The continued global pandemic of coronavirus disease 2019 (COVID-19) poses a serious threat to global public health and social stability and it has become a serious global public health problem. Unfortunately, existing diagnostic and therapeutic approaches for the prevention and control of COVID-19 have many shortcomings. In recent years, the emerging CRISPR/Cas technology can complement the problems of traditional methods. Biological tools based on CRISPR/Cas systems have been widely used in biomedicine. In particular, they are advantageous in pathogen detection, clinical antiviral therapy, drug, and vaccine development. Therefore, CRISPR/Cas technology may have great potential for application in the prevention and control of COVID-19 and emerging infectious diseases in the future. This article summarizes the existing applications of CRISPR/Cas technology in infectious diseases with the aim of providing effective strategies for the prevention and control of COVID-19 and other emerging infectious diseases in the future.

Background: Vaccination is a highly effective strategy for the prevention of enterovirus A71 (EV-A71)—hand, foot, and mouth disease (HFMD). Three inactivated EV-A71 vaccines in China have demonstrated remarkable efficacy against EV-A71-HFMD during clinical trials, exhibiting vaccine effectiveness (VE) exceeding 90% and few adverse events (AEs). However, the effectiveness of vaccines in the real world and its impact on the epidemiological characteristics of HFMD after the use of EV-A71 inactivated vaccine are uncertain. Methods: The odd ratio (OR) and 95% confidence (CI) were used as the effect estimates of the meta-analysis in the test-negative design (TND), and the OR was used to calculate VE: VE = (1 − OR) × 100%. Results: According to the literature search strategy, a comprehensive search was conducted in PubMed, Web of Science (including Chinese Science Citation Database and MEDLINE), and Embase, and 18 records were ultimately included in this study. Subsequently, the overall VE and 95% CI of different vaccine doses were analyzed, with the one-dose vaccine at 66.9% (95% CI: 45.2–80.0%) and the two-dose vaccine at 84.2% (95% CI: 79.4–87.9%). Additionally, the most reported AEs were mild general reactions without any rare occurrences. Simultaneously, the widespread use of the EV-A71 vaccine would lead to a reduction in both the incidence of EV-A71-associated HFMD and severe cases caused by EV-A71. Conclusion: The administration of the two-dose EV-A71 vaccine is highly effective in preventing HFMD in the real world, and the widespread use of the EV-A71 vaccine leads to a reduction in the incidence of EV-A71-associated HFMD and that of severe cases caused by EV-A71. The findings suggest that administering the two-dose EV-A71 inactivated vaccine to children aged 6 months to 71 months can be effective in preventing EV-A71-associated HFMD, highlighting the need for developing a multivalent HFMD vaccine for preventing cases not caused by EV-A71.

The increase in the antimicrobial resistance (AMR) of Staphylococcus aureus (S. aureus) has become a global public health concern. This study globally monitored the large-scale longitudinal trend of AMR in S. aureus and examined the various human and environmental climate factors that influence the occurrence and spread of AMR in S. aureus, which might provide valuable data to support the development of a global surveillance system for S. aureus AMR and provide a theoretical basis for coordinated actions to control the emergence and development of AMR from multiple perspectives. There was a significantly positive correlation between the number of antibiotic resistance genes (ARGs) in S. aureus and the collection year, with a sharp increase in ARGs over time. The number of ARGs in S. aureus genomes significantly increased each decade, with the average number of ARGs per genome rising from 10.37 ± 3.55 before 1990 to 12.75 ± 4.04 after 2010, suggesting a growing problem of S. aureus AMR. The Spearman correlation results indicated that the human development index (HDI), antibiotic consumption, and mobile genetic elements (MGEs) were significantly associated with the AMR of S. aureus, and these factors played a crucial role in the emergence and development of S. aureus AMR. The results of structural equation modeling showed that the HDI significantly promoted an increase in antibiotic consumption, thereby indirectly enhancing the AMR of S. aureus. Antibiotic consumption also indirectly facilitated the progression of AMR in S. aureus through its impact on MGEs. The results of restricted cubic spline and generalized linear models showed that climate change also played a significant role in the progression of S. aureus AMR. In summary, this study provides a theoretical framework for monitoring the longitudinal trend of ARGs in S. aureus isolates and examining the possible influencing variables of ARGs in these isolates.

Bloodstream infections (BSIs) caused by antibiotic-resistant bacteria (ARB) represent a significant disease burden worldwide. However, a comprehensive analysis of the mortality rates and global epidemiology across different ARB species associated with BSIs is currently lacking. We conducted a systematic review by searching multiple databases (PubMed, Web of Science, and Embase) for studies reporting ARB-related BSIs data up to June 19, 2023. Additionally, we performed genomic analyses of all the publicly available bacterial genomes associated with BSIs to elucidate their molecular characteristics. A total of 322 articles (N = 90,672 patients) were included in this study. For 28 or 30-day mortality, the overall mortality rate for all ARB species was 32.0%. Among them, antibiotic-resistant A. baumannii exhibited the highest rate (54.2%). And the top three ARB types with the highest mortality rates at 28 or 30-day were CefeR-PA (cefepime-resistant P. aeruginosa), CREC (carbapenem-resistant E. coli), and CRAB (carbapenem-resistant A. baumannii), all exceeding 50%, whereas the mortality rates of CRKP (carbapenem-resistant K. pneumoniae), CRPA (carbapenem-resistant P. aeruginosa), and VREfm (vancomycin-resistant E. faecium) were at least 40%. A total of 9,289 ARB genomes related to BSIs were acquired from the NPDIB database and are predominantly distributed in North America, Asia, and Europe. Antibiotic resistance gene (ARG) analysis identified a total of 613 ARG subtypes from the top six ARB species, with numbers ranging from 48 for E. faecium to 253 for K. pneumoniae. Furthermore, specific clones of ARB species were strongly associated with BSIs, such as ST131 in E. coli, ST8, and ST5 in S. aureus, ST2 in A. baumannii, and ST11 and ST258 in K. pneumoniae. ARB contributed to the burden of BSIs, with a 30-day all-cause mortality rate as high as 32.0%. ARB strains causing BSIs display high genetic diversity, highlighting the importance of continuing to monitor high-risk clones to control the development of antibiotic resistance. Differences in ARGs patterns require tailored antibiotic management strategies for each ARB species.

CRISPR systems are often encoded by many prokaryotes as adaptive defense against mobile genetic elements (MGEs), but several MGEs also recruit CRISPR components to perform additional biological functions. Type IV-A systems are identified in Klebsiella plasmids, yet the distribution, characterization, and role of these plasmids carrying CRISPR systems in the whole Klebsiella genus remain unclear. Here, we performed large-scale comparative analysis of these plasmids using publicly available plasmid genomes.