Achromobacter xylosoxidans infection presenting as a pulmonary nodule mimicking cancer

Fine Particulate Matter Perturbs the Pulmonary Microbiota in Broiler Chickens

(1) Fine particulate matter (PM2.5) seriously affects the respiratory tract health of both animals and humans. Growing evidence indicates that the pulmonary microbiota is involved in the development of respiratory tract health; however, there is still much that is unknown about the specific changes of pulmonary microbiota caused by PM2.5 in broilers. (2) In this experiment, a total of 48 broilers were randomly divided into a control group and PM-exposure group. The experiment lasted for 21 days. Microbiota, inflammation biomarkers, and histological markers in the lungs were determined. (3) On the last day of the experiment, PM significantly disrupted the structure of lung tissue and induced chronic pulmonary inflammation by increasing IL-6, TNFα, and IFNγ expression and decreasing IL-10 expression. PM exposure significantly altered the α and β diversity of pulmonary microbiota. At the phylum level, PM exposure significantly decreased the Firmicutes abundance and increased the abundance of Actinobacteria and Proteobacteria. At the genus level, PM exposure significantly increased the abundance of Rhodococcus, Achromobacter, Pseudomonas, and Ochrobactrum. We also observed positive associations of the above altered genera with lung TNFα and IFNγ expression. (4) The results suggest that PM perturbs the pulmonary microbiota and induces chronic inflammation, and the pulmonary microbiota possibly contributes to the development of lung inflammation.

Clinicomicrobiological Profile of Infections by Achromobacter: An Emerging Nosocomial Pathogen in Indian Hospitals

Background

Achromobacter causes opportunistic nosocomial infections in immunocompromised patients with high mortality. It is underreported as it is often misidentified by conventional microbiological methods.

Aims

The aim of the study is to access the clinicomicrobiological profile and antibiogram of Achromobacter spp. from clinical isolates.

Materials and Methods

It is an observational study done from July 2020 to December 2021 in our hospital. All nonduplicate isolates of Achromobacter from blood and respiratory samples were initially identified with VITEK-2 GN card system and further confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Antibiogram and treatment outcomes were also studied.

Results

Achromobacter spp. was isolated from 14 patients. Blood samples yielded most isolates (71.4%; n = 10) followed by tracheal aspirate and bronchoalveolar lavage fluid. Bacteremia followed by pneumonia was the most common clinical manifestation of Achromobacter infection. All the isolates were identified as A. xylosoxidans denitrificans and showed 100% susceptibility to minocycline and piperacillin-tazobactam. Diabetes mellitus and malignancy were the most common underlying condition in these patients. A favorable outcome was seen in 78.6% of the individuals with timely institution of antibiotics and proper diagnosis.

Conclusion

Infections due to Achromobacter are on the rise in developing countries like India. Resistance to many classes of antimicrobials makes its treatment more challenging therefore it should always be guided by antibiograms. The present study highlights the significance of this rare bacterium in patients with malignancies in India and advocates greater vigilance toward appropriate identification of this organism.

Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria

Achromobacter xylosoxidans is a rod-shaped Gram-negative bacterium linked with causing several infections which mostly includes hematological malignancies. It has been recently reported to be associated with the development and progression of lung cancer and is an emerging respiratory disease-causing bacterium. The treatment of individuals infected with A. xylosoxidans bacteremia is difficult due to the fact that this pathogen has both intrinsic and acquired resistance mechanisms, typically resulting in a phenotype of multidrug resistance (MDR). Efforts are needed to design effective therapeutic strategies to curtail the emergence of this bacterium. Computational vaccine designing has proven its effectiveness, specificity, safety, and stability compared to conventional approaches of vaccine development. Therefore, the whole proteome of A. xylosoxidans was screened for the characterization of potential vaccine targets through subtractive proteomics pipeline for therapeutics design. Annotation of the whole proteome confirmed the three immunogenic vaccine targets, such as (E3HHR6), (E3HH04), and (E3HWA2), which were used to map the putative immune epitopes. The shortlisted epitopes, specific against Cytotoxic T Lymphocytes, Helper T-cell Lymphocytes, and linear B-Cell, were used to design the mRNA and multi-epitopes vaccine (MEVC). Initial validations confirmed the antigenic and non-allergenic properties of these constructs, followed by docking with the immune receptor, TLR-5, which resulted in robust interactions. The interaction pattern that followed in the docking complex included formation of 5 hydrogen bonds, 2 salt bridges, and 165 non-bonded contacts. This stronger binding affinity was also assessed through using the mmGBSA approach, showing a total of free binding energy of -34.64 kcal/mol. Further validations based on in silico cloning revealed a CAI score of 0.98 and an optimal percentage of GC contents (54.4%) indicated a putatively higher expression of the vaccine construct in Escherichia coli. Moreover, immune simulation revealed strong antibodies production upon the injection of the designed MEVC that resulted in the highest peaks of IgM+ IgG production (>3,500) between 10 and 15 days. In conclusion the current study provide basis for vaccine designing against the emerging A. xylosoxidans, which demands further experimental studies for in vitro and in vivo validations.

Distinct tumor bacterial microbiome in lung adenocarcinomas manifested as radiological subsolid nodules

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Subsolid nodules have higher microbiome diversity compared with solid nodules

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Microbiome composition of Subsolid nodules is distinct from that of solid nodules

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Microbial signatures show robust performance to predict lung adenocarcinoma or subsolid nodules

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Some lung microbial species are associated with clinical characteristics

Objectives

Increasing evidence indicates that microbiota dysbiosis in the human body may play vital roles in carcinogenesis. However, the relationship between microbiome and lung cancer remains unclear. In this study, we aimed to characterize the microbiome in early stage of lung adenocarcinoma (LUAD), which presented as subsolid nodules (SSN) or solid nodules (SN).

Materials and Methods

We performed 16S rRNA sequencing of 35 pairs (10 SSN and 25 SN) of LUAD tumor tissues and paired adjacent normal tissues. Machine learning was used to identify microbial signatures and construct predictive models.

Results

SSN has higher microbiome richness and diversity compared with SN (richness p = 0.017, Shannon index p = 0.17), and the microbiome composition of SSN is distinct from that of SN (Bray-Curtis p = 0.013, unweighted unifrac p = 0.001). Phylum Chloroflexi (p = 0.009), Gemmatimonadetes (p = 0.018) and genus including Cloacibacterium (p = 0.003), Subdoligranulum (p = 0.002), and Mycobacterium (p = 0.034) were significantly increased in SSN. Tumor and normal tissues had similar richness and diversity, as well as overall microbiome composition. Probiotics with anti-cancer potential, like Lactobacillus, showed elevated levels in normal tissues (p = 0.018). A random forest model with 20 genera-based biomarkers achieved high accuracy for LUAD prediction (area under curve, AUC = 0.879). Meanwhile, a five genera-based signature can accurately discriminate SSN between SN (AUC = 0.950). Cross-validation of these two models also showed high predictive performance (LUAD AUC = 0.813, SSN AUC = 0.933).

Conclusions

This study demonstrates, for the first time, the tumor bacterial microbiome composition of LUAD manifested as SSN is distinct from that presented as SN, which adds new knowledge to SSN in the perspective of microbiome. Furthermore, microbiome signatures showed good performance to predict LUAD or SSN.

The effect of essential oils and their combinations on bacteria from the surface of fresh vegetables

During the study, we determined the antimicrobial activity of different selected essential oils (thyme, lemongrass, juniper, oregano, sage, fennel, rosemary, mint, rosehips, dill) on some pathogenic and spoilage bacteria isolated from the surface of various fresh vegetables. At the same time, in the case of some volatile oil combinations we followed the phenomena of synergism and antagonism. The identification of the isolated bacterial strains was made using 16S rDNA gene sequence analysis. The most resistant isolates appeared to be Curtobacterium herbarum, Achromobacter xylosoxidans, and Enterobacter ludwigii, while Pseudomonas hibiscicola was the most sensitive. Of the chosen plant essential oils, the most pronounced antimicrobial effect was detected in the case of oregano. The essential oils of thyme and mint also showed elevated antimicrobial activity. A synergistic effect was observed in case of five combinations of essential oil. Based on the results, we find that some individual essential oils and mixture compositions (due to synergic effect) could be good candidates for the preservation of fresh vegetables. These preliminary findings suggest that essential oils from locally grown spices could contribute to decreasing the health risk and also to the suppression of emergence of antibiotic resistance.

Nosocomial Achromobacter xylosoxidans Infection Presenting as a Cavitary Lung Lesion in a Lung Cancer Patient

Achromobacter xylosoxidans is a Gram-negative bacillus that is known to cause nosocomial infections, primarily in patients with hematological malignancies. The most common primary manifestation is bacteremia. We report a novel case of primary A. xylosoxidans infection presenting as a cavitary lung lesion with associated pneumonia in a lung cancer patient who showed no evidence of malignant disease progression after radiation therapy. Our patient was initially admitted for acute hypoxic respiratory failure requiring mechanical ventilation. Initial computed tomography (CT) revealed a cavitary lesion in the right upper lobe of the lung. Diagnostic bronchoscopy with bronchoalveolar lavage (BAL) was performed and was negative for infectious etiologies including tuberculosis (TB) and fungal infections. Cytology was also negative for malignancy. However, the bacterial culture grew A. xylosoxidans. Antimicrobial therapy was initiated based on culture susceptibilities and the patient showed significant improvement in oxygen requirements. Due to poor functional status, the palliative care route was pursued and mechanical ventilation weaning was not performed. Cavitary pulmonary infections secondary to A. xylosoxidans are rarely reported in the medical literature. After conducting a thorough PubMed database search of the medical literature, we believe this is the first case of A. xylosoxidans infection manifesting as a cavitary lung lesion with associated pneumonia in a lung cancer patient.

First Documented Case of Percutaneous Endoscopic Gastrostomy (PEG) Tube-Associated Bacterial Peritonitis due to Achromobacter Species with Literature Review

Introduction. Achromobacter species (spp.) peritonitis has seldom been identified in medical literature. Scarce cases of Achromobacter peritonitis described previously have been correlated with peritoneal dialysis and more sparingly with spontaneous bacterial peritonitis. Achromobacter exhibits intrinsic and acquired resistance, especially in chronic infections, to most antibiotics. This article conducts a literature review of all previously reported Achromobacter spp. peritonitis and describes the first reported case of Achromobacter peritonitis as a complication of percutaneous endoscopic gastrostomy (PEG) tube placement. Discussion. Achromobacter peritonitis as a complication of PEG-tube placement has not been previously reported. In our patients' case, the recently placed PEG-tube with ascitic fluid leakage was identified as the most plausible infection source. Although a rare bacterial peritonitis pathogen, Achromobacter may be associated with wide antimicrobial resistance and unfavorable outcomes. Conclusion. No current guidelines provide significant guidance on treatment of PEG-tube peritonitis regardless of microbial etiology. Infectious Disease Society of America identifies various broad-spectrum antibiotics targeting nosocomial intra-abdominal coverage; some of these antimicrobial selections (such as cefepime and metronidazole combination) may yet be inadequate for widely resistant Achromobacter spp. Recognizably, the common antibiotics utilized for spontaneous bacterial peritonitis, i.e., third generation cephalosporins and fluoroquinolones, to which Achromobacter is resistant and variably susceptible, respectively, would be extensively insufficient. Piperacillin/tazobactam (P/T) and carbapenem were identified to provide the most reliable coverage in vitro; clinically, 5 out of the 8 patients who received either P/T or a carbapenem, or both, eventually experienced clinical improvement.

Community-acquired Achromobacter xylosoxidans infection presenting as a cavitary lung disease in an immunocompetent patient

Achromobacter xylosoxidans is a gram-negative bacterium that can oxidize xylose. It is commonly found in contaminated soil and water but does not normally infect immunocompetent humans. We report a case of a cavitary lung lesion associated with community-acquired A. xylosoxidans infection, which mimicked pulmonary tuberculosis or lung cancer in an immunocompetent man. The patient was hospitalized due to hemoptysis, and chest computed tomography (CT) revealed a cavitary lesion in the superior segment of the left lower lobe. We performed bronchoscopy and bronchial washing, and subsequent bacterial cultures excluded pulmonary tuberculosis and identified A. xylosoxidans. We performed antibiotic sensitivity testing and treated the patient with a 6-week course of amoxicillin/clavulanate. After 2 months, follow-up chest CT revealed complete resolution of the cavitary lesion.

Achromobacter xylosoxidans in idiopathic cystic bronchiectasis

This is the first case in the English language describing Achromobacter xylosoxidans in a patient with idiopathic bronchiectasis. A 66-year-old man with bronchiectasis presented with shortness of breath to the emergency department of our institution, a district hospital in the UK. His medications included long-term supplemental oxygen therapy and prophylactic azithromycin. Following 2 days admission to the respiratory unit, his saturations significantly deteriorated, and the patient was admitted to intensive care with type II respiratory failure. Following a week of intubation and ventilation, multidrug resistant A. xylosoxidans was isolated from the tracheal aspiration secretions. The patient recovered after receiving targeted intravenous antimicrobial therapy.

PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin

Non-small cell lung cancer (NSCLC) is the major form of lung cancer, with adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being its major subtypes. Smoking alone cannot completely explain the lung cancer etiology. We hypothesize that altered lung microbiome and chronic inflammatory insults in lung tissues contribute to carcinogenesis. Here we explore the microbiome composition of LUAD samples, compared to LUSC and normal samples. Extraction of microbiome DNA in formalin-fixed, paraffin-embedded (FFPE) lung tumor and normal adjacent tissues was meticulously performed. The 16S rRNA product from extracted microbiota was subjected to microbiome amplicon sequencing. To assess the contribution of the host genome, CD36 expression levels were analyzed then integrated with altered NSCLC subtype-specific microbe sequence data. Surprisingly phylum Cyanobacteria was consistently observed in LUAD samples. Across the NSCLC subtypes, differential abundance across four phyla (Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes) was identified based on the univariate analysis (p-value < 6.4e-4 to 3.2e-2). In silico metagenomic and pathway analyses show that presence of microcystin correlates with reduced CD36 and increased PARP1 levels. This was confirmed in microcystin challenged NSCLC (A427) cell lines and Cyanobacteria positive LUAD tissues. Controlling the influx of Cyanobacteria-like particles or microcystin and the inhibition of PARP1 can provide a potential targeted therapy and prevention of inflammation-associated lung carcinogenesis.

Treatment of Achromobacter Ventilator-Associated Pneumonia in Critically Ill Trauma Patients

BACKGROUND

Achromobacter sp are nonfermenting Gram-negative bacilli (NFGNB) that rarely cause severe infections, including ventilator-associated pneumonia (VAP). Data on the treatment of Achromobacter pneumonia are very limited, and the organism has been associated with a high mortality rate. Thus, more data are needed on treating this organism.

OBJECTIVE

To evaluate the treatment of Achromobacter VAP in critically ill trauma patients.

METHODS

This retrospective, observational study evaluated critically ill trauma patients who developed Achromobacter VAP. A previously published pathway for the diagnosis and management of VAP was used according to routine patient care. This included the use of quantitative bronchoscopic bronchoalveolar lavage cultures to definitively diagnose VAP.

RESULTS

A total of 37 episodes of Achromobacter VAP occurred in 34 trauma intensive care unit patients over a 15-year period. The most commonly used definitive antibiotics were imipenem/cilastatin, cefepime, or trimethoprim/sulfamethoxazole. The primary outcome of clinical success was achieved in 32 of 37 episodes (87%). This is similar to previous studies of other NFGNB VAP (eg, Pseudomonas, Acinetobacter) from the study center. Microbiological success was seen in 21 of 28 episodes (75%), and VAP-related mortality was 9% (3 of 34 patients).

CONCLUSIONS

Achromobacter is a rare but potentially serious cause of VAP in critically ill patients. In this study, there was an acceptable success rate compared with other causes of NFGNB VAP in this patient population.

Deep sequencing approach for investigating infectious agents causing fever

Acute undifferentiated fever (AUF) poses a diagnostic challenge due to the variety of possible aetiologies. While the majority of AUFs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. This study evaluated the utility of deep sequencing in fever investigation. DNA and RNA were isolated from plasma/sera of AUF cases being investigated at Cairns Hospital in northern Australia, including eight control samples from patients with a confirmed diagnosis. Following isolation, DNA and RNA were bulk amplified and RNA was reverse transcribed to cDNA. The resulting DNA and cDNA amplicons were subjected to deep sequencing on an Illumina HiSeq 2000 platform. Bioinformatics analysis was performed using the program Kraken and the CLC assembly-alignment pipeline. The results were compared with the outcomes of clinical tests. We generated between 4 and 20 million reads per sample. The results of Kraken and CLC analyses concurred with diagnoses obtained by other means in 87.5 % (7/8) and 25 % (2/8) of control samples, respectively. Some plausible causes of fever were identified in ten patients who remained undiagnosed following routine hospital investigations, including Escherichia coli bacteraemia and scrub typhus that eluded conventional tests. Achromobacter xylosoxidans, Alteromonas macleodii and Enterobacteria phage were prevalent in all samples. A deep sequencing approach of patient plasma/serum samples led to the identification of aetiological agents putatively implicated in AUFs and enabled the study of microbial diversity in human blood. The application of this approach in hospital practice is currently limited by sequencing input requirements and complicated data analysis.

Achromobacter respiratory infections

Achromobacteria are ubiquitous environmental organisms that may also become opportunistic pathogens in certain conditions, such as cystic fibrosis, hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. Some members of this genus, such as xylosoxidans, cause primarily nosocomially acquired infections affecting multiple organ systems, including the respiratory tract, urinary tract, and, less commonly, the cardiovascular and central nervous systems. Despite an increasing number of published case reports and literature reviews suggesting a global increase in achromobacterial disease, most clinicians remain uncertain of the organism's significance when clinically isolated. Moreover, effective treatment can be challenging due to the organism's inherent and acquired multidrug resistance patterns. We reviewed all published cases to date of non-cystic fibrosis achromobacterial lung infections to better understand the organism's pathogenic potential and drug susceptibilities. We found that the majority of these cases were community acquired, typically presenting as pneumonias (88%), and were most frequent in individuals with hematologic and solid organ malignancies. Our findings also suggest that achromobacterial lung infections are difficult to treat, but respond well to extended-spectrum penicillins and cephalosporins, such as ticarcillin, piperacillin, and cefoperazone.

Antimicrobial resistance in hospital-acquired gram-negative bacterial infections

Aerobic gram-negative bacilli, including the family of Enterobacteriaceae and non-lactose fermenting bacteria such as Pseudomonas and Acinetobacter species, are major causes of hospital-acquired infections. The rate of antibiotic resistance among these pathogens has accelerated dramatically in recent years and has reached pandemic scale. It is no longer uncommon to encounter gram-negative infections that are untreatable using conventional antibiotics in hospitalized patients. In this review, we provide a summary of the major classes of gram-negative bacilli and their key mechanisms of antimicrobial resistance, discuss approaches to the treatment of these difficult infections, and outline methods to slow the further spread of resistance mechanisms.

Pulmonary Infection Caused by Achromobacter xylosoxidans in a Patient with Carcinoma of Epiglottis: A Rare Case

Achromobacter xylosoxidans is an aerobic, motile, oxidase and catalase positive, non-fermenting, gram negative bacillus. It is an opportunistic pathogen which is responsible for various nosocomial and community-acquired infections. However, there are only very few reports of pulmonary infections caused by this bacterium in cancer patients. We are presenting a case of a patient with carcinoma of epiglottis, who developed pulmonary infection caused by Achromobacter xylosoxidans. According to the available literature, this is the first case of pulmonary infection caused by Achromobacter xylosoxidans, which was detected in a cancer patient in India. Since Achromobacter xylosoxidans demonstrates resistance to many classes of antimicrobials, vigilant and efficient microbiological work-ups and surveillances are needed, to diagnose infections caused by this rare pathogen in clinical settings.

Identification and clinical significance of Helcococcus species, with description of Helcococcus seattlensis sp. nov. from a patient with urosepsis

Helcococcus spp. are Gram-positive, catalase-negative, facultatively anaerobic cocci that are associated with wound and prosthetic joint infections as well bacteremia and empyema. Five Helcococcus spp. strains were isolated from our patient population, including 2 strains of Helcococcus kunzii from trauma-associated wounds, 2 Helcococcus sueciensis strains from blood and abscess, and a novel Helcococcus spp. strain from blood associated with urosepsis. Based on the phenotypic and phylogenetic evidence, we propose that the unknown bacterium be classified as Helcococcus seattlensis sp. nov. We found that all 5 tested Helcococcus strains grew as satellite colonies around Staphylococcus aureus and, interestingly, both H. kunzii strains were isolated together with S. aureus. In addition to 16S rRNA gene sequencing, conventional methods for leucine aminopeptidase (LAP) and pyrrolidonyl arylamidase (PYR) testing can be cost-effective and efficient for differentiation of Helcococcus spp. from Abiotrophia and Granulicatella species. Using nonstandard methods, we found that all tested Helcococcus spp. had high MICs of >4/76 μg/ml for trimethoprim-sulfamethoxazole, an antibiotic commonly used to treat urinary tract infections. High MICs for erythromycin, azithromycin, and clindamycin, and intermediate to high MICs for moxifloxacin, levofloxacin, and gentamicin were also observed among the Helcococcus strains.

Open-lung biopsy in patients with undiagnosed lung lesions referred at a tertiary cancer center is safe and reveals noncancerous, noninfectious entities as the most common diagnoses

We evaluated the diagnostic yield of open-lung biopsies (OLBs) in a large tertiary cancer center to determine the role of infectious diseases as causes of undiagnosed pulmonary lesions. All consecutive adult patients with either single or multiple pulmonary nodules or masses who underwent a diagnostic OLB over a period of 10 years (1998-2007) were retrospectively identified. Their risk factors for malignancy and clinical and radiological characteristics were reviewed, and their postoperative complications were assessed. We evaluated 155 patients with a median age of 57 years (range, 19-83 years). We identified infectious etiologies in 29 patients (19 %). The most common diagnosis in this group was histoplasmosis (12 [41 %]), followed by nontuberculous mycobacterial infection (7 [24 %]) and aspergillosis (4 [14 %]). The majority of the 126 remaining patients had nonmalignant diagnoses, the most prevalent being nonspecific granuloma (26 %), whereas only 17 % had malignant diagnoses. We observed no significant differences among the patients with infectious, malignant, or both noninfectious and nonmalignant final diagnoses regarding their demographic, laboratory, and clinical characteristics. Six percent of the patients had at least one post-OLB complication, and the post-OLB mortality rate was 1 %. OLB is a safe diagnostic procedure which frequently identifies a wide variety of infectious and inflammatory diseases.