The Role of Bacterial Secretion Systems in the Virulence of Gram-Negative Airway Pathogens Associated with Cystic Fibrosis

The exoS, exoT, exoU and exoY Virulotypes of the Type 3 Secretion System in Multidrug Resistant Pseudomonas aeruginosa as a Death Risk Factor in Pediatric Patients

The poor prognosis of infections associated with multidrug-resistant Pseudomonas aeruginosa can be attributed to several conditions of the patient and virulence factors of the pathogen, such as the type III secretion system (T3SS), which presents the ability to inject four effectors into the host cell: ExoS, ExoT, ExoU and ExoY. The aim of this study was to analyze the distribution of exo genes through multiplex polymerase chain reaction in P. aeruginosa strains isolated from patients at a third-level pediatric hospital and their relationships with clinical variables, e.g., the origin of the sample, susceptibility profile and outcome, through a multinomial logistic regression model. A total of 336 bacterial strains were obtained from cystic fibrosis (CF; n = 55) and bloodstream infection (BSI; n = 281) samples, and eleven presence (+)/absence (-) exo virulotype patterns were identified. The virulotype V3 (exoU-/exoS+/exoT+/exoY+) was observed in 64.28%, followed by V1 (exoU+/exoS-/exoT+/exoY+) with 11.60%. Additionally, V2 (exoU+/exoS-/exoT+/exoY-) was present in 11.60%, and V7 (exoU-/exoS+/exoT+/exoY-) was present in 4.17%. The remaining virulotypes (8.33%) identified were clustered in the other virulotype (OV) group (V4, V5, V6, V8, V9, V10 and V11). The clinical records of 100 patients and their outcomes were reviewed. Fifteen patients died (CF = 4; BSI = 11). V2 and V1 were the virulotypes most related to pandrug resistance (PDR), whereas the V1 relative risk of death was determined to be almost four-fold greater than that of V3, followed by V2 and OV. In summary, the virulotypes V1, V2 and CF are related to death. This study highlights the association of T3SS virulotypes with the susceptibility profile, clinical origin and their potential for predicting a poor prognosis.

Structural determinants of protein kinase A essential for CFTR channel activation

Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), the anion channel mutated in cystic fibrosis (CF) patients, is activated by the catalytic subunit of protein kinase A (PKA-C). PKA-C activates CFTR both noncatalytically, through binding, and catalytically, through phosphorylation of multiple serines in CFTR's regulatory (R) domain. Here, we identify key molecular determinants of the CFTR/PKA-C interaction essential for these processes. By comparing CFTR current activation in the presence of ATP or an ATP analog unsuitable for phosphotransfer, as well as pseudosubstrate peptides of various lengths, we identify two distinct specific regions of the PKA-C surface which interact with CFTR to cause noncatalytic and catalytic CFTR stimulation, respectively. Whereas the "substrate site" mediates CFTR phosphorylation, a distinct hydrophobic patch (the "docking site") is responsible for noncatalytic CFTR activation, achieved by stabilizing the R domain in a "released" conformation permissive to channel gating. Furthermore, by comparing PKA-C variants with different posttranslational modification patterns, we find that direct membrane tethering of the kinase through its N-terminal myristoyl group is an unappreciated fundamental requirement for CFTR activation: PKA-C demyristoylation abolishes noncatalytic, and profoundly slows catalytic, CFTR stimulation. For the F508del CFTR mutant, present in ~90% of CF patients, maximal activation by demyristoylated PKA-C is reduced by ~10-fold compared to that by myristoylated PKA-C. Finally, in bacterial genera that contain common CF pathogens, we identify virulence factors that demyristoylate PKA-C in vitro, raising the possibility that during recurrent bacterial infections in CF patients, PKA-C demyristoylation may contribute to the exacerbation of lung disease.

The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism

Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic "effectors" against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.

Plant-derived virulence arresting drugs as novel antimicrobial agents: Discovery, perspective, and challenges in clinical use

Antimicrobial resistance (AMR) emerges as a severe crisis to public health and requires global action. The occurrence of bacterial pathogens with multi-drug resistance appeals to exploring alternative therapeutic strategies. Antivirulence treatment has been a positive substitute in seeking to circumvent AMR, which aims to target virulence factors directly to combat bacterial infections. Accumulated evidence suggests that plant-derived natural products, which have been utilized to treat infectious diseases for centuries, can be abundant sources for screening potential virulence-arresting drugs (VADs) to develop advanced therapeutics for infectious diseases. This review sums up some virulence factors and their actions in various species of bacteria, as well as recent advances pertaining to plant-derived natural products as VAD candidates. Furthermore, we also discuss natural VAD-related clinical trials and patents, the perspective of VAD-based advanced therapeutics for infectious diseases and critical challenges hampering clinical use of VADs, and genomics-guided identification for VAD therapeutic. These newly discovered natural VADs will be encouraging and optimistic candidates that may sustainably combat AMR.

Genomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh

The increasing antimicrobial resistance in Providencia stuartii (P. stuartii) worldwide, particularly concerning for immunocompromised and burn patients, has raised concern in Bangladesh, where the significance of this infectious opportunistic pathogen had been previously overlooked, prompting a need for investigation. The two strains of P. stuartii (P. stuartii SHNIBPS63 and P. stuartii SHNIBPS71) isolated from wound swab of two critically injured burn patients were found to be multidrug-resistant and P. stuartii SHNIBPS63 showed resistance to all the 22 antibiotics tested as well as revealed the co-existence of blaVEB-6 (Class A), blaNDM-1 (Class B), blaOXA-10 (Class D) beta lactamase genes. Complete resistance to carbapenems through the production of NDM-1, is indicative of an alarming situation as carbapenems are considered to be the last line antibiotic to combat this pathogen. Both isolates displayed strong biofilm-forming abilities and exhibited resistance to copper, zinc, and iron, in addition to carrying multiple genes associated with metal resistance and the formation of biofilms. The study also encompassed a pangenome analysis utilizing a dataset of eighty-six publicly available P. stuartii genomes (n = 86), revealing evidence of an open or expanding pangenome for P. stuartii. Also, an extensive genome-wide analysis of all the P. stuartii genomes revealed a concerning global prevalence of diverse antimicrobial resistance genes, with a particular alarm raised over the abundance of carbapenem resistance gene blaNDM-1. Additionally, this study highlighted the notable genetic diversity within P. stuartii, significant informations about phylogenomic relationships and ancestry, as well as potential for cross-species transmission, raising important implications for public health and microbial adaptation across different environments.

Metal manipulators and regulators in human pathogens: A comprehensive review on microbial redox copper metalloenzymes "multicopper oxidases and superoxide dismutases"

The chemistry of metal ions with human pathogens is essential for their survival, energy generation, redox signaling, and niche dominance. To regulate and manipulate the metal ions, various enzymes and metal chelators are present in pathogenic bacteria. Metalloenzymes incorporate transition metal such as iron, zinc, cobalt, and copper in their reaction centers to perform essential metabolic functions; however, iron and copper have gained more importance. Multicopper oxidases have the ability to perform redox reaction on phenolic substrates with the help of copper ions. They have been reported from Enterobacteriaceae, namely Salmonella enterica, Escherichia coli, and Yersinia enterocolitica, but their role in virulence is still poorly understood. Similarly, superoxide dismutases participate in reducing oxidative stress and allow the survival of pathogens. Their role in virulence and survival is well established in Salmonella typhimurium and Mycobacterium tuberculosis. Further, to ensure survival against stress, like metal starvation or metal toxicity, redox metalloenzymes and metal transportation systems of pathogens actively participate in metal homeostasis. Recently, the omics and protein structure biology studies have helped to predict new targets for regulation the colonization potential of the pathogenic strains. The current review is focused on the major roles of redox metalloenzymes, especially MCOs and SODs of human pathogenic bacteria.

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance

India is one of the largest consumers and producers of antibiotics and a hot spot for the emergence and proliferation of antimicrobial resistance genes (ARGs). Indian hospital wastewater (HWW) accumulates ARGs from source hospitals and often merges with urban wastewater, with the potential for environmental and human contamination. Despite its putative clinical importance, there is a lack of high-resolution resistome profiling of Indian hospital wastewater, with most studies either relying on conventional PCR-biased techniques or being limited to one city. In this study, we comprehensively analyzed antibiotic resistomes of wastewater from six Indian hospitals distributed in rural and urban areas of northern India through shotgun metagenomics. Our study revealed the predominance of ARGs against aminoglycoside, macrolide, carbapenem, trimethoprim, and sulfonamide antibiotics in all the samples through both read-based analysis and assembly-based analysis. We detected the mobile colistin resistance gene mcr-5.1 for the first time in Indian hospital sewage. blaNDM-1 was present in 4 out of 6 samples and was carried by Pseudomonas aeruginosa in HWW-2, Klebsiella pneumoniae in HWW-4 and HWW-6, and Acinetobacter baumanii in HWW-5. Most ARGs were plasmid-mediated and hosted by Proteobacteria. We identified virulence factors and transposable elements flanking the ARGs, highlighting the role of horizontal gene transmission of ARGs. IMPORTANCE There is a paucity of research on detailed antibiotic resistome and microbiome diversity of Indian hospital wastewater. This study reports the predominance of clinically concerning ARGs such as the beta-lactamases blaNDM and blaOXA and the colistin resistance gene mcr and their association with the microbiome in six different Indian hospital wastewaters of both urban and rural origin. The abundance of plasmid-mediated ARGs and virulence factors calls for urgent AMR crisis management. The lack of proper wastewater management strategies meeting international standards and open drainage systems further complicates the problem of containing the ARGs at these hospitals. This metagenomic study presents the current AMR profile propagating in hospital settings in India and can be used as a reference for future surveillance and risk management of ARGs in Indian hospitals.

SurA-like and Skp-like Proteins as Important Virulence Determinants of the Gram Negative Bacterial Pathogens

In the Gram-negative bacteria, many important virulence factors reach their destination via two-step export systems, and they must traverse the periplasmic space before reaching the outer membrane. Since these proteins must be maintained in a structure competent for transport into or across the membrane, they frequently require the assistance of chaperones. Based on the results obtained for the model bacterium Escherichia coli and related species, it is assumed that in the biogenesis of the outer membrane proteins and the periplasmic transit of secretory proteins, the SurA peptidyl-prolyl isomerase/chaperone plays a leading role, while the Skp chaperone is rather of secondary importance. However, detailed studies carried out on several other Gram-negative pathogens indicate that the importance of individual chaperones in the folding and transport processes depends on the properties of client proteins and is species-specific. Taking into account the importance of SurA functions in bacterial virulence and severity of phenotypes due to surA mutations, this folding factor is considered as a putative therapeutic target to combat microbial infections. In this review, we present recent findings regarding SurA and Skp proteins: their mechanisms of action, involvement in processes related to virulence, and perspectives to use them as therapeutic targets.

Functional Annotation of Hypothetical Proteins From the Enterobacter cloacae B13 Strain and Its Association With Pathogenicity

Enterobacter cloacae B13 strain is a rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. It can cause respiratory and urinary tract infections, and is responsible for several outbreaks in hospitals. E. cloacae has become an important pathogen and an emerging global threat because of its opportunistic and multidrug resistant ability. However, little knowledge is present about a large portion of its proteins and functions. Therefore, functional annotation of the hypothetical proteins (HPs) can provide an improved understanding of this organism and its virulence activity. The workflow in the study included several bioinformatic tools which were utilized to characterize functions, family and domains, subcellular localization, physiochemical properties, and protein-protein interactions. The E. cloacae B13 strain has overall 604 HPs, among which 78 were functionally annotated with high confidence. Several proteins were identified as enzymes, regulatory, binding, and transmembrane proteins with essential functions. Furthermore, 23 HPs were predicted to be virulent factors. These virulent proteins are linked to pathogenesis with their contribution to biofilm formation, quorum sensing, 2-component signal transduction or secretion. Better knowledge about the HPs’ characteristics and functions will provide a greater overview of the proteome. Moreover, it will help against E. cloacae in neonatal intensive care unit (NICU) outbreaks and nosocomial infections.

Host–Bacterial Interactions: Outcomes of Antimicrobial Peptide Applications

The bacterial membrane is part of a secretion system which plays an integral role to secrete proteins responsible for cell viability and pathogenicity; pathogenic bacteria, for example, secrete virulence factors and other membrane-associated proteins to invade the host cells through various types of secretion systems (Type I to Type IX). The bacterial membrane can also mediate microbial communities’ communication through quorum sensing (QS), by secreting auto-stimulants to coordinate gene expression. QS plays an important role in regulating various physiological processes, including bacterial biofilm formation while providing increased virulence, subsequently leading to antimicrobial resistance. Multi-drug resistant (MDR) bacteria have emerged as a threat to global health, and various strategies targeting QS and biofilm formation have been explored by researchers worldwide. Since the bacterial secretion systems play such a crucial role in host–bacterial interactions, this review intends to outline current understanding of bacterial membrane systems, which may provide new insights for designing approaches aimed at antimicrobials discovery. Various mechanisms pertaining interaction of the bacterial membrane with host cells and antimicrobial agents will be highlighted, as well as the evolution of bacterial membranes in evasion of antimicrobial agents. Finally, the use of antimicrobial peptides (AMPs) as a cellular device for bacterial secretion systems will be discussed as emerging potential candidates for the treatment of multidrug resistance infections.

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

The transcriptional regulatory network (TRN) of Pseudomonas aeruginosa coordinates cellular processes in response to stimuli. We used 364 transcriptomes (281 publicly available + 83 in-house generated) to reconstruct the TRN of P. aeruginosa using independent component analysis. We identified 104 independently modulated sets of genes (iModulons) among which 81 reflect the effects of known transcriptional regulators. We identified iModulons that (i) play an important role in defining the genomic boundaries of biosynthetic gene clusters (BGCs), (ii) show increased expression of the BGCs and associated secretion systems in nutrient conditions that are important in cystic fibrosis, (iii) show the presence of a novel ribosomally synthesized and post-translationally modified peptide (RiPP) BGC which might have a role in P. aeruginosa virulence, (iv) exhibit interplay of amino acid metabolism regulation and central metabolism across different carbon sources and (v) clustered according to their activity changes to define iron and sulfur stimulons. Finally, we compared the identified iModulons of P. aeruginosa with those previously described in Escherichia coli to observe conserved regulons across two Gram-negative species. This comprehensive TRN framework encompasses the majority of the transcriptional regulatory machinery in P. aeruginosa, and thus should prove foundational for future research into its physiological functions.

Pathogenic arsenal of Pseudomonas aeruginosa: an update on virulence factors

The emergence of Pseudomonas aeruginosa as a potential threat in persistent infections can be attributed to the plethora of virulence factors expressed by it. This review discusses the various virulence factors that help this pathogen to establish an infection and regulatory systems controlling these virulence factors. Cell-associated virulence factors such as flagella, type IV pili and non-pilus adhesins have been reviewed. Extracellular virulence factors have also been explained. Quorum-sensing systems present in P. aeruginosa play a cardinal role in regulating the expression of virulence factors. The identification of novel virulence factors in hypervirulent strains indicate that the expression of virulence is dynamic and constantly evolving. An understanding of this is critical for the better clinical management of infections.

An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion

Bacterial biofilms represent multicellular communities embedded in a matrix of extracellular polymeric substances, conveying increased resistance against environmental stress factors but also antibiotics. They are shaped by secreted enzymes such as proteases, which can aid pathogenicity by degrading host proteins of the connective tissue or the immune system. Importantly, both secreted proteases and the capability of biofilm formation are considered key virulence factors. In this review, we focus on the basic aspects of proteolysis and protein secretion, and highlight various secreted bacterial proteases involved in biofilm establishment and dispersal, and how they aid bacteria in immune evasion by degrading immunoglobulins and components of the complement system. Thus, secreted proteases represent not only prominent antimicrobial targets but also enzymes that can be used for dedicated applications in biotechnology and biomedicine, including their use as laundry detergents, in mass spectrometry for the glycoprofiling of antibodies, and the desensitization of donor organs intended for positive crossmatch patients.

Characteristics of the sputum microbiome in COPD exacerbations and correlations between clinical indices

Background

Chronic obstructive pulmonary disease (COPD) is a prevalent, progressive respiratory disease, and acute exacerbations of COPD (AECOPD) can accelerate the deterioration of the disease. Increasing evidence suggests that airway bacterial dysbiosis is associated with AECOPD. However, the exact relationship between changes in the sputum microbiome during AECOPD and clinical indices remains unclear.

Methods

In this study, a total of 76 sputum samples were collected from patients with AECOPD (n = 28), stable COPD (n = 23), recovery (n = 15) and healthy controls (HCs; n = 10). The sputum microbiome profile was analysed by sequencing the V3‑V4 amplicon of the 16S rRNA (ribosomal RNA) gene.

Results

The bacterial diversity (Shannon and Simpson’s index) was found to be significantly decreased in the AECOPD and recovery groups when compared to that in the stable COPD and HC groups. The most dominant phylum identified in the sputum samples of AECOPD patients was Proteobacteria, accounting for 30% of the microbiome. Compared to the stable COPD groups, the relative abundances of Firmicutes and Bacteroidetes were decreased, whereas those of Proteobacteria and Actinobacteria were increased in AECOPD patients. Furthermore, discriminative bacteria, such as Haemophilus, were identified as being specific taxa in AECOPD patients. Functional analysis showed that genes involved in membrane transport and signal transduction metabolism were enriched in the AECOPD group. Importantly, the proportions of Veillonella were positively correlated with lung function, and Staphylococcus was positively correlated with inflammatory indices.

Conclusion

Our study revealed variations in the sputum microbiome of AECOPD (based on composition and function) in a Chinese cohort and highlighted its correlation to clinical indices. These results indicated that microbial dysbiosis may contribute to disease progression and provide microbial biomarkers for the diagnosis of AECOPD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03278-x.

Identification of genes involved in exoprotein release using a high-throughput exoproteome screening assay in Yersinia entomophaga

Bacterial protein secretion is crucial to the maintenance of viability and pathogenicity. Although many bacterial secretion systems have been identified, the underlying mechanisms regulating their expression are less well explored. Yersinia entomophaga MH96, an entomopathogenic bacterium, releases an abundance of proteins including the Yen-Tc into the growth medium when cultured in Luria Bertani broth at ≤ 25°C. Through the development of a high-throughput exoproteome screening assay (HESA), genes involved in MH96 exoprotein production were identified. Of 4,080 screened transposon mutants, 34 mutants exhibited a decreased exoprotein release, and one mutation located in the intergenic region of the Yen-Tc operon displayed an elevated exoprotein release relative to the wild-type strain MH96. DNA sequencing revealed several transposon insertions clustered in gene regions associated with lipopolysaccharide (LPSI and LPSII), and N-acyl-homoserine lactone synthesis (quorum sensing). Twelve transposon insertions were located within transcriptional regulators or intergenic regions. The HESA will have broad applicability for identifying genes associated with exoproteome production in a range of microorganisms.

Characteristics in gut microbiome is associated with chemotherapy-induced pneumonia in pediatric acute lymphoblastic leukemia

Background

Children with acute lymphoblastic leukemia (ALL) undergoing chemotherapy experience a relatively high risk of infection. And the disturbance of gut microbiota is generally believed to impair intestinal barrier function and may induce bacterial infections and inflammation. The study aimed to investigate the alterations in the gut microbiota and assess its relationship with chemotherapy-induced pneumonia in pediatric ALL patients.

Methods

We conducted a case–control study with 14 cases affected by pneumonia and 44 unaffected subjects and characterized the physiological parameters and gut microbiota by microarray-based technique.

Results

There were significant differences in α- and β-diversity in the affected group compared with the control group. At species level, the LEfSe analysis revealed that Enterococcus malodoratus, Ochrobactrum anthropi and Actinomyces cardiffensis were significantly abundant in the affected subjects. A receiver operating characteristic (ROC) curve yielded the area under the curve (AUC) of 0.773 for classification between the two groups. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways involved in the bacterial secretion system were more enriched in the affected group than in the control group.

Conclusions

Gut microbiota alteration was associated with chemotherapy-induced pneumonia in pediatric ALL patients, which provided a new perspective on the personalized clinical care of pediatric ALL.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08917-y.

Extracellular Proteome Analysis Shows the Abundance of Histidine Kinase Sensor Protein, DNA Helicase, Putative Lipoprotein Containing Peptidase M75 Domain and Peptidase C39 Domain Protein in Leptospira interrogans Grown in EMJH Medium

Leptospirosis is a re-emerging form of zoonosis that is caused by the spirochete pathogen Leptospira. Extracellular proteins play critical roles in the pathogenicity and survival of this pathogen in the host and environment. Extraction and analysis of extracellular proteins is a difficult task due to the abundance of enrichments like serum and bovine serum albumin in the culture medium, as is distinguishing them from the cellular proteins that may reach the analyte during extraction. In this study, extracellular proteins were separated as secretory proteins from the culture supernatant and surface proteins were separated during the washing of the cell pellet. The proteins identified were sorted based on the proportion of the cellular fractions and the extracellular fractions. The results showed the identification of 56 extracellular proteins, out of which 19 were exclusively extracellular. For those proteins, the difference in quantity with respect to their presence within the cell was found to be up to 1770-fold. Further, bioinformatics analysis elucidated characteristics and functions of the identified proteins. Orthologs of extracellular proteins in various Leptospira species were found to be closely related among different pathogenic forms. In addition to the identification of extracellular proteins, this study put forward a method for the extraction and identification of extracellular proteins.

Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases

The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesize that microbiome diversity and composition, and their genomic features are associated with different pathological conditions of these human respiratory tract diseases. To test this hypothesis, we analyzed 21 RNASeq metagenomic data including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the microbiome diversity and related genomic metabolic functions. The metagenomic data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19 > COPD > URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively. However, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID samples, respectively, and of them 34.50% strains shared between the conditions. Functional annotation of the metagenomic data identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, virulence, disease and defense, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, we detected comparatively higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful in developing microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.

The involvement of PacIRA system of Stenotrophomonas maltophilia in the uptake of Pseudomonas aeruginosa pyochelin and intraspecies competition for iron acquisition

BACKGROUND

Stenotrophomonas maltophilia, a species of highly genetic diversity, has emerged as an important nosocomial pathogen. S. maltophilia and Pseudomonas aeruginosa are often co-isolated from pneumonia patients. In our previous study, we have demonstrated that the pacIRA cluster present in some but not all clinical S. maltophilia isolates. Proteins encoded by pacIRA operon are an extracytoplasmic function (ECF) sigma factor, a transmembrane anti-sigma regulator, and a TonB-dependent receptor. This study aimed to elucidate PacIRA system function and its significance to S. maltophilia.

METHODS

The pacI, pacR, and pacA genes were individually or totally deleted from the chromosome of KJΔEnt, a pacIRA-positive and siderophore-null strain. Growth promotion assay was performed to examine the implication of pacIRA system in iron utilization. Gene expression was quantified by quantitative real time PCR (qRT-PCR). Growth competition assay was executed to investigate the significance of pacIRA operon to S. maltophilia.

RESULTS

PacIRA system contributed to utilize ferri-pyochelin of P. aeruginosa as iron sources for growth in an iron-depleted condition, but hardly utilized ferric citrate, hemin, ferri-stenobactin, and ferri-pyoverdine. PacIRA was founded to belong to Fur regulon and upregulated in response to iron-depleted stress. Growth competition assay demonstrated that pacIRA-positive S. maltophilia had a superiority over pacIRA-negative S. maltophilia in iron acquisition when they were co-cultured in P. aeruginosa ferri-pyochelin-supplemented medium.

CONCLUSIONS

PacIRA system of S. maltophilia is a xenosiderophore uptake implement, involving in the acquisition of pyochelin of P. aeruginosa.

Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa

OBJECTIVES

Klebsiella michiganensis is an emerging pathogen implicated in nosocomial infections. Here we report on the resistome, virulome and mobilome of a carbapenemase-producing K. michiganensis isolate from urban hospital effluent in Pietermaritzburg, KwaZulu-Natal, South Africa. Klebsiella sp. isolate KP124 was originally isolated from the final effluent of an urban tertiary hospital in Pietermaritzburg, KwaZulu-Natal.

METHODS

Following phenotypic characterisation and antibiotic susceptibility testing, the genome of carbapenemase-producing isolate KP124 was sequenced using an Illumina MiSeq platform, de novo assembled and analysed using established bioinformatics tools.

RESULTS

The draft genome of strain KP124 was 6 544 586 bp in length, comprising 203 contigs >200 bp. Following confirmation of isolate KP124 as K. michiganensis using reference genomes, the bla_OXA-181 carbapenemase gene as well as 11 additional genes encoding resistance against β-lactams, aminoglycosides, fluoroquinolones and sulfonamides were detected. Virulence factors enabling iron acquisition and cell adherence, capsule locus type and plasmid replicon types were identified.

CONCLUSION

This study represents the first report of an OXA-181 carbapenemase-producing K. michiganensis isolate from hospital effluent in South Africa. The presence of such a strain in the environment owing to the absence of hospital effluent treatment presents a potential risk to informal communities that may use contaminated surface water domestically.

Review of Potential Pseudomonas Weaponry, Relevant to the Pseudomonas-Aspergillus Interplay, for the Mycology Community

Pseudomonas aeruginosa is one of the most prominent opportunistic bacteria in airways of cystic fibrosis patients and in immunocompromised patients. These bacteria share the same polymicrobial niche with other microbes, such as the opportunistic fungus Aspergillus fumigatus. Their inter-kingdom interactions and diverse exchange of secreted metabolites are responsible for how they both fare in competition for ecological niches. The outcomes of their contests likely determine persistent damage and degeneration of lung function. With a myriad of virulence factors and metabolites of promising antifungal activity, P. aeruginosa products or their derivatives may prove useful in prophylaxis and therapy against A. fumigatus. Quorum sensing underlies the primary virulence strategy of P. aeruginosa, which serves as cell–cell communication and ultimately leads to the production of multiple virulence factors. Understanding the quorum-sensing-related pathogenic mechanisms of P. aeruginosa is a first step for understanding intermicrobial competition. In this review, we provide a basic overview of some of the central virulence factors of P. aeruginosa that are regulated by quorum-sensing response pathways and briefly discuss the hitherto known antifungal properties of these virulence factors. This review also addresses the role of the bacterial secretion machinery regarding virulence factor secretion and maintenance of cell–cell communication.

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

BACKGROUND

The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection.

RESULTS

Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes.

CONCLUSIONS

This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza. Video abstract.

Tolerability of inhaled N-chlorotaurine in humans: a double-blind randomized phase I clinical study

BACKGROUND

N-chlorotaurine (NCT), a long-lived oxidant produced by human leukocytes, can be synthesized chemically and used topically as a well-tolerated antiseptic to different body regions including sensitive ones. The aim of this study was to test the tolerability of inhaled 1% NCT in aqueous solution upon repeated application.

METHODS

The study was performed double-blind and randomized with a parallel test group (1% NCT) and control group (0.9% NaCl as placebo). There were two Austrian centres involved, the hospitals, Natters and Vöcklabruck. Healthy, full age volunteers were included, 12 in each centre. A total of 12 patients were treated with NCT, and 12 with placebo, exactly half of each group from each centre. The single dose was 1.2 ml inhaled over a period of 10 min using an AKITA JET nebulizer. One inhalation was done every day for five consecutive days. The primary criterion of evaluation was the forced expiratory volume in 1 second (FEV₁). Secondary criteria were subjective sensations, further lung function parameters such as airway resistance, physical examination, and blood analyses (gases, electrolytes, organ function values, pharmacokinetic parameters taurine and methionine, immune parameters).

RESULTS

All included 15 females and 9 males completed the treatment and the control examinations according to the study protocol. FEV₁ (100.83% ± 8.04% for NCT and 92.92% ± 11.35% for controls) remained unchanged and constant during the treatment and in control examinations 1 week and 3 months after the treatment (98.75% ± 7.37% for NCT and 91.17% ± 9.46% for controls, p > 0.082 between time points within each group). The same was true for all other objective parameters. Subjective mild sensations with a higher frequency in the test group were chlorine taste ( p < 0.01) and occasional tickle in the throat ( p = 0.057). Taurine and methionine plasma concentrations did not change within 60 min after inhalation or later on.

CONCLUSIONS

Inhaled NCT is well tolerated as in other applications of different body regions. Side effects are mild, topical and transitory. The study was registered prospectively in the European Clinical Trials Database of the European Medicines Agency. The EudraCT number is 2012-003700-12.

Bartonella Species, an Emerging Cause of Blood-Culture-Negative Endocarditis

Since the reclassification of the genus Bartonella in 1993, the number of species has grown from 1 to 45 currently designated members. Likewise, the association of different Bartonella species with human disease continues to grow, as does the range of clinical presentations associated with these bacteria. Among these, blood-culture-negative endocarditis stands out as a common, often undiagnosed, clinical presentation of infection with several different Bartonella species. The limitations of laboratory tests resulting in this underdiagnosis of Bartonella endocarditis are discussed. The varied clinical picture of Bartonella infection and a review of clinical aspects of endocarditis caused by Bartonella are presented. We also summarize the current knowledge of the molecular basis of Bartonella pathogenesis, focusing on surface adhesins in the two Bartonella species that most commonly cause endocarditis, B. henselae and B. quintana. We discuss evidence that surface adhesins are important factors for autoaggregation and biofilm formation by Bartonella species. Finally, we propose that biofilm formation is a critical step in the formation of vegetative masses during Bartonella-mediated endocarditis and represents a potential reservoir for persistence by these bacteria.

Bactericidal and Fungicidal Activity of N-Chlorotaurine Is Enhanced in Cystic Fibrosis Sputum Medium

Lung infections with multiresistant pathogens are a major problem among patients suffering from cystic fibrosis (CF). N-Chlorotaurine (NCT), a microbicidal active chlorine compound with no development of resistance, is well tolerated upon inhalation. The aim of this study was to investigate the in vitro bactericidal and fungicidal activity of NCT in artificial sputum medium (ASM), which mimics the composition of CF mucus. The medium was inoculated with bacteria (Staphylococcus aureus, including some methicillin-resistant S. aureus [MRSA] strains, Pseudomonas aeruginosa, and Escherichia coli) or spores of fungi (Aspergillus fumigatus, Aspergillus terreus, Candida albicans, Scedosporium apiospermum, Scedosporium boydii, Lomentospora prolificans, Scedosporium aurantiacum, Scedosporium minutisporum, Exophiala dermatitidis, and Geotrichum sp.), to final concentrations of 10⁷ to 10⁸ CFU/ml. NCT was added at 37°C, and time-kill assays were performed. At a concentration of 1% (10 mg/ml, 55 mM) NCT, bacteria and spores were killed within 10 min and 15 min, respectively, to the detection limit of 10² CFU/ml (reduction of 5 to 6 log₁₀ units). Reductions of 2 log₁₀ units were still achieved with 0.1% (bacteria) and 0.3% (fungi) NCT, largely within 10 to 30 min. Measurements by means of iodometric titration showed oxidizing activity for 1, 30, 60, and >60 min at concentrations of 0.1%, 0.3%, 0.5%, and 1.0% NCT, respectively, which matches the killing test results. NCT demonstrated broad-spectrum microbicidal activity in the milieu of CF mucus at concentrations ideal for clinical use. The microbicidal activity of NCT in ASM was even stronger than that in buffer solution; this was particularly pronounced for fungi. This finding can be explained largely by the formation, through transhalogenation, of monochloramine, which rapidly penetrates pathogens.

E. coli Group 1 Capsular Polysaccharide Exportation Nanomachinary as a Plausible Antivirulence Target in the Perspective of Emerging Antimicrobial Resistance

Bacteria evolving resistance against the action of multiple drugs and its ability to disseminate the multidrug resistance trait(s) across various strains of the same bacteria or different bacterial species impose serious threat to public health. Evolution of such multidrug resistance is due to the fact that, most of the antibiotics target bacterial survival mechanisms which exert selective pressure on the bacteria and aids them to escape from the action of antibiotics. Nonetheless, targeting bacterial virulence strategies such as bacterial surface associated polysaccharides biosynthesis and their surface accumulation mechanisms may be an attractive strategy, as they impose less selective pressure on the bacteria. Capsular polysaccharide (CPS) or K-antigen that is located on the bacterial surface armors bacteria from host immune response. Thus, unencapsulating bacteria would be a good strategy for drug design, besides CPS itself being a good vaccine target, by interfering with CPS biosynthesis and surface assembly pathway. Gram-negative Escherichia coli uses Wzy-polymerase dependent (Groups 1 and 4) and ATP dependent (Groups 1 and 3) pathways for CPS production. Considering E. coli as a case in point, this review explains the structure and functional roles of proteins involved in Group 1 Wzy dependent CPS biosynthesis, surface expression and anchorage in relevance to drug and vaccine developments.