Whole genome sequencing of resistance and virulence genes in multi-drug resistant Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa is an opportunistic bacterium that causes serious hospital-acquired infections. To assess the risk of clinically isolated P. aeruginosa to human health, we analyzed the resistance and virulence mechanisms of a collection of clinical isolates.

METHODS

This was a retrospective study in which P. aeruginosa isolates collected from January 1, 2018 to August 31, 2019 were analyzed using phenotypic and whole-genome sequencing (WGS) methods. The analysis included 48 clinical samples. Median patient age was 54.0 (29.5) years, and 58.3% of patients were women. Data from the microbiology laboratory database were reviewed to identify P. aeruginosa isolates. All unique isolates available for further testing were included, and related clinical data were collected. Infections were defined as hospital acquired if the index culture was obtained at least 48 h after hospitalization.

RESULTS

High-risk P. aeruginosa clones, including sequence types (STs) ST235 and ST111, were identified, in addition to 12 new STs. The isolates showed varying degrees of biofilm formation ability when evaluated at room temperature, along with reduced metabolic activity, as measured by metabolic staining, suggesting their ability to evade antimicrobial therapy. Most isolates (77.1%) were multidrug resistant (MDR), with the highest resistance and susceptibility rates to beta-lactams and colistimethate sodium, respectively.

CONCLUSIONS

The MDR phenotypes of the examined isolates can be explained by the high prevalence of efflux-mediated resistance- and hydrolytic enzyme-encoding genes. These isolates had high cytotoxic potential, as indicated by the detection of toxin production-related genes.

A genotypic analysis of patients receiving Zidovudine with either Lamivudine, Didanosine or Zalcitabine dual therapy using the LiPA point mutation assay to detect genotypic variation at codons 41, 69, 70, 74, 184 and 215

BACKGROUND

The Murex-Innogenetics LiPA HIV-1 RT assay can be used to identify the presence of mutations of the reverse transcriptase gene at codons 41, 69, 70, 74, 184 and 215 of HIV-1, which have been shown to confer resistance to the nucleoside analogs Zidovudine (ZDV), Lamivudine (3TC), Didanosine (ddI) and Zalcitabine (ddC). The M184V mutation of the reverse transcriptase gene of HIV-1 has been associated with resistance to 3TC, ddC and ddI. This mutation has also been observed in patients receiving ZDV+ddC and ZDV+ddI. We used LiPA HIV-1 RT assay to identify the presence of either consensus methionine 184 or the mutant valine 184 with three groups of patients who were treated with ZDV/3TC, ZDV/ddI or ZDV/ddC combination therapy.

OBJECTIVES

The aim of our study was to determine the viral genotype of patients who were considered to be failing therapy, by two ways: using sequencing and LiPA assays. In particular we were interested in establishing a possible correlation between these methods.

STUDY DESIGN

The study group consisted of a consecutive series of 33 patients with a treatment failure, 18 of whom received ZDV+3TC therapy, seven received ZDV+ddI and eight received ZDV+ddC therapy. We also examined a small cohort of seven seroconverters.

RESULTS

The M184V mutation was observed in 47.0% of patients receiving ZDV+3TC combination therapy but was not observed in either patient group receiving either ddI or ddC as co-therapy with ZDV. There was no evidence of the L74V mutation in our study group in either the ZDV/ddI or ZDV/ddC combination therapy group. We found the frequency of the K70R mutation to be higher in patients treated with ZDV/ddI (P=0.033) or ZDV/ddC (P=0.3) when compared with patients treated with ZDV/3TC.

CONCLUSION

The LiPA assay allowed for the rapid detection of wild type and amino acid variations at key positions conferring resistance to the most used antiviral RT inhibitors. This represented a rapid, quite sensitive, and simple genotyping test. For these reasons the LiPA assay proved to be useful in studying genetic resistance in large screenings, when key RT mutations could be useful in guiding an effective HIV-1 suppressing regimen.

Use of molecular assays in diagnosis and monitoring of cytomegalovirus disease following renal transplantation

We compared two commercial molecular assays (the Murex Hybrid Capture CMV DNA assay [HCA], version 2, and the Roche Amplicor plasma PCR assay) with a standard shell vial assay in detecting and predicting cytomegalovirus (CMV) disease in a group of renal transplant patients and assessed the role of viral load measurements (using the HCA) in their management. The sensitivity of the HCA and Amplicor assay in terms of disease detection was 100%, compared to 71% for the shell vial assay. Both the HCA and the PCR assay detected all cases of disease, at medians of 11 and 12.5 days before the onset of symptoms, respectively. Significantly higher viral loads were detected in those patients with symptoms (7.9 x 10(5) copies/ml) than in patients without symptoms (7.9 x 10(4) copies/ml; P < 0.0001). There was also a trend towards higher viral loads in those patients with primary infections (7.8 x 10(5) copies/ml) than in those patients with reactivations of CMV disease or reinfections. Successful treatment with ganciclovir was associated with a >90% reduction in viral load. Both of these new assays are sensitive and easy to use. A comparison of accurate quantitation is also useful in monitoring responses to antiviral therapy.

Causes of death of persons with developmental disabilities: comparison of institutional and community residents

Between 1993 and 1995, 1,878 persons transferred from California institutions into the community. By early 1996, 45 had died--significantly more than expected (Strauss, Shavelle, Baumeister, and Anderson, 1998). We report here on the death certificates for this group, using a comparison group of 45 certificates for institutional residents. Thirty-two of the community deaths versus 10 of the institution deaths were "sudden" or "subacute." All of the institution deaths versus 79% of the community deaths were reported to the coroner, and 55% of the institutional deaths were followed by autopsy compared to 33% in the community. Six deaths were due to perforated bowels, 5 of which were in individuals residing in the community.

Pediatric death rates and donor yield: a medical examiner's view

Problems relating to organ procurement for transplantation are examined from the medical examiner's perspective. A protocol developed in September 1991 for the County of San Bernardino, California, is described. Procurement statistics and lessons learned during the first 18 months the protocol was used are reviewed. A revised protocol and documentation forms are included. Emphasis is on pediatric donors, especially victims of child abuse. As a result of this program, organ procurement agencies in the area experience fewer denials by the Coroner's Office and organ recoveries have increased by 60%. Internal organs have been recovered from homicide victims, including children, without significant problems occurring during subsequent legal proceedings. There is increasing acceptance of the protocol by all concerned including deputy coroner investigators, homicide detectives, and the District Attorney's Office.

Lipomas of the mesencephalic tectum and rostral pons associated with sleep apnea syndrome

Two patients with mixed sleep apnea and autopsy-documented lipomas of the mesencephalic tectum and rostral pons are presented. Microscopically, the locus ceruleus was unilaterally invaded by a tumor in one case and may have been compressed in the other. Adipocytes and fibrous tissue were present adjacent to pial surfaces and around small blood vessels within the parenchyma. There was prominent astrogliosis in the adjacent neuropil. Although respiratory control is a complex, multifocal phenomena, these findings raise the possibility that the locus ceruleus or adjacent brain stem regions may be affected in some instances of sleep apnea.