Quantitative proteome profiling of C. burnetii under tetracycline stress conditions

Entomopathogenic fungus treatment changes the gut bacterial diversity of Rhipicephalus microplus ticks

BACKGROUND

Ticks are obligate bloodsucking parasites responsible for significant economic losses and concerns with human and animal health, mainly due to the transmission of pathogens. Entomopathogenic fungi have been intensively studied as an alternative strategy for tick control that can be used in combination with synthetic acaricides in the integrated management of ticks. Here, we investigated how the gut bacterial community of Rhipicephalus microplus is shaped after Metarhizium anisopliae treatment and how the tick susceptibility to the fungus is affected after disrupting gut bacterial microbiota.

METHODS

Partially engorged tick females were artificially fed with pure bovine blood or blood plus tetracycline. Two other groups received the same diet and were topically treated with M. anisopliae. The guts were dissected, and the genomic DNA was extracted 3 days after the treatment; the V3-V4 variable region of the bacterial 16S rRNA gene was amplified.

RESULTS

The gut of ticks that received no antibiotic but were treated with M. anisopliae exhibited lower bacterial diversity and a higher occurrence of Coxiella species. The Simpson diversity index and Pielou equability coefficient were higher in the gut bacterial community when R. microplus were fed with tetracycline and fungus-treated. Ticks from fungus-treated groups (with or without tetracycline) exhibited lower survival than untreated females. Previous feeding of ticks with the antibiotic did not change their susceptibility to the fungus. Ehrlichia spp. were not detected in the gueated groups.

CONCLUSIONS

These findings suggest that myco-acaricidal action would not be impacted if the calf hosting these ticks is under antibiotic therapy. Moreover, the hypothesis that entomopathogenic fungi can affect the bacterial community in the gut of R. microplus engorged females is endorsed by the fact that ticks exposed to M. anisopliae exhibited a dramatic reduction in bacterial diversity. This is the first report of an entomopathogenic fungus affecting the tick gut microbiota.

Pathogenic and Endosymbiotic Bacteria and Their Associated Antibiotic Resistance Biomarkers in Amblyomma and Hyalomma Ticks Infesting Nguni Cattle (Bos spp.)

Deciphering the interactions between ticks and their microbiome is key to revealing new insights on tick biology and pathogen transmission. However, knowledge on tick-borne microbiome diversity and their contribution to drug resistance is scarce in sub–Saharan Africa (SSA), despite endemism of ticks. In this study, high-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used to characterize the bacterial community structure and associated antibiotic resistance markers in Amblyomma variegatum, A. hebraeum, and Hyalomma truncatum ticks infesting Nguni cattle (Bos spp.). Twenty-one (seven families and fourteen genera) potentially pathogenic and endosymbiotic bacterial taxa were differentially enriched in two tick genera. In H. truncatum ticks, a higher abundance of Corynebacterium (35.6%), Porphyromonas (14.4%), Anaerococcus (11.1%), Trueperella (3.7%), and Helcococcus (4.7%) was detected. However, Rickettsia (38.6%), Escherichia (7%), and Coxiellaceae (2%) were the major differentially abundant taxa in A. variegatum and A. hebraeum. Further, an abundance of 50 distinct antibiotic resistance biomarkers relating to multidrug resistance (MDR) efflux pumps, drug detoxification enzymes, ribosomal protection proteins, and secretion systems, were inferred in the microbiome. This study provides theoretical insights on the microbiome and associated antibiotic resistance markers, important for the design of effective therapeutic and control decisions for tick-borne diseases in the SSA region.

Proteomic and Transcriptomic Analyses Indicate Reduced Biofilm-Forming Abilities in Cefiderocol-Resistant Klebsiella pneumoniae

The advent of cefiderocol provides hope for the clinical treatment of multi-drug resistant gram-negative bacteria (GNB), especially those with carbapenem resistance. Resistance of Klebsiella pneumoniae to cefiderocol can be enhanced by acclimatization. In the present study, we collected cefiderocol resistant K. pneumoniae isolates during a 36-day acclimatization procedure while increasing the cefiderocol concentration in the culture medium. Strains were studied for changes in their biological characteristics using proteomics and transcriptomics. A decrease in biofilm formation ability was the main change observed among the induced isolates. Downregulation of genes involved in biofilm formation including hdeB, stpA, yhjQ, fba, bcsZ, uvrY, bcsE, bcsC, and ibpB were the main factors that reduced the biofilm formation ability. Moreover, downregulation of siderophore transporter proteins including the iron uptake system component efeO, the tonB-dependent receptor fecA, and ferric iron ABC transporter fbpA may be among the determining factors leading to cefiderocol resistance and promoting the reduction of biofilm formation ability of K. pneumoniae. This is the first study to investigate cefiderocol resistance based on comprehensive proteomic and transcriptomic analyses.

Relevance of peroxiredoxins in pathogenic microorganisms

The oxidative and nitrosative responses generated by animals and plants are important defenses against infection and establishment of pathogenic microorganisms such as bacteria, fungi, and protozoa. Among distinct oxidant species, hydroperoxides are a group of chemically diverse compounds that comprise small hydrophilic molecules, such as hydrogen peroxide and peroxynitrite, and bulky hydrophobic species, such as organic hydroperoxides. Peroxiredoxins (Prx) are ubiquitous enzymes that use a highly reactive cysteine residue to decompose hydroperoxides and can also perform other functions, like molecular chaperone and phospholipase activities, contributing to microbial protection against the host defenses. Prx are present in distinct cell compartments and, in some cases, they can be secreted to the extracellular environment. Despite their high abundance, Prx expression can be further increased in response to oxidative stress promoted by host defense systems, by treatment with hydroperoxides or by antibiotics. In consequence, some isoforms have been described as virulence factors, highlighting their importance in pathogenesis. Prx are very diverse and are classified into six different classes (Prx1-AhpC, BCP-PrxQ, Tpx, Prx5, Prx6, and AhpE) based on structural and biochemical features. Some groups are absent in hosts, while others present structural peculiarities that differentiate them from the host's isoforms. In this context, the intrinsic characteristics of these enzymes may aid the development of new drugs to combat pathogenic microorganisms. Additionally, since some isoforms are also found in the extracellular environment, Prx emerge as attractive targets for the production of diagnostic tests and vaccines. KEY POINTS: • Peroxiredoxins are front-line defenses against host oxidative and nitrosative stress. • Functional and structural peculiarities differ pathogen and host enzymes. • Peroxiredoxins are potential targets to microbicidal drugs.

Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges

Research to discover and develop antibacterial and antiviral drugs with potent activity against pathogens of biothreat concern presents unique methodological and process-driven challenges. Herein, we review laboratory approaches for finding new antibodies, antibiotics, and antiviral molecules for pathogens of biothreat concern. Using high-throughput screening techniques, molecules that directly inhibit a pathogen’s entry, replication, or growth can be identified. Alternatively, molecules that target host proteins can be interesting targets for development when countering biothreat pathogens, due to the modulation of the host immune response or targeting proteins that interfere with the pathways required by the pathogen for replication. Monoclonal and cocktail antibody therapies approved by the Food and Drug Administration for countering anthrax and under development for treatment of Ebola virus infection are discussed. A comprehensive tabular review of current in vitro, in vivo, pharmacokinetic and efficacy datasets has been presented for biothreat pathogens of greatest concern. Finally, clinical trials and animal rule or traditional drug approval pathways are also reviewed.

Opinions; interpretations; conclusions; and recommendations are those of the authors and are not necessarily endorsed by the US Army.

Proteomics approach to understand bacterial antibiotic resistance strategies

Introduction: The understanding of novel antibiotic resistance mechanisms is essential to develop strategies against antibiotic-resistant pathogens, which has become an urgent task due to the worldwide emergence of antibiotic resistance. Areas covered: In this review, the authors summarize the recent progress on antibiotic resistance caused by lab-evolved bacteria and clinical multidrug-resistant bacterial pathogens from the proteomics perspective. Expert opinion: Proteomics provides a new platform for a comprehensive understanding of change in protein pathways that are engaged in antibiotics resistance, which is different from a genetic view that focuses on the role of an individual gene or protein. Further work is required to understand why and how the involved pathways are integrated for surviving antibiotic-mediated killing, to use other OMICs for better comprehension of antibiotic resistance mechanisms, and to develop reprogramming proteomics, which reverts an 'antibiotic resistance proteome' to an 'antibiotic sensitive or antibiotic sensitive-like' proteome, for the control of antibiotic-resistant pathogens.

Proteomic analysis revealed the survival strategy of Coxiella burnetii to doxycycline exposure

Antibiotic resistance is a global threat with a top concern in healthcare. Doxycycline is an antibiotic highly permeable to cell membrane used for treating a broad variety of bacteria, including Coxiella burnetii. This intracellular pathogen is the causative agent of Q fever, a re-emerging zoonosis found worldwide. Hence, C. burnetii has a considerable impact on the farming industry and public health, it is essential to explore its antibiotic adaptation/tolerance strategy to ensure effective therapy. Herein, we tracked changes in the bacterium induced by doxycycline exposure. Our proteomic analysis detected fifteen significantly altered proteins. Adjustments of some key proteins were verified by gene expression analysis. We also observed an increasing in hydrogen peroxide as a consequence of treatment, indicating deregulation of redox balance. Thus, our data suggests the reduction of protein synthesis to minimal levels, activation of the defense mechanism against oxidative stress and maintenance of cell envelope integrity as the key processes ensuring C. burnetii survival under doxycycline exposure. SIGNIFICANCE: Infection by intracellular microorganisms like C. burnetii requires long periods of treatment, thus antibiotic resistance development is a risk. In this report, 2-DE quantitative proteomics was used to identify changes in the proteome that occurs when C. burnetii is exposed to high concentrations of doxycycline. The identification of pathways impacted by doxycycline could be helpful to understand the mechanism of how C. burnetii is dealing with antibiotic stress.

The effect of measuring serum doxycycline concentrations on clinical outcomes during treatment of chronic Q fever

Background

First choice treatment for chronic Q fever is doxycycline plus hydroxychloroquine. Serum doxycycline concentration (SDC) >5 μg/mL has been associated with a favourable serological response, but the effect on clinical outcomes is unknown.

Objectives

To assess the effect of measuring SDC during treatment of chronic Q fever on clinical outcomes.

Methods

We performed a retrospective cohort study, to assess the effect of measuring SDC on clinical outcomes in patients treated with doxycycline and hydroxychloroquine for chronic Q fever. Primary outcome was the first disease-related event (new complication or chronic Q fever-related mortality); secondary outcomes were all-cause mortality and PCR-positivity. Multivariable analysis was performed with a Cox proportional hazards model, with shared-frailty terms for different hospitals included.

Results

We included 201 patients (mean age 68 years, 83% male): in 167 patients (83%) SDC was measured, 34 patients (17%) were treated without SDC measurement. First SDC was >5 μg/mL in 106 patients (63%), all with 200 mg doxycycline daily. In patients with SDC measured, dosage was adjusted in 41% (n = 68), concerning an increase in 64 patients. Mean SDC was 4.1 μg/mL before dosage increase, and 5.9 μg/mL afterwards. SDC measurement was associated with a lower risk for disease-related events (HR 0.51, 95% CI 0.26-0.97, P = 0.04), but not with all-cause mortality or PCR-positivity.

Conclusions

SDC measurement decreases the risk for disease-related events, potentially through more optimal dosing or improved compliance. We recommend measurement of SDC and striving for SDC >5 μg/mL and <10 μg/mL during treatment of chronic Q fever.

Genotyping of Coxiella burnetii in sheep and goat abortion samples

Background

Q fever, caused by Coxiella burnetii, is a zoonosis that presents a worldwide distribution and affects both humans and animals. The route of dispersal of the pathogen by ruminants into the environment usually involves stages of abortion and parturition, nevertheless the agent can, also, be detected in other animal samples. Therefore it is considered as important in terms of proper diagnosis, as well as, for epidemiology and surveillance purposes, to genotype the pathogen. The aim of the current study was to investigate the presence of different genotypes of the agent in animals that had suffered from abortion during a two-year survey in Greece.

Results

Sixty nine tissue samples (37 stomach contents, 11 liver samples, 21 cotyledons) were collected from 59 abortion cases in sheep (N = 45) and goats (N = 14) from 65 farms at eight different areas of Greece. Samples were screened by qPCR and positive ones were further genotyped using a 10-locus multiple loci (ms 1, 3, 7, 12, 20, 21, 22, 26, 30 and 36) variable number of tandem repeat analysis (MLVA) method.

Three genotypes were identified in sheep (A, B, C). Samples representing each of the obtained MLVA profile were further used for MST genotyping. Ten spacers (Cox 2, 5, 6, 18, 20, 22, 37, 51, 56 and 57) were amplified. A close relatedness among the identified MLVA genotypes was confirmed since they all belonged to MST group 32.

Conclusions

The current study introduces into the aspect of genotyping of C. burnetii in Greece. Further studies are needed to explore the presence of more genotypes, to associate the genotypes circulating in the animal and tick population with those causing human disease in order to further expand on the epidemiological aspects of the pathogen.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1353-y) contains supplementary material, which is available to authorized users.

Stress response of Escherichia coli to essential oil components - insights on low-molecular-weight proteins from MALDI-TOF

The antibacterial effects of essential oils and their components (EOCs) are usually attributed to effects on membranes and metabolism. Studies of the effects of EOCs on protein expression have primarily analysed proteins larger than 10 kDa using gel electrophoresis. In the present study, we used MALDI-TOF-MS to investigate the effects of EOCs on low-molecular-weight proteins. From 297 m/z features, we identified 94 proteins with important differences in expression among untreated samples, samples treated with EOCs, and samples treated with antibiotics, peroxide, or chlorine. The targets of these treatments obviously differ, even among EOCs. In addition to ribosomal proteins, stress-, membrane- and biofilm-related proteins were affected. These findings may provide a basis for identifying new targets of essential oils and synergies with other antibiotics.

Systematically integrated metabonomic-proteomic studies of Escherichia coli under ciprofloxacin stress

Many antibiotics are used to kill pathogenic Escherichia coli each year, resulting in an increase in the number of antibiotic-resistant strains. In this study, an integrated metabonomic-proteomic method was performed to systematically compare the profiles of metabolites and proteins with or without ciprofloxacin (CFLX) treatment. Proteomics identified 290 altered proteins including 143 with decreased and 147 increased expression, respectively. Metabonomics identified 65 altered metabolites including 58 and 7 with decreased and increased expression, respectively. The integrated analysis showed that the CFLX inhibited the DNA replication and increased the expression of DNA gyrase and DNA topoisomerase 1, while causing a sharp decrease in metabolic activity such as the alanine, aspartate and glutamate metabolism. Moreover, CFLX affected the biosynthesis of aminoacyl- transfer RNAs (tRNAs), leading to an increase in aminoacyl-tRNAs ligases, but limited the aminoacyl-tRNAs-mediated-biosynthesis of related amino acids. In this study, we identified the metabolite and protein profiles under CFLX stress, indicating the mode of action of antibiotics in E. coli. Furthermore, the decreasing metabolic activity in E. coli may be an effective strategy to escape killing by antimicrobials or toxic compounds. The results of this study will advance our understanding of the mechanisms underlying the resistance of bacteria to antibiotics.

BIOLOGICAL SIGNIFICANCE

To investigate the biological impact of antibiotics stress on Escherichia coli, we applied an integrated metabonomic-proteomic method to systematically compare the profiles of metabolites and proteins between with and without antibiotics ciprofloxacin (CFLX) treatment. Following bioinformatics analysis showed that CFLX inhibited the DNA replication and increased the expression of DNA gyrase and DNA topoisomerase, while causing a sharp increase in the alanine, aspartate and glutamate metabolism. Moreover, CFLX affected the biosynthesis of tRNAs and limited the generation of related amino acids metabolites. In a summary, our results will provide the metabolite and protein profiles under CFLX stress, indicating the mode of action of antibiotics in E. coli. The results of this study will advance our understanding of the mechanisms underlying the resistance of bacteria to antibiotics.

Proteomic characterization and bio-informatic analysis of differentially expressed E. coli Nissle 1917 proteins with response to cocoti wine stress

The present study emphases the comparative proteomic analysis of Escherichia coli Nissle 1917 under cocoti palm wine stress and identified differentially expressed proteins. Protein samples were analyzed by 2-D, MALDI-TOF combined with MS access. In 2-D electrophoresis, eight differentially expressed proteins were identified: five up-regulated, two down-regulated and one newly expressed protein. Protein spots were digested with trypsin for MALDI-TOF-MS analysis; protein sequences were obtained from MASCOT search. Sequences were aligned with template using Swiss Model server. Phyre-2 was used to predict homology modeling, RasMol was used to analyze the modeling structures, PSVS server was utilized to validate the protein structure by Ramachandran's plot analysis, physical and chemical properties were analyzed using ProtParam server, Phylogenetic tree was constructed by Mega4. UniProt search helps to find protein functional information of differentially expressed proteins, involved in catalytic activities, regulation mechanisms, DNA damage stimulus, anti-termination and termination process, protein binding, electron transport mechanism, and cell signaling process functions. A detailed exploration of the proteins under cocoti palm wine stress have provided the composition, structure and functions of the expressed proteins for further investigation.

Sharpening Host Defenses during Infection: Proteases Cut to the Chase

The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered. Recently, proteomic techniques have been developed that can identify proteolytically processed proteins across the proteome. These “degradomics” approaches can identify human substrates of microbial proteases during infection in vivo and expose the molecular-level changes that occur in the human proteome during infection as an operational network to develop hypotheses for further research as well as new therapeutics. This Perspective Article reviews how proteases are utilized during infection by both the human host and invading bacterial pathogens, including archetypal virulence-associated microbial proteases, such as the Clostridia spp. botulinum and tetanus neurotoxins. We highlight the potential knowledge that degradomics studies of host–pathogen interactions would uncover, as well as how degradomics has been successfully applied in similar contexts, including use with a viral protease. We review how microbial proteases have been targeted in current therapeutic approaches and how microbial proteases have shaped and even contributed to human therapeutics beyond infectious disease. Finally, we discuss how, moving forward, degradomics research can greatly contribute to our understanding of how microbial pathogens cause disease in vivo and lead to the identification of novel substrates in vivo, and the development of improved therapeutics to counter these pathogens.

Quantitative proteome analysis of an antibiotic resistant Escherichia coli exposed to tetracycline reveals multiple affected metabolic and peptidoglycan processes

Tetracyclines are among the most commonly used antibiotics administrated to farm animals for disease treatment and prevention, contributing to the worldwide increase in antibiotic resistance in animal and human pathogens. Although tetracycline mechanisms of resistance are well known, the role of metabolism in bacterial reaction to antibiotic stress is still an important assignment and could contribute to the understanding of tetracycline related stress response. In this study, spectral counts-based label free quantitative proteomics has been applied to study the response to tetracycline of the environmental-borne Escherichia coli EcAmb278 isolate soluble proteome. A total of 1484 proteins were identified by high resolution mass spectrometry at a false discovery rate threshold of 1%, of which 108 were uniquely identified under absence of tetracycline whereas 126 were uniquely identified in presence of tetracycline. These proteins revealed interesting difference in e.g. proteins involved in peptidoglycan-based cell wall proteins and energy metabolism. Upon treatment, 12 proteins were differentially regulated showing more than 2-fold change and p<0.05 (p value corrected for multiple testing). This integrated study using high resolution mass spectrometry based label-free quantitative proteomics to study tetracycline antibiotic response in the soluble proteome of resistant E. coli provides novel insight into tetracycline related stress.

SIGNIFICANCE

The lack of new antibiotics to fight infections caused by multidrug resistant microorganisms has motivated the use of old antibiotics, and the search for new drug targets. The evolution of antibiotic resistance is complex, but it is known that agroecosystems play an important part in the selection of antibiotic resistance bacteria. Tetracyclines are still used as phytopharmaceutical agents in crops, selecting resistant bacteria and changing the ecology of farm soil. Little is known about the metabolic response of genetically resistant populations to antibiotic exposure. Indeed, to date there are no quantitative tetracycline resistance studies performed with the latest generation of high resolution mass spectrometers allowing high mass accuracy in both MS and MS/MS scans. Here, we report the proteome profiling of a soil-borne Escherichia coli upon tetracycline stress, so that this new perspective could provide a broaden understanding of the metabolic responses of E. coli to a widely used antibiotic.

The contribution of genomics to the study of Q fever

Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis that can result in large outbreaks. The birth of genomics and sequencing of C. burnetii strains has revolutionized many fields of study of this infection. Accurate genotyping methods and comparative genomic analysis have enabled description of the diversity of strains around the world and their link with pathogenicity. Genomics has also permitted the development of qPCR tools and axenic culture medium, facilitating the diagnosis of Q fever. Moreover, several pathophysiological mechanisms can now be predicted and therapeutic strategies can be determined thanks to in silico genome analysis. An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence.

Fluctuation of multiple metabolic pathways is required for Escherichia coli in response to chlortetracycline stress

Bacterial antibiotic resistance has become a worldwide challenge with the overuse and misuse of drugs.

Chronic exposure of river sediments to environmentally relevant levels of tetracycline affects bacterial communities but not denitrification rates

The effects of tetracycline (TC) at chronic sub-inhibitory exposure concentrations on benthic denitrification rates and bacterial communities were explored. River sediments were continuously exposed to different TC concentrations (0.5, 20 and 10,000 μg L(-1)) for 2 weeks in flow-through reactors allowing denitrification and bacterial growth conditions. Bacterial communities were fingerprinted by Denaturing Gradient Gel Electrophoresis of 16S rRNA gene amplification products. Cultivable denitrifiers enriched from the sediment were tested for TC resistance (2-128 mg L(-1)). Denitrification rates were unaffected by exposure to TC, regardless of concentration. In contrast, the bacterial community composition changed significantly from sub-inhibitory (ng-μg L(-1)) to therapeutic (mg L(-1)) exposure concentrations. Furthermore the cultivable denitrifiers showed a high TC sensitivity (<4 mg L(-1)). Maintenance of efficient benthic denitrification rates, even at the highest level of TC exposure most likely originated from an adaptation of the autochthonous bacterial community where dominant species become those that acquire, or already have resistance to antibiotics.

Bacterial resistance mechanism: what proteomics can elucidate

Antibiotics are important therapeutic agents commonly used for the control of bacterial infectious diseases; however, resistance to antibiotics has become a global public health problem. Therefore, effective therapy in the treatment of resistant bacteria is necessary and, to achieve this, a detailed understanding of mechanisms that underlie drug resistance must be sought. To fill the multiple gaps that remain in understanding bacterial resistance, proteomic tools have been used to study bacterial physiology in response to antibiotic stress. In general, the global analysis of changes in the protein composition of bacterial cells in response to treatment with antibiotic agents has made it possible to construct a database of proteins involved in the process of resistance to drugs with similar mechanisms of action. In the past few years, progress in using proteomic tools has provided the most realistic picture of the infective process, since these tools detect the end products of gene biosynthetic pathways, which may eventually determine a biological phenotype. In most bacterial species, alterations occur in energy and nitrogen metabolism regulation; glucan biosynthesis is up-regulated; amino acid, protein, and nucleotide synthesis is affected; and various proteins show a stress response after exposing these microorganisms to antibiotics. These issues have been useful in identifying targets for the development of novel antibiotics and also in understanding, at the molecular level, how bacteria resist antibiotics.