Emerging bacterial pathogens: the past and beyond

Leptospira spp. and Rickettsia spp. as pathogens with zoonotic potential causing acute undifferentiated febrile illness in a central-eastern region of Peru

OBJETIVE

this study was to determine the relationship between acute febrile illness and bacterial pathogens with zoonotic potential that cause emerging and re-emerging diseases in a central-eastern region of Peru.

RESULTS

Out of the 279 samples analyzed, 23 (8.2%) tested positive for infection by Rickettsia spp., while a total of 15 (5.4%) tested positive for Leptospira spp. Women had a higher frequency of infection by Rickettsia spp., with 13 cases (53.3%), while men had a higher frequency of infection by Leptospira spp., with 10 cases (66.7%). The most frequently reported general symptom was headache, with 100.0% (n = 23) of patients with Rickettsia (+) and 86.7% (n = 13) of patients with Leptospira (+) experiencing it. Arthralgia was the second most frequent symptom, reported by 95.6% (n = 22) and 60% (n = 9) of patients with Rickettsia (+) and Leptospira (+), respectively. Myalgia was reported by 91.3% (n = 21) and 66.7% (n = 10) of patients with Rickettsia (+) and Leptospira (+), respectively. Retroocular pain, low back pain, and skin rash were also present, but less frequently. Among the positives, no manifestation of bleeding was recorded, although only one positive case for Leptospira spp. presented a decrease in the number of platelets.

Comparative resistomics analysis of multidrug-resistant Chryseobacteria

Chryseobacteria consists of important human pathogens that can cause a myriad of nosocomial infections. We isolated four multidrug-resistant Chryseobacterium bacteria from activated sludge collected at domestic wastewater treatment facilities in the New York Metropolitan area. Their genomes were sequenced with Nanopore technology and used for a comprehensive resistomics comparison with 211 Chryseobacterium genomes available in the public databases. A majority of Chryseobacteria harbor 3 or more antibiotic resistance genes (ARGs) with the potential to confer resistance to at least two types of commonly prescribed antimicrobials. The most abundant ARGs, including β-lactam class A (blaCGA-1 and blaCIA) and class B (blaCGB-1 and blaIND) and aminoglycoside (ranA and ranB), are considered potentially intrinsic in Chryseobacteria. Notably, we reported a new resistance cluster consisting of a chloramphenicol acetyltransferase gene catB11, a tetracycline resistance gene tetX, and two mobile genetic elements (MGEs), IS91 family transposase and XerD recombinase. Both catB11 and tetX are statistically enriched in clinical isolates as compared to those with environmental origins. In addition, two other ARGs encoding aminoglycoside adenylyltransferase (aadS) and the small multidrug resistance pump (abeS), respectively, are found co-located with MGEs encoding recombinases (e.g., RecA and XerD) or transposases, suggesting their high transmissibility among Chryseobacteria and across the Bacteroidota phylum, particularly those with high pathogenicity. High resistance to different classes of β-lactam, as well as other commonly used antimicrobials (i.e., kanamycin, gentamicin, and chloramphenicol), was confirmed and assessed using our isolates to determine their minimum inhibitory concentrations. Collectively, though the majority of ARGs in Chryseobacteria are intrinsic, the discovery of a new resistance cluster and the co-existence of several ARGs and MGEs corroborate interspecies and intergenera transfer, which may accelerate their dissemination in clinical environments and complicate efforts to combat bacterial infections.

A novel vaccine strategy using quick and easy conversion of bacterial pathogens to unnatural amino acid-auxotrophic suicide derivatives

We propose a novel strategy for quick and easy preparation of suicide live vaccine candidates against bacterial pathogens. This method requires only the transformation of one or more plasmids carrying genes encoding for two types of biological devices, an unnatural amino acid (uAA) incorporation system and toxin-antitoxin systems in which translation of the antitoxins requires the uAA incorporation. Escherichia coli BL21-AI laboratory strains carrying the plasmids were viable in the presence of the uAA, whereas the free toxins killed these strains after the removal of the uAA. The survival time after uAA removal could be controlled by the choice of the uAA incorporation system and toxin-antitoxin systems. Multilayered toxin-antitoxin systems suppressed escape frequency to less than 1 escape per 109 generations in the best case. This conditional suicide system also worked in Salmonella enterica and E. coli clinical isolates. The S. enterica vaccine strains were attenuated with a >105 fold lethal dose. Serum IgG response and protection against the parental pathogenic strain were confirmed. In addition, the live E. coli vaccine strain was significantly more immunogenic and provided greater protection than a formalin-inactivated vaccine. The live E. coli vaccine was not detected after inoculation, presumably because the uAA is not present in the host animals or the natural environment. These results suggest that this strategy provides a novel way to rapidly produce safe and highly immunogenic live bacterial vaccine candidates.

IMPORTANCE

Live vaccines are the oldest vaccines with a history of more than 200 years. Due to their strong immunogenicity, live vaccines are still an important category of vaccines today. However, the development of live vaccines has been challenging due to the difficulties in achieving a balance between safety and immunogenicity. In recent decades, the frequent emergence of various new and old pathogens at risk of causing pandemics has highlighted the need for rapid vaccine development processes. We have pioneered the use of uAAs to control gene expression and to conditionally kill host bacteria as a biological containment system. This report proposes a quick and easy conversion of bacterial pathogens into live vaccine candidates using this containment system. The balance between safety and immunogenicity can be modulated by the selection of the genetic devices used. Moreover, the uAA-auxotrophy can prevent the vaccine from infecting other individuals or establishing the environment.

Unraveling the ligand specificity and promiscuity of the Staphylococcus aureus NorA efflux pump: a computational study

Staphylococcus aureus, a gram-positive bacterial pathogen, develops antibiotic resistance partly through enhanced activity of transmembrane multi-drug efflux pump proteins like NorA. Being a prominent member of the Major Facilitator Superfamily (MFS), NorA transports various small molecules including hydrophilic fluoroquinolone antibiotics across the cell membrane. Intriguingly, NorA is inhibited by a structurally diverse set of small molecule inhibitors as well, indicating a highly promiscuous ligand/inhibitor recognition. Our study aims to elucidate the structural facets of this promiscuity. Known NorA inhibitors were grouped into five clusters based on chemical class and docked into ligand binding pockets on NorA conformations generated via molecular dynamics simulations. We discovered that several key residues, such as I23, E222, and F303, are involved in inhibitor binding. Additionally, residues I244, T223, F303, and F140 were identified as prominent in interactions with specific ligand clusters. Our findings suggest that NorA's substrate binding site, encompassing residues aiding ligand recognition based on chemical nature, facilitates the recognition of chemically diverse ligands. This insight into NorA's structural promiscuity in ligand recognition not only enhances understanding of antibiotic resistance mechanisms in S. aureus but also sets the stage for the development of more effective efflux pump inhibitors, vital for combating multidrug resistance.Communicated by Ramaswamy H. Sarma.

Advances in electrochemical-optical dual-mode biosensors for detection of environmental pathogens

Electrochemical techniques are commonly used to analyze and screen various environmental pathogens. When used in conjunction with other optical recognition methods, it can extend the sensing range, lower the detection limit, and offer mutual validation. Nowadays, electrochemical-optical dual-mode biosensors have ensured the accuracy of test results by integrating two signals into one, indicating their potential use in primary food safety quantitative assays and screening tests. Particularly, visible optical signals from electrochemical/colorimetric dual-mode biosensors could meet the demand for real-time screening of microbial pathogens. While electrochemical-optical dual-mode probes have been receiving increasing attention, there is limited emphasis on the design approaches for sensors intended for microbial pathogens. Here, we review the recent progress in the merging of optical and electrochemical techniques, including fluorescence, colorimetry, surface plasmon resonance (SPR), and surface enhanced Raman spectroscopy (SERS). This study particularly emphasizes the reporting of various sensing performances, including sensing principles, types, cutting-edge design approaches, and applications. Finally, some concerns and upcoming advancements in dual-mode probes are briefly outlined.

From Stress Tolerance to Virulence: Recognizing the Roles of Csps in Pathogenicity and Food Contamination

Be it for lab studies or real-life situations, bacteria are constantly exposed to a myriad of physical or chemical stresses that selectively allow the tolerant to survive and thrive. In response to environmental fluctuations, the expression of cold shock domain family proteins (Csps) significantly increases to counteract and help cells deal with the harmful effects of stresses. Csps are, therefore, considered stress adaptation proteins. The primary functions of Csps include chaperoning nucleic acids and regulating global gene expression. In this review, we focus on the phenotypic effects of Csps in pathogenic bacteria and explore their involvement in bacterial pathogenesis. Current studies of csp deletions among pathogenic strains indicate their involvement in motility, host invasion and stress tolerance, proliferation, cell adhesion, and biofilm formation. Through their RNA chaperone activity, Csps regulate virulence-associated genes and thereby contribute to bacterial pathogenicity. Additionally, we outline their involvement in food contamination and discuss how foodborne pathogens utilize the stress tolerance roles of Csps against preservation and sanitation strategies. Furthermore, we highlight how Csps positively and negatively impact pathogens and the host. Overall, Csps are involved in regulatory networks that influence the expression of genes central to stress tolerance and virulence.

The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective

The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.

Microbial and heavy metal contamination in herbal medicine: a prospective study in the central region of Saudi Arabia

INTRODUCTION

Herbal medicine is a medical system based on the utilization of plants or plant extracts for therapy. The continual increase in global consumption and the trade of herbal medicine has raised safety concerns in many regions. These concerns are mainly linked to microbial contamination, which could spread infections with multi-resistant bacteria in the community, and heavy metal contamination that may lead to cancers or internal organs' toxicity.

METHODS

This study was performed using an experimental design. A total of 47 samples, herbal medicine products sold in local stores in Qassim region, were used in the experiments. They were tested for bacterial contamination, alongside 32 samples for heavy metal analysis. Bacterial contamination was determined by the streak plate method and further processed to determine their antimicrobial susceptibility patterns using MicroScan WalkAway96 pulse; heavy metals were determined using a spectrometer instrument.

RESULTS

A total of 58 microorganisms were isolated. All samples were found to be contaminated with at least one organism except three samples. The majority of the isolated bacterial species were gram negative bacteria, such as Klebsiella spp., Pseudomonas spp. and E. coli., which could be of fecal origin and may lead to pneumonia, skin, or internal infections. Furthermore, most of the gram-positive bacteria were found to be multi-drug resistant. Moreover, for heavy metals, all samples had levels exceeding the regulatory limits.

CONCLUSION

This study demonstrated the presence of bacteria and heavy metals in samples of herbal medicines. Using these contaminated products may spread resistant infections, metal toxicities, or even cancers in the community.

New insights into the genetic predisposition of brucellosis and its effect on the gut and vaginal microbiota in goats

Goats contribute significantly to the global food security and industry. They constitute a main supplier of meat and milk for large proportions of people in Egypt and worldwide. Brucellosis is a zoonotic infectious disease that causes a significant economic loss in animal production. A case-control genome-wide association analysis (GWAS) was conducted using the infectious status of the animal as a phenotype. The does that showed abortion during the last third period of pregnancy and which were positive to both rose bengal plate and serum tube agglutination tests, were considered as cases. Otherwise, they were considered as controls. All animals were genotyped using the Illumina 65KSNP BeadChip. Additionally, the diversity and composition of vaginal and fecal microbiota in cases and controls were investigated using PCR-amplicone sequencing of the V4 region of 16S rDNA. After applying quality control criteria, 35,818 markers and 66 does were available for the GWAS test. The GWAS revealed a significantly associated SNP (P = 5.01 × 10-7) located on Caprine chromosome 15 at 29 megabases. Four other markers surpassed the proposed threshold (P = 2.5 × 10-5). Additionally, fourteen genomic regions accounted for more than 0.1% of the variance explained by all genome windows. Corresponding markers were located within or in close vicinity to several candidate genes, such as ARRB1, RELT, ATG16L2, IGSF21, UBR4, ULK1, DCN, MAPB1, NAIP, CD26, IFIH1, NDFIP2, DOK4, MAF, IL2RB, USP18, ARID5A, ZAP70, CNTN5, PIK3AP1, DNTT, BLNK, and NHLRC3. These genes play important roles in the regulation of immune responses to the infections through several biological pathways. Similar vaginal bacterial community was observed in both cases and controls while the fecal bacterial composition and diversity differed between the groups (P < 0.05). Faeces from the control does showed a higher relative abundance of the phylum Bacteroidota compared to cases (P < 0.05), while the latter showed more Firmicutes, Spirochaetota, Planctomycetota, and Proteobacteria. On the genus level, the control does exhibited higher abundances of Rikenellaceae RC9 gut group and Christensenellaceae R-7 group (P < 0.05), while the infected does revealed higher Bacteroides, Alistipes, and Prevotellaceae UCG-003 (P < 0.05). This information increases our understanding of the genetics of the susceptibility to Brucella in goats and may be useful in breeding programs and selection schemes that aim at controlling the disease in livestock.

Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology

Full Laboratory Automation is revolutionizing work habits in an increasing number of clinical microbiology facilities worldwide, generating huge streams of digital images for interpretation. Contextually, deep learning architectures are leading to paradigm shifts in the way computers can assist with difficult visual interpretation tasks in several domains. At the crossroads of these epochal trends, we present a system able to tackle a core task in clinical microbiology, namely the global interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. This is achieved by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture we call DeepColony. Working on a large stream of clinical data and a complete set of 32 pathogens, the proposed system is capable of effectively assist plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of Urinary Tract Infections. Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.

Aerococcus urinae urinary tract infection in a hospitalised patient: an increasingly common infection

An elderly male with an extensive medical history was admitted for sepsis of unspecified origin; the source was later found to be an Aerococcus urinae urinary tract infection. Urinalysis and conventional urine culture were used in diagnosing this infection, and it was successfully treated with a 7-day course of intravenous ceftriaxone. The patient had no recurrence of urinary symptoms or development of complications at his follow-up. While A. urinae has traditionally been described as an uncommon and relatively avirulent source of urinary tract infections, increasing reports of positive isolation suggest its incidence may be higher than previously believed. Cases have been more frequently reported among elderly males with multimorbidity and repeat hospitalisation. A lower threshold of suspicion for A. urinae urinary tract infections in this population may better guide empiric therapy and help avoid potentially life-threatening complications.

MicroRNA therapeutics and nucleic acid nano-delivery systems in bacterial infection: a review

Bacteria that have worked with humans for thousands of years pose a major threat to human health even today, as drug resistance has become a prominent problem. Compared to conventional drug therapy, nucleic acid-based therapies are a promising and potential therapeutic strategy for diseases in which nucleic acids are delivered through a nucleic acid delivery system to regulate gene expression in specific cells, offering the possibility of curing intractable diseases that are difficult to treat at this stage. Among the many nucleic acid therapeutic ideas, microRNA, a class of small nucleic acids with special properties, has made great strides in biology and medicine in just over two decades, showing promise in preclinical drug development. In this review, we introduce recent advances in nucleic acid delivery systems and their clinical applications, highlighting the potential of nucleic acid therapies, especially miRNAs extracted from traditional herbs, in combination with the existing set of nucleic acid therapeutic systems, to potentially open up a new line of thought in the treatment of cancer, viruses, and especially bacterial infectious diseases.

Antimicrobial and Antioxidant Properties of Chemically Analyzed Essential Oil of Artemisia annua L. (Asteraceae) Native to Mediterranean Area

Artemisia annua (AA) is an aromatic plant belonging to the Asteraceae family, which has long been known for its several medicinal virtues. In addition, essential oils (EOs) extracted from AA have a wide range of therapeutic properties. Therefore, this study aimed to investigate the phytochemical composition, anti-microbial, and anti-oxidant properties of Artemisia annua essential oil (EOAA). EO was extracted, and its chemical constituents were ascertained by the use of GC-MS analysis. EOAA shows remarkable antioxidant capacities of DPPH free radical scavenging with an IC50 value of 29 ± 5.3 μg/mL and ferric reducing antioxidant power with an EC50 value of 9.21 ± 0.3 µg/mL, and it also has a good total antioxidant capacity of 911.59 ± 115.71 milligrams of ascorbic acid equivalence per gram of EO (mg AAE/g EO). Moreover, the in vitro antimicrobial screening results indicate that EOAA has shown promising antibacterial activity, especially against the Escherichia coli strain, and it also shows significant antifungal activity against Fusarium oxysporum and Candida albicans yeasts. Taken together, our findings highlight the importance of EOAA as a source of strong antioxidant and antimicrobial agents, which could be used as an alternative form to control free radicals and combat drug-resistant microbes.

Genomic and functional analysis of phage-mediated horizontal gene transfer in Pseudomonas syringae on the plant surface

Many strains of Pseudomonas colonise plant surfaces, including the cherry canker pathogens, Pseudomonas syringae pathovars syringae and morsprunorum. We have examined the genomic diversity of P. syringae in the cherry phyllosphere and focused on the role of prophages in transfer of genes encoding Type 3 secreted effector (T3SE) proteins contributing to the evolution of virulence. Phylogenomic analysis was carried out on epiphytic pseudomonads in the UK orchards. Significant differences in epiphytic populations occurred between regions. Nonpathogenic strains were found to contain reservoirs of T3SE genes. Members of P. syringae phylogroups 4 and 10 were identified for the first time from Prunus. Using bioinformatics, we explored the presence of the gene encoding T3SE HopAR1 within related prophage sequences in diverse P. syringae strains including cherry epiphytes and pathogens. Results indicated that horizontal gene transfer (HGT) of this effector between phylogroups may have involved phage. Prophages containing hopAR1 were demonstrated to excise, circularise and transfer the gene on the leaf surface. The phyllosphere provides a dynamic environment for prophage-mediated gene exchange and the potential for the emergence of new more virulent pathotypes. Our results suggest that genome-based epidemiological surveillance of environmental populations will allow the timely application of control measures to prevent damaging diseases.

Antibacterial Effect of Acoustic Cavitation Promoted by Mesoporous Silicon Nanoparticles

As-prepared mesoporous silicon nanoparticles, which were synthesized by electrochemical etching of crystalline silicon wafers followed by high-energy milling in water, were explored as a sonosensitizer in aqueous media under irradiation with low-intensity ultrasound at 0.88 MHz. Due to the mixed oxide-hydride coating of the nanoparticles' surfaces, they showed both acceptable colloidal stability and sonosensitization of the acoustic cavitation. The latter was directly measured and quantified as a cavitation energy index, i.e., time integral of the magnitude of ultrasound subharmonics. The index turned out to be several times greater for nanoparticle suspensions as compared to pure water, and it depended nonmonotonically on nanoparticle concentration. In vitro tests with Lactobacillus casei revealed a dramatic drop of the bacterial viability and damage of the cells after ultrasonic irradiation with intensity of about 1 W/cm² in the presence of nanoparticles, which themselves are almost non-toxic at the studied concentrations of about 1 mg/mL. The experimental results prove that nanoparticle-sensitized cavitation bubbles nearby bacteria can cause bacterial lysis and death. The sonosensitizing properties of freshly prepared mesoporous silicon nanoparticles are beneficial for their application in mild antibacterial therapy and treatment of liquid media.

Synthesis, Characterization, DFT Mechanistic Study, Antimicrobial Activity, Molecular Modeling, and ADMET Properties of Novel Pyrazole-isoxazoline Hybrids

A series of new heterocycle hybrids incorporating pyrazole and isoxazoline rings was successfully synthesized, characterized, and evaluated for their antimicrobial responses. The synthesized compounds were obtained utilizing N-alkylation and 1,3-dipolar cycloaddition reactions, as well as their structures were established through spectroscopic methods and confirmed by mass spectrometry. To get more light on the regioselective synthesis of new hybrid compounds, mechanistic studies were performed using DFT calculations with B3LYP/6-31G(d,p) basis set. Additionally, the results of the preliminary screening indicate that some of the examined hybrids showed potent antimicrobial activity, compared to standard drugs. The results confirm that the antimicrobial activity is strongly dependent on the nature of the substituents linked pyrazole and isoxazoline rings. Furthermore, molecular docking studies were conducted to highlight the interaction modes between the investigated hybrid compounds and the Escherichia coli and Candida albicans receptors. Notably, the results demonstrate that the investigated compounds have strong protein binding affinities. The stability of the formed complexes by the binding between the hybrid compound 6c, and the target proteins was also confirmed using a 100 ns molecular dynamics simulation. Finally, the prediction of ADMET properties suggests that almost all hybrid compounds possess good pharmacokinetic profiles and no signs of observed toxicity, except for compounds 6e, 6f, and 6g.

A comprehensive list of bacterial pathogens infecting humans

There exists an enormous diversity of bacteria capable of human infection, but no up-to-date, publicly accessible list is available. Combining a pragmatic definition of pathogenicity with an extensive search strategy, we report 1513 bacterial pathogens known to infect humans described pre-2021. Of these, 73 % were regarded as established (have infected at least three persons in three or more references) and 27 % as putative (fewer than three known cases). Pathogen species belong to 10 phyla and 24 classes scattered throughout the bacterial phylogeny. We show that new human pathogens are discovered at a rapid rate. Finally, we discuss how our results could be expanded to a database, which could provide a useful resource for microbiologists. Our list is freely available and archived on GitHub and Zenodo and we have provided walkthroughs to facilitate access and use.

Exploring the microbiome, antibiotic resistance genes, mobile genetic element, and potential resistant pathogens in municipal wastewater treatment plants in Brazil

Wastewater treatment plants (WWTPs) have been widely investigated in Europe, Asia and North America regarding the occurrence and fate of antibiotic resistance (AR) elements, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and antibiotic resistant bacteria and pathogens. However, monitoring data about AR elements in municipal WWTPs in Brazil are scarce. This study investigated the abundance of intI1, five ARGs (sul1, tetA, blaTEM, ermB and qnrB) and 16S rRNA in raw and treated wastewater of three WWTPs, using different sewage treatments named CAS (Conventional activated sludge), UASB/BTF (UASB followed by biological trickling filter) and MAS/UV (modified activated sludge with UV disinfection stage). Bacterial diversity and the presence of potentially pathogenic groups were also evaluated, and associations between genetic markers and the bacterial populations were presented. All WWTPs decreased the loads of genetic markers finally discharged to receiving water bodies and showed no evidence of being hotspots for antimicrobial resistance amplification in wastewater, since the abundances of intI1 and ARGs within the bacterial population were not increased in the treated effluents. UASB/BTF showed a similar performance to that of the CAS and MAS/UV, reinforcing the sanitary and environmental advantages of this biological treatment, widely applied for wastewater treatment in warm climate regions. Bacterial diversity and richness increased after treatments, and bacterial communities in wastewater samples differed due to catchment areas and treatment typologies. Potential pathogenic population underwent considerable decrease after the treatments; however, strong significant correlations with intI1 and ARGs revealed potential multidrug-resistant pathogenic bacteria (Aeromonas, Arcobacter, Enterobacter, Escherichia-Shigella, Stenotrophomonas and Streptococcus) in the treated effluents, although in reduced relative abundances. These are contributive results for understanding the fate of ARGs, MGEs and potential pathogenic bacteria after wastewater treatments, which might support actions to mitigate their release into Brazilian aquatic environments in the near future.

Sonochemical synthesis of a copper reduced graphene oxide nanocomposite using honey and evaluation of its antibacterial and cytotoxic activities

The combination of graphene-based materials and inorganic nanoparticles for the enhancement of the nanomaterial properties is extensively explored nowadays. In the present work, we used a sonochemical method to synthesize a copper/reduced graphene oxide (Cu/RGO) nanocomposite using Australian honey and vitamin C as capping and reducing agents, respectively. The honey-mediated copper/reduced graphene oxide (H/Cu/RGO) nanocomposite was then characterized through UV-visible, XRD, HRTEM, and FTIR analysis. The copper nanoparticles (Cu-NPs) in the nanocomposite formed uniform spherical shapes with a size of 2.20 ± 0.70 nm, which attached to the reduced graphene oxide (RGO) layers. The nanocomposite could suppress bacterial growth in both types of bacteria strains. However, in this study, the nanocomposite exhibited good bactericidal activity toward the Gram-positive bacteria than the Gram-negative bacteria. It also showed a cytotoxic effect on the cancer colorectal cell line HCT11, even in low concentrations. These results suggested that the H/Cu/RGO nanocomposite can be a suitable component for biomedical applications.

Fe-Doped MoS2 Nanozyme for Antibacterial Activity and Detoxification of Mustard Gas Simulant

The peroxidase-like catalytic activity of various nanozymes was extensively applied in various fields. In this study, we have demonstrated the preparation of Fe-doped MoS₂ (Fe@MoS₂) nanomaterials with enhanced peroxidase-like activity of MoS₂ in a co-catalytic pathway. In view of Fenton reaction, the peroxidase-like Fe@MoS₂ nanozyme prompted the decomposition of hydrogen peroxide (H₂O₂) to a reactive hydroxyl radical (·OH). The efficient decomposition of H₂O₂ in the presence of Fe@MoS₂ has been employed toward the antibacterial activity and detoxification of mustard gas simulant. The combined effect of Fe@MoS₂ and H₂O₂ showed remarkable antibacterial activity against the drug-resistant bacterial strain methicillin-resistant Staphylococcus aureus and Escherichia coli with the use of minimal concentration of H₂O₂. Fe@MoS₂ was further applied for the detoxification of the chemical warfare agent sulfur mustard simulant, 2-chloroethyl ethyl sulfide, by selective conversion to the nontoxic sulfoxide. This work demonstrates the development of a hybrid nanozyme and its environmental remediation from harmful chemicals to microbes.

Morganella Phage Mecenats66 Utilizes an Evolutionarily Distinct Subtype of Headful Genome Packaging with a Preferred Packaging Initiation Site

Both recognized species from the genus Morganella (M. morganii and M. psychrotolerans) are Gram-negative facultative anaerobic rod-shaped bacteria that have been documented as sometimes being implicated in human disease. Complete genomes of seven Morganella-infecting phages are publicly available today. Here, we report on the genomic characterization of an insect associated Morganella sp. phage, which we named Mecenats66, isolated from dead worker honeybees. Phage Mecenats66 was propagated, purified, and subjected to whole-genome sequencing with subsequent complete genome annotation. After the genome de novo assembly, it was noted that Mecenats66 might employ a headful packaging with a preferred packaging initiation site, although its terminase amino acid sequence did not fall within any of the currently recognized headful packaging subtype employing phage (that had their packaging strategy experimentally verified) with clusters on a terminase sequence phylogenetic tree. The in silico predicted packaging strategy was verified experimentally, validating the packaging initiation site and suggesting that Mecenats66 represents an evolutionarily distinct headful genome packaging with a preferred packaging initiation site strategy subtype. These findings can possibly be attributed to several of the phages already found within the public biological sequence repositories and could aid newly isolated phage packaging strategy predictions in the future.

Culture-Free Quantification of Bacteria Using Digital Fluorescence Imaging in a Tunable Magnetic Capturing Cartridge for Onsite Food Testing

Accurate, onsite detection of pathogenic bacteria from food matrices is required to rapidly respond to pathogen outbreaks. However, accurately detecting whole-cell bacteria in large sample volumes without an enrichment step remains a challenge. Therefore, bacterial samples must be concentrated, identified, and quantified. We developed a tunable magnetic capturing cartridge (TMCC) and combined it with a portable digital fluorescence reader for quick, onsite, quantitative detection of Staphylococcus aureus. The TMCC platform integrates an absorption pad impregnated with water-soluble polyvinyl alcohol (PVA) with an injection-molded polycarbonate (PC) plate that has a hard magnet on its back and an acrylonitrile-butadiene-styrene case. An S. aureus-specific antibody conjugated with magnetic nanoparticles was used to concentrate bacteria from a large-volume sample and capture bacteria within the TMCC. The retention time for capturing bacteria on the TMCC was adjusted by controlling the concentration and volume of the PVA solution. Concentrated bacterial samples bound to target-specific aptamer probes conjugated with quantum dots were loaded into the TMCC for a controlled time, followed by attachment of the bacteria to the PC plate and removal of unbound aptamer probes with wash buffer. The captured bacteria were quantified using a digital fluorescence reader equipped with an embedded program that automatically counts fluorescently tagged bacteria. The bacterial count made using the TMCC was comparable to a standard plate count (R² = 0.9898), with assay sensitivity and specificity of 94.3 and 100%, respectively.

Genomic characterization of Streptococcus parasuis, a close relative of Streptococcus suis and also a potential opportunistic zoonotic pathogen

Streptococcus parasuis (S. parasuis) is a close relative of Streptococcus suis (S. suis), composed of former members of S. suis serotypes 20, 22 and 26. S. parasuis could infect pigs and cows, and recently, human infection cases have been reported, making S. parasuis a potential opportunistic zoonotic pathogen. In this study, we analysed the genomic characteristics of S. parasuis, using pan-genome analysis, and compare some phenotypic determinants such as capsular polysaccharide, integrative conjugative elements, CRISPR-Cas system and pili, and predicted the potential virulence genes by associated analysis of the clinical condition of isolated source animals and genotypes. Furthermore, to discuss the relationship with S. suis, we compared these characteristics of S. parasuis with those of S. suis. We found that the characteristics of S. parasuis are similar to those of S. suis, both of them have "open" pan-genome, their antimicrobial resistance gene profiles are similar and a srtF pilus cluster of S. suis was identified in S. parasuis genome. But S. parasuis still have its unique characteristics, two novel pilus clusters are and three different type CRISPR-Cas system were found. Therefore, this study provides novel insights into the interspecific and intraspecific genetic characteristics of S. parasuis, which can be useful for further study of this opportunistic pathogen, such as serotyping, diagnostics, vaccine development, and study of the pathogenesis mechanism.

Predicting the pathogenicity of bacterial genomes using widely spread protein families

Background

The human body is inhabited by a diverse community of commensal non-pathogenic bacteria, many of which are essential for our health. By contrast, pathogenic bacteria have the ability to invade their hosts and cause a disease. Characterizing the differences between pathogenic and commensal non-pathogenic bacteria is important for the detection of emerging pathogens and for the development of new treatments. Previous methods for classification of bacteria as pathogenic or non-pathogenic used either raw genomic reads or protein families as features. Using protein families instead of reads provided a better interpretability of the resulting model. However, the accuracy of protein-families-based classifiers can still be improved.

Results

We developed a wide scope pathogenicity classifier (WSPC), a new protein-content-based machine-learning classification model. We trained WSPC on a newly curated dataset of 641 bacterial genomes, where each genome belongs to a different species. A comparative analysis we conducted shows that WSPC outperforms existing models on two benchmark test sets. We observed that the most discriminative protein-family features in WSPC are widely spread among bacterial species. These features correspond to proteins that are involved in the ability of bacteria to survive and replicate during an infection, rather than proteins that are directly involved in damaging or invading the host.

Intelligent design of polymersomes for antibacterial and anticancer applications

Polymersomes (or polymer vesicles) have attracted much attention for biomedical applications in recent years because their lumen can be used for drug delivery and their coronas and membrane can be modified with a variety of functional groups. Thus, polymersomes are very suitable for improved antibacterial and anticancer therapy. This review mainly highlighted recent advances in the synthetic protocols and design principles of intelligent antibacterial and anticancer polymersomes. Antibacterial polymersomes are divided into three categories: polymersomes as antibiotic nanocarriers, intrinsically antibacterial polymersomes, and antibacterial polymersomes with supplementary means including photothermal and photodynamic therapy. Similarly, the anticancer polymersomes are divided into two categories: polymersomes-based delivery systems and anticancer polymersomes with supplementary means. In addition, the bilateral relationship between bacteria and cancer is addressed, since more and more evidences show that bacteria may cause cancer or promote cancer progression. Finally, prospective on next-generation antibacterial and anticancer polymersomes are discussed. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Biology-Inspired Nanomaterials > Lipid-Based Structures.

Can microplastics facilitate the emergence of infectious diseases?

Plastic pollution is a major environmental problem. Small plastic particles (called microplastics) have been reported to have pernicious effects on human and wildlife health, by altering physiological functions (e.g., immunity, metabolism) and interfering with commensal microorganisms. However, in addition to these direct toxic effects, we suggest that microplastic pollution might also exert deleterious effects, modifying (i) the exposure to pathogens (e.g., multi-drug resistant bacteria) and (ii) the dynamics of vector-borne diseases. Therefore, we argue that microplastics should be considered as a ubiquitous environmental hazard, potentially promoting the (re)emergence of infectious diseases. The implementation of multi- and interdisciplinary research projects are crucial to properly evaluate if microplastic pollution should be added to the current list of global health threats.

The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans

In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.

Occurrence and Risk Factors of Dog Bites in Northern Indigenous Communities: A Scoping Review

The relationship between northern Indigenous people and dogs has evolved over the past years alongside events such as colonization, settlement, proliferation of snowmobiling and other socio-cultural and environmental changes. These changes have had negative impacts on this relationship, and with the endemic presence of arctic fox rabies, dog bites have become an important public health burden. The objective of this study was to synthesize the state of knowledge regarding the occurrence of dog bites and associated risk factors in the specific context of northern Indigenous communities. A scoping review was conducted in seven bibliographic databases, from June 2018 to May 2020. From this search, 257 original studies were identified and eight papers were included for final analysis. Annual occurrence of dog bites in northern Indigenous communities ranged from 0.61 to 59.6/10,000 inhabitants. Dog bites affected 27–62.9% of the population in those regions during their lifetime. Very few studies compared the occurrence of dog bites between people living in northern communities with other populations or settings, but available evidence suggests that Indigenous people living in northern communities are at higher risk of dog bites than the rest of the population. Several individual and environmental risk factors were identified in the selected studies, although the strength of evidence varied significantly. Age (children) and gender (male) were well documented individual risk factors. Other factors, such as organizational barriers to dog management and lack of access to veterinary services, were identified and discussed by several authors. The results of this study support concerns about the higher risk of bites in northern Indigenous communities, and underscore the urgent need for more research into the contextual and environmental factors that impact the mitigation of these risks.

Exploring the applications of hyaluronic acid-based nanoparticles for diagnosis and treatment of bacterial infections

Hyaluronic acid (HA) has become a topic of significant interest in drug delivery research due to its excellent properties, including biosafety, biodegradability, and nonimmunogenicity. Moreover, due to its ease of modification, HA can be used to prepare several HA‐based nanosystems using various approaches. These approaches involve conjugating/grafting of hydrophobic moieties, polyelectrolytes complexation with cationic polymers, or surface modification of various nanoparticles using HA. These nanoparticles are able to selectively deliver antibacterial drugs or diagnostic molecules into the site of infections. In addition, HA can bind with overexpressed cluster of differentiation 44 (CD44) receptors in macrophages and also can be degraded by a family of enzymes called hyaluronidase (HAase) to release drugs or molecules. By binding with these receptors or being degraded at the infection site by HAase, HA‐based nanoparticles allow enhanced and targeted antibacterial delivery. Herein, we present a comprehensive and up‐to‐date review that highlights various techniques of preparation of HA‐based nanoparticles that have been reported in the literature. Furthermore, we also discuss and critically analyze numerous types of HA‐based nanoparticles that have been employed in antibacterial delivery to date. This article offers a critical overview of the potential of HA‐based nanoparticles to overcome the challenges of conventional antibiotics in the treatment of bacterial infections. Moreover, this review identifies further avenues of research for developing multifunctional and biomimetic HA‐based nanoparticles for the treatment, prevention, and/or detection of pathogenic bacteria.

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology

Therapeutic Approaches and Drug Discovery > Emerging Technologies

Impact of Dietary Egg Yolk IgY Powder on Behavior, Meat Quality, Physiology, and Intestinal Escherichia coli Colonization of Broiler Chicks

The current study investigated the impact of different concentrations of purified egg yolk immunoglobulin Y (IgY) supplemental food on the growth performance, behaviors, cecal contents of Escherichia coli, and the meat quality of broiler chicks. Four dietary groups were given to 180 female Ross broiler chicks at random (n = 45 for each). The control group was fed a standard diet only, whereas the other three experimental groups were fed the same basic diet supplemented with 1,500, 3,000, and 4,000 μg/ml IgY for a duration of 42 days. Significant greater behavioral activities, including, feeding, drinking, and dust bathing (p &lt; 0.05), in the birds fed 4,000 μg/ml of IgY compared to the control group were observed. Greater weight gains of the crop, proventriculus, gizzard, and intestine (p &lt; 0.05) were observed for broiler chicks fed 4,000 μg/ml of IgY when compared to the control group. After 3 weeks of feeding, the groups fed 3,000 and 4,000 μg/ml IgY had significant lower E. coli counts in the muscle and cecal contents (p &lt; 0.05) when compared to the control group. Moreover, dietary supplementation with 4,000 μg/ml IgY in the third week and 3,000 μg/ml IgY in the sixth week resulted in greater weight gain (p &lt; 0.01) when compared to the control group. Also, at week 3, chicks fed 4,000 μg/ml of IgY had a lower feed conversion ratio (FCR) when compared to the control group (p &lt; 0.05). At week 6, chicks fed 3,000 μg/ml of IgY had lower FCR than the control (p &lt; 0.05). The circulating heterophile/lymphocyte ratio was simply altered in birds fed variable IgY concentrations (1,500, 3,000, and 4,000 μg/ml), with no significant differences compared to the control group due to the individual resistance of each bird to physiological stress. The addition of 4,000 μg/ml IgY to the diet enhanced the nutritive value of meat, including protein, fat, and ash content (p &lt; 0.05). Our study concluded that dietary supplementation of 3,000 and/or 4,000 μg/ml IgY improved the growth rates, behavioral activities, intestinal health indices, and meat quality of broiler chicks.

SERS-based CRISPR/Cas assay on microfluidic paper analytical devices for supersensitive detection of pathogenic bacteria in foods

Rapid and point-of-need (PON) detection of bacteria is crucial to directly provide rapid and reliable diagnostics information during on-site tests, allowing more room for taking proactive measures. By taking the multifaceted advantages of CRISPR/Cas12a and surface-enhanced Raman scattering (SERS), for the first time, we designed a recombinase polymerase amplification (RPA)-integrated microfluidic paper-based analytical device (μPAD), coined RPA-Cas12a-μPAD for supersensitive SERS detection. Single-stranded DNAs were designed to "pull down" SERS nanoprobes. The amplicons of the invA gene triggered the trans-cleavage of Cas12a, resulting in the indiscriminate shredding of linker ssDNA. Thus, the degree of aggregation of SERS nanoprobes was dependent on the concentration of Salmonella typhimurium (S. typhi), which was determined on a μPAD and monitored by a Raman spectrometer. The limit of detection for S. typhi was approximately 3-4 CFU/mL for spiked milk and meat samples with a dynamic detection range from 1 to 10⁸ CFU/mL. The RPA-Cas12a-μPAD secured accurate tests for food samples in 45 min. This work expands the reach of CRISPR-based diagnostics (CRISPR-Dx) and provides a novel and robust bacterial PON detection platform.

Bacteria Detection at a Single-Cell Level through a Cyanotype-Based Photochemical Reaction

The detection of living organisms at very low concentrations is necessary for the early diagnosis of bacterial infections, but it is still challenging as there is a need for signal amplification. Cell culture, nucleic acid amplification, or nanostructure-based signal enhancement are the most common amplification methods, relying on long, tedious, complex, or expensive procedures. Here, we present a cyanotype-based photochemical amplification reaction enabling the detection of low bacterial concentrations up to a single-cell level. Photocatalysis is induced with visible light and requires bacterial metabolism of iron-based compounds to produce Prussian Blue. Bacterial activity is thus detected through the formation of an observable blue precipitate within 3 h of the reaction, which corresponds to the concentration of living organisms. The short time-to-result and simplicity of the reaction are expected to strongly impact the clinical diagnosis of infectious diseases.

Isolation and identification of Streptomyces tunisiensis from Garmsar salt cave soil with antibacterial and gene expression activity against Pseudomonas aeruginosa

It is known that more than 70% of the current antibiotics have been produced by Streptomyces; therefore, the main goal of the present study was to isolate halophiles Streptomyces to investigate their antimicrobial properties on the expression of the pathogenic genes of clinically resistant Pseudomonas aeruginosa. To this aim, isolation of Streptomyces from soil was performed by serial dilution method, and cultivation on ISP2 and SCA medium. The secondary metabolite was extracted by ethyl acetate method. The presence of exo A, alg D and oprl genes were determined by PCR in 50 clinical isolates of Pseudomonas aeruginosa. The inhibitory effect of active metabolites on gene expression were investigated by employing the real-time PCR technique. The purification of secondary metabolites were performed by employing the HPLC technique. Moreover, the FTIR technique was employed to determine the functional groups to help performing identifications by employing the LC-MS technique. Finally, selected Streptomyces was identified by 16S ribosomal RNA gene. Accordingly, the possible forms of Streptomyces were isolated and identified, in which Streptomyces number 25 had the highest growth inhibition zone against the clinical strains of Pseudomonas aeruginosa. The obtained results of molecular analysis showed 95.4% similarity to Streptomyces tunisiensis. The effect of selected Streptomyces secondary metabolites reduced expressions of both of exo A and algD genes in 1024μg/mL concentration. In this regard, the potent fraction could be known as an isobutyl Nonactin analogue. The concluding remarks of this work showed the antimicrobial activity of halophilus Streptomyces species against the resistant strains of Pseudomonas aeruginosa with the ability of producing antibiotics proposing for running further investigations to determine the active compound structures.

Objectionable microorganisms in pharmaceutical production: Validation of a decision tree

The release of quality, safe, and effective non-sterile drugs needs to exclude the presence of objectionable microorganisms, which include microorganisms potentially involved in product degradation, or considered as poor hygiene indicator during manufacturing, or causing adverse effect on patient's health. In this paper, a method allowing objective and verifiable evaluations has been investigated through the development of a suitable decision tree with a template for data collection. The decision tree has been used to establish which microorganisms were objectionables, using several hypothetical scenarios in which 24 different biological agents, both harmless microorganisms and opportunistic pathogens, were combined with 9 different products, representing each type of administration route for non-sterile drugs. The results showed that the use of aforementioned approach makes the microorganisms evaluation easy and verifiable and highlighted that even the microbes initially considered harmless could be objectionable.

Model development for evidence-based prioritisation of policy action on emerging chemical and microbial drinking water risks

While the burden of disease from well-studied drinking water contaminants is declining, risks from emerging chemical and microbial contaminants arise because of social, technological, demographic and climatological developments. At present, emerging chemical and microbial drinking water contaminants are not assessed in a systematic way, but reactively and incidence based. Furthermore, they are assessed separately despite similar pollution sources. As a result, risks might be addressed ineffectively. Integrated risk assessment approaches are thus needed that elucidate the uncertainties in the risk evaluation of emerging drinking water contaminants, while considering risk assessors' values. This study therefore aimed to (1) construct an assessment hierarchy for the integrated evaluation of the potential risks from emerging chemical and microbial contaminants in drinking water and (2) develop a decision support tool, based on the agreed assessment hierarchy, to quantify (uncertain) risk scores. A multi-actor approach was used to construct the assessment hierarchy, involving chemical and microbial risk assessors, drinking water experts and members of responsible authorities. The concept of value-focused thinking was applied to guide the problem-structuring and model-building process. The development of the decision support tool was done using Decisi-o-rama, an open-source Python library. With the developed decision support tool (uncertain) risk scores can be calculated for emerging chemical and microbial drinking water contaminants, which can be used for the evidence-based prioritisation of actions on emerging chemical and microbial drinking water risks. The decision support tool improves existing prioritisation approaches as it combines uncertain indicator levels with a multi-stakeholder approach and integrated the risk assessment of chemical and microbial contaminants. By applying the concept of value-focused thinking, this study addressed difficulties in evidence-based decision-making related to emerging drinking water contaminants. Suggestions to improve the model were made to guide future research in assisting policy makers to effectively protect public health from emerging drinking water risks.

Responsive Quaternized PDMAEMA Copolymers with Antimicrobial Action

In this work, the antimicrobial action of partially quaternized poly(2-(dimethylamino)ethyl methacrylate) (PQDMAEMA) copolymers using different alkyl halides is presented. The poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) homopolymer was synthesized by group transfer polymerization, followed by the modification of its tertiary amine groups, using bromoethane, iodoethane, bromohexane and bromoethanol, to introduce permanent cationic, quaternary ammonium salt moieties, randomly distributed along the polymer chains. In all cases, the degree of quaternization was low, at ~10 mol%, as verified by proton nuclear magnetic resonance spectroscopy to preserve the thermo-responsive character of the PDMAEMA precursor polymer. The biocidal activity of the lightly quaternized PQDMAEMA copolymers against Escherichia coli and Staphylococcus aureus was evaluated by calculating the minimum inhibitory concentration (MIC) as well as the minimum bactericidal concentration (MBC) of the polymers and by comparing them to the respective values of the precursor non-quaternized PDMAEMA homopolymer. The antibacterial mechanism of action in the solution was studied by zeta potential measurements, scanning electron microscopy and protein leakage tests signifying the disruption of the outer membrane of the bacterial cells to release their periplasmic proteins.

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

BACKGROUND

Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).

RESULTS

Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.

CONCLUSIONS

Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.

Synthesis, in silico studies and antibacterial assessment of α-amino phosphonates derivatives

The widespread of multi-resistant strains due to the lack of specific treatment and the propagation of infectious diseases requires all resources to remedy this scourge. This study is therefore aimed to assess the antibacterial activity of four synthetic α-Aminophosphonate 4(a-d). Methods: Firstly, α-Aminophosphonate has been synthesized and characterized, then molecular docking of these compounds 4(a-d) into the active binding site of Escherichia coli MurB enzyme (PDB Id: 1MBT) was performed to gain a comprehensive understanding of their biological activity. These compounds have been subjected to in vitro antibacterial screening against three multi-resistant strains E. coli, S. aureus, and L. monocytogenes. These compounds showed crucial antibacterial behavior against all studied strains. Thus, their docking estimation supported the in vitro results and showed that the 4c derivative has considerable binding energy towards the active site of Escherichia coli MurB. These findings provide critical information for the exploration of α-amino phosphonates as novel antibacterial agents.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

Deep learning-based real-time detection of novel pathogens during sequencing

Novel pathogens evolve quickly and may emerge rapidly, causing dangerous outbreaks or even global pandemics. Next-generation sequencing is the state of the art in open-view pathogen detection, and one of the few methods available at the earliest stages of an epidemic, even when the biological threat is unknown. Analyzing the samples as the sequencer is running can greatly reduce the turnaround time, but existing tools rely on close matches to lists of known pathogens and perform poorly on novel species. Machine learning approaches can predict if single reads originate from more distant, unknown pathogens but require relatively long input sequences and processed data from a finished sequencing run. Incomplete sequences contain less information, leading to a trade-off between sequencing time and detection accuracy. Using a workflow for real-time pathogenic potential prediction, we investigate which subsequences already allow accurate inference. We train deep neural networks to classify Illumina and Nanopore reads and integrate the models with HiLive2, a real-time Illumina mapper. This approach outperforms alternatives based on machine learning and sequence alignment on simulated and real data, including SARS-CoV-2 sequencing runs. After just 50 Illumina cycles, we observe an 80-fold sensitivity increase compared to real-time mapping. The first 250 bp of Nanopore reads, corresponding to 0.5 s of sequencing time, are enough to yield predictions more accurate than mapping the finished long reads. The approach could also be used for screening synthetic sequences against biosecurity threats.

Adaptation of the WHO Hand Hygiene Observation Form for Application in Optometry Training Facilities

BACKGROUND

The link between hand and surface hygiene and the spread of disease has been reported by various studies and understanding the appropriate use of hand hygiene is important in healthcare. The World Health Organization (WHO) introduced the "My Five Moments for Hand Hygiene" model to educate healthcare workers about the importance of hand hygiene to stop the spread of disease.

OBJECTIVE

The objectives of this paper were to determine if the WHO Hand Hygiene Observation Form could be used to monitor for hand and personal hygiene practices of Optometry students, and what their actual hygiene practices are in an Optometry training facility in South Africa.

METHODS

This cross-sectional study was performed at an Optometry training facility in South Africa using third (n=32) and fourth year (n=39) students. The Hand Hygiene Knowledge Questionnaire for Health Care Workers by the WHO was used to determine their knowledge regarding hand hygiene. After completing the questionnaire, participants were observed in the clinic while consulting patients to determine the hand and surface hygiene practices they apply.

RESULTS

The WHO hand hygiene observation rubric was not appropriate to evaluate hand and surface hygiene in Optometry facilities. The adapted observation rubric created was a better tool to evaluate student hygiene practices and was able to record which hand or surface hygiene were missed when presented with such opportunities. Although 90.1% of the students knew that germs could be transferred to the patients via hands, only 46.5% routinely used an alcohol-based hand sanitizer.

CONCLUSION

This observation rubric developed during this study can assist in creating awareness with students about their own hand and surface hygiene deficiencies when interacting with patients.

Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model

Instead of conventional serotyping and virulence gene combination methods, methods have been developed to evaluate the pathogenic potential of newly emerging pathogens. Among them, the machine learning (ML)-based method using whole-genome sequencing (WGS) data are getting attention because of the recent advances in ML algorithms and sequencing technologies. Here, we developed various ML models to predict the pathogenicity of Shiga toxin-producing Escherichia coli (STEC) isolates using their WGS data. The input dataset for the ML models was generated using distinct gene repertoires from positive (pathogenic) and negative (nonpathogenic) control groups in which each STEC isolate was designated based on the source attribution, the relative risk potential of the isolation sources. Among the various ML models examined, a model using the support vector machine (SVM) algorithm, the SVM model, discriminated between the two control groups most accurately. The SVM model successfully predicted the pathogenicity of the isolates from the major sources of STEC outbreaks, the isolates with the history of outbreaks, and the isolates that cannot be assessed by conventional methods. Furthermore, the SVM model effectively differentiated the pathogenic potentials of the isolates at a finer resolution. Permutation importance analyses of the input dataset further revealed the genes important for the estimation, proposing the genes potentially essential for the pathogenicity of STEC. Altogether, these results suggest that the SVM model is a more reliable and broadly applicable method to evaluate the pathogenic potential of STEC isolates compared with conventional methods.

Hsp100 Molecular Chaperone ClpB and Its Role in Virulence of Bacterial Pathogens

This review focuses on the molecular chaperone ClpB that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and its biological function in selected bacterial pathogens, causing a variety of human infectious diseases, including zoonoses. It has been established that ClpB disaggregates and reactivates aggregated cellular proteins. It has been postulated that ClpB’s protein disaggregation activity supports the survival of pathogenic bacteria under host-induced stresses (e.g., high temperature and oxidative stress), which allows them to rapidly adapt to the human host and establish infection. Interestingly, ClpB may also perform other functions in pathogenic bacteria, which are required for their virulence. Since ClpB is not found in human cells, this chaperone emerges as an attractive target for novel antimicrobial therapies in combating bacterial infections.

Rapid detection of Klebsiella pneumoniae producing extended spectrum β lactamase enzymes by infrared microspectroscopy and machine learning algorithms

Antimicrobial drugs have played an indispensable role in decreasing morbidity and mortality associated with infectious diseases. However, the resistance of bacteria to a broad spectrum of commonly-used antibiotics has grown to the point of being a global health-care problem. One of the most important classes of multi-drug resistant bacteria is Extended Spectrum Beta-Lactamase-producing (ESBL+) bacteria. This increase in bacterial resistance to antibiotics is mainly due to the long time (about 48 h) that it takes to obtain lab results of detecting ESBL-producing bacteria. Thus, rapid detection of ESBL+ bacteria is highly important for efficient treatment of bacterial infections. In this study, we evaluated the potential of infrared microspectroscopy in tandem with machine learning algorithms for rapid detection of ESBL-producing Klebsiella pneumoniae (K. pneumoniae) obtained from samples of patients with urinary tract infections. 285 ESBL+ and 365 ESBL-K. pneumoniae samples, gathered from cultured colonies, were examined. Our results show that it is possible to determine that K. pneumoniae is ESBL+ with ∼89% accuracy, ∼88% sensitivity and ∼89% specificity, in a time span of ∼20 minutes following the initial culture.