The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes.

Repeated exposure to antibiotics and changes in the diet and environment shift the gut microbial diversity and composition, making the host susceptible to pathogenic infection. The emergence and ongoing spread of AMR pathogens is a challenging public health issue. Recent evidence showed that probiotics and prebiotics may play a role in decolonizing drug-resistant pathogens by enhancing the colonization resistance in the gut. This review aims to analyze available evidence from human-controlled trials to determine the effect size of probiotic interventions in decolonizing AMR pathogenic bacteria from the gut. We further studied the effects of prebiotics in human and animal studies. PubMed, Embase, Web of Science, Scopus, and CINAHL were used to collect articles. The random-effects model meta-analysis was used to pool the data. GRADE Pro and Cochrane collaboration tools were used to assess the bias and quality of evidence. Out of 1395 citations, 29 RCTs were eligible, involving 2871 subjects who underwent either probiotics or placebo treatment to decolonize AMR pathogens. The persistence of pathogenic bacteria after treatment was 22%(probiotics) and 30.8%(placebo). The pooled odds ratio was 0.59(95% CI:0.43-0.81), favoring probiotics with moderate certainty (p = 0.0001) and low heterogeneity (I2 = 49.2%, p = 0.0001). The funnel plot showed no asymmetry in the study distribution (Kendall'sTau = -1.06, p = 0.445). In subgroup, C. difficile showed the highest decolonization (82.4%) in probiotics group. Lactobacillus-based probiotics and Saccharomyces boulardii decolonize 71% and 77% of pathogens effectively. The types of probiotics (p < 0.018) and pathogens (p < 0.02) significantly moderate the outcome of decolonization, whereas the dosages and regions of the studies were insignificant (p < 0.05). Prebiotics reduced the pathogens from 30% to 80% of initial challenges. Moderate certainty of evidence suggests that probiotics and prebiotics may decolonize pathogens through modulation of gut diversity. However, more clinical outcomes are required on particular strains to confirm the decolonization of the pathogens. Protocol registration: PROSPERO (ID = CRD42021276045).

Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning.

BACKGROUND: Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), exhibits a broad host range, manifesting as both a beneficial commensal and an opportunistic pathogen across various species. In humans, it poses significant risks, causing neonatal sepsis and meningitis, along with severe infections in adults. Additionally, it impacts livestock by inducing mastitis in bovines and contributing to epidemic mortality in fish populations. Despite its wide host spectrum, the mechanisms enabling GBS to adapt to specific hosts remain inadequately elucidated. Therefore, the development of a rapid and accurate method differentiates GBS strains associated with particular animal hosts based on genome-wide information holds immense potential. Such a tool would not only bolster the identification and containment efforts during GBS outbreaks but also deepen our comprehension of the bacteria's host adaptations spanning humans, livestock, and other natural animal reservoirs. METHODS AND RESULTS: Here, we developed three machine learning models-random forest (RF), logistic regression (LR), and support vector machine (SVM) based on genome-wide mutation data. These models enabled precise prediction of the host origin of GBS, accurately distinguishing between human, bovine, fish, and pig hosts. Moreover, we conducted an interpretable machine learning using SHapley Additive exPlanations (SHAP) and variant annotation to uncover the most influential genomic features and associated genes for each host. Additionally, by meticulously examining misclassified samples, we gained valuable insights into the dynamics of host transmission and the potential for zoonotic infections. CONCLUSIONS: Our study underscores the effectiveness of random forest (RF) and logistic regression (LR) models based on mutation data for accurately predicting GBS host origins. Additionally, we identify the key features associated with each GBS host, thereby enhancing our understanding of the bacteria's host-specific adaptations.

Synergism of colistin and globular endolysins against multidrug-resistant gram-negative bacteria.

Endolysins (lysins), a novel class of antibacterial agents derived from bacteriophages, efficiently lyse bacteria by degrading the peptidoglycan layer within the bacterial wall. Colistin, a classic peptide antibiotic with the ability to permeabilize the outer membrane, has recently shown great promise in synergizing with lysins against gram-negative bacteria. However, the exact mechanisms responsible for their synergy remain unclear. Here, we first demonstrated the synergistic bacterial killing of various lysin and colistin combinations. With a model lysin, LysAB2, we then confirmed that there is a threshold concentration of colistin causing sufficient permeabilization of the outer membrane for lysin to access the peptidoglycan layer and subsequently exert its lytic ability. The threshold colistin concentrations were found to range 0.2-0.8 µM for the tested bacteria, with the exact value largely depending on the density of lipopolysaccharides on the outer membrane. Beyond the threshold colistin level, LysAB2 could synergize with colistin at a concentration as low as 0.31 µM. Next, we proved for the first time that lysin-induced degradation of the peptidoglycan layer facilitated the disruption of cytoplasmic membrane by colistin, elevated the level of reactive oxygen species in bacterial cells, and boosted the killing effect of colistin. Additionally, the colistin-lysin combination could effectively eliminate established biofilms due to the biofilm dispersal ability of lysin. The in-vivo efficacy was preliminary confirmed in a Galleria mellonella infection model for combination with colistin doses (≥ 1.8 µg/larvae), which could reach beyond the threshold concentration, and a fixed LysAB2 dose (10 µg/larvae). In summary, our study provided the first experimental evidence unravelling the mechanisms behind the synergy of colistin and lysins. All these findings provided important insights in guiding the dosing strategy for applying this combination in future development.

Global epidemiology of asymptomatic colonisation of methicillin-resistant Staphylococcus aureus in the upper respiratory tract of young children: a systematic review and meta-analysis.

OBJECTIVE: To estimate the global prevalence of asymptomatic colonisation, and determine the associated risk factors, antibiotic resistance and genotypes of methicillin-resistant Staphylococcus aureus (MRSA) in the upper respiratory tract of young children. DESIGN: Four bibliometric databases were searched for publications between 2010 and 2022 according to the protocol registered in PROSPERO. Cross-sectional or cohort studies describing the prevalence of asymptomatic colonisation of S. aureus and MRSA in young children were included. Data extraction and analysis were carried out by two reviewers independently according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 statement. Pooled prevalence was estimated using a random effects model. SETTING AND STUDIES: We included studies where children without respiratory tract infection or Staphylococcal infection were recruited from the community, children's institutions (ie, nurseries, kindergartens, daycare centres and preschools) and healthcare centre visits and assessed for asymptomatic colonisation with S. aureus and MRSA. MAIN OUTCOME MEASURES: The pooled prevalence of asymptomatic colonisation of S. aureus and MRSA of young children globally. RESULTS: In this systematic review and meta-analysis of 21 416 young children, the pooled global prevalence of asymptomatic S. aureus colonisation was 25.1% (95% CI 21.4 to 28.8) and MRSA colonisation was 3.4% (95% CI 2.8 to 4.1). The clones of MRSA strains included healthcare-associated MRSA, community-associated MRSA and livestock-associated MRSA. CONCLUSION: This study provides evidence of increased MRSA colonisation globally among young children, underlining the critical role of asymptomatic carriers in MRSA transmission and the need for control measures. PROSPERO REGISTRATION NUMBER: CRD 42022328385.

Characterization of group A streptococci causing invasive diseases in Sri Lanka.

Group A ß haemolytic streptococcus (GAS) or Streptococcus pyogenes is a human pathogen that causes an array of infections, including pharyngitis, cellulitis, impetigo, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. The present study characterizes 51 GAS isolates from invasive infections in Sri Lanka, focusing on resistance profiles, genetic determinants of resistance, and virulence markers. Isolates were tested for sensitivity to penicillin, erythromycin, clindamycin, and tetracycline. The presence of erm(A), erm(B), and mef(A) was detected in erythromycin-resistant isolates, while tet(M) was detected in the tetracycline-resistant isolates. PCR was used to identify SpeA, SpeB, SpeC, SpeF, SpeG, smez, and ssa as virulence markers. Selected GAS isolates were emm-typed using the updated CDC protocol. All 51 isolates were susceptible to penicillin. The number of isolates non-susceptible to erythromycin was 16. The commonest resistance determinant identified was erm(B) (11/16). Tetracycline non-susceptibility was found in 36 (70.6 %) isolates and 26 of them contained the tet(M) gene. Thirteen (25.5 %) isolates were resistant to both tetracycline and erythromycin, while 12 (23.5 %) isolates were sensitive to both antibiotics. The commonest virulence markers detected among the isolates were SpeB (44, 86.3 %), SpeG (36, 70.6 %), and SpeF (35, 68.6 %), while SpeJ (15, 29.4 %), SpeA (10, 19.6 %), and ssa (5,9.8 %) were less common. The emm types were diverse. In conclusion, the GAS isolates studied showed resistance to erythromycin and tetracycline, while retaining universal susceptibility to penicillin. Additionally, these isolates exhibited diverse genetic backgrounds, displaying varying patterns of virulence genes and emm types.

Storage stability of lysostaphin solution and its pulmonary delivery.

Methicillin-resistant Staphylococcus aureus (MRSA) has become a leading causative pathogen of nosocomial pneumonia with an alarming in-hospital mortality rate of 30%. Last resort antibiotic, vancomycin, has been increasingly used to treat MRSA infections, but the rapid emergence of vancomycin-resistant strains urges the development of alternative treatment strategies against MRSA-associated pneumonia. The bacteriolytic enzyme, lysostaphin, targeting the cell wall peptidoglycan of S. aureus, has been considered as a promising alternative for MRSA infections. Its proteinaceous nature is likely benefit from direct delivery to the lungs, but the challenges for successful pulmonary delivery of lysostaphin lying on a suitable inhalation device and a formulation with sufficient storage stability. In this study, the applicability of a vibrating mesh nebulizer (Aerogen Solo®) and a soft mist inhaler (Respimat®) was investigated. Both devices were capable of aerosolizing lysostaphin solution into inhalable droplets and caused minimum antibacterial activity loss. In addition, lysostaphin stabilized with phosphate-buffered saline and 0.1% Tween 80 was proved to have acceptable stability for at least 12 months when stored at 4 °C. These promising data encourage further clinical development of lysostaphin for management of MRSA-associated lung infections.

Implants coating strategies for antibacterial treatment in fracture and defect models: A systematic review of animal studies.

Objective: Fracture-related infection (FRI) remains a major concern in orthopaedic trauma. Functionalizing implants with antibacterial coatings are a promising strategy in mitigating FRI. Numerous implant coatings have been reported but the preventive and therapeutic effects vary. This systematic review aimed to provide a comprehensive overview of current implant coating strategies to prevent and treat FRI in animal fracture and bone defect models. Methods: A literature search was performed in three databases: PubMed, Web of Science and Embase, with predetermined keywords and criteria up to 28 February 2023. Preclinical studies on implant coatings in animal fracture or defect models that assessed antibacterial and bone healing effects were included. Results: A total of 14 studies were included in this systematic review, seven of which used fracture models and seven used defect models. Passive coatings with bacteria adhesion resistance were investigated in two studies. Active coatings with bactericidal effects were investigated in 12 studies, four of which used metal ions including Ag+ and Cu2+; five studies used antibiotics including chlorhexidine, tigecycline, vancomycin, and gentamicin sulfate; and the other three studies used natural antibacterial materials including chitosan, antimicrobial peptides, and lysostaphin. Overall, these implant coatings exhibited promising efficacy in antibacterial effects and bone formation. Conclusion: Antibacterial coating strategies reduced bacterial infections in animal models and favored bone healing in vivo. Future studies of implant coatings should focus on optimal biocompatibility, antibacterial effects against multi-drug resistant bacteria and polymicrobial infections, and osseointegration and osteogenesis promotion especially in osteoporotic bone by constructing multi-functional coatings for FRI therapy. The translational potential of this paper: The clinical treatment of FRI is complex and challenging. This review summarizes novel orthopaedic implant coating strategies applied to FRI in preclinical studies, and offers a perspective on the future development of orthopaedic implant coatings, which can potentially contribute to alternative strategies in clinical practice.

Predicting antibiotic susceptibility in urinary tract infection with artificial intelligence-model performance in a multi-centre cohort.

Objective: To develop an artificial intelligence model to predict an antimicrobial susceptibility pattern in patients with urinary tract infection (UTI). Materials and methods: 26 087 adult patients with culture-proven UTI during 2015-2020 from a university teaching hospital and three community hospitals in Hong Kong were included. Cases with asymptomatic bacteriuria (absence of diagnosis code of UTI, or absence of leucocytes in urine microscopy) were excluded. Patients from 2015 to 2019 were included in the training set, while patients from the year 2020 were included as the test set.Three first-line antibiotics were chosen for prediction of susceptibility in the bacterial isolates causing UTI: namely nitrofurantoin, ciprofloxacin and amoxicillin-clavulanate. Baseline epidemiological factors, previous antimicrobial consumption, medical history and previous culture results were included as features. Logistic regression and random forest were applied to the dataset. Models were evaluated by F1-score and area under the curve-receiver operating characteristic (AUC-ROC). Results: Random forest was the best algorithm in predicting susceptibility of the three antibiotics (nitrofurantoin, amoxicillin-clavulanate and ciprofloxacin). The AUC-ROC values were 0.941, 0.939 and 0.937, respectively. The F1 scores were 0.938, 0.928 and 0.906 respectively. Conclusions: Random forest model may aid judicious empirical antibiotics use in UTI. Given the reasonable performance and accuracy, these accurate models may aid clinicians in choosing between different first-line antibiotics for UTI.

LOX-1 acts as an N6-methyladenosine-regulated receptor for Helicobacter pylori by binding to the bacterial catalase.

The role of N6-methyladenosine (m6A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulates host m6A methylases and increases m6A levels in gastric epithelial cells. Reducing m6A methylase activity via hemizygotic deletion of methylase-encoding gene Mettl3 in mice, or via small interfering RNAs targeting m6A methylases, enhances H. pylori colonization. We identify LOX-1 mRNA as a key m6A-regulated target during H. pylori infection. m6A modification destabilizes LOX-1 mRNA and reduces LOX-1 protein levels. LOX-1 acts as a membrane receptor for H. pylori catalase and contributes to bacterial adhesion. Pharmacological inhibition of LOX-1, or genetic ablation of Lox-1, reduces H. pylori colonization. Moreover, deletion of the bacterial catalase gene decreases adhesion of H. pylori to human gastric sections. Our results indicate that m6A modification of host LOX-1 mRNA contributes to protection against H. pylori infection by downregulating LOX-1 and thus reducing H. pylori adhesion.