1.What is shigellosis? What bacteria cause shigellosis? How is infection acquired? How is infection treated? Shigellosis is a public health threat in developed as well as developing countries, it is an infectious disease caused by a group of bacteria called Shigella. The genus Shigella having four pathogenic serogroups (Shigella dysenteriae, Shigella flexneri, Shigella sonnei, and Shigella boydii). Shigellosis causes diarrhea, fever, and stomach cramps. One can contract Shigellosis by putting something in their mouths or swallow something that has come into contact with the stool of someone else who is sick with shigellosis. Antibiotic therapy is the current, mainstay of treatment for shigellosis, such as ciprofloxacin and azithromycin but there is an emergence of multidrug-resistant strains of shigella. Lytic bacteriophages which destroy antibiotic resistant Shigella spp. have great potential in this context and hence their identification and detailed characterization is necessary. The bacteriophage Sfin-1 shows potent lytic activity against multidrug-resistant isolates of Shigella flexneri, Shigella dysenteriae, Shigella sonnei. 
2.Where were bacteriophages collected? A water sample was collected from the Ganga River, in the state of West Bengal, India. The water sample was then mixed with S. flexneri 2a strains, 10% (w/v) peptone and it was incubated at 37◦C for 24 hours to enrich the concentration of bacteriophages. All the different bacteriophage sequences were aligned using ClustalW in MEGA7 with default parameters. 
3.Describe the morphology of phage Sfin-1. (Figure 1) Phage Sfin-1 show potent lytic activity against multidrug-resistant isolates. The phage has an isometric head and non-contractile tail with which a basal tuft is attached.
4.Describe bacterial viability after infection with Sfin-1. Do you see any differences with different multiplicities of infection (MOIs)? (Figure 2) The result of host cell lysis caused by phage Sfin-1 showed that MOI (multiplicity of infection) is directly related to cell death. If higher number of phages are applied on cells, destabilization of the outer membrane occurs, which in turn causes cell lysis. Phage Sfin-1 displays a MOI of 0.001, 0.01 and 0.1. The viability of bacterial cells was significantly decreased when infected with MOI of 0.1, 0.01, and 0.001.
5.Describe the thermal and pH stability of Sfin-1. (Figure 3) The activity of phage Sfin-1 remained moderately same when warmed at 37◦C or 50◦C for 5 min. Activity decreased significantly into 0.1–0.01% when incubated at 60◦C or 70◦C for 5 min. When heated at 80◦C or 90◦C for 5 min only 0.001% activity was retained. Most of the phages remained active even after 60 min incubation at 37◦C or 50◦C, whereas only 0.1 and 0.01% phages were active after 60 min incubation at 60 and 70◦C, respectively, the phage activity remarkably decreased at 80◦C or 90◦C after 60 min incubation. This result suggests that the phage Sfin-1 is moderately stable toward heat stress at both 37 and 50◦C. Highest activity was observed after 1 h incubation at pH 7.0 at 37◦C, while reduction of activity was observed at different pH. Around 42.7% or 10.8% recovery of infectious phage Sfin-1 was found at pH 5.0 and 12.0, respectively. This result suggested that extreme pH as well as lower pH though affect the phage stability but a remarkable fraction of Sfin-1 remained active.
6.What was the latent period and burst size for Sfin-1? (Figure 4) Burst size was determined as a ratio of the average bacteriophage particles produced after the burst and the average number of phage particles absorbed. Sfin-1 propagated on S. flexneri 2a and S. dysenteriae1 showed a latent period of ~ 5 min and the average burst size was 27– 28 PFU/cell. While in case of S. sonnei, the latent period was 10 min and the average burst size was estimated to be 146 PFU/cell. A larger burst size is more advantageous in therapy.
7.Which genes are predicted to be involved in forming the viral head and tail components? Do these genes show any sequence homology to other phages? If so, which phages? Sequenced based prediction of the phage Sfin-1 genome identified that upstream and downstream cluster genes are involved in viral head morphogenesis and tail component formation. CDS3, CDS4, and CDS5 which are likely to produce phage capsid and scaffold protein belong to Phage Mu F like protein family. Members of this family are required for viral head morphogenesis. 
8.Which genes are involved in cell lysis? How do they work? What does the presence of these genes in the Sfin-1 genome mean? The genes involved in cell lysis are the LPS genes because the outer membrane on a gram-negative bacterium contributing to the structural integrity of the bacteria and protecting it from chemical attack. 
9.What is the host cell receptor for Sfin-1? (Figure 9) The adsorption of phage Sfin-1 to the host is mediated by the outer membrane complex LPS structure. When LPS is used as phage receptor, phage shows strain specificity.
10.What are the main conclusions of this paper? What evidence is presented that supports these conclusions? In the current study they have concluded a thermostable and wide range pH tolerant Siphoviridae phage Sfin-1 that infects and lyses the important antibiotic resistant enteropathogens Shigella spp. This is the first reported phage which infects both S. flexneri and S. dysenteriae. The article presents complete physical characterizations, sequence analysis and detailed genome annotation of phage Sfin-1. Phage structural proteins have also been identified through LC-MS/MS study. Phylogenetic analysis concludes that Sfin-1 belongs to the T1-like bacteriophage and thus it may be packaged by headful packaging method. With further analysis of phage Sfin-1 cell wall receptor revealed that bacteriophage Sfin-1 recognizes LPS O-antigen as its primary receptor for adsorption. This study proved that Sfin-1 phage will be useful for a therapeutic application against multidrug-resistant shigellosis.
11.Describe two things you learned from this paper. I learned that the activity of phages depends upon it’s pH and thermal stability causing the phage to either be active or inactive. It was also interesting to learn about the bacterium Shigellosis and its extreme relevance in society and just how easily it is spread/commonness of it in human beings