Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts

Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health

Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.

Herbaspirillum seropedicae Bacteremia Secondary to Pneumonia in a Patient With Chronic Obstructive Pulmonary Disease

Herbaspirillum seropedicae is a species of bacteria commonly found in vegetation, but in rare cases, can cause opportunistic infections in human hosts. Infections typically occur due to environmental exposure to the pathogen, such as through agriculture or gardening. However, these incidents typically only involve immunocompromised patients. Our present report describes a case of sepsis secondary to pneumonia in an adult with a history of chronic obstructive pulmonary disease who presented with complaints of shortness of breath and hypoxia. Although initially misidentified as Burkholderia cepacia, blood culture and reference lab eventually confirmed H. seropedicae bacteremia. The patient was admitted for treatment with intravenous antibiotics with significant improvement and subsequent discharge. H. seropedicae is often clinically misidentified due to its rarity. As we observe the increasing pathogenicity of H. seropedicae, clinicians must be better prepared to recognize the symptoms of its infection. Technologies such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have proven to be useful in distinguishing H. seropedicae from other similarly presenting species.

Tumor-associated microbiota in colorectal cancer with vascular tumor thrombus and neural invasion and association with clinical prognosis

Neural invasion (NI) and vascular tumor thrombus (VT) are associated with poor prognosis in patients with colorectal cancer (CRC). In this study, we apply 16S rRNA amplicon sequencing to tumor tissues and adjacent normal tissues in patients with CRC to determine the microbial differences. A discovery cohort, including 30 patients with NI, 23 with VT, and 35 with double-negative CRC tissue, is utilized. Then, we analyze the relationship between the specific bacterial taxa and indicators of different dimensions in separate cohorts. In the discovery cohort, the diversity and composition of the gut microbiome distinctly differ between the tumor and nontumor tissues in the NI and VT groups. A high abundance of Cupriavidus is found to be related to a short survival time of NI CRC, while Herbaspirillum is a potential microbial biomarker predicting the prognosis of patients with CRC with NI or VT. Moreover, the abundance of Cupriavidus or Herbaspirillum is associated with some clinical patient characteristics and prognosis, respectively. In conclusion, this study is the first to comprehensively elaborate the differences in the gut microbiota of patients with CRC with different invasion statuses and to prove the relationship between some gut microbiota and clinical patient characteristics.

Molecular and evolutionary basis of O-antigenic polysaccharide-driven phage sensitivity in environmental pseudomonads

IMPORTANCE

The application of plant-beneficial microorganisms to protect crop plants is a promising alternative to the usage of chemicals. However, biocontrol research often faces difficulties in implementing this approach due to the inconsistency of the bacterial inoculant to establish itself within the root microbiome. Beneficial bacterial inoculants can be decimated by the presence of their natural predators, notably bacteriophages (also called phages). Thus, it is important to gain knowledge regarding the mechanisms behind phage-bacteria interactions to overcome this challenge. Here, we evidence that the major long O-antigenic polysaccharide (O-PS, O-antigen) of the widely used model plant-beneficial bacterium Pseudomonas protegens CHA0 is the receptor of its natural predator, the phage ΦGP100. We examined the distribution of the gene cluster directing the synthesis of this O-PS and identified signatures of horizontal gene acquisitions. Altogether, our study highlights the importance of bacterial cell surface structure variation in the complex interplay between phages and their Pseudomonas hosts.

Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types

Microbiome-based diagnosis of cancer is an increasingly important supplement for the genomics approach in cancer diagnosis, yet current models for microbiome-based diagnosis of cancer face difficulties in generality: not only diagnosis models could not be adapted from one cancer to another, but models built based on microbes from tissues could not be adapted for diagnosis based on microbes from blood. Therefore, a microbiome-based model suitable for a broad spectrum of cancer types is urgently needed. Here we have introduced DeepMicroCancer, a diagnosis model using artificial intelligence techniques for a broad spectrum of cancer types. Built based on the random forest models it has enabled superior performances on more than twenty types of cancers' tissue samples. And by using the transfer learning techniques, improved accuracies could be obtained, especially for cancer types with only a few samples, which could satisfy the requirement in clinical scenarios. Moreover, transfer learning techniques have enabled high diagnosis accuracy that could also be achieved for blood samples. These results indicated that certain sets of microbes could, if excavated using advanced artificial techniques, reveal the intricate differences among cancers and healthy individuals. Collectively, DeepMicroCancer has provided a new venue for accurate diagnosis of cancer based on tissue and blood materials, which could potentially be used in clinics.

Tracking Antibiotic Resistance from the Environment to Human Health

Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.

Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum

The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.

Antibiotic resistance and siderophores production by clinical Escherichia coli strains

The phenomenon of antibiotic resistance has dramatically increased in the last few decades, especially in enterobacterial pathogens. Different strains of Escherichia coli have been reported to produce a variety of structurally different siderophores. In the present study, 32 E. coli strains were collected from different clinical settings in Cairo, Egypt and subjected to the antibiotic susceptibility test by using 19 antibiotics belonging to 7 classes of chemical groups. The results indicated that 31 strains could be considered as extensively drug-resistant and only one strain as pan drug-resistant. Siderophores production by all the tested E. coli strains was determined qualitatively and quantitatively. Two E. coli strains coded 21 and 49 were found to be the most potent siderophores producers, with 79.9 and 46.62%, respectively. Bacterial colonies with cured plasmids derived from strain 49 showed susceptibility to all the tested antibiotics. Furthermore, E. coli DH5α cells transformed with the plasmid isolated from E. coli strain 21 or E. coli strain 49 were found to be susceptible to ansamycins, quinolones, and sulfonamide groups of antibiotics. In contrast, both plasmid-cured and plasmid-transformed strains did not produce siderophores, indicating that the genes responsible for siderophores production were located on plasmids and regulated by genes located on the chromosome. On the basis of the obtained results, it could be concluded that there is a positive correlation between antibiotic resistance, especially to quinolones and sulfonamide groups, and siderophores production by E. coli strains used in this study.

Comparative genomic analysis reveals the evolution and environmental adaptation of Acinetobacter johnsonii

Genome plasticity is a key determinant that Acinetobacter johnsonii could widely distribute in natural and clinical environments. However, little attention has been paid to figure out the changes in the genome during A. johnsonii's evolution. Here, a comparative genomic analysis of A. johnsonii isolated from clinical and environmental sources was conducted. In this study, we found A. johnsonii has an open pan-genome and has great adaptability to different environments. Based on the results of the phylogenetic tree, ANI value and the distribution of accessory genes, we found that strains from the same habitat had a high degree of similarity. Though genes associated with the fundamental process were mostly conserved in evolution, clinical-derived isolates accumulate more genes associated with translational modification, β-lactamase and defense mechanisms, whereas environmental-derived isolates enriched more genes related to substances degradation. In addition, clinical-derived strains harbored some "strong" virulence islands and resistance islands. This study highlights the evolutionary relationship of A. johnsonii isolates from clinical and environmental sources.

High Genomic Identity between Clinical and Environmental Strains of Herbaspirillum frisingense Suggests Pre-Adaptation to Different Hosts and Intrinsic Resistance to Multiple Drugs

The genus Herbaspirillum is widely studied for its ability to associate with grasses and to perform biological nitrogen fixation. However, the bacteria of the Herbaspirillum genus have frequently been isolated from clinical samples. Understanding the genomic characteristics that allow these bacteria to switch environments and become able to colonize human hosts is essential for monitoring emerging pathogens and predicting outbreaks. In this work, we describe the sequencing, assembly, and annotation of the genome of H. frisingense AU14559 isolated from the sputum of patients with cystic fibrosis, and its comparison with the genomes of the uropathogenic strain VT-16-41 and the environmental strains GSF30, BH-1, IAC152, and SG826. The genes responsible for biological nitrogen fixation were absent from all strains except for GSF30. On the other hand, genes encoding virulence and host interaction factors were mostly shared with environmental strains. We also identified a large set of intrinsic antibiotic resistance genes that were shared across all strains. Unlike other strains, in addition to unique genomic islands, AU14559 has a mutation that renders the biosynthesis of rhamnose and its incorporation into the exopolysaccharide unfeasible. These data suggest that H. frisingense has characteristics that provide it with the metabolic diversity needed to infect and colonize human hosts.

The Mexican giant maize of Jala landrace harbour plant-growth-promoting rhizospheric and endophytic bacteria

The giant landrace of maize Jala is a native crop cultured in Nayarit and Jalisco States in the occident of México. In this study, after screening 374 rhizospheric and endophytic bacteria isolated from rhizospheric soil, root, and seed tissues of maize Jala, a total of 16 bacterial strains were selected for their plant-growth-promoting potential and identified by 16S rRNA phylogenetic analysis. The isolates exhibited different combinations of phenotypic traits, including solubilisation of phosphate from hydroxyapatite, production of a broad spectrum of siderophores such as cobalt, iron, molybdenum, vanadium, or zinc (Co²⁺, Fe³⁺, Mo^2 +, V⁵⁺, Zn²⁺), and nitrogen fixation capabilities, which were detected in both rhizospheric and endophytic strains. Additional traits such as production of 1-aminocyclopropane-1-carboxylate deaminase and a high-rate production of Indoleacetic Acid were exclusively detected on endophytic isolates. Among the selected strains, the rhizospheric Burkholderia sp., and Klebsiella variicola, and the endophytic Pseudomonas protegens significantly improved the growth of maize plants in greenhouse assays and controlled the infection against Fusarium sp. 50 on fresh maize cobs. These results present the first deep approach on handling autochthonous microorganisms from native maize with a potential biotechnological application in sustainable agriculture as biofertilizers or biopesticides.

Environmental and clinical isolates of Herbaspirillum induce pulmonary infection in mice and its secretome is cytotoxic to human lung cells

Introduction. In recent years, the Herbaspirillum genus has emerged as a pathogen in healthcare-related infections and has became stablished as an opportunistic pathogen.Hypothesis/Gap Statement. Little is known about the pathogenesis induced by Herbaspirillum genus.Aim. To evaluate the cytotoxic effects of genus Herbaspirillum, its ability to adhere to lung human cells and the ability of environmental and clinical strains of Herbaspirillum to induce pneumonia in mice.Methodology. Environmental and clinical isolates of Herbaspirillum were examined for their cytotoxic effects on the Calu-3 cell lineage. Cytotoxic activity of secretome was tested using MTT/neutral red assays and cell morphology analysis. Herbaspirillum adhesion on Calu-3 cells was assessed using bright-field microscopy and cell-associated bacteria were counted. A mouse model of acute lung infection was done using a clinical and an environmental strain. Adult male mice were used, and the pneumonia was inducted by intra-tracheal inoculation of 10⁸ or 10⁹ bacteria. Mice weight variations were evaluated at the end of the experiment. Bronchoalveolar lavage was collected and evaluated for total and differential cytology. A histological examination of lungs was performed giving a histological score.Results. The secretomes of all the strains induced morphological alterations in cells, but only H. seropedicae SmR1 were cytotoxic in MTT and neutral red assays. Clinical strains of H. frisingense AU14459 and H. hutttiense subsp. huttiense AU11883 exhibited low adherence to lung cells, while SmR1 was non-adhesive. Following intratracheal inoculation, mice treated with 10⁹ c.f.u. of the SmR1 and AU11883 strains lost 18 and 6% of their weight over 7 days, respectively, and presented moderate clinical signs. Infected mice showed inflammatory cell infiltration in the perivascular and peribroncheal/peribronchiolar spaces. Bronchoalveolar fluid of mice inoculated with SmR1 10⁹ c.f.u. presented an increase in total leucocyte cells and in neutrophils population.Conclusion. These in vivo and in vitro results provide insights into how some Herbaspirillum strains cause infection in humans, providing a basis for the characterization of pathogenesis studies on this emerging infectious agent.

Bloodstream infection due to Herbaspirillum sp.: case series and review of literature

Herbaspirillum species are Gram-negative bacteria belonging to the class Betaproteobacteria, order Burkholderiales. The phylogenetic and phenotypic similarities among these groups easily lead to species misidentification. Herbaspirillum bacteraemia is an uncommon clinical entity. The objective of this review is to collect information to contribute to the management of this infection. We describe our own case series and review the cases reported in the literature. Cancer appears as the major underlying disease. The main source of bacteraemia was respiratory. Phenotypic identification methods often misidentify this species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and molecular methods identify at genus level, but species assignment is not reliable. Herbaspirillum spp. showed a highly susceptible antimicrobial profile. β-Lactams showed good activity with low MIC values, except ampicillin. All isolates were resistant to colistin, suggesting an intrinsic resistance mechanism. Herbaspirillum spp. is an uncommon pathogen. MALDI-TOF MS or molecular methods are necessary to achieve a reliable genus identification. These species are not multidrug resistant. Piperacillin/tazobactam or ceftazidime might be a good treatment for this microorganism.

Herbaspirillum Infection in Humans: A Case Report and Review of Literature

Introduction. Herbaspirillum seropedicae are Gram-negative oxidase-positive nonfermenting rods of Betaproteobacteria class, commonly found in rhizosphere. More recently, some Herbaspirillium species have transitioned from environment to human hosts, mostly as opportunistic (pathogenic) bacteria. We present a 58-year-old female with non-small-cell lung cancer (NSCLC) who presented with pneumonia and was found to have Herbaspirillum seropedicae bacteremia. Case History. A 58-year-old woman with NSCLC on Pralsetinib presented with fevers and rigors for 2 days. Coarse breath sounds were auscultated on the right upper lung field. Labs revealed leukopenia and mild neutropenia. CT chest revealed right upper lobe pneumonia. She was admitted for sepsis secondary to pneumonia and placed on broad spectrum antibiotics with intravenous piperacillin-tazobactam and vancomycin. The patient continued to have fever 2 days after admission (max: 102.8°F). Preliminary blood cultures grew Gram-negative rods. The patient continued to have temperature spikes on the 3rd day of antibiotics (T_max 101.5°F). Blood cultures revealed oxidase-positive nonfermenting rods. The patient's antibiotic was changed to IV meropenem on the 4th day of hospitalization. Ultimately, on the seventh day of hospitalization, the blood culture was confirmed from outside lab as Herbaspirillum seropedicae. The patient started feeling better and defervesced after about 24 hours. Discussion. More recently, Herbaspirillum spp. have been recovered from humans. Our patient had Herbaspirillum bacteremia, and reported regularly cleaning her pond and weeding her garden with possible exposure to this environmental proteobacterium. Herbaspirillum may be more prevalent than earlier thought owing to misidentification. With the institution of appropriate antimicrobial therapy, the outcomes seem mostly favorable.