Human Pathogen Research Articles

First report and genomic characterization of Escherichia coli O111:H12 serotype from raw mussels in Türkiye

BackgroundThis study aimed to assess the prevalence and genomic characteristics of Shiga-toxigenic (STEC) and Enteroaggregative E. coli (EAEC) strains in raw mussels and ready-to-eat (RTE)-stuffed mussels, focusing on potential public health implications for identifying virulence and antimicrobial resistance genes.ResultsThe genome sequence analysis identified the E. coli strain named 23EM as serotype O111:H12, with adhesion (fimH-54) and fumarate hydratase (fumC-11) genes. The draft genome (4.9 Mb, 50.6% GC content, 111 contigs, 4,688 genes) is available in NCBI GenBank (accession JAWXVJ000000000). The strain, classified as ST292 and CC ST10, showed high similarity to nonpathogenic E. coli MG1655 but was distinct from pathogenic strains such as EAEC and ExPEC. In silico serotyping revealed the presence of O111-antigen flippase (wzx) and H12-antigen flagellin (fliC) genes. The strain harbors an IncFII (pCoo) plasmid with 96.95% identity. PathogenFinder predicted a 92% probability of being a human pathogen, supported by 720 pathogenic protein families. CRISPR analysis identified one high-evidence sequence with nine spacers and six low-evidence sequences. Phylogenetic analysis using RAxML positioned 23EM close to nonpathogenic E. coli but distant from other pathogenic strains. Antimicrobial resistance genes across multiple classes, including macrolides, fluoroquinolones, and aminoglycosides, were identified. The strain also contains several virulence factors, such as adhesins (e.g., ECP, ELF, TIF, type IV pili), and autotransporter genes (espP, pic), highlighting its significant pathogenic potential and public health risk.ConclusionsThis study highlights the ability of the detection of E. coli strains harboring virulence and antimicrobial resistance genes in mussels, thus emphasizing the importance of ongoing surveillance and careful consideration of the potential risks associated with the consumption of these shellfish.

Streptococcus equi Subspecies zooepidemicus Endocarditis and Meningitis in a 62-Year-Old Horse Rider Patient: A Case Report and Literature Review

The present article presents a case report and literature review concerning the Streptococcus equi subspecies zooepidemicus (SEZ), a rare zoonotic pathogen in humans. The case involves a 62-year-old man with no prior heart disease, presenting with endocarditis, pneumonia, and meningitis following close contact with a horse. The patient underwent urgent aortic valve replacement due to severe valvular damage caused by the infection. Blood and cerebrospinal fluid cultures confirmed the presence of SEZ, and the patient was treated with a combination of antibiotics, followed by a successful step-down to oral therapy using linezolid. A review of 25 additional Streptococcus equi endocarditis cases highlights the rarity of the condition, its association with animal contact, and its tendency to cause multi-site infections, such as pneumonia and meningitis. Early diagnosis, appropriate antibiotic therapy, and, in severe cases, surgical intervention are critical for a favorable outcome. This report emphasizes the importance of recognizing zoonotic infections in at-risk populations and the potential need for public health surveillance in these scenarios.

Bioorthogonal Monomycolate of Trehalose Disclosed the O-Mycoloylation of Mycoloyltransferases and Other Cell Envelope Proteins in C. glutamicum.

Protein mycoloylation is a recently identified unusual post-translational modification (PTM) exclusively observed in Mycobacteriales, an order of bacteria that includes several human pathogens. These bacteria possess a distinctive outer membrane, known as the mycomembrane, composed of very long-chain fatty acids called mycolic acids. It has been demonstrated that a few mycomembrane proteins undergo covalent modification with mycolic acids in the model organism Corynebacterium glutamicum through the action of mycoloyltransferase MytC. This PTM represents the first example of protein O-acylation in prokaryotes and also the first example of protein modification by mycolic acid. Many questions about the specificity of protein O-mycoloylation remain crucial for understanding its evolutionary significance in Mycobacteriales and its role in cell physiology. We have developed the first bioorthogonal mycolate donor featuring the natural mycolic acid pattern, enabling direct, unambiguous transfer of the lipid moiety to its acceptors and efficient metabolic labeling and enrichment of MytC protein substrates. Mass spectrometry analysis of the labeled proteins and comparative proteomic analysis of the cell envelope proteome between wild-type and ΔmytC strains identified an unbiased list of 21 proteins likely mycoloylated in the cell. The robustness of our approach is demonstrated by the successful biological validation of mycoloylation in 6 candidate proteins within wild-type cells, revealing the characteristic profile of proteins modified with natural mycolates. These findings provide interesting insights into the significance of this new lipidation pathway and pave the way for understanding their function, especially concerning the mycoloyltransferase family that includes the essential Antigen85 enzymes in Mycobacteria.

INFECÇÃO POR HELICOBACTER PYLORI E SUAS MANIFESTAÇÕES CLÍNICAS

Helicobacter pylori (H. pylori) is one of the most prevalent pathogens in humans, contributing significantly to gastroduodenal diseases. Despite being widely researched, there are still gaps in the understanding of this pathology. The general objective of this study is to analyze the existing literature on the clinical manifestation of H. pylori infection in humans and its epidemiological correlations. The specific objective is to update academics and health professionals on the epidemiology and clinical manifestations of H. pylori infection in humans. To carry out this bibliographic review, consensus statements on H. pylori, guidelines and scientific articles available in the PubMed and SciELO databases were consulted. The inclusion criteria adopted were: publications from 2016 to 2024, free access to the full text, clinical trials, systematic reviews, controlled and randomized tests, and writing in Portuguese, English and/or Spanish. The selected articles contribute relevant concepts to outline ideas related to the topic of this study. Works that were not aligned with the objectives of this study were excluded, and those that were not fully available free of charge, only abstracts and those with inadequate methodology or low scientific quality. It was found that additional studies on H. pylori are essential to fully elucidate the pathogenesis of this infection, however, there is evidence that the process is influenced by genetic and environmental factors, which also require further research. Furthermore, it is essential to raise awareness among legislators when planning public health policies and, thus, improve patients' quality of life.

Intrinsic Natural Resistance of Various Plant Pathogens to Ipflufenoquin, a New DHODH (Dihydroorotate Dehydrogenase)-inhibiting Fungicide, in Relation to Unaltered Amino Acid Sequence of the Target Site.

In recent years, increasingly stringent pesticide regulations have made the development of new chemistries challenging. Under these regulations, the new fungicide ipflufenoquin (FRAC Code 52) was first released in Japan. Its mode of action is new; it inhibits dihydroorotate dehydrogenase (DHODH), a key enzyme in the biosynthesis of pyrimidine-based nucleotides. However, because it is a single-site inhibitor, the risk of resistance developing in pathogens must be carefully considered. The risk for dual use of DHODH inhibitors in agriculture and medicine has also become a great concern because a new antifungal olorofim is under development against human pathogens now and cross-resistance has recently been reported between ipflufenoquin and olorofim in Aspergillus fumigatus. In this study, the sensitivity to ipflufenoquin was examined in culture and in plants using "baseline" isolates, which had never been exposed to DHODH inhibitors. Isolates of Alternaria alternata, Botrytis cinerea, B. elliptica, Colletotrichum fioriniae, C. fructicola, C. nymphaeae, C. orbiculare, C. siamense, C. tropicale, C. truncatum, and Sclerotinia sclerotiorum were highly sensitive to ipflufenoquin in culture, but isolates of Coniella vitis, Corynespora cassiicola, Pseudocercospora fuligena, and Rhizoctonia solani were inherently resistant. Ipflufenoquin had low efficacy against C. cassiicola and C. vitis after inoculation of cucumber and grapevine leaves, respectively. To understand the mechanism of natural resistance, we analyzed the partial sequence of pyrE genes, which encode the DHODH enzyme, but did not find any differences in the deduced amino acids that were thought to be associated with resistance. Thus, mechanisms other than target-site mutations might be involved in the intrinsic resistance.

Malaria mosquitoes, Plasmodium parasites and skin microbiota, towards control of malaria: A review

Vector-borne pathogens are transmitted by bites of infected arthropod species. The pathogens require two different host species to complete their lifecycle, usually a vertebrate and an invertebrate host, of which the latter transmits the pathogen between vertebrate hosts. Blood-feeding mosquitoes are important vectors of several human pathogens, including arboviruses namely: chikungunya, dengue fever, Rift Valley fever, yellow fever and Zika transmitted by Aedes mosquitoes amongst others. Culex mosquitoes on the other hand transmit Saint Louis and Japanese encephalitis, lymphatic filariasis, West Nile fever and Rift Valley Fever virus while Anopheles mosquitoes transmit malaria. The contact rate between vectors and their vertebrate hosts affects the intensity of pathogen transmission, and hence disease epidemiology. The ability of vectors to locate their blood hosts therefore is crucial in disease maintenance and perseverance. Host odour is known to play an important role in mosquito host-seeking behaviour and hence influences the contact rate between vectors and hosts. This literature review focuses on interactions between malaria parasites, humans, mosquitoes and how skin bacterial volatiles mediate host-seeking behaviour of mosquitoes.

Capsular Polysaccharide Production in Bacteria of the Mycoplasma Genus: A Huge Diversity of Pathways and Synthases for So-Called Minimal Bacteria.

Mycoplasmas are wall-less bacteria with many species spread across various animal hosts in which they can be pathogenic. Despite their reduced anabolic capacity, some mycoplasmas are known to secrete hetero- and homopolysaccharides, which play a role in host colonization through biofilm formation or immune evasion, for instance. This study explores how widespread the phenomenon of capsular homopolysaccharide secretion is within mycoplasmas, and investigates the diversity of both the molecules produced and the synthase-type glycosyltransferases responsible for their production. Fourteen strains representing 14 (sub)species from four types of hosts were tested invitro for their polysaccharide secretion using both specific (immunodetection) and nonspecific (sugar dosage) assays. We evidenced a new, atypical homopolymer of β-(1 → 6)-glucofuranose (named glucofuranan) in the human pathogen Mycoplasma (M.) fermentans, as well as a β-(1 → 6)-glucopyranose polymer for the turkey pathogen M. iowae and galactan (β-(1 → 6)-galactofuranose) and β-(1 → 2)-glucopyranose for M. bovigenitalium infecting ruminants. Sequence and phylogenetic analyses revealed a huge diversity of synthases from varied Mycoplasma species. The clustering of these membrane-embedded glycosyltransferases into three main groups was only partially correlated to the structure of the produced homopolysaccharides.

Use of stable isotope combined with intact cell lipidomic by routine MALDI mass spectrometry analysis for rapid drug susceptibility assay in mycobacteria.

Rapid, accurate, and easy-to-perform diagnostic assays are required to address the current need for the diagnosis of resistant pathogens. That is particularly the case for mycobacteria, such as the human pathogen Mycobacterium tuberculosis, which requires up to 2weeks for the determination of the drug susceptibility profile using the conventional broth microdilution method. To address this challenge, we investigated the incorporation of deuterium, the stable isotope of hydrogen, into lipids as a read out of the drug susceptibility profile. Deuterium is incorporated into newly synthesized proteins or lipids in place of hydrogen as bacterial cells grow, increasing the mass of the macromolecules, which can then be observed via matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). As proof-of-concept, we used the non-pathogenic Mycobacterium smegmatis mc2155 strain, which is susceptible to the aminoglycoside antibiotic kanamycin, and M.smegmatis mc2155 containing the empty vector pVV16, which is kanamycin-resistant. Bacteria were incubated in a culture medium containing 50% of deuterium oxide (D2O) and either 1 or 2 times the minimal inhibitory concentration (MIC50) of kanamycin. Lipids were then analyzed using the MBT lipid Xtract matrix combined with routine MALDI mass spectrometry in the positive ion mode to evaluate the changes in the lipid profile. Using this approach, we were able to distinguish susceptible from resistant bacteria in less than 5h, a process that would take 72 h using the conventional broth microdilution method. We therefore propose a solution for the rapid determination of drug susceptibility profiles using a phenotypic assay combining D2O stable isotope labelling and lipid analysis by routine MALDI mass spectrometry.

Helicobacter pylori biofilm interference by N-acyl homoserine lactonases: in vitro and in silico approaches.

Qurom quenching enzyme have an impact on treatment efficacy and prevent the recurrence of Helicobacter pylori biofilm-related infections, although it has not been thoroughly investigated in vitro and in silico. The current study aims to characterize the N-acyl homoserine lactonase, the quorum quenching AiiA protein of Bacillus licheniformis against H. pylori biofilm. In this study, AiiA protein were screened for their anti-biofilm activity, was found to effectively control biofilm formation of H. pylori with concentrations ranging from 2 to 10µg/mL. According to CLSM and COMSTAT analysis, the untreated substratum had the robust biofilm biomass of 25-18 µM and biovolume of 3-4 mm3 /mm2. The total biofilm biovolume and average biofilm thickness were considerably reduced by 40% with a single application of 10µg/mL of AiiA protein. The biofilm treated with AiiA exhibited a lower urease and polysaccharides than to the untreated biofilm. Further, in silico analysis, exhibited a greater interaction of AiiA against the outer membrane proteins of H. pylori compared to virulence factors. The conserved domains in the binding pockets of AiiA proteins showed a highest binding affinity proving the catalytic activity of the protein. In this study, the H. pylori biofilm architecture, exopolysaccharide and urease were significantly controlled by our purified N-acyl homoserine lactonase from B. licheniformis. Furthermore, the molecular docking showed the significant interaction between AiiA and key biofilm forming and virulence proteins proved an excellent antibiofilm activity controlling the infections of H. pylori human pathogen.

Large-scale genomic analysis of Elizabethkingia anophelis

The recent emergence of Elizabethkingia anophelis as a human pathogen is a major concern for global public health. This organism has the potential to cause severe infections and has inherent antimicrobial resistance. The potential for widespread outbreaks and rapid global spread highlights the critical importance of understanding the biology and transmission dynamics of this infectious agent. We performed a large-scale analysis of available 540 E. anophelis, including one novel strain isolated from raw milk and sequenced in this study. Pan-genome analysis revealed an open and diverse pan-genome in this species, characterized by the presence of many accessory genes. This suggests that the species has a high level of adaptability and can thrive in a variety of environments. Phylogenetic analysis has also revealed a complex population structure, with limited source-lineage correlation. We identified diverse antimicrobial resistance factors, including core-genome and accessory ones often associated with mobile genetic elements within specific lineages. Mobilome analysis revealed a dynamic landscape primarily composed of genetic islands, integrative and conjugative elements, prophage elements, and small portion of plasmids emphasizing a complex mechanism of horizontal gene transfer. Our study underscores the adaptability of E. anophelis, characterized by a diverse range of antimicrobial resistance genes, putative virulence factors, and genes enhancing fitness. This adaptability is also supported by the organism’s ability to acquire genetic material through horizontal gene transfer, primarily facilitated by mobile genetic elements such as integrative and conjugative elements (ICEs). The potential for rapid evolution of this emerging pathogen poses a significant challenge to public health efforts.

Production of bacteriocin-like inhibitory substance (BLIS) by Staphylococcus spp. isolates from dogs.

In the present study, 39 canine isolates of Staphylococcus spp. were tested for antimicrobial substance (AMS) production. Seven AMS producers were identified, whose products exhibited a non-acidic character and a proteinaceous nature, therefore being considered bacteriocin-like inhibitory substances (BLIS). The producer strains of BLIS P1, P16 and I3 showed a broad spectrum of antimicrobial activity. Human, veterinary and plant pathogens, such as Listeria monocytogenes, Klebsiella pneumoniae, Staphylococcus spp. and Clavibacter michiganensis, were among the inhibited micro-organisms, suggesting the potential biotechnological application of these peptides. MALDI-TOF mass spectrometry and 16S rDNA sequencing identified the producer strains of BLIS P1, P16 and I3 as Staphylococcus pseudintermedius P1, Staphylococcus schleiferi P16 and Staphylococcus pseudintermedius I3. The plasmid profile of these strains suggests that the BLIS production is linked to biosynthetic genes located on plasmids. PCR analyses revealed that BLIS P1, P16 and I3 are different from 11 staphylococcins already described in the literature and that their genomic DNAs do not carry the most prevalent staphylococcal enterotoxin genes. The highest levels of BLIS production were achieved after 18-24h of growth of the producer strains in TSB medium. Moreover, BLIS P1 and I3 exhibited high resistance to temperature and pH variations, and BLIS P16 maintained 100% of its activity in almost all conditions tested. The characteristics associated with BLIS P1, P16 and I3 described in this work encourage further investigation of these substances, in addition to this study being the first report of BLIS production by a strain of S. schleiferi.

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology.

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured--with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

Unraveling the full impact of SPD_0739: a key effector in S. pneumoniae iron homeostasis.

S. pneumoniae obtains growth essential iron from hemoglobin and other host hemoproteins. Still, the bacterial mechanisms involved are only partially understood, and there are inconsistent reports regarding the function of several transporters implicated in iron uptake. In this study, we clarified the role of PnrA/Spbhp-37, a ligand-binding protein previously linked to nucleoside or heme by different studies. We present data supporting a role in nucleoside scavenging rather than heme import and reveal that PnrA/Spbhp-37 modulates iron and heme uptake, likely by influencing the nucleoside cellular pool. Hence, this work provides a new understanding of a process critical to the pathophysiology of a significant human pathogen. Moreover, PnrA/Spbhp-37 is an abundant and immunogenic surface protein that is highly conserved. Hence, this study also clarifies the function of a promising vaccine target.

Acanthamoeba polyphaga de novo transcriptome and its dynamics during Mimivirus infection

Mimivirus bradfordmassiliense (Mimivirus) is a giant virus that infects Acanthamoeba species – opportunistic human pathogens. Long- and short-read sequencing were used to generate a de novo transcriptome of the host and followed the dynamics of both host and virus transcriptomes over the course of infection. The assembled transcriptome of the host included 22,604 transcripts and 13,043 genes, with N50 = 2,372 nucleotides. Functional enrichment analysis revealed major changes in the host transcriptome, namely, enrichment in downregulated genes associated with cytoskeleton homeostasis and DNA replication, repair, and nucleotide synthesis. These modulations, together with those implicated by other enriched processes, indicate cell cycle arrest, which was demonstrated experimentally. We also observed upregulation of host genes associated with transcription, secretory pathways and, as reported here for the first time, peroxisomes and the ubiquitin-proteasome system. In Mimivirus, the early stages of infection were marked by upregulated genes related to DNA replication, transcription, translation, and nucleotide metabolism, and in later stages, enrichment in genes associated with lipid metabolism, carbohydrates, and proteases. Some of the changes observed in the amoebal transcriptome likely point to Mimivirus infection causing dismantling of host cytoskeleton and translocation of endoplasmic reticulum membranes to viral factory areas.

Additions to the genus Kirschsteiniothelia (Dothideomycetes); Three novel species and a new host record, based on morphology and phylogeny

During a survey of microfungi associated with forest plants, four specimens related to Kirschsteiniothelia were collected from decaying wood in Guizhou, Hainan and Yunnan Provinces, China. Kirschsteiniothelia species have sexual and asexual forms. They are commonly found as saprophytes on decaying wood and have been reported as disease-causing pathogens in humans as well. In this study, we introduce three novel Kirschsteiniothelia species (K. bulbosapicalis, K. dendryphioides and K. longirostrata) and describe a new host record for K. atra, based on morphology and multi-gene phylogenetic analyses of a concatenated ITS, LSU and SSU rDNA sequence data. These taxa produced a dendryphiopsis- or sporidesmium-like asexual morph and detailed descriptions and micromorphological illustrations are provided. Furthermore, we provide a checklist for the accepted Kirschsteiniothelia species, including detailed host information, habitat preferences, molecular data, existing morphological type, country of origin and corresponding references.

Poultry farms as a One health priority for Aspergillus section Fumigati surveillance

Abstract In poultry production environments, particulate matter (PM) is considered one of the harmful air pollutants [2]. Considering potential biological pathogens, the genus Aspergillus in particular, Aspergillus fumigatus, is a widely recognized human and animal pathogen [3]. Hot-humid farm environments could contribute to the proliferation of these fungi [4]. Therefore, poultry production workers, besides animals [4], may be at a higher risk of inhaling fungi spores [4,5]. This study aimed to determine particulate matter (PM) contamination and analyze the prevalence of Aspergillus section Fumigati in air samples from poultry pavilions. Indoor and outdoor air samples were taken in the 1st, 2nd and 3rd weeks of birds growth cycle (n = 58). Air was collected through the impaction method (MAS-100) onto polycarbonate filters, set at 100 L/min, for 5 min. Followed by DNA extraction, and real-time PCR detection of Aspergillus section Fumigati. For PM evaluation, portable direct-reading equipment (Lighthouse, model 3016 IAQ) was used. Particle concentrations were measured (n = 67) at five distinct fractions during 5 min. Considering particles fractions, PM10 and PM5 where prevalent in 1st (58% PM10; 28% PM5), 2nd (63% PM10; 26% PM5) and 3rd (64% PM10; 25% PM5) weeks. These results evidence that coarse particles (between 2.5 and 10 µm) are the most relevant PM present in this setting. Regarding fungal detection, Aspergillus section Fumigati was widespread inside poultry pavilions (62%, 26 out of 42), highlighting this environment has a potential reservoir of microbial pathogens [7]. Furthermore, PM can act as a host of biological fragments [6]. Overall, in addition to molecular analysis, future studies should consider using culture-based methods to assess the viability of pathogenic microorganisms and their infection potential [3]. From a One Health perspective, quantitative and qualitative research is required to fully understand this environment. Key messages • This study evidence that coarse particles (between 2.5 and 10 µm) are the most relevant PM present and Aspergillus section Fumigati is widespread in poultry pavilions. • A One health intervention should be considered in future studies.

Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium.

Establishing suitable in vitro culture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, including Pneumocystis jirovecii, remain unculturable, hampering research efforts. P. jirovecii is a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact of Pneumocystis on human health, limited progress has been made in dissecting the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organism in vitro. We present a comprehensive in silico genome-scale metabolic model of Pneumocystis growth and metabolism, to identify metabolic requirements and imbalances that hinder growth in vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ relaxed Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of the Pneumocystis growth medium. Our findings offer insights into the biology of Pneumocystis and provide a novel strategy to overcome the longstanding challenge of culturing this pathogen in vitro.

Rational Exploration of 2,4-Diaminopyrimidines as DHFR Inhibitors Active against Mycobacterium abscessus and Mycobacterium avium, Two Emerging Human Pathogens.

Nontuberculous mycobacteria (NTM) are emerging human pathogens linked to severe pulmonary diseases. Current treatments involve the prolonged use of multiple drugs and are often ineffective. Bacterial dihydrofolate reductase (DHFR) is a key enzyme targeted by antibiotics in Gram-negative bacterial infections. However, existing DHFR inhibitors designed for Gram-negative bacteria often fail against mycobacterial DHFRs. Here, we detail the rational design of NTM DHFR inhibitors based on P218, a malarial DHFR inhibitor. We identified compound 8, a 2,4-diaminopyrimidine exhibiting improved pharmacological properties and activity against purified DHFR, and whole cell cultures of two predominant NTM species: Mycobacterium avium and Mycobacterium abscessus. This study underscores the potential of compound 8 as a promising candidate for the in vivo validation of DHFR as an effective treatment against NTM infections.

Optimizing SureQuant for Targeted Peptide Quantification: a Technical Comparison with PRM and SWATH-MS Methods.

Bacterial infections are a major threat to human health worldwide. A better understanding of the properties and physiology of bacterial pathogens in human tissues is required to develop urgently needed novel control strategies. Mass spectrometry-based proteomics could yield such data, but identifying and quantifying scarce bacterial proteins against a preponderance of human proteins is challenging. Here, we explored the recently introduced SureQuant method for highly sensitive targeted mass spectrometry. Using a major human pathogen, the Gram-positive bacteria Staphylococcus aureus, as an example, we evaluated several parameters, including the number of targets and intensity thresholds, for optimal qualitative and quantitative protein analysis. By comparison, we found that SureQuant achieved the same quantitative performance as standard parallel reaction monitoring while allowing accurate and precise quantification of up to 400 targets. SureQuant also surpassed the sensitivity and quantification capabilities of global data-independent acquisition methods. Finally, to facilitate method development, we provide optimized MS parameters for the sensitive quantification of different peptide panel sizes. This study provides a foundation for the broader application of SureQuant in the analysis of clinical specimens containing trace amounts of bacterial proteins as well as other studies requiring ultrasensitive detection of low-abundant proteins.

Coal mining activities driving the changes in bacterial community

The mechanism of the difference in bacterial community composition caused by environmental factors in the underground coal mine is unclear. In order to reveal the influence of coal mining activities on the characteristics of bacterial community structure in coal seam, 16S rRNA gene amplicon sequencing technology was used to determine the species abundance, biodiversity, and gene abundance of bacterial community in a coal mine in Shanxi Province, and the environmental factors such as metal elements, non-metal elements, pH value, and gas concentration of coal samples were determined. The results showed that environmental factors and bacterial communities had obvious regional characteristics. Mining activities greatly affected the α diversity of bacterial communities, mining working face > main airway > roadway roof > unexposed coal seam > tunneling roadway. The bacterial community composition of each sample point is also very different. The main airway, roadway roof, and unexposed coal seam are dominated by Actinobacteria while the mining working face and tunneling roadway are dominated by Proteobacteria. Among the gene abundances of metabolic pathways in each site, Citrate cycle had the greatest difference, followed by glycine, serine and threonine metabolism, and oxidative phosphorylation and methane metabolism had little difference. RDA analysis showed that the environmental factors affecting the bacterial community were mainly cadmium, oxygen, hydrogen, and gas content. CCA analysis divided the bacterial community into three categories. Degradation functional bacteria are located in mining working face, bacteria that tolerate poor environments are located in main airway and tunneling roadway, and human pathogens are mostly located in roadway roof and unexposed coal seam. The research results would provide support for realizing green and safe mining in coal mines.