Acute infective endocarditis caused by Delftia acidovorans, a rare pathogen complicating intravenous drug use

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

Retrospective Cohort Study on Delftia acidovorans Infections in Patients: A Rare and Significant Infection

Background

In recent years, Delftia acidovorans has gained attention for its rare occurrence in patient infections. The literature consists mostly of case reports, necessitating further research to comprehensively understand risk factors, clinical characteristics, and management strategies.

Methods

We conducted a retrospective cohort study involving patients diagnosed with Delftia acidovorans infection at a tertiary teaching hospital between January 2014 and December 2022. The data included demographic details, comorbidities, bacterial cultures, antibiotic susceptibility, and treatment outcomes.

Results

There were 26 patients diagnosed with Delftia acidovorans infection who were predominantly older with multiple comorbidities. Approximately 76.9% of Delftia acidovorans infection patients had polymicrobial infections. Twenty-one patients had received antibiotics within three months before they developed the Delftia acidovorans infection, and these antibiotics were primarily third-generation cephalosporins, glycopeptides and fluoroquinolones. Antibiotic susceptibility testing showed resistance to aminoglycosides and susceptibility to imipenem, meropenem, ceftazidime, and piperacillin/tazobactam. Treatment outcome showed a mortality rate of 11.5%, mainly in patients with malignancy and advanced age.

Conclusion

Delftia acidovorans infections predominantly affect older patients with multiple comorbidities. In terms of antibiotic therapy, carbapenems, cephalosporins, and piperacillin/tazobactam with antipseudomonal activity could all be considered.

Delftia acidovorans: An Unusual Pathogen from an Adenocarcinoma Lung Patient with Pleural Effusion

Delftia acidovorans (D. acidovorans) is an aerobic, nonfermentative Gram-negative bacillus infrequently isolated from clinical specimens. The pathogenicity and clinical significance of the organism has not been ascertained due to uncommon clinical isolation and suspected low virulence. The organism has been reported to be inherently resistant to aminoglycoside group of drugs which remain as a widely used first-line drug of choice for febrile neutropenic patients. Hereby, we report a case of D. acidovorans-associated pleural effusion in a patient of metastatic adenocarcinoma diagnosed and treated timely and successfully with appropriate antibiotics.

Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations

Delftia is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. Delftia spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of Delftia and supported their role as generalists.

Small molecule natural products in human nasal/oral microbiota

Small molecule natural products are a chemically diverse class of biomolecules that fulfill myriad biological functions, including autoregulation, communication with microbial neighbors and the host, interference competition, nutrient acquisition, and resistance to oxidative stress. Human commensal bacteria are increasingly recognized as a potential source of new natural products, which may provide insight into the molecular ecology of many different human body sites as well as novel scaffolds for therapeutic development. Here, we review the scientific literature on natural products derived from residents of the human nasal/oral cavity, discuss their discovery, biosynthesis, and ecological roles, and identify key questions in the study of these compounds.

Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS production

The proportion of Staphylococcus aureus in the skin microbiome is associated with the severity of inflammation in the skin disease atopic dermatitis. Staphylococcus epidermidis, a commensal skin bacterium, inhibits the growth of S. aureus in the skin. Therefore, the balance between S. epidermidis and S. aureus in the skin microbiome is important for maintaining healthy skin. In the present study, we demonstrated that the heat-treated culture supernatant of Delftia acidovorans, a member of the skin microbiome, inhibits the growth of S. epidermidis, but not that of S. aureus. Comprehensive gene expression analysis by RNA sequencing revealed that culture supernatant of D. acidovorans increased the expression of genes related to glycolysis and the tricarboxylic acid cycle (TCA) cycle in S. epidermidis. Malonate, an inhibitor of succinate dehydrogenase in the TCA cycle, suppressed the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis. Reactive oxygen species production in S. epidermidis was induced by the heat-treated culture supernatant of D. acidovorans and suppressed by malonate. Further, the inhibitory effect of the heat-treated culture supernatant of D. acidovorans on the growth of S. epidermidis was suppressed by N-acetyl-L-cysteine, a free radical scavenger. These findings suggest that heat-resistant substances secreted by D. acidovorans inhibit the growth of S. epidermidis by inducing the production of reactive oxygen species via the TCA cycle.

First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core

Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.

A New Type of Chronic Wound Infection after Wisdom Tooth Extraction: A Diagnostic Approach with 16S-rRNA Gene Analysis, Next-Generation Sequencing, and Bioinformatics

Delayed-onset infections are rare postoperative complications of lower third molar extractions. This article presents a case of a chronic combined hard and soft tissue infection after the extraction of a third molar, where the causative organisms could only be elucidated by molecular methods. Experimental 16S-rRNA gene analysis with next-generation sequencing and bioinformatics was used to identify the bacterial spectrum of the infection. 16S-rRNA gene analysis delivered the microbiome of the abscessing inflammation while standard culture and laboratory examinations were all sterile. The microbiome showed a mixed bacterial infection with a dominance of Delftia and Alcanivorax (spp.) besides other bacteria of the normal oral flora. Using 16S-rRNA-gene analysis, next-generation sequencing, and bioinformatics, a new type of chronic wound infection after wisdom tooth extraction was found. The property of Delftia and Alcanivorax (spp.) as water-affine environmental bacteria raises suspicion of infection from contaminated water from a dental unit. Thus, osteotomies of teeth should only be done with sterile cooling water. The 16S-rRNA gene analysis should become a part of the routine diagnostics in medical microbiology.

Delftibactin-A, a Non-ribosomal Peptide With Broad Antimicrobial Activity

The rapid emergence of drug resistant bacteria is occurring worldwide, outpacing the development of new antibiotics. It is known that some of the main sources of antibiotics are the bacteria themselves, many of which are secondary metabolites of Gram positive bacteria. Siderophores, which are secondary metabolites, function as natural chelators (e.g., iron). They are produced and secreted by many bacteria and have been experimented on as "carriers" of several types of antibiotics that pass the cell membrane of challenging Gram negative bacteria. Delftibactin A is a non-ribosomal peptide (NRP), which is known to detoxify gold in Delftia spp. and form gold nuggets, and is considered to be a siderophore. In this study we demonstrate that the supernatant from novel environmental isolates of Delftia spp. have antimicrobial activity. We characterized the active fraction and identified delftibactin A as a compound with antimicrobial activity. Delftibactin A exhibits potent antimicrobial activity against Gram positive multi drug resistant (MDR) bacteria like Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin resistant Enterococcus (VRE), and also against the Gram negative pathogens Acinetobacter baumannii and Klebsiella pneumoniae. We discovered that the production of delftibactin A is greatly influenced by temperature. Furthermore, we have demonstrated the possibility of utilizing delftibactin A as a siderophore carrier of toxic metals such as gallium into Gram negative bacteria. These findings expose new opportunities of yet unexploited natural products such as delftibactin A, which have been known for other bacterial uses, as potent factors in the battle against MDR bacteria.

Conjunctival dysbiosis in mucosa-associated lymphoid tissue lymphoma

To investigate the conjunctival microbiota and the association between the development of conjunctival mucosa-associated lymphoid tissue (MALT) lymphoma and dysbiosis, DNA samples were collected from 25 conjunctival MALT lymphoma patients and 25 healthy controls. To compare the microbiota, samples were collected from the following four body locations: conjunctiva, meibomian gland, periocular skin and hand. Extracted DNA was analyzed by 16S rRNA sequences, and libraries were sequenced on an Illumina MiSeq sequencer. The differences in bacteria were characterized by using principal coordinate analysis of metagenomics data, and the differences in bacterial compositions were evaluated by linear discriminant analysis effect size. The conjunctival microbiota of MALT lymphoma patients was compositionally different from that of healthy controls. For the conjunctival MALT lymphoma patients, alterations in the microbial composition were detected, and a remarkable change was detected at the conjunctiva. Detailed analysis showed that a specific population of the microbiota, the genus Delftia, was significantly more abundant in conjunctival MALT lymphoma patients, and the genera Bacteroides and Clostridium were less abundant in the MALT lymphoma patients. A specific microbiota on the ocular surface in conjunctival MALT lymphoma patients was detected, and dysbiosis may play an important role in the pathophysiology of conjunctival MALT lymphoma.

Delftia acidovorans: A rare cause of septic pulmonary embolism from catheter-related infection: Case report and literature review

Septic pulmonary emboli is a rare condition due to the dislodgement of an infected thrombus traveling to the pulmonary vasculature via the venous system. Staphylococcus spp. and Candida spp. are the most common causative agents. The most common risk factor is intravenous drug abuse, but there has been an association with intravenous catheters. Delftia acidovorans (DA) is a rare organism causing catheter-related infection, which has a tendency to embolize and clog up major vessels. It is highly resistant to all available aminoglycoside agents. There are only a few cases reported in children showing DA as a cause of septic emboli with none of the cases reported in a young patient. We report a similar case but in a young adult who developed septic emboli due to DA that was caused by an infected peripherally inserted central catheter (PICC) line. Since the organism is highly susceptible to recurrent embolization, the PICC line was removed and the patient was treated successfully with an appropriate antibiotic regime.

Cutaneous alternariosis in an immunocompromised dog successfully treated with cold plasma and cessation of immunosuppressive medication

A cutaneous infection with Alternaria spp. was diagnosed in a 2-year-old male intact Irish setter dog, presenting with multifocal papules, plaques and ulcerations involving all four distal limbs, shoulder blades, scrotum, pinnae and nasal mucous membranes. The dog had been treated for inflammatory bowel disease and lymphangiectasia with immunosuppressive doses of cyclosporine and prednisolone for approximately 3 months. The diagnosis was based on clinical signs, the demonstration of fungal elements within skin biopsies, deep fungal culture and fungal PCR from a formalin-fixed tissue specimen. Complete clinical remission was achieved by tapering and cessation of the immunosuppressive medication, treatment with cold atmospheric-pressure plasma (CAPP) and topical enilconazole within 8 weeks.

Rhizobium radiobacter Endocarditis in an Intravenous Drug User: Clinical Presentation, Diagnosis, and Treatment

Rhizobium radiobacter, a soil-based organism, is not, usually, pathogenic unless in the immunecompromised. Endocarditis, in the immunocompromised, is a typical presentation generally as a result of catheter-based infections. We describe the presentation of R. radiobacter prosthetic valve endocarditis and the inherent challenges in its presentation and diagnosis. A patient presented with acute limb ischemia secondary to R. radiobacter-mediated endocarditis and subsequent thromboembolization of the distal superior femoral and proximal popliteal arteries in the left lower limb. He underwent an uneventful thrombolectomy that restored blood flow distal to the occlusion and restored the patency of the affected arteries. Postoperatively, the patient maintained several unexplained febrile episodes. Blood cultures remained negative for infection. A cardiac work-up demonstrated the presence of vegetative growth on the prosthetic mitral and native aortic valves. Histopathologic analysis of the extracted thrombus confirmed the presence of R. radiobacter. On further history, it was elucidated that the patient was an intravenous drug user who routinely stored drug paraphernalia in plant beds. The patient recovered uneventfully after Piptazobactam was administered. R. radiobacter, and similarly other soil-based pathogens, should be considered as a potential source of endocarditic infection and thromboembolization in patients who similarly describe a history of intravenous drug use.

Delftia acidovorans: A rare pathogen in immunocompetent and immunocompromised patients

Delftia acidovorans is an aerobic, nonfermenting Gram-negative bacillus. It is usually a nonpathogenic environmental organism and is rarely clinically significant. Although D acidovorans infection most commonly occurs in hospitalized or immunocompromised patients, there are also several reports documenting the infection in immunocompetent patients. The present article describes a B cell lymphoblastic leukemia patient with D acidovorans pneumonia who was successfully treated with antibiotic therapy. The present report indicates that unusual pathogens may be clinically significant in both immunocompromised and immunocompetent patients. D acidovorans is often resistant to aminoglycosides; therefore, rapid detection of this microorganism is important.

Emergency management of heat exchanger leak on cardiopulmonary bypass with hypothermia

Heat exchanger leak on cardiopulmonary bypass is very rare, but serious. The exact incidence is not known. It is an emergency associated with the potential risk of blood contamination, air embolism and haemolysis, difficulty with re-warming, acidosis, subsequent septic shock, multi-organ failure and death. We present a prompt, highly co-ordinated algorithm for the successful management of this important rare complication. There is need for further research to look for safety devices that detect leaks and techniques to reduce bacterial load. It is essential that teams practice oxygenator change-out routines and have a well-established change-out protocol.

Delftia lacustris septicemia in a pheochromocytoma patient: case report and literature review

We report the first case of true Delftia lacustris bacteremia in a patient with pheochromocytoma. The organism was identified using 16S rRNA gene sequencing and biochemical tests. A peripheral intravenous catheter was the suspected source of infection, and the patient was successfully treated with piperacillin/tazobactam. We also present a review of the literature describing bacteremia caused by Delftia species.