Ralstonia pickettii Bacteremia: An Emerging Infection in a Tertiary Care Hospital Setting

Genomic analysis of Ralstonia pickettii reveals the genetic features for potential pathogenicity and adaptive evolution in drinking water

Ralstonia pickettii, the most critical clinical pathogen of the genus Ralstonia, has been identified as a causative agent of numerous harmful infections. Additionally, Ralstonia pickettii demonstrates adaptability to extreme environmental conditions, such as those found in drinking water. In this study, we conducted a comprehensive genomic analysis to investigate the genomic characteristics related to potential pathogenicity and adaptive evolution in drinking water environments of Ralstonia pickettii. Through phylogenetic analysis and population genetic analysis, we divided Ralstonia pickettii into five Groups, two of which were associated with drinking water environments. The open pan-genome with a large and flexible gene repertoire indicated a high genetic plasticity. Significant differences in functional enrichment were observed between the core- and pan-genome of different groups. Diverse mobile genetic elements (MGEs), extensive genomic rearrangements, and horizontal gene transfer (HGT) events played a crucial role in generating genetic diversity. In drinking water environments, Ralstonia pickettii exhibited strong adaptability, and the acquisition of specific adaptive genes was potentially facilitated by genomic islands (GIs) and HGT. Furthermore, environmental pressures drove the adaptive evolution of Ralstonia pickettii, leading to the accumulation of unique mutations in key genes. These mutations may have a significant impact on various physiological functions, particularly carbon metabolism and energy metabolism. The presence of virulence-related elements associated with macromolecular secretion systems, virulence factors, and antimicrobial resistance indicated the potential pathogenicity of Ralstonia pickettii, making it capable of causing multiple nosocomial infections. This study provides comprehensive insights into the potential pathogenicity and adaptive evolution of Ralstonia pickettii in drinking water environments from a genomic perspective.

Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study

BACKGROUND

Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise.

METHODS

This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients.

RESULTS

A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test.

CONCLUSIONS

This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.

Metagenomic next-generation sequencing versus traditional laboratory methods for the diagnosis of central nervous system opportunistic infections in HIV-infected Chinese adults

To evaluate clinical value of metagenomic next-generation sequencing (mNGS) in people living with HIV/AIDS (PLWHA) who had CNS disorders. Cerebrospinal fluid (CSF) samples from 48 PLWHA presenting with CNS disorders were sequenced using mNGS and compared with clinical conventional diagnostic methods. In total, 36/48 ss(75%) patients were diagnosed with pathogen(s) infection by mNGS, and the positive detection proportion by mNGS was higher than that by clinical conventional diagnostic methods (75% vs 52.1%, X² = 5.441, P = 0.020). Thirteen out of 48 patients (27.1%) were detected with 3-7 pathogens by mNGS. Moreover, 77 pathogen strains were detected, of which 94.8% (73/77) by mNGS and 37.0% (30/77) by clinical conventional methods (X² = 54.206, P < 0.001). The sensitivity and specificity of pathogens detection by mNGS were 63.9% (23/36) and 66.7% (8/12), respectively, which were superior to that by clinical conventional methods (23/36 vs 9/25, X² = 4.601, P = 0.032; 8/12 vs 5/23, X² = 5.029, P = 0.009). The application of mNGS was superior for its ability to detect a variety of unknown pathogens and multiple pathogens infection, and relatively higher sensitivity and specificity in diagnosis of CNS disorders in PLWHA.

Pediococcus pentosaceus PR-1 modulates high-fat-died-induced alterations in gut microbiota, inflammation, and lipid metabolism in zebrafish

Introduction

Obesity is a health issue worldwide. This study aimed to evaluate the beneficial effects of Pediococcus pentococcus PR-1 on the modulating of gut microbiota, inflammation and lipid metabolism in high-fat-diet (HFD)-fed zebrafish.

Methods

Adult zebrafish were fed a commercial (C), high fat (H, 25% fat), probiotic (P, 10⁶ CFU/g), or high fat with probiotic (HP) diets twice daily for 5 weeks. Gut microbiota were analysed using 16S rRNA gene sequencing. Gene expressions of intestinal cytokine, intestinal TJ protein, and liver lipid metabolism were analysed by quantitative real-time polymerase chain reaction. Biochemical and histological analysis were also performed.

Results and discussion

P. pentosaceus PR-1 reduced body weight and BMI, indicating its anti-obesity effect. The 16S rRNA sequencing results showed HFD induced a distinct gut microbiota structure from C group, which was restored by probiotic. P. pentosaceus PR-1 improved gut health by decreasing the abundance of Ralstonia and Aeromonas which were increased induced by HFD. Moreover, probiotic restored abundance of Fusobacteria, Cetobacterium and Plesiomonas, which were decreased in HFD-fed zebrafish. The results of quantitative real-time polymerase chain reaction showed probiotic suppressed HFD-induced inflammation by decreasing the expressions of IL-1b and IL-6. Levels of hepatic TNF-α, IL-1ß, and IL-6 were reduced by probiotic in HFD-fed zebrafish. Probiotic also ameliorated gut barrier function by increasing the expressions of occludin, Claudin-1, and ZO-1. Probiotic exerted anti-adipogenic activity through regulating the expressions of SREBP1, FAS and LEPTIN. Levels of hepatic triglyceride, total cholesterol, low density lipoprotein were also reduced by probiotic. Histological analysis showed probiotic alleviated liver steatosis and injury induced by HFD. P. pentosaceus PR-1 might be useful as a dietary health supplement, especially for reducing obesity.

[Rapid identification of Ralstonia pickettii using PCR-nucleic acid test strips]

OBJECTIVE

To develop a method for rapid detection of Ralstonia pickettii in water for pharmaceutical purpose using PCR-nucleic acid test strips.

METHODS

The genomic DNA of Ralstonia pickettii was extracted by boiling method. A pair of specific primers targeting the 16S rDNA with FITC and biotin labeling of the 5' ends was designed and cloned into competent E. coli DH5α cells. The nucleic acid test strips were assembled, and the workload of streptavidin labeled with colloidal gold and antibody concentration in the reaction system was optimized. After verification of the reaction mechanism and assessment of the test sensitivity, specificity and stability, the test strip was used for detecting 7 known strains of Ralstonia pickettii detected in pharmaceutical water, and an evolutionary tree was constructed to analyze the source of contamination.

RESULTS

The genomic DNA extracted by boiling method had a purity between 1.8 and 2.0, and the PCR products showed a 100% similarity of with Ralstonia pickettii 16S rDNA registered in GenBank. Using the colloidal gold amplification principle, in every 100 μL colloidal gold solution, 3.5 μL streptavidin was added; the detection line on nitrocellulose membrane was 2.0 mg·mL-1 anti FITC antibody, and the quality control line was 1.2 mg · mL-1 biotinylated BSA, and they generate a red band after binding with positive amplification product. Specificity test of the assembled test strip yielded consistent result with agarose gel electrophoresis without cross reaction with Acinetobacter, Aeromonas, Pseudomonas, or Leclercia adecarboxylata. Sensitivity test of the strip showed a lower detection limit for DNA concentration of 10-5 ng/μL, with a sensitivity 1000 times that of agarose gel electrophoresis. The test strip still had good performance after storage for 3, 6, 9 and 12 months.

CONCLUSION

We successfully developed a PCR-nucleic acid test strip for convenient and cost-effective detection of Ralstonia pickettii with good specificity and sensitivity and low cost to facilitate daily monitoring of pharmaceutical water contaminations.

cleanSURFACES® intervention reduces microbial activity on surfaces in a senior care facility

As one of the top public health challenges outlined by the Centers for Disease Control (CDC), estimates report that hospital acquired infections (HAIs) claim the lives of 99,000 Americans and cost healthcare providers over $28 billion each year. In addition to underlying conditions related to age, elderly patients in long-term care facilities are at an elevated risk of acquiring HAIs. A large percentage of HAIs is attributable to contaminated surfaces and medical devices. To that end, this study utilized a metatranscriptomic sequencing workflow (CSI-Dx™) to profile active microbial communities from surfaces in the HJ Heinz Community Living Center, a long-term care facility in the Veterans Affairs Pittsburgh Health Care System. Swabs were collected from high-touch surfaces (Keyboard, Ledge, Workstation on Wheels, Worksurfaces) before (Baseline) and after cleanSURFACES^® were installed at 4 timepoints (Day 1, Day 7, Day 14, and Day 30). Microbial richness was significantly reduced after cleanSURFACES^® intervention (Wilcoxon test with Holm correction, p=0.000179). Beta diversity results revealed distinct clustering between Baseline and Post-intervention samples (Adonis, p<0.001). Reduction in bacterial (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis) and fungal (Malassezia restricta, Candida albicans, Candida glabrata, and Candida orthopsilosis) expression of opportunistic pathogens was observed. Additionally, a subset of taxa (Corynebacterium, Cutibacterium acnes, and Ralstonia pickettii) was present in specific Post-intervention timepoints and surface types. This study revealed decreased microbial activity, highlighting the potential for the combinatorial application of cleanSURFACES^® and regular decontamination practices to reduce the prevalence of microbes causing HAIs.

Oldukça Nadir Görülen Toplum Kaynaklı Yara Yeri Enfeksiyonu Etkeni: Ralstonia pickettii

Ralstonia pickettii (R. pickettii), Ralstonia cinsi içerisinde en sık rastlanılan tür olup non-fermenter, aerobik, Gram-negatif bir basildir. Fırsatçı bir patojen olan bakteri, hastane ortamından ve çevresel kaynaklardan bulaşabilir. R. pickettii immunkompetan bireylerde oral flora ve üst solunum yolu florasında kommensal olarak yaşayabilirken immun-kompromize kişilerde şiddetli enfeksiyonlara neden olabilmektedir. R. pickettii ile ilgili toplum kaynaklı rapor edilmiş az sayıda vaka bildirilmişken, genellikle hastane kaynaklı enfeksiyonlar rapor edilmiştir. Bu olguda ise toplum kökenli yara yeri enfeksiyonu olan erişkin bir hasta sunulmuştur. Alt ekstremitede seropürülan akıntılı açık lezyon şikayeti ile başvuran 69 yaşında kadın hastanın laboratuvar parametrelerinden lökosit ve nötrofil sayısı ile sedimantasyon hızı değeri normalden yüksek olarak değerlendirildi. Yara kültürü alınan hastaya sefuroksim aksetil 2 x 500 mg/gün tablet tedavisi ampirik olarak başlandı. Numuneden hazırlanan Gram boyalı preparatta bol PMNL ve gram negatif basiller görüldü, Q-skoru Q3 olarak değerlendirildi. Kültürde üremiş olan koloniler Vitek 2 Compact (bioMerieux, Fransa) otomatize sistemi ile R. pickettii olarak tanımlandı. Mikroorganizmanın antibiyotik duyarlılık testi yine aynı otomatize sistem ile çalışıldı. Suş gentamisin, amikasin, piperasilin-tazobaktam, seftazidim, sefepim, siprofloksasin ve meropeneme standart dozda duyarlı iken trimetoprim-sulfametoksazole dirençliydi. 3 gün sonra poliklinik kontrolüne gelen hastanın yarasında iyileşme gözlendiği için mevcut antimikrobiyal tedavi devam ettirildi. Bu olgu sunumunda, R. pickettii’nin toplumdan edinilmiş yara yeri enfeksiyonlarında karşımıza çıkabileceğine dikkat çekmek istedik. Genellikle kontaminant olarak kabul edilen bazı mikroorganizmaların enfeksiyon etkeni olabileceği akılda tutulmalı, toplum kökenli R.pickettii enfeksiyonu olasılığı göz ardı edilmemelidir. Yapılan literatür taramasında ülkemizden bildirilmiş R. pickettii’ye bağlı toplum kaynaklı yara yeri enfeksiyonuna rastlanmadı. Dolayısı ile vakamız bildiğimiz kadarıyla, Türkiye’de bildirilen R. pickettii’ye bağlı ilk toplum kaynaklı yara yeri enfeksiyonu vakasıdır.

Volatile Organic Compounds and 16S Metabarcoding in Ice-Stored Red Seabream Pagrus major

The profiles of bacterial communities and volatile organic compounds (VOCs) of farmed red seabream (Pagrus major) from two batches during ice storage were studied using 16S metabarcoding (culture independent approach) and headspace Solid Phase Micro-Extraction—Gas Chromatography/Mass Spectrometry (SPME-GC/MS) analysis, respectively. Sensory attributes and microbiological parameters were also evaluated. At Day 12 (shelf-life for both batches based on sensory evaluation), using classical microbiological analysis, Total Viable Counts (TVC) were found at the levels of 7–8 log cfu/g, and Pseudomonas and/or H2S producing bacteria dominated. On the other hand, the culture independent 16S metabarcoding analysis showed that Psychrobacter were the most abundant bacteria in fish tissue from batch 1, while Pseudomonas and Psychrobacter (at lower abundance) were the most abundant in fish from batch 2. Differences were also observed in VOC profiles between the two batches. However, combining the VOC results of the two batches, 15 compounds were found to present a similar trend during fish storage. Of them, 2-methylbutanal, 3-methylbutanal, 3-methyl-1-butanol, ethanol, 2,4 octadiene (2 isomers), ethyl lactate, acetaldehyde and (E)-2-penten-1-ol could be used as potential spoilage markers of red seabream because they increased during storage, mainly due to Psychrobacter and/or Pseudomonas activity and/or chemical activity (e.g., oxidation). Additionally, VOCs such as propanoic acid, nonanoic acid, decanoic acid, 1-propanol, 3,4-hexanediol and hexane decreased gradually with time, so they could be proposed as freshness markers of red seabream. Such information will be used to develop intelligent approaches for the rapid evaluation of spoilage course in red seabream during ice storage.

The Role of a Rapid Prevention of Ralstonia pickettii Growth during Dialysis in a Frail Patient

Ralstonia pickettii is an opportunistic bacillus found in Pseudomonas species, with the ability to induce systemic infections. We report the case of a 69-year-old man, with a clinical history of myeloma, Type IIdiabetes, renal failure (grade IV), and colon cancer, that developed a severe bacterial infection, with acute asthenia and a fever, that appeared at the end of dialysis. Using theMALDI-TOF technology, the bacillus Ralstonia pickettii was identified, and an antimicrobial treatment was quickly started with a rapid microbiological remission.

Altered Microbial Composition of Drug-Sensitive and Drug-Resistant TB Patients Compared with Healthy Volunteers

Mycobacterium tuberculosis infection has three discernible outcomes: active tuberculosis, latent tuberculosis, or clearance of the bacterium. The outcome of the infection depends on the interaction of the bacterium, the immune system, and the microbiome of the host. The current study uses 16S rRNA sequencing to determine the diversity and composition of the respiratory microbiome of drug-resistant and drug-sensitive tuberculosis patients as well as healthy volunteers. Tuberculosis patients exhibited increased microbial diversity and differentially abundant bacteria than healthy volunteers. Compositional differences were also observed when comparing drug-sensitive or -resistant tuberculosis patients. Finally, we defined and assessed the differences in the core sputum microbiota between tuberculosis patients and healthy volunteers. Our observations collectively suggest that in sputum, Mycobacterium tuberculosis infection is related to altered bacterial diversity and compositional differences of core members of the microbiome, with potential implications for the bacterial pulmonary ecosystem's stability and function.

Host-Pathogen Molecular Factors Contribute to the Pathogenesis of Rhizopus spp. in Diabetes Mellitus

Purpose of Review

Infectious diseases represent up to 12% of all deaths in people with diabetes mellitus (DM). The development and progression of DM generate a chronic inflammatory state with unique characteristics that have been exploited by some pathogens; one of them is Rhizopus spp., a fungus considered the causative agent of mucormycosis. This disease has a poor prognosis with high mortality rates, and the apparition of resistant isolates each year has become a worrying concern. DM is an actual and continuing health problem, and for that reason, it is of foremost importance to study the pathogenesis of mucormycosis to generate new prevention and treatment strategies.

Recent Findings

The worldwide incidence of mucormycosis has increased in recent years. The pathogenic mechanisms and factors identified in Rhizopus spp. are the cell wall, spore germination, proteins, and enzymes related to iron sequestration, CotH fungal protein, positive regulation of the GRP78 cell receptor, and immune evasion due to survival within phagocytes, among others. The physiopathology of DM offers favorable conditions for the successful replication of Rhizopus spp.

Summary

The main reason for increase of incidence of mucormycosis caused by Rhizopus spp. has been associated with the rise of worldwide prevalence of DM. Knowing the fungal pathogenic mechanisms as well as the relationships between Rhizopus with the microenvironment found in the human body will undoubtedly help generate better antifungals to enhance treatment outcomes. Nowadays, some strategies to combat the fungus are based on the knowledge of its proteins, cellular interactions, and iron metabolism.

Identification and Elimination of the Clinically Relevant Multi-Resistant Environmental Bacteria Ralstonia insidiosa in Primary Cell Culture

In times of spreading multidrug-resistant bacteria, species identification and decontamination of cell cultures can be challenging. Here, we describe a mobile cell culture contaminant with “black dot”-like microscopic appearance in newly established irreplaceable hybridoma cell lines and its identification. Using 16S rRNA gene sequencing, species-specific PCRs, whole genome sequencing (WGS), and MALDI-TOF mass spectrometry, the contaminant was identified as the ubiquitous environmental and clinically relevant Gram-negative bacterium Ralstonia insidiosa (R. insidiosa), a strong biofilm producer. Further characterizations by transmission electron microscopy (TEM) and biochemical API test were not conclusive. Whole genome sequencing of our R. insidiosa isolate revealed numerous drug-resistance determinants. Genome-wide comparison to other Ralstonia species could not unambiguously designate our isolate to R. insidiosa (<95% average nucleotide identity) suggesting a potential novel species or subspecies, closely related to R. insidiosa and R. pickettii. After determining the antibiotic susceptibility profile, the hybridoma cell culture was successfully decontaminated with ciprofloxacin without affecting antibody production.