Bacteriophages benefit from generalized transduction.

Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.

Epidemiology and clinical characteristics of Morganella morganii infections: A multicenter retrospective study.

BACKGROUND: Morganella morganii is a Gram-negative, opportunistic pathogen that can cause a variety of infections, including bloodstream infections, especially in those with compromised immune systems. It is often resistant to antibiotics, making it a difficult organism to treat. Limited studies have addressed M. morganii, but the organism is becoming increasingly recognized as a public health threat. More research is needed to understand the epidemiology and virulence factors of M. morganii in Saudi Arabia, as well as to develop effective treatment strategies. METHODS: This retrospective study included all M. morganii bloodstream infections patients admitted to five tertiary care hospitals in Saudi Arabia between 2015 and 2022. RESULTS: The study population included 75 patients (45 males and 30 females) between the age of 53-72 with a 54% ICU admission rate. The most comorbidities were hypertension followed by diabetes. The most common symptoms were fever, cough, shortness of breath, vomiting, and fatigue. The study also found that M. morganii was often resistant to multiple antibiotics, including ciprofloxacin, trimethoprim/sulfamethoxazole, gentamicin, amoxicillin, nitrofurantoin, and colistin. The most common treatment for M. morganii bacteremia was carbapenems, followed by aminoglycosides, ciprofloxacin, and colistin. Source control measures, such as surgery, line removal, drainage, and tissue removal, were also used in some cases. The study found that the in-hospital mortality rate for M. morganii bacteremia was 41%. The risk of mortality was increased in patients who were admitted to the ICU, who were older than 65 years, and who had Klebsiella pneumoniae co-infection. CONCLUSION: M. morganii bacteremia is a serious infection that is often resistant to antibiotics. Elderly patients and patients with comorbidities are at increased risk of mortality. Source control measures and appropriate antibiotic therapy are important for improving outcomes.

An Explorative Review on Advanced Approaches to Overcome Bacterial Resistance by Curbing Bacterial Biofilm Formation.

The continuous emergence of multidrug-resistant pathogens evoked the development of innovative approaches targeting virulence factors unique to their pathogenic cascade. These approaches aimed to explore anti-virulence or anti-infective therapies. There are evident concerns regarding the bacterial ability to create a superstructure, the biofilm. Biofilm formation is a crucial virulence factor causing difficult-to-treat, localized, and systemic infections. The microenvironments of bacterial biofilm reduce the efficacy of antibiotics and evade the host's immunity. Producing a biofilm is not limited to a specific group of bacteria; however, Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus biofilms are exemplary models. This review discusses biofilm formation as a virulence factor and the link to antimicrobial resistance. In addition, it explores insights into innovative multi-targeted approaches and their physiological mechanisms to combat biofilms, including natural compounds, phages, antimicrobial photodynamic therapy (aPDT), CRISPR-Cas gene editing, and nano-mediated techniques.

Towards promising antimicrobial alternatives: The future of bacteriophage research and development in Saudi Arabia.

The escalating threat of antibiotic-resistant pathogens resulting from the rapid emergence of antimicrobial resistance (AMR) is a significant health and economic concern worldwide, exacerbated by the misuse of antibiotics in both humans and livestock. This has led to critical challenges when treating infections by multi-drug resistant (MDR) pathogens, which often display high mortality and morbidity rates. An international action plan and multisectoral cooperative approach are therefore needed to combat and halt AMR dissemination. Critical to these efforts are enhanced research programs aimed at identifying new antimicrobial agents, as well as the use of advanced biotechnology tools to develop alternative antimicrobial approaches. Bacteriophages (phages)-viruses that infect and kill bacteria-represent a promising tool for combatting the global threat of antibiotic-resistant pathogens. Phages and their potential applications have been extensively studied in Europe and the United States (US) for decades. However, although health authorities in the Gulf Health Council (GHC), including Saudi Arabia, have developed an action plan to combat AMR, phage research in the Middle East has lagged behind global scientific efforts. Thus, there is still a paucity of phage-related studies in this region, including those focused on therapeutic applications, clinical trials, biotechnology, and biocontrol. This article highlights the importance of bacteriophage research and development and discusses the potential implementation of phage-based therapies in Saudi Arabia.

Screening for Highly Transduced Genes in Staphylococcus aureus Revealed Both Lateral and Specialized Transduction.

Bacteriophage-mediated transduction of bacterial DNA is a major route of horizontal gene transfer in the human pathogen, Staphylococcus aureus. Transduction involves the packaging of bacterial DNA by viruses and enables the transmission of virulence and resistance genes between cells. To learn more about transduction in S. aureus, we searched a transposon mutant library for genes and mutations that enhanced transfer mediated by the temperate phage, ϕ11. Using a novel screening strategy, we performed multiple rounds of transduction of transposon mutant pools selecting for an antibiotic resistance marker within the transposon element. When determining the locations of transferred mutations, we found that the screen had selected for just 1 or 2 transposon mutant(s) within each pool of 96 mutants. Subsequent analysis showed that the position of the transposon, rather than the inactivation of bacterial genes, was responsible for the phenotype. Interestingly, from multiple rounds, we identified a pattern of transduction that encompassed mobile genetic elements as well as chromosomal regions both upstream and downstream of the phage integration site. The latter was confirmed by DNA sequencing of purified phage lysates. Importantly, transduction frequencies were lower for phage lysates obtained by phage infection rather than induction. Our results confirmed previous reports of lateral transduction of bacterial DNA downstream of the integrated phage but also indicated a novel form of specialized transduction of DNA upstream of the phage. These findings illustrated the complexity of transduction processes and increased our understanding of the mechanisms by which phages transfer bacterial DNA. IMPORTANCE Horizontal transfer of DNA between bacterial cells contributes to the spread of virulence and antibiotic resistance genes in human pathogens. For Staphylococcus aureus, bacterial viruses play a major role in facilitating the horizontal transfer. These viruses, termed bacteriophages, can transfer bacterial DNA between cells by a process known as transduction, which despite its importance is only poorly characterized. Here, we employed a transposon mutant library to investigate transduction in S. aureus. We showed that the genomic location of bacterial DNA relative to where bacteriophages integrated into that bacterial genome affected how frequently that DNA was transduced. Based on serial transduction of transposon mutant pools and direct sequencing of bacterial DNA in bacteriophage particles, we demonstrated both lateral and specialized transduction. The use of mutant libraries to investigate the genomic patterns of bacterial DNA transferred between cells could help us understand how horizontal transfer influences virulence and resistance development.

Learning From Mistakes: The Role of Phages in Pandemics.

The misuse of antibiotics is leading to the emergence of multidrug-resistant (MDR) bacteria, and in the absence of available treatments, this has become a major global threat. In the middle of the recent severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic, which has challenged the whole world, the emergence of MDR bacteria is increasing due to prophylactic administration of antibiotics to intensive care unit patients to prevent secondary bacterial infections. This is just an example underscoring the need to seek alternative treatments against MDR bacteria. To this end, phage therapy has been proposed as a promising tool. However, further research in the field is mandatory to assure safety protocols and to develop appropriate regulations for its use in clinics. This requires investing more in such non-conventional or alternative therapeutic approaches, to develop new treatment regimens capable of reducing the emergence of MDR and preventing future global public health concerns that could lead to incalculable human and economic losses.

Fitness Tradeoffs of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli.

Evolutionary trade-offs occur when selection on one trait has detrimental effects on other traits. In pathogenic microbes, it has been hypothesized that antibiotic resistance trades off with fitness in the absence of antibiotic. Although studies of single resistance mutations support this hypothesis, it is unclear whether trade-offs are maintained over time, due to compensatory evolution and broader effects of genetic background. Here, we leverage natural variation in 39 extraintestinal clinical isolates of Escherichia coli to assess trade-offs between growth rates and resistance to fluoroquinolone and cephalosporin antibiotics. Whole-genome sequencing identifies a broad range of clinically relevant resistance determinants in these strains. We find evidence for a negative correlation between growth rate and antibiotic resistance, consistent with a persistent trade-off between resistance and growth. However, this relationship is sometimes weak and depends on the environment in which growth rates are measured. Using in vitro selection experiments, we find that compensatory evolution in one environment does not guarantee compensation in other environments. Thus, even in the face of compensatory evolution and other genetic background effects, resistance may be broadly costly, supporting the use of drug restriction protocols to limit the spread of resistance. Furthermore, our study demonstrates the power of using natural variation to study evolutionary trade-offs in microbes.