A controlled comparison of the BacT/ALERT® 3D and VIRTUO™ microbial detection systems.

The performance of the next-generation BacT/ALERT® VIRTUO™ Microbial Detection System (VIRTUO™, bioMérieux Inc., Hazelwood, MO) was compared to the BacT/ALERT® 3D Microbial Detection System (3D, bioMérieux Inc., Durham, NC) using BacT/ALERT® FA Plus (FA Plus), BacT/ALERT® PF Plus (PF Plus), BacT/ALERT® FN Plus (FN Plus), BacT/ALERT® Standard Aerobic (SA), and BacT/ALERT® Standard Anaerobic (SN) blood culture bottles (bioMérieux Inc., Durham, NC). A seeded limit of detection (LoD) study was performed for each bottle type in both systems. The LoD studies demonstrated that both systems were capable of detecting organisms at nearly identical levels [<10 colony-forming units (CFU) per bottle], with no significant difference. Following LoD determination, a seeded study was performed to compare the time to detection (TTD) between the systems using a panel of clinically relevant microorganisms inoculated at or near the LoD with 0, 4, or 10 mL of healthy human blood. VIRTUO™ exhibited a faster TTD by an average of 3.5 h, as well as demonstrated a significantly improved detection rate of 99.9% compared to 98.8% with 3D (p-value <0.05).

Antimicrobial binding and growth kinetics in BacT/ALERT® FA Plus and BACTEC® Aerobic/F Plus blood culture media.

The capacity of absorbent beads in BacT/ALERT® FA Plus and BACTEC® Aerobic/F Plus blood culture bottles to bind and neutralize antibiotics was compared. Binding was established using reverse-phase HPLC, and inactivation was based on the recovery of susceptible test stains from simulated blood cultures. The FA Plus medium demonstrated more rapid and better overall binding kinetics for each drug tested, resulting in significantly better overall recovery rates. Differences in time to detection favored the FA Plus medium for three drug/organism combinations and Aerobic/F Plus for two.

Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory.

The identification and/or prediction of the antimicrobial resistance of microorganisms in clinical materials solely by molecular means in the diagnostic microbiology laboratory is not novel. However, the ability to sequence multitudes of bacterial genomes and deliver and interpret the resultant sequence information in near "real-time" is the basis of next-generation sequencing (NGS) technologies. There have been numerous applications and successes of NGS applications in the clinical and public health domain. However, none have, as yet, delivered perhaps the most sought after application, i.e., the generation of microbial sequence data for "real-time" patient management. In this review, we discuss the use of NGS and whole-genome sequencing (WGS) of microorganisms as a logical next step for the routine diagnosis of infection and the prediction of antimicrobial susceptibility in the clinical microbiology laboratory.

Epithelial apoptosis in mechanistically distinct methods of injury in the murine small intestine.

Gut epithelial apoptosis is involved in the pathophysiology of multiple diseases. This study characterized intestinal apoptosis in three mechanistically distinct injuries with different kinetics of cell death. FVB/N mice were subjected to gamma radiation, Pseudomonas aeruginosa pneumonia or injection of monoclonal anti-CD3 antibody and sacrificed 4, 12, or 24 hours post-injury (n=10/time point). Apoptosis was quantified in the jejunum by hematoxylin and eosin (H&E), active caspase-3, terminal deoxynucleotidyl transferase dUTP-mediated nick end labeling (TUNEL), in situ oligoligation reaction (ISOL,) cytokeratin 18, and annexin V staining. Reproducible results were obtained only for H&E, active caspase-3, TUNEL and ISOL, which were quantified and compared against each other for each injury at each time point. Kinetics of injury were different with early apoptosis highest following radiation, late apoptosis highest following anti CD3, and more consistent levels following pneumonia. ISOL was the most consistent stain and was always statistically indistinguishable from at least 2 stains. In contrast, active caspase-3 demonstrated lower levels of apoptosis, while the TUNEL assay had higher levels of apoptosis in the most severely injured intestine regardless of mechanism of injury. H&E was a statistical outlier more commonly than any other stain. This suggests that regardless of mechanism or kinetics of injury, ISOL correlates to other quantification methods of detecting gut epithelial apoptosis more than any other method studied and compares favorably to other commonly accepted techniques of quantifying apoptosis in a large intestinal cross sectional by balancing sensitivity and specificity across a range of times and levels of death.

Use of pyrosequencing to identify point mutations in domain V of 23S rRNA genes of linezolid-resistant Staphylococcus aureus and Staphylococcus epidermidis.

A pyrosequencing assay was used for the rapid characterization of linezolid-resistant isolates of Staphylococcus aureus and Staphylococcus epidermidis. The assay identified base substitutions in copies of the 23S rRNA gene and determined the percentage of alleles with the mutation. Modifications of the assay were necessary to identify all mutations in the 23S rRNA genes of S. epidermidis that were associated with linezolid resistance. A C2534T mutation was identified in S. epidermidis that was not previously reported in a linezolid-resistant isolate.

Chronic colonization with Pandoraea apista in cystic fibrosis patients determined by repetitive-element-sequence PCR.

Pandoraea apista is recovered with increasing frequency from the lungs of patients with cystic fibrosis (CF) and may represent an emerging pathogen (I. M. Jorgensen et al., Pediatr. Pulmonol. 36:439-446, 2003). We identified two CF patients from our hospital whose sputum specimens were culture positive for P. apista over the course of several years. Repetitive-element-sequence PCR was employed to determine whether sequential isolates that were recovered from these patients represented a single clone and whether each patient had been chronically colonized with the same strain. Banding patterns generated with ERIC primers, REP primers, and BOX primers showed that individual patient isolates had a high degree of similarity (>97%) and were considered identical. However, only the banding patterns from the ERIC primers and BOX primers were able to show that the strains from patients I and II were unique (similarity indices of 79.8% and 70.0%, respectively). We concluded that all strains of P. apista from patient I were identical, as were all strains from patient II, establishing chronic colonization. Only two of the three methods employed indicate that the strains from the two patients are distinct. This implied that the organism was not transferred from one patient to the other, suggesting that the choice of methodology could generate misleading results when examining person-to-person transmission regarding this organism.

Evaluation of a multiplexed bead assay for assessment of Epstein-Barr virus immunologic status.

Currently, serological assays using either indirect immunofluorescence assay or enzyme-linked immunosorbent assay (ELISA) are performed to evaluate the status of Epstein-Barr virus (EBV) infection in humans. Although these methods are reliable, they are limited to testing an antibody response to a single viral antigen per reaction, thus necessitating a panel of assays to complete the evaluation. In contrast, a new bead-based method (BioPlex 2200; Bio-Rad Laboratories, Hercules, Calif.) can analyze the humoral response to multiple antigens in a single tube. This approach potentially reduces overall cost, turnaround time, and sample volume. The aim of this study was to evaluate the multiplexed EBV serologic assays performed on the BioPlex 2200 platform compared to results of conventional heterophile and ELISA-based assays. A total of 167 nonconsecutive, stored serum samples from adult and pediatric patients submitted for EBV serologic studies were used in the evaluation. Concordance between results generated by the BioPlex 2200 system and conventional assays was calculated. The anti-EA-D assay had the lowest concordance at 91%. The BioPlex 2200 system showed 97% agreement with conventional heterophile and anti-nuclear antigen assays and 92% agreement with the anti-VCA IgG and immunoglobulin M assays. Agreement between the BioPlex 2200 system and conventional testing was 92% with respect to categorization of acute versus nonacute EBV disease. The correlation between these two systems with regard to assignment into one of four categories of EBV status was also good (82%). In summary, there is excellent correlation between contemporary EBV serologic testing and the BioPlex 2200 system.

Neisseria elongata subsp. elongata, as a cause of human endocarditis.

Neisseria elongata subsp. elongata, previously considered nonpathogenic, is a potential agent of human endocarditis. We report the second case of human endocarditis caused by this organism. The patient was successfully treated with Ceftriaxone alone for a total of six weeks.

Comparison of results generated by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence PCR used to characterize penicillin-resistant pneumococci from the United States.

One hundred forty-seven isolates of Streptococcus pneumoniae with high-level penicillin resistance collected during a national surveillance program in the United States were characterized by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence (BOX element) PCR. The results generated by each method were compared by frequency of association to examine whether relationships existed between the various typing methods and statistically to determine association with the geographic source of the isolate or the age of the patient from whom the isolate was obtained. When the data were examined by pairwise analysis of individual strain classifications produced by each typing method, no statistically significant relationships between strain type, geographic location, or patient age were identified, suggesting that distinct clones of penicillin-resistant S. pneumoniae have been widely distributed throughout the United States. However, we did observed shared expression of two or three typing markers at a high frequency (>50%) among clusters of strains, indicating a certain level of concordance between the various typing methods used to classify penicillin-resistant S. pneumoniae.

Evaluation of two rapid modifications of the 4-nitrophenyl-beta-D-glucopyranosiduronic acid (PGUA) assay for the identification of Escherichia coli from urine.

Two rapid modifications of a tube assay for the detection of beta-glucuronidase activity (PGUA assay) were evaluated for the identification of Escherichia coli from urine cultures. A microwell and filter paper adaptation of the PGUA assay were tested using 1,234 oxidase-negative, Gram-negative rods isolated from urine on MacConkey agar in clinically significant numbers. There was perfect correlation between both methods and 676 of 797 E. coli isolates were PGUA-positive within 2 h while all of remaining isolates were PGUA-negative (sensitivity = 85%; specificity = 100%). We conclude that either modified format of the PGUA assay provides a useful, inexpensive, and rapid alternative spot test for the definitive identification of E. coli from urine because of the high degree of specificity.

Comparison of selective broth medium plus neomycin-nalidixic acid agar and selective broth medium plus Columbia colistin-nalidixic acid agar for detection of group B streptococcal colonization in women.

The combination of neomycin-nalidixic acid (NNA) agar and a selective broth medium (SBM) has recently been shown to improve the sensitivity of screening cultures for group B streptococcal (GBS) carriage in women. Because of the relatively high cost of NNA agar, a study was initiated to determine whether Columbia colistin-nalidixic acid (CNA) agar would be an equally sensitive, more economical alternative. A total of 580 cervical-vaginal and/or rectal specimens submitted for detection of GBS were included in the study. Each was plated onto NNA and CNA agar and then inoculated into SBM. GBS were recovered from 95 of 580 (16.4%) specimens, including 61 isolates from CNA, 74 from NNA, 73 from the CNA-SMB combination, and 86 from the NNA-SMB tandem. Of those, 22 isolates were recovered on NNA but not CNA, 9 were cultured on CNA but not NNA, 52 were isolated on both media, and 12 were recovered from subcultures of SBM only. The overall sensitivity of CNA alone (64. 2%) was statistically significantly less than that of NNA agar (77. 9%), as was the sensitivity of combination of CNA plus SBM (76.8%) compared to that of NNA plus SBM (90.5%). Based on these findings, CNA should not be considered an acceptable alternative to NNA for the detection of GBS colonization in women despite potential cost savings.

Antimicrobial activity of merocyanine 540: a photosensitizing dye.

The antimicrobial activity of merocyanine 540 (MC 540), a photosensitizing dye previously used to purge malignant cells from autologous bone marrow grafts, was evaluated against a panel of Gram-positive and Gram-negative bacteria and Candida albicans in the presence and absence of light. In the absence of light, MC 540 demonstrated no antibacterial activity against any of the organisms tested. When combined with increasing intervals of photoillumination, growth inhibition was observed with all Gram-positive organisms tested except Mycobacterium fortuitum. Photosensitizing growth inhibition was also observed with Moraxella catarrhalis but not with any other Gram-negative bacilli including members of the Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophila, or Burkhoderia cepacia. These results suggested that differences in cell wall structure confer resistance to the photodamaging effects of the dye. MC 540 exhibited no antimicrobial activity against C. albicans in the presence or absence of light.

Comparison of NNA agar culture and selective broth culture for detection of group B streptococcal colonization in women.

In 1996, the Centers for Disease Control and Prevention recommended the use of a selective broth culture for the improved detection of genital tract or anorectal carriage of group B streptococci (GBS) in pregnant women. In order to verify this recommendation in our laboratory, we compared the sensitivity of Todd-Hewitt medium with gentamicin and nalidixic acid (SBM) with our current method of direct plating on blood agar medium containing neomycin and nalidixic acid (NNA). Five hundred consecutive cervicovaginal and anorectal specimens submitted for GBS culture were included in the study. Swabs were plated onto NNA and the swabs were immersed in SBM, followed by overnight incubation at 35 degrees C. On the following day, the NNA plates were examined for colonies typical of GBS and the organisms were identified by the CAMP test or by latex agglutination. SBM cultures were subcultured onto blood agar and CNA agar plates, and the plates were reincubated for 24 h. Negative specimens from either medium were incubated for an additional 24 h and were examined again before finalization of the results. GBS were recovered from 78 specimens by both methods; from SBM only for 17 specimens (sensitivity, 86%) and from NNA only for 16 specimens (sensitivity, 85%). A moderate to heavy growth of Enterococcus faecalis was observed on plates containing NNA-positive, SBM-negative specimens. Competitive growth studies suggested that E. faecalis suppressed the growth potential of GBS in SBM. Our study suggests that direct plating on NNA, as a single method, is equivalent in sensitivity to SBM for the recovery of GBS, and the results are often available 24 h sooner. However, it appears that both direct plating and selective broth amplification techniques are required for the maximum level of identification of colonization with GBS in pregnant women.

Four-day incubation period for blood culture bottles processed with the Difco ESP blood culture system.

Blood culture records from 1994 to 1995 from five U.S. medical centers all using the Difco ESP continuous monitoring blood culture system were reviewed retrospectively. Among a total of 7,362 isolates of bacteria and yeasts, only 0.1% of possibly significant isolates would have been missed had blood cultures been routinely incubated for 4 days instead of the 5 days recommended by the manufacturer. Conversely, numerous contaminants, detected only on day 5, would have been eliminated by a 4-day incubation period.

Clonal dissemination and colony morphotype variation of vancomycin-resistant Enterococcus faecium isolates in metropolitan Detroit, Michigan.

Thirty-two isolates of vancomycin-resistant Enterococcus faecium (VRE) recovered from 25 patients hospitalized at six hospitals in the metropolitan Detroit, Mich., area over a 32-month period were examined for relatedness by repetitive-sequence PCR (rep-PCR). All isolates were shown to carry the vanA gene by PCR. The rep-PCR patterns generated from each isolate showed that the first three VRE isolates obtained from hospital A between June 1992 and February 1994 were distinct strains. Thereafter, all VRE isolates originating from hospital A and those collected from five other area hospitals had identical rep-PCR patterns. On detailed examination, subcultures of 25 of the 32 VRE isolates produced two distinct colony types characterized phenotypically by a rough and a smooth appearance, respectively. Both colony types retained the vanA locus and the rep-PCR pattern of the primary isolate. These data suggest that a single strain of VRE with the capacity to produce two colonial variants has been disseminated to several Detroit-area hospitals. The clinical significance of the colonial morphotypes is unclear.

Epidemiological investigation of infections due to Alcaligenes species in children and patients with cystic fibrosis: use of repetitive-element-sequence polymerase chain reaction.

Twenty-one isolates of Alcaligenes species were recovered from the respiratory tract of 16 patients at Texas Children's Hospital over a 1-year period. All but one were identified as Alcaligenes xylosoxidans; the remaining isolate was identified as Alcaligenes faecalis (formerly Alcaligenes odorans). Thirteen of 21 isolates were from the sputum of eight patients with cystic fibrosis (CF), two of whom were persistently colonized. The remaining isolates were recovered from intubated children. Patterns produced by repetitive-element-sequence polymerase chain reaction (rep-PCR), with use of either repetitive extragenic palindromic (REP) or enterobacterial repetitive intergenic consensus (ERIC) primers, showed that strains from different patients were distinct. This observation ruled out a common-source outbreak. Strains repeatedly cultured from the two persistently colonized patients over several months had identical rep-PCR patterns. We conclude that, similar to Pseudomonas aeruginosa, Alcaligenes species (most often A. xylosoxidans) colonize the respiratory tract of intubated children and of patients with CF. Colonization of patients with CF was associated with an exacerbation of pulmonary symptoms.

An analysis of lymph node DNA for possible bacterial agents of cat-scratch disease.

Recent investigations have implicated Afipia felis and Rochalimaea henselae as possible agents of cat-scratch disease (CSD). We studied lymph nodes with necrotizing granulomas characteristic of CSD for A. felis and R. henselae DNA so that the relationship of these organisms to lymph nodes with necrotizing granulomas of unknown etiology might be better defined. We examined formalin-fixed, paraffin-embedded lymph node biopsies with necrotizing granulomas suggestive of CSD from 28 children obtained over the last 10 years. None had identifiable bacteria, fungi, or acid-fast organisms on routine staining. Pleomorphic bacillary structures consistent with the CSD bacillus were seen with the Steiner stain in 17 cases. We performed the polymerase chain reaction (PCR) on the extracted lymph node DNA with DNA primers for these organisms after demonstrating the presence of amplifiable DNA with c-K-Ras primers. R. henselae was identified in two samples. A. felis DNA was found in just one specimen. These putative CSD bacteria are infrequently associated with necrotizing granulomas using standard PCR techniques. It is possible that some of the patients did not have clinical CSD. The preservation of DNA or numbers of bacteria in the extracted sections may be inadequate for demonstration by DNA amplification methods. These bacilli may be responsible for a small proportion of these characteristic lesions of unknown etiology, or the typical CSD histology, including the presence of pleomorphic bacillary structures, may be nonspecific.