<i>In silico</i> design of a novel chimeric <i>shigella</i> IpaB fused to C terminal of <i>clostridium perfringens</i> enterotoxin as a vaccine candidate

<p>This study aimed to design a novel chimeric protein <i>in silico</i> to serve as a serotype-independent vaccine candidate against <i>Shigella</i>. The chimera contains amino acid residues 240–460 of <i>Shigella</i> invasion plasmid antigen B (IpaB) and the C-terminus of <i>Clostridium perfringens</i> enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE_290–319, IpaB-CPE_184–319, IpaB-CPE_194–319 and 537 newly designed IpaB-linker-CPE_290–319 constructs with varying linker regions were predicted. These predicted 3D structures were merged with the 3D structures of native IpaB_240–460, CPE_194–319, CPE_184–319 and CPE_290–319 to select the structure most similar to native IpaB and C-CPE. Several <i>in silico</i> tools were used to determine the suitability of the selected IpaB-C-CPE structure as a vaccine candidate. None of the 537 linkers was capable of preserving the native structure of CPE_290–319 within the IpaB-linker-CPE_290–319 structure. <i>In silico</i> analysis determined that the IpaB-CPE_194–319 3D structure was the most similar to the 3D structure of the respective native CPE domain and that it was a stable chimeric protein exposing multiple B-cell epitopes. IpaB-CPE_194–319 was designed for its capability to bind to human intestinal epithelial and M cells and to accumulate on these cells. The predicted B-cell epitopes are likely to be capable of inducing a mucosal antibody response in the human intestine against <i>Shigella</i> IpaB. This study also showed that the higher binding affinities of CPE_184–319 and CPE_194–319 to claudin molecules than those of CPE_290–319 is the result of preserving the 3D structures of CPE_184–319 and CPE_194–319 when they are linked to the C-termini of other proteins.</p

Changes in antimicrobial resistance patterns and dominance of extended spectrum β-lactamase genes among faecal <i>Escherichia coli</i> isolates from broilers and workers during two rearing periods

<p>The emergence of antibiotic-resistant <i>Escherichia coli</i>, especially extended–spectrum β-lactamase (ESBL)–producing strains, in the intestinal tract of broilers could be a threat to poultry and human. We investigated changes of antimicrobial resistance patterns and frequency of ESBL genes among faecal <i>E. coli</i> isolates of broilers and workers in five different farms during two rearing periods in Iran. In this regard, <i>E. coli</i> was isolated from rectal swabs of the workers and cloacal swabs of the broilers. After detection of antibiotic resistance patterns, phenotypic and genotypic characterisation of ESBL phenotype in these strains, carriage of the resistance genes on their crude plasmid extracts and diversity of plasmid profiles were analysed. Accordingly, multidrug-resistant (MDR) patterns were detected in a high percentage of <i>E. coli</i> strains from the workers (72.7%) and poultry (92.3%). ESBL-producing <i>E. coli</i> strains were identified in these farms throughout the two periods of rearing (6.3%). <i>bla</i>_CTX-M-1, <i>bla</i>_CTX-M-61, <i>bla</i>_TEM-116 and <i>bla</i>_TEM-1 were characterised in 6 (Period I/II: 4/2), 1 (Period I), 2 (Period II) and 9 (Period I/II: 5/4) strains, respectively. The first isolation of <i>E. coli</i> strains harbouring the <i>bla</i>_TEM116 gene in chicken is reported in this study. In conclusion, results of this study showed that chickens could serve as a reservoir for ESBL-producing <i>E. coli</i> strains. These strains could carry clinically important ESBL or new emerging β-lactamases genes. Early colonisation and selection of the resistant strains during rearing periods proposed illegal use of antimicrobials as the cause of change in resistance patterns in the studied farms.</p