of Fourier-Transform Infrared Spectroscopy for Typing of Candida albicans Strains Isolated in Intensive Care Units 
Journal of Clinical Microbiology  2003;41(3):954-959.
Comparative studies of Candida albicans strains are essential for proving cross-infections in epidemiological investigations. Typing of C. albicans strains is mainly based on genotypic methods. Fourier-transform infrared (FTIR) spectroscopy is described in this study as a novel phenotypic approach to the typing of C. albicans. The first step in the approach was the standardization of sample preparation (culture conditions and sampling parameters) and acquisition and classification parameters (spectral acquisition, spectral window selection, classification algorithm, and heterogeneity threshold). The second step consisted of validating the established parameters with a set of 79 strains of C. albicans isolated over 4 months from nine patients hospitalized in two intensive care units. Strains were isolated from multiple anatomical sites with repeated sampling. FTIR spectroscopy results were compared to randomly amplified polymorphic DNA (RAPD) results; this analysis showed that the amplification patterns of strains isolated from a given patient were identical and that different patients had different profiles. FTIR spectroscopy data were analyzed by hierarchical clustering performed with the second-derivative spectra. This classification revealed nine groups, one per patient. Only one spectrum out of 79 was misclassified by the FTIR spectroscopy method. RAPD and FTIR spectroscopy results were in good agreement, showing that, when nosocomial candidiasis transmission is suspected and urgent information is needed, this technique may be useful as a quick identification tool to give solid clues before confirmation by a genotypic method.
doi:10.1128/JCM.41.3.954-959.2003
PMCID: PMC150280  PMID: 12624015
21.  DNA AND INFLAMMATORY MEDIATORS IN BRONCHOALVEOLAR LAVAGE FLUID FROM CHILDREN WITH ACUTE INHALATIONAL INJURIES 
Objective
Assess the feasibility of using serial bronchoalveolar lavage fluids (BALF) to characterize the course of cell damage and inflammation in airways of pediatric patients with acute burn or inhalation injury.
Design
Prospective, longitudinal descriptive pilot study.
Setting
Burn and Pediatric Intensive Care Units in a tertiary-care medical center.
Subjects
Six consecutive intubated, mechanically ventilated pediatric patients with acute inhalational injuries were studied.
Interventions
Serial BALF specimens from clinically-indicated bronchoscopies were used to measure DNA and cytokine levels.
Measurements and Main Results
BALF DNA levels for the 6 pediatric burn subjects were highest within the first 72 hours after burn injury and declined thereafter. At the early stages after injury, BALF DNA levels (median [min, max] 3789 [1170,11917] ng/ml) were similar to those in adult burn patients and pediatric cystic fibrosis or bronchiectasis patients, and higher than those in pediatric recurrent pneumonia patients. BALF DNA levels in children and adults with inhalation injury correlated significantly with BALF IL-6, IL-8, and TGF-β1 levels. The patient with the most severe early visible airway mucosal damage and soot pattern at bronchoscopy, as well as the most extensive burns, also had the highest average early BALF DNA level (11917ng/ml) and the longest ventilator course and hospital stay. Procedures were well tolerated.
Conclusions
In children with acute burn and inhalational injury, airway cellular damage and inflammation (reflected in high BALF DNA levels) appear to peak during the first 72 hours after burns or inhalation injury followed by a slow decline. Serial analysis of factors in airway secretions is feasible and has the potential to reveal important pathophyisiologic pathways and therapeutic targets for treatment of acute inhalational injuries.
doi:10.1097/BCR.0b013e31825d5126
PMCID: PMC3567221  PMID: 23128126
DNA; BALF; cytokines; inhalation injury; pediatric; burn
22.  A study of a hospital cluster of systemic candidosis using DNA typing methods. 
Epidemiology and Infection  1994;112(2):393-398.
A cluster of disseminated Candida albicans infections, which occurred at the Intensive Care Unit of the Department of Heart Surgery, was investigated. Ten patients became infected and seven died. A wide microbiological surveillance was carried out. A total of 14 isolates of Candida albicans, four environmental and ten human, were examined using the Restriction Endonuclease Analysis (REA) of DNA. The isolates were classified into five different main groups. Five of the clinical isolates had the predominant pattern Ab and two more clinical strains were very closely related. Two more isolates from the emergency kit desk and the hands of a nurse gave the same REA profile. Such a relationship proved the epidemic nature of the cluster, with most of the patients cross-infected, and strongly suggested transmission on the hands of the staff as a determinant of the epidemic. Thus, REA has the potential to address many important questions in the study of nosocomial epidemiology of Candida albicans.
Images
PMCID: PMC2271449  PMID: 8150013
23.  Molecular tracking of Candida albicans in a neonatal intensive care unit: long-term colonizations versus catheter-related infections. 
Journal of Clinical Microbiology  1997;35(12):3032-3036.
Nosocomial neonatal candidiasis is a major problem in infants requiring intensive therapy. The subjects of this retrospective study were nine preterm infants admitted to the neonatal intensive care unit of the Hospital Central de Asturias between March 1993 and August 1994. The infants were infected with or colonized by Candida albicans. Five patients developed C. albicans bloodstream infections. A total of 36 isolates (including isolates from catheters and parenteral nutrition) were examined for molecular relatedness by PCR fingerprinting and restriction fragment length polymorphism (RFLP) analysis. The core sequence of phage M13 was used as a single primer in the PCR-based fingerprinting procedure, and RFLP analysis was performed with C. albicans-specific DNA probe 27A. Both techniques were evaluated with a panel of eight C. albicans reference strains, and each technique showed eight different patterns. With the 36 isolates from neonates, each technique enabled us to identify by PCR and RFLP analysis seven and six different patterns, respectively. The combination of these two methods (composite DNA type) identified eight different profiles. A strain with one of these profiles was present in three patients and in their respective catheters. Patients infected with or colonized by this isolate profile were clustered in time. Among the other patients, each patient was infected over time and at multiple anatomic sites with a C. albicans strain with a distinct DNA type. We conclude that C. albicans was most commonly producing long-term colonizations, although horizontal transmission probably due to catheters also occurred.
PMCID: PMC230117  PMID: 9399489
24.  Ventilator-associated pneumonia in a surgical intensive care unit: epidemiology, etiology and comparison of three bronchoscopic methods for microbiological specimen sampling 
Critical Care  2001;5(3):167-173.
Background:
Ventilator-associated bacterial pneumonia (VAP) is a important intensive care unit (ICU)-acquired infection in mechanically ventilated patients. Early and correct diagnosis of VAP is difficult but is an urgent challenge for an optimal antibiotic treatment. The aim of the study was to evaluate the incidence and microbiology of ventilator-associated pneumonia and to compare three quantitative bronchoscopic methods for diagnosis.
Methods:
A prospective, open, epidemiological clinical study was performed in a surgical ICU. In a prospective study, 279 patients admitted to a 14-bed surgical ICU during a 1-year period were evaluated with regard to VAP. Three quantitative culture bronchoscopic techniques for identifying the etiological agent were compared [bronchoalveolar lavage (BAL), protected specimen brush (PSB) and bronchoscopic tracheobronchial secretion (TBS)].
Results:
Among 103 long-term ventilated patients, 49 (48%) developed one or more VAPs (a total of 60 VAPs). The incidence was 24 VAPs per 100 ventilated patients or 23 VAPs per 1000 ventilator days. BAL, PSB and TBS with quantitative measurements were equivalent in identifying the bacterial etiology. The VAP was caused predominantly by Staphylococcus aureus in 38% of cases, followed by Pseudomonas aeruginosa in 10%, Haemophilus influenzae in 10% and Klebsiella sp. in 9%. We did not find an increased mortality rate in patients undergoing long-term ventilation who acquired VAP in comparison with patients without VAP.
Conclusion:
For the identification of the microbiological etiology of VAP, one of three available bronchoscopic methods analysed by quantitative measurements is sufficient. In our study, quantitative bronchoscopic tracheal secretion analysis was very promising. Before accepting this method as a standard technique, other studies will have to confirm our results.
PMCID: PMC31581  PMID: 11353934
bronchoscopic techniques; microbial etiology; surgical intensive care unit; ventilator-associated pneumonia
25.  The Role of the IL-12 Cytokine Family in Directing T-Cell Responses in Oral Candidosis 
Candida albicans is an opportunistic fungal pathogen that normally exists as a harmless commensal in humans. In instances where host debilitation occurs, Candida can cause a range of clinical infections, and whilst these are primarily superficial, effecting mucosal membranes, systemic infections can develop in severely immunocompromised individuals. The mechanism of host immunity during commensal carriage of C. albicans has been intensively studied. In this paper, we present the most recent information concerning host recognition of C. albicans leading to cytokine production and the subsequent T-cell responses generated in response to C. albicans. Particular focus is given to the role of the IL-12 cytokine family including IL-12, IL-23, IL-27, and IL-35, in host immunity to Candida. CD4+ T-cells are considered crucial in the regulation of immunity and inflammation. In this regard, the role of Th1/2, helper cells, together with the recently identified Th17 and Treg cells in candidosis will be discussed. Understanding the detailed mechanisms that underlie host immunity to Candida not only will be of benefit in terms of the infections caused by this organism but could also be exploited in the development of therapeutic interventions for other diseases.
doi:10.1155/2011/697340
PMCID: PMC2963117  PMID: 20981280

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