Modelling the spatiotemporal complexity of interactions between pathogenic bacteria and a phage with a temperature-dependent life cycle switch

Pattern formation by bacteria-phage interactions

The interactions between bacteria and phages-viruses that infect bacteria-play critical roles in agriculture, ecology, and medicine; however, how these interactions influence the spatial organization of both bacteria and phages remain largely unexplored. Here, we address this gap in knowledge by developing a theoretical model of motile, proliferating bacteria that aggregate via motility-induced phase separation (MIPS) and encounter phage that infect and lyse the cells. We find that the non-reciprocal predator-prey interactions between phage and bacteria strongly alter spatial organization, in some cases giving rise to a rich array of finite-scale stationary and dynamic patterns in which bacteria and phage coexist. We establish principles describing the onset and characteristics of these diverse behaviors, thereby helping to provide a biophysical basis for understanding pattern formation in bacteria-phage systems, as well as in a broader range of active and living systems with similar predator-prey or other non-reciprocal interactions.

Characterization of Mu-Like Yersinia Phages Exhibiting Temperature Dependent Infection

Yersinia pestis is the etiological agent of plague. Marmota himalayana of the Qinghai-Tibetan plateau is the primary host of flea-borne Y. pestis. This study is the report of isolation of Mu-like bacteriophages of Y. pestis from M. himalayana. The isolation and characterization of four Mu-like phages of Y. pestis were reported, which were named as vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 according to their morphology. Comparative genome analysis revealed that vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 are phylogenetically closest to Escherichia coli phages Mu, D108 and Shigella flexneri phage SfMu. The role of LPS core structure of Y. pestis in the phages' receptor was pinpointed. All the phages exhibit "temperature dependent infection," which is independent of the growth temperature of the host bacteria and dependent of the temperature of phage infection. The phages lyse the host bacteria at 37°C, but enter the lysogenic cycle and become prophages in the chromosome of the host bacteria at 26°C. IMPORTANCE Mu-like bacteriophages of Y. pestis were isolated from M. himalayana of the Qinghai-Tibetan plateau in China. These bacteriophages have a unique temperature dependent life cycle, follow a lytic cycle at the temperature of warm-blooded mammals (37°С), and enter the lysogenic cycle at the temperature of its flea-vector (26°С). A switch from the lysogenic to the lytic cycle occurred when lysogenic bacteria were incubated from lower temperature to higher temperature (initially incubating at 26°C and shifting to 37°C). It is speculated that the temperature dependent lifestyle of bacteriophages may affect the population dynamics and pathogenicity of Y. pestis.

Identification and characterization of P2-like bacteriophages of Yersinia pestis

Yersinia pestis is the cause of plague, historically known as the "Black Death". Marmota himalayana in the Qinghai-Tibet Plateau (QTP) natural plague focus is the primary host in China. Although several phages originating from Y. pestis have been characterized. This is the first report of isolation of P2-like phages of Y. pestis from M. himalayana. In this study, the isolation and characterization of three P2-like phages of Y. pestis were reported, which were named as vB_YpM_22, vB_YpM_46 and vB_YpM_50. Comparative genome analysis revealed that vB_YpM_22, vB_YpM_46 and vB_YpM_50 are members of the nonlambdoid P2 family, and are highly similar and collinear with enterobacteriophage P2, plague diagnostic phage L-413C and enterobacteriophage fiAA91-ss. The role of LPS core structure of Y. pestis in the phages' receptor was pinpointed. The findings of this study contribute an advance in our current knowledge of Y. pestis phages and will also play a key role in understanding the evolution of Y. pestis phages.

Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems

Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetic analysis of the cold-sensitive growth phenotype of Burkholderia pseudomallei/thailandensis bacteriophage AMP1

Bacteriophages related to phage Bp_AMP1 are the most widely spread group of phages infecting Burkholderia pseudomallei-the causative agent of melioidosis. These viruses are also infective against the nonpathogenic host Burkholderia thailandensis, allowing experimental work with them without any special safety precautions. The indirect data as well as the results of the mathematical modelling suggest that the AMP1-like viruses may act as natural biocontrol agents influencing the population levels of B. pseudomallei in soil and water habitats in endemic regions. The cold sensitivity of the lytic growth (CSg) of these phages was suggested to be an important feature modulating the effect of viral infection on host populations in nature. We performed genetic analysis to determine the molecular background of the CSg phenotype of the AMP1 phage. The results indicate that CSg is not due to the lack of any function or product missing at low temperature (25 °C) but results in growth inhibition by a phage-encoded temperature-sensitive genetic switch. We identified phage ORF3 and ORF14 to be involved in the genetic determination of this mechanism.

Generation of Distinct Differentially Culturable Forms of Burkholderia following Starvation at Low Temperature

Bacteria have developed unique mechanisms to adapt to environmental stresses and challenges of the immune system. Here, we report that Burkholderia pseudomallei, the causative agent of melioidosis, and its laboratory surrogate, Burkholderia thailandensis, utilize distinct mechanisms for surviving starvation at different incubation temperatures. At 21°C, Burkholderia are present as short rods which can rapidly reactivate and form colonies on solid media. At 4°C, Burkholderia convert into coccoid forms that cannot be cultured on solid agar but can be resuscitated in liquid media supplemented with supernatant obtained from logarithmic phase cultures of B. thailandensis, or catalase and Tween 80, thus displaying characteristics of differentially culturable bacteria (DCB). These DCB have low intensity fluorescence when stained with SYTO 9, have an intact cell membrane (propidium iodide negative), and contain 16S rRNA at levels comparable with growing cells. We also present evidence that lytic transglycosylases, a family of peptidoglycan-remodeling enzymes, are involved in the generation of coccoid forms and their resuscitation to actively growing cells. A B. pseudomallei ΔltgGCFD mutant with four ltg genes deleted did not produce coccoid forms at 4°C and could not be resuscitated in the liquid media evaluated. Our findings provide insights into the adaptation of Burkholderia to nutrient limitation and the generation of differentially culturable bacteria. IMPORTANCE Bacterial pathogens exhibit physiologically distinct forms that enable their survival in an infected host, the environment and following exposure to antimicrobial agents. B. pseudomallei causes the disease melioidosis, which has a high mortality rate and is difficult to treat with antibiotics. The bacterium is endemic to several countries and detected in high abundance in the environment. Here, we report that during starvation at low temperature, B. pseudomallei produces coccoid forms that cannot grow in standard media and which, therefore, can be challenging to detect using common tools. We provide evidence that the formation of these cocci is mediated by cell wall-specialized enzymes and lytic transglycosylases, and that resuscitation of these forms occurs following the addition of catalase and Tween 80. Our findings have important implications for the disease control and detection of B. pseudomallei, an agent of both public health and defense interest.

Mathematical model of COVID-19 with comorbidity and controlling using non-pharmaceutical interventions and vaccination

Pandemic is an unprecedented public health situation, especially for human beings with comorbidity. Vaccination and non-pharmaceutical interventions only remain extensive measures carrying a significant socioeconomic impact to defeating pandemic. Here, we formulate a mathematical model with comorbidity to study the transmission dynamics as well as an optimal control-based framework to diminish COVID-19. This encompasses modeling the dynamics of invaded population, parameter estimation of the model, study of qualitative dynamics, and optimal control problem for non-pharmaceutical interventions (NPIs) and vaccination events such that the cost of the combined measure is minimized. The investigation reveals that disease persists with the increase in exposed individuals having comorbidity in society. The extensive computational efforts show that mean fluctuations in the force of infection increase with corresponding entropy. This is a piece of evidence that the outbreak has reached a significant portion of the population. However, optimal control strategies with combined measures provide an assurance of effectively protecting our population from COVID-19 by minimizing social and economic costs.