Safety and efficacy of phage application in bacterial decolonisation: a systematic review

Real-Time in Vivo Bacterial Imaging by Computed Tomography and Fluorescence Using Phage-Gold Nanorod Bioconjugates as Contrast Agents

Real-time in vivo imaging of bacterial infections is an important goal to aid the study and treatment of bacterial infections. Phages can be genetically engineered to ensure a particular biomolecular target specificity, and gold nanomaterials can be conjugated to phages for a variety of applications including biosensing. In this paper, we describe methods to use phage-gold nanorod conjugates for in vivo detection and imaging of the bacterial species Pseudomonas aeruginosa in mice. The imaging modalities are computed tomography (CT), using gold as a contrast agent, and fluorescence, which can be applied when the FDA-approved near-infrared (NIR) dye indocyanine green (ICG) is also chemically cross-linked to the bioconjugates. In addition, rapid protocols for validating bioconjugate synthesis and the initial assessment of toxicity are given. In this example, the phage-gold nanorod probe is shown to specifically highlight P. aeruginosa without cross-reactivity to another Gram-negative organism (V. cholerae) in vivo and appears to be biocompatible. Phage-directed imaging probes may thus be useful for the characterization and diagnosis of bacterial infections.

Trial design of bacteriophage therapy for nontuberculous mycobacteria pulmonary disease in cystic fibrosis: The POSTSTAMP study

Bacteriophages (phages) are viruses that selectively infect bacteria and have been utilized to treat Mycobacterium abscessus (Mab) with varying success. The POSTSTAMP study is an ongoing, multi-site phage therapy protocol for treatment-refractory pulmonary Mab disease in people with cystic fibrosis (pwCF). Participants (n = 10) are prospectively assessed while utilizing FDA investigational new drug (IND) approval for compassionate use. Participants are >6 years old, able to produce sputum, have been treated with guideline-based antibiotic therapy (GBT) for >12 months without culture conversion, and are currently receiving GBT with at least 3 and ≥ 80 % positive Mab cultures in the prior year. At enrollment, an isolate is assessed for the availability of lytic phage(s). Open-label phage therapy consists of 1 or 2 phages administered intravenously twice daily for 52 weeks. Participants without a phage match will be followed on GBT as a comparison group. Follow-up visits will occur monthly, with one follow-up visit at completion and intermittent visits for a year after phage therapy. Efficacy will be assessed by culture, standard clinical measures and a patient-reported quality-of-life instrument. Frequency of Mab detection 12 months prior to treatment will be compared with the 12-month period beginning 6 months after treatment initiation. Individual-level tests of difference in percent positive cultures within subjects will be used to identify "responders". Collectively and including all persons, a mixed-effect model will be used to test for a difference in frequency of Mab detection following treatment or without treatment. The trial will also test for markers of treatment failure and pathogen adaptation in participants who did not achieve microbiological response, and will monitor for safety and tolerance.

Stool carriage of CTX-M/CMY-producing Salmonella enterica in a Chinese tertiary hospital in Shenzhen, China

Salmonellosis, caused by non-typhoidal Salmonella, is a common foodborne gastrointestinal infection. Third-generation cephalosporins are recommended as the first-line treatment for Salmonella infections. Our study aimed to investigate the molecular epidemiology, antimicrobial resistance, and the transmission of extended-spectrum β-lactamases (ESBL) genes in 96 clinical Salmonella isolates collected between 2020 and 2022 at a tertiary hospital in Shenzhen, China. We performed antimicrobial susceptibility testing and whole-genome sequencing to identify serotypes, multilocus sequence typing, antimicrobial resistance genes in these isolates, and the genetic structures of the bla CTX-M/bla CMY genes. Seventeen Salmonella serotypes were identified, with S. 4,[5],12:i:- (37.5%) being the most common, followed by S. Enteritidis (15.63%), S. Typhimurium (14.58%), S. London (7.29%), and S. Rissen (5.21%). MLST analysis revealed 19 distinct sequence types (STs), with ST34 being the most prevalent (36.46%), followed by ST11 (15.63%) and ST19 (13.54%). Antimicrobial resistance testing showed those isolates had high levels of resistance to ampicillin (72.92%) and tetracycline (71.88%), with 70.83% of isolates as multidrug-resistant (MDR). Three bla CTX-M genes (bla CTX-M-14, bla CTX-M-55, and bla CTX-M-65) and bla CMY-2 were identified among 18 cefotaxime-resistant strains, of which one and 12 isolates successfully transferred bla CMY or bla CTX-M to E. coli C600 via conjugation, respectively. The bla CTX-M/bla CMY-2-carrying contigs in nine Salmonella isolates ranged from 2,156 to 164,862 bp, were located either on the chromosome (n=1) or plasmids (IncI1, IncK1, IncA/C) (n=9), and the bla CTX-M/bla CMY-2 genes were associated with ISEcp1. Our study demonstrates the diversity of MDR Salmonella serotypes in clinical isolates, and highlights the role of plasmids and mobile genetic elements in the horizontal transfer of bla CTX-M/bla CMY, emphasizing the need for continuous surveillance of Salmonella in clinical samples.

Cutibacterium acnes bacteriophage therapy: exploring a new frontier in acne vulgaris treatment

The skin microbiome, encompassing a variety of microorganisms, plays a critical role in skin health and function. Acne vulgaris, affecting approximately 9.4% of the global population, is a prevalent skin condition primarily targeting pilosebaceous units rich in sebaceous glands. The condition is influenced by factors such as hormonal changes, sebaceous gland dysfunction, and the activity of Cutibacterium acnes, a gram-positive bacterium linked to acne development. The skin's immune system, particularly keratinocytes with pattern recognition receptors like Toll-like receptors (TLRs), plays a crucial role in recognizing and responding to bacterial presence. The onset of acne is often linked to adolescence, marked by significant hormonal fluctuations. Genetics also plays a role, with family history being a notable risk factor. Acne is characterized by distinct alterations in the C. acnes composition, with specific phylotypes associated with either commensal or pathogenic behavior. Traditional treatments include antibiotics, but the rise of antibiotic resistance has led to exploring alternative therapies, such as bacteriophage therapy. Bacteriophages offer a targeted approach to treating acne by targeting C. acnes strains, potentially reducing antibiotic resistance and enhancing treatment efficacy. Phage therapy shows promise, but further research is needed to fully understand its effectiveness and potential in clinical applications. Additionally, combining phages with antibiotics may offer a synergistic approach to overcoming antibiotic resistance and managing acne.

In vitro characterization and genome sequencing of two novel lytic phages against Salmonella Infantis isolated from poultry feces

Introduction

Salmonella spp. is the second most common bacteria associated with foodborne gastrointestinal outbreaks in humans, with the highest contamination levels in meat, especially poultry. Salmonella enterica subsp. enterica serovar Infantis is the primary serovar isolated from broilers, without causing any symptomatic disease. Conversely, certain human strains can result in symptomatic illness (fever, headache, and diarrhoea). Therefore, reducing S. Infantis colonization in broilers is important before slaughter, to prevent this pathogen carryover along the food chain.

Methods

Here, we report the characterization of two S. Infantis virulent phages, isolated from broiler feces. Isolates were phenotypically and genetically characterized.

Results and discussion

Phages (ɸ) SaI_NFG_5581 and SaI_NFG_5577 were characterized as strictly lytic versus S. Infantis but with different bacteriolytic activities and genetic features. They both belong to the Caudoviricetes class, but ɸSaI_NFG_5581 (genome length 112,970 bp) belongs to the Demerecviridae family while ɸSaI_NFG_5577 (genome length 42,481 bp) to the Guernseyvirinae family. Genomic analysis excluded the presence of lysogeny, toxin, or antimicrobial resistance genes, and for those reasons, the two phages could be considered safe. Phages are stable under a broad range of pH (4-10) and temperature (4°C-50°C) conditions. In vitro, both ɸSaI_NFG_5581 and ɸSaI_NFG_5577 were able to lower Salmonella counts of about 2.2 LOG/mL and 3.4 LOG CFU/mL respectively, at MOI 0.1 after 2 h of treatment. After 24 h, Salmonella counts treated with both phages remained lower than the control (non-phage-treated Salmonella). These newly isolated phages have promising features, which could be exploited and further studied for potential in vivo application.

Expression, purification and characterization of CTP synthase PyrG in Staphylococcusaureus

Staphylococcus aureus (S. aureus) presents a significant challenge in both nosocomial and community settings due to its pathogenicity. The emergence of drug-resistant strains exacerbates S. aureus infections, leading to increased mortality rates. PyrG, a member of the cytidine triphosphate (CTP) synthase family, serves as a crucial therapeutic target against S. aureus due to the pivotal role of CTP in cellular metabolism. However, the structural and mechanistic details of S. aureus PyrG remains unknown. Here, we successfully expressed and purified monomeric PyrG. Mutational experiments were conducted based on the results of molecular docking. Based on the results of the molecular docking, we carried out mutation experiments and found that Q386A dramatically decreased the CTP synthase activity compared to the wild-type protein, while Y54A almost completely abolished the activity. Exposure of S. aureus to the kinase inhibitor crizotinib increased expression of gene pyrG. Our results identify the two key sites on PyrG for the CTP synthase activity, and present PyrG gene expression increased during the treatment of crizotinib, which may eventually provide valuable guidance for the development of new drugs against S. aureus infections.

Phage-based delivery systems: engineering, applications, and challenges in nanomedicines

Bacteriophages (phages) represent a unique category of viruses with a remarkable ability to selectively infect host bacteria, characterized by their assembly from proteins and nucleic acids. Leveraging their exceptional biological properties and modifiable characteristics, phages emerge as innovative, safe, and efficient delivery vectors. The potential drawbacks associated with conventional nanocarriers in the realms of drug and gene delivery include a lack of cell-specific targeting, cytotoxicity, and diminished in vivo transfection efficiency. In contrast, engineered phages, when employed as cargo delivery vectors, hold the promise to surmount these limitations and attain enhanced delivery efficacy. This review comprehensively outlines current strategies for the engineering of phages, delineates the principal types of phages utilized as nanocarriers in drug and gene delivery, and explores the application of phage-based delivery systems in disease therapy. Additionally, an incisive analysis is provided, critically examining the challenges confronted by phage-based delivery systems within the domain of nanotechnology. The primary objective of this article is to furnish a theoretical reference that contributes to the reasoned design and development of potent phage-based delivery systems.

Persistent Colonization of Ciprofloxacin-Resistant and Extended-Spectrum β-Lactamase (ESBL)-Producing Salmonella enterica Serovar Kentucky ST198 in a Patient with Inflammatory Bowel Disease

Objective

Salmonella enterica serovar Kentucky ST198 has emerged as a global threat to humans. In this study, we aimed to characterize the prolonged carriage of ciprofloxacin-resistant and extended-spectrum β-lactamase (ESBL)-producing S. Kentucky ST198 in a single patient with inflammatory bowel disease (IBD).

Methods

Three S. Kentucky strains were collected from a single patient with IBD on 11th January, 23rd January, and 8th February, 2022, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis with 38 previously described Chinese S. Kentucky ST198 strains from patients and food were performed.

Results

All three S. Kentucky isolates belonged to ST198. They carried identical 16 resistance genes, such as blaCTX-M-55, tet(A), and qnrS1, and had identical mutations within gyrA (S83F and D87N) and parC (S80I). Therefore, they exhibited identical multidrug-resistant profiles, including the clinically important antibiotics cephalosporins (ceftazidime and cefepime), fluoroquinolones (ciprofloxacin and levofloxacin), and third-generation tetracycline (tigecycline). Our three S. Kentucky strains were classified into the subclade ST198.2-2, and were genetically identical (2-6 SNPs) to each other. They exhibited a close genetic similarity (15-20 SNPs) to the isolate NT-h3189 from a patient and AH19MCS1 from chicken meat in China, indicating a possible epidemiological link between these S. Kentucky ST198 isolates from the patients and chicken meat.

Conclusion

Long-term colonization of ciprofloxacin-resistant and ESBL-producing S. Kentucky ST198 in a single patient is a matter of concern. Due to the potential transfer of S. Kentucky ST198 from food sources to humans, ongoing surveillance of this particular clone in animals, animal-derived food products, and humans should be strengthened.