Shigella dysenteriae type 1-specific bacteriophage from environmental waters in Bangladesh

The changing epidemiology of shigellosis in Australia, 2001-2019

Shigellosis is an increasing cause of gastroenteritis in Australia, with prolonged outbreaks reported in remote Aboriginal and Torres Strait Islander (hereafter "First Nations") communities and among men who have sex with men (MSM) in major cities. To determine associations between Shigella species and demographic and geographic factors, we used multivariate negative binomial regression to analyse national case notifications of shigellosis from 2001 to 2019. Between 2001 and 2019, Australian states and territories reported 18,363 shigellosis cases to the National Notifiable Diseases Surveillance System (NNDSS), of which age, sex and organism information were available for >99% (18,327/18,363) of cases. Of the cases included in our analysis, 42% (7,649/18,327) were S. sonnei, 29% (5,267/18,327) were S. flexneri, 1% (214/18,327) were S. boydii, less than 1% (87/18,327) were S. dysenteriae, and species information was unknown for 28% (5,110/18,327) of cases. Males accounted for 54% (9,843/18,327) of cases, and the highest proportion of cases were in children aged 0-4 years (19%; 3,562/18,327). Crude annual notification rates ranged from 2.2 cases per 100,000 in 2003 and 2011 to 12.4 cases per 100,000 in 2019. Nationally, notification rates increased from 2001 to 2019 with yearly notification rate ratios of 1.04 (95% CI 1.02-1.07) for S. boydii and 1.05 (95% CI 1.04-1.06) for S. sonnei. Children aged 0-4 years had the highest burden of infection for S. flexneri, S. sonnei and S. boydii; and males had a higher notification rate for S. sonnei (notification rate ratio 1.24, 95% CI 1.15-1.33). First Nations Australians were disproportionately affected by shigellosis, with the notification rate in this population peaking in 2018 at 92.1 cases per 100,000 population. Over the study period, we also observed a shift in the testing method used to diagnose shigellosis, with culture independent diagnostic testing (CIDT) increasing from 2014; this also coincided with an increase in notifications of untyped Shigella. This change in testing methodology may have contributed to the observed increase in shigellosis notifications since 2014, with CIDT being more sensitive than culture dependent testing methods. The findings of this study provide important insights into the epidemiological characteristics of shigellosis in Australia, including identification of high-risk groups. This can be used to inform public health prevention and control strategies, such as targeted communication programs in First Nations communities and places with high levels of interaction between young children, such as childcare centres. Our study findings also highlight the implications of culture independent testing on shigellosis surveillance, particularly a reduction in the availability of species level information. This emphasises the continued importance of culture dependant testing for national surveillance of shigellosis.

Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis

Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.

In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System

Shigellosis caused by Shigella dysenteriae is a major public health concern worldwide, particularly in developing countries. The bacterial genome is known, but there are many hypothetical proteins whose functions are yet to be discovered. A hypothetical protein (accession no. WP_128879999.1, 161 residues) of S. dysenteriae ATCC 12039 strain was selected in this study for comprehensive structural and functional analysis. Subcellular localization and different physicochemical properties of this hypothetical protein were estimated indicating it as a stable, soluble, and extracellular protein. Functional annotation tools, such as NCBI-CD Search, Pfam, and InterProScan, predicted our target protein to be an amidase effector protein 4 (Tae4) of type-VI secretion system (T6SS). Multiple sequence alignment of the homologous sequences coincided with previous findings. Random coil was found to be predominant in secondary structure. Three-dimensional (3D) structure of the protein was obtained using homology modeling method by SWISS-MODEL server using a template protein (PDB ID: 4J30) of 80.12% sequence identity. The 3D structure became more stable after YASARA energy minimization and was validated by several quality assessment tools like PROCHECK, QMEAN, Verify3D, and ERRAT. Superimposition of the target with the template protein by UCSF Chimera generated RMSD value of 0.115 Å, suggesting a reliable 3D structure. The active site of the modeled structure was predicted and visualized by CASTp server and PyMOL. Interestingly, similar binding affinity and key interacting residues were found for the target protein and a Salmonella enterica Tae4 protein with the ligand L-Ala D-Glu-mDAP by molecular docking analysis. Protein-protein docking was also performed between the target protein and hemolysin coregulated protein 1 of T6SS. Finally, the protein was found to be a unique protein of S. dysenteriae nonhomologous to human by comparative genomics approach indicating a potential therapeutic target. Most pathogens harboring T6SS in their system pose a significant threat to the human health. Many T6SSs and their effectors are associated with interbacterial competition, pathogenesis, and virulency; however, relationships between these effectors and pathogenicity of S. dysenteriae are yet to be determined. The study findings provide a lucrative platform for future antibacterial treatment.

Combatting intracellular pathogens using bacteriophage delivery

Intracellular pathogens reside in specialised compartments within the host cells restricting the access of antibiotics. Insufficient intracellular delivery of antibiotics along with several other resistance mechanisms weaken the efficacy of current therapies. An alternative to antibiotic therapy could be bacteriophage (phage) therapy. Although phage therapy has been in practice for a century against various bacterial infections, the efficacy of phages against intracellular bacteria is still being explored. In this review, we will discuss the advancement and challenges in phage therapy, particularly against intracellular bacterial pathogens. Finally, we will highlight the uptake mechanisms and approaches to overcome the challenges to phage therapy against intracellular bacteria.

Prevalence of Shigella boydii in Bangladesh: Isolation and Characterization of a Rare Phage MK-13 That Can Robustly Identify Shigellosis Caused by Shigella boydii Type 1

Shigellosis, caused by Shigella boydii type 1, is understudied and underreported. For 3 years, GEMS study identified 5.4% of all Shigella as S. boydii. We showed the prevalent serotypes of S. boydii in Bangladesh and phage-based diagnosis of S. boydii type 1, a rapid and low-cost approach. Previously typed 793 clinical S. boydii strains were used for serotype distribution. Twenty-eight environmental water samples were collected for isolation of Shigella phages. Forty-eight serotypes of Shigella and other enteric bacteria were used for testing the susceptibility to phage MK-13. Electron microscopy, restriction enzyme analysis, whole genome sequencing (WGS), and annotation were performed for extensive characterization. S. boydii type 1 is the second most prevalent serotype among 20 serotypes of S. boydii in Bangladesh. We isolated a novel phage, MK-13, which specifically lyses S. boydii type 1, but doesn’t lyse other 47 serotypes of Shigella or other enteric bacteria tested. The phage belongs to the Myoviridae family and distinct from other phages indicated by electron microscopy and restriction enzyme analysis, respectively. MK-13 genome consists of 158 kbp of circularly permuted double-stranded DNA with G + C content of 49.45%, and encodes 211 open reading frames including four tRNA-coding regions. The genome has 98% identity with previously reported phage, ΦSboM-AG3, reported to have a broader host range infecting most of the S. boydii and other species of Shigella tested. To our knowledge, MK-13 is the first phage reported to be used as a diagnostic marker to detect S. boydii type 1, especially in remote settings with limited laboratory infrastructure.

Genomic and Proteomic Characterizations of Sfin-1, a Novel Lytic Phage Infecting Multidrug-Resistant Shigella spp. and Escherichia coli C

Shigellosis is a public health threat in developed as well as developing countries like “India.” While antibiotic therapy is the mainstay of treatment for shigellosis, current emergence of multidrug-resistant strains of Shigella spp. has posed the problem more challenging. Lytic bacteriophages which destroy antibiotic resistant Shigella spp. have great potential in this context and hence their identification and detailed characterization is necessary. In this study we presented the isolation and a detailed characterization of a novel bacteriophage Sfin-1, which shows potent lytic activity against multidrug-resistant isolates of Shigella flexneri, Shigella dysenteriae, Shigella sonnei obtained from clinical specimens from shigellosis patients. It is also active against Escherichia coli C. The purified phage is lytic in nature, exhibited absorption within 5–10 min, a latent period of 5–20 min and burst size of ∼28 to ∼146 PFU/cell. The isolated phage shows stability in a broad pH range and survives an hour at 50°C. Genome sequencing and phylogenetic analyses showed that Sfin-1 is a novel bacteriophage, which is very closely related to T1-like phages (89.59% identity with Escherichia virus T1). In silico analysis indicates that Sfin-1 genome consists of double stranded linear DNA of 50,403 bp (GC content of 45.2%) encoding 82 potential coding sequences, several potential promoters and transcriptional terminators. Under electron microscopy, Sfin-1 shows morphology characteristics of the family Siphoviridae with an isometric head (61 nm) and a non-contractile tail (155 nm). This is most likely the first report of a lytic bacteriophage that is active against three of the most virulent multidrug-resistant Shigella species and therefore might have a potential role in phage therapy of patients infected with these organisms.

Bacteriophage application for biocontrolling Shigella flexneri in contaminated foods

Shigellosis (bacillary dysentery) is an acute enteric infection caused by members of Shigella genus. It causes annual deaths of approximately five million children in developing countries. Among Shigella spp., S. flexneri causes more serious forms of dysentery than other Shigella species. Due to the appearance of multidrug-resistant strains of Shigella spp., it is necessary to find alternative antimicrobial agents. The aims of this study were the isolation of a novel species-specific phage against S. flexneri and to evaluate its potential and efficacy for biocontrolling of S. flexneri in foods. Shigella flexneri PTCC 1234 was used as the host strain for bacteriophage isolation from waste water. A lytic phage of the Siphoviridae family was isolated and designated as vB_SflS-ISF001. The phage activity remained at high levels after 1 h of incubation at - 20 to 50 °C and was fairly stable for 1 h at pH values ranging from 7 to 9. The latent period and burst size were approximately 20 min and 53 ± 4 phages per host cell, respectively. Raw and cooked chicken breast were inoculated with a predetermined amount of S. flexneri and subjected to biocontrol test. The results showed that using vB_SflS-ISF001 phage led to more than two logs reduction in the count of viable S. flexneri. It was demonstrated that using vB_SflS-ISF001 phage is of high potential for developing an alternative strategy against S. flexneri contamination in foodstuffs.

Bacteriophages for managing Shigella in various clinical and non-clinical settings

The control of shigellosis in humans enjoys a prominent position in the history of bacteriophage therapy. d’Herelle first demonstrated the efficacy of phage therapy by curing 4 patients of shigellosis, and several subsequent studies confirmed the ability of phages to reduce Shigella based infection. Shigella spp continue to cause millions of illnesses and deaths each year and the use of phages to control the disease in humans and the spread of the bacteria within food and water could point the way forward to the effective management of an infectious disease with global influence.

Acanthamoeba castellanii an environmental host for Shigella dysenteriae and Shigella sonnei

The interaction between Shigella dysenteriae or Shigella sonnei and Acanthamoeba castellanii was studied by viable counts, gentamicin assay and electron microscopy. The result showed that Shigella dysenteriae or Shigella sonnei grew and survived in the presence of amoebae for more than 3 weeks. Gentamicin assay showed that the Shigella were viable inside the Acanthamoeba castellanii which was confirmed by electron microscopy that showed the Shigella localized in the cytoplasm of the Acanthamoeba castellanii. In conclusion, the relationship between Shigella dysenteriae and Shigella sonnei with Acanthamoeba castellanii is symbiotic, and accordingly free-living amoebae may serve as a transmission reservoir for Shigella in water.

Prevalence of the stx 2 Gene in Coliform Populations from Aquatic Environments

Shiga toxin-producing Escherichia coli strains are human pathogens linked to hemorrhagic colitis and hemolytic uremic syndrome. The major virulence factors of these strains are Shiga toxins Stx1 and Stx2. The majority of the genes coding for these toxins are borne by bacteriophages. Free Stx2-encoding bacteriophages have been found in aquatic environments, but there is limited information about the lysogenic strains and bacteria present in the environment that are susceptible to phage infection. The aim of this work was to study the prevalence and the distribution of the stx 2 gene in coliform bacteria in sewage samples of different origins. The presence of the stx 2 gene was monitored every 2 weeks over a 1-year period in a municipal sewage treatment plant. A mean value of 10 2 genes/ml was observed without significant variation during the study period. This concentration was of the same order of magnitude in raw municipal sewage of various origins and in animal wastewater from several slaughterhouses. A total of 138 strains carrying the stx 2 gene were isolated by colony hybridization. This procedure detected approximately 1 gene-carrying colony per 1,000 fecal coliform colonies in municipal sewage and around 1 gene-carrying colony per 100 fecal coliform colonies in animal wastewaters. Most of the isolates belonged to E. coli serotypes other than E. coli O157, suggesting a low prevalence of strains of this serotype carrying the stx 2 gene in the wastewater studied.