Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.

We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.

Genetic Lineages and Antimicrobial Resistance in Pseudomonas spp. Isolates Recovered from Food Samples.

Raw food is a reservoir of Pseudomonas isolates that could be disseminated to consumers. The presence of Pseudomonas spp. was studied in food samples, and the phenotypic and genotypic characterizations of the recovered isolates were analyzed. Two samples of meat (3%, turkey and beef) and 13 of vegetables (22%, 7 green peppers and 6 tomatoes) contained Pseudomonas spp. A total of 20 isolates were identified, and were classified as follows (number of isolates): P. aeruginosa (5), P. putida (5), P. nitroreducens (4), P. fulva (2), P. mosselli (1), P. mendocina (1), P. monteilii (1), and Pseudomonas sp. (1). These 20 Pseudomonas isolates were clonally different by pulsed-field-gel-electrophoresis, and were resistant to the following antibiotics: ticarcillin (85%), aztreonam (30%), cefepime (10%), imipenem (10%), and meropenem (5%), but were susceptible to ceftazidime, piperacillin, piperacillin-tazobactam, doripenem, gentamicin, tobramycin, amikacin, ciprofloxacin, norfloxacin, and colistin. Only one strain (Ps158) presented a class 1 integron lacking the 3' conserved segment. The five P. aeruginosa strains were typed by multilocus sequence typing in five different sequence-types (ST17, ST270, ST800, ST1455, and ST1456), and different mutations were detected in protein OprD that were classified in three groups. One strain (Ps159) showed a new insertion sequence (ISPa47) truncating the oprD gene, and conferring resistance to imipenem.

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum.

Defining the essential genome of bacterial pathogens is central to developing an understanding of the biological processes controlling disease. This has proven elusive for Pseudomonas aeruginosa during chronic infection of the cystic fibrosis (CF) lung. In this paper, using a Monte Carlo simulation-based method to analyze high-throughput transposon sequencing data, we establish the P. aeruginosa essential genome with statistical precision in laboratory media and CF sputum. Reconstruction of the global requirements for growth in CF sputum compared with defined growth conditions shows that the latter requires several cofactors including biotin, riboflavin, and pantothenate. Comparison of P. aeruginosa strains PAO1 and PA14 demonstrates that essential genes are primarily restricted to the core genome; however, some orthologous genes in these strains exhibit differential essentiality. These results indicate that genes with similar molecular functions may have distinct genetic roles in different P. aeruginosa strains during growth in CF sputum. We also show that growth in a defined growth medium developed to mimic CF sputum yielded virtually identical fitness requirements to CF sputum, providing support for this medium as a relevant in vitro model for CF microbiology studies.

Assessment of panobacumab as adjunctive immunotherapy for the treatment of nosocomial Pseudomonas aeruginosa pneumonia.

The fully human anti-lipopolysaccharide (LPS) immunoglobulin M (IgM) monoclonal antibody panobacumab was developed as an adjunctive immunotherapy for the treatment of O11 serotype Pseudomonas aeruginosa infections. We evaluated the potential clinical efficacy of panobacumab in the treatment of nosocomial pneumonia. We performed a post-hoc analysis of a multicenter phase IIa trial (NCT00851435) designed to prospectively evaluate the safety and pharmacokinetics of panobacumab. Patients treated with panobacumab (n = 17), including 13 patients receiving the full treatment (three doses of 1.2 mg/kg), were compared to 14 patients who did not receive the antibody. Overall, the 17 patients receiving panobacumab were more ill. They were an average of 72 years old [interquartile range (IQR): 64-79] versus an average of 50 years old (IQR: 30-73) (p = 0.024) and had Acute Physiology and Chronic Health Evaluation II (APACHE II) scores of 17 (IQR: 16-22) versus 15 (IQR: 10-19) (p = 0.043). Adjunctive immunotherapy resulted in an improved clinical outcome in the group receiving the full three-course panobacumab treatment, with a resolution rate of 85 % (11/13) versus 64 % (9/14) (p = 0.048). The Kaplan-Meier survival curve showed a statistically significantly shorter time to clinical resolution in this group of patients (8.0 [IQR: 7.0-11.5] versus 18.5 [IQR: 8-30] days in those who did not receive the antibody; p = 0.004). Panobacumab adjunctive immunotherapy may improve clinical outcome in a shorter time if patients receive the full treatment (three doses). These preliminary results suggest that passive immunotherapy targeting LPS may be a complementary strategy for the treatment of nosocomial O11 P. aeruginosa pneumonia.

Bioconversion of sodium dodecyl sulphate to rhamnolipid by Pseudomonas aeruginosa: a novel and cost-effective production strategy.

The utility of rhamnolipids in industry is currently limited due to the high constraints in its economic production. In this scenario, the novel utility of sodium dodecyl sulphate (SDS) as carbon source could serve as promising cost-effective strategy. Screening of effective SDS biodegraders led to the isolation of Pseudomonas aeruginosa S15 capable of concomitant SDS degradation and biosurfactant synthesis. SDS-based rhamnolipid production was proved on SDS minimal agar plates using cetyl trimethylammonium bromide-methylene blue method and optimised in SDS-based minimal salt (SBS) medium. SDS proved to be an ideal carbon source for rhamnolipid synthesis with a high substrate to product conversion rate yielding 6.9 g/l of rhamnolipids from 1 g/l SDS in 5 days. Fast atom bombardment mass spectroscopy analysis of the purified biosurfactant proved the presence of mono- and di-rhamnolipids, viz., Rha-C(10)-C(10), Rha-C(10)-C(12) and Rha-Rha-C(10)-C(10) with surface active properties. The secreted rhamnolipids were not utilised by S15 as a carbon source, but it caused a dispersion of bacterial biofilms in SBS medium. To the best of our knowledge, this is the first report on bioconversion of synthetic detergent to biodetergent. This SDS-based novel methodology presents a more economised mode of rhamnolipid synthesis utilising SDS as sole carbon source.

Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness.

Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.

Economic effects of an eradication protocol for first appearance of Pseudomonas aeruginosa in cystic fibrosis patients: 1995 vs. 2009.

BACKGROUND: Acquisition of Pseudomonas aeruginosa (Psa) and infection with mucoid strains is associated with repeated pulmonary exacerbations which often require intravenous and long-term nebulised antibiotic treatments, repeated hospitalizations and leads to a more precipitous decline in lung function. Anti-Psa antibiotic therapy early in the course of Psa infection in patients with cystic fibrosis (CF) may result in eradication of Psa and prevention or delay of colonization with the organism. From January 1995 to December 2009 our paediatric CF clinic has followed an early eradication protocol for the first appearance of Psa. In this paper we report on the economic effects after 15 years as reflected in hospitalization and antibiotic usage and cost. METHODS: The Psa-eradication protocol includes 2 weeks of IV piperacillin and tobramycin, followed by oral ciprofloxacin for 3 weeks, and nebulised colistimethate for 6 months. The same protocol is used for newly diagnosed CF patients who grow Psa on their first visit or who grow a mucoid strain, multiresistant strain of Psa or whose Psa co-cultured with Burkholderia cepacia complex, and for patients in whom Psa recurs after initial clearance. RESULTS: 195 Psa eradication courses were completed from 1995 to 2009 with an overall Psa clearance rate of 90%. Patients that only cultured a Psa classic (non-mucoid) strain had a clearance rate was 96.5%. The percentage of children chronically infected with Psa has declined from 44% in 1994 to 15% in 2009.Total days spent in hospital for all reasons declined by 43%; chronic Psa hospital days declined by 75%; IV and nebulised anti-Psa antibiotic costs reduced by 44%. CONCLUSIONS: Results indicate that application of a Pseudomonas eradication protocol as described in this report has economic and resource utilization benefits in addition to clinical benefits.

Identification of an imipenem-resistant Pseudomonas aeruginosa clone among patients in a hospital in Rio de Janeiro.

A total of 85 Pseudomonas aeruginosa isolates were obtained from October 1999 to April 2000 in a tertiary care hospital in Rio de Janeiro, Brazil. The imipenem susceptibility was evaluated by disk diffusion and agar dilution methods, and the clonal relationship among 67 isolates was examined by macrorestriction profile analysis following pulsed-field gel electrophoresis. Imipenem resistance was observed in 52 (61.2%) isolates. Imipenem-resistant P. aeruginosa isolates were separated into 10 genotypes, 73% of which belonged to genotype A. Identification of a single P. aeruginosa clone with a high rate of imipenem resistance emphasizes the need to control the transmission of this organism among patients.

Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis.

Pseudomonas aeruginosa lung infection is an important cause of morbidity and mortality in cystic fibrosis (CF). Longitudinal assessment of the phenotypic changes in P. aeruginosa isolated from young children with CF is lacking. This study investigated genotypic and phenotypic changes in P. aeruginosa from oropharynx (OP) and bronchoalveolar lavage fluid (BALF) in a cohort of 40 CF patients during the first 3 years of life; antibody response was also examined. A high degree of genotypic variability was identified, and each patient had unique genotypes. Early isolates had a phenotype distinct from those of usual CF isolates: generally nonmucoid and antibiotic susceptible. Genotype and phenotype correlated between OP and BALF isolates. As determined by culture, 72.5% of patients demonstrated P. aeruginosa during their first 3 years. On the basis of combined culture and serologic results, 97.5% of patients had evidence of infection by age 3 years, which suggests that P. aeruginosa infection occurs early in CF and may be intermittent or undetectable by culture.

Quantitation of Pseudomonas aeruginosa in wound biopsy samples: from bacterial culture to rapid 'real-time' polymerase chain reaction.

STATEMENT OF FINDINGS: We developed a real-time detection (RTD) polymerase chain reaction (PCR) with rapid thermal cycling to detect and quantify Pseudomonas aeruginosa in wound biopsy samples. This method produced a linear quantitative detection range of 7 logs, with a lower detection limit of 103 colony-forming units (CFU)/g tissue or a few copies per reaction. The time from sample collection to result was less than 1h. RTD-PCR has potential for rapid quantitative detection of pathogens in critical care patients, enabling early and individualized treatment.

The Automicrobic System for urines.

An evaluation of the Automicrobic System (AMS) for Urines (Vitek Systems, Inc.) was carried out under the auspices of the Product Evaluation Committee of the College of American Pathologists from the period June 1977 through October 1978. Data generated during this evaluation indicated that, when comparing the AMS methodology to our clinical microbiology laboratory methodology, a 37% time saving could be realized by utilizing the AMS. Quantitation with the AMS showed a 99% correlation with the clinical microbiology laboratory method except for yeast which correlated only 50% of the time. The average overall identification accuracy was 95%. Negative response accuracy was 99%. Other members of the Enterobacteriaceae which the instrument is not designed to identify may produce erroneous results if they occur in urine specimens. Specimens containing two organisms were identified with a 94% correlation when compared to our conventional methodology. The time when a well becomes positive may be used as a fairly reliable indicator of significance (count greater than 70,000 colony-forming units per ml) for Escherichia coli, Klebsiella-Enterobacter group, and group D Enterococcus, but not for Proteus sp., Pseudomonas aeruginosa, and yeast. Specimen collection must be performed properly since specimens considered as contaminated by conventional plating-out techniques may be reported out by the AMS as only one or two organisms and thus lead to an erroneous assumption as to significance. Cost per specimen was $1.83 more by utilizing the AMS method as compared to our conventional method. This is offset by a saving of 1.74 h daily of personnel time and a final report in 13 h. At least 30 urine specimens would be needed daily to pay for the instrument and specimen costs in 1 year. The AMS can provide significant aid to a clinical microbiology laboratory when all factors are considered.