Study of Drug-Resistant Bacterial Load and Microbial Safety of Bangladeshi Nursing Assignment Help

Assignment Task

List of Tables

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Table 1 Materials, collected area, and characteristics of Bangladesh fermented milk samples
Table 2 Values of pH and viable counts (Log CFU/g) in Bangladesh fermented milk products
Table 3 Salinity, composition of sugars, organic acids and ethanol content of Bangladesh fermented milk samples
Table 4 Total read number, OTUs, and Shannon-Wienner index of 16S rDNA gene and ITS region sequencing with MiSeq
Table 5 Values of pH and salinity in ready to eat foods distributed in Bangladesh
Table 6 Viable bacteria count and detection with the selective agar plates with enrichment in the RTE food samples
Table 7 Isolates from DHL agar plates showing no clear zone (NCZ) against three or more drugs
Table 8 Isolates from MS and NGKG agar plates showing no clear zone (NCZ) and resistance (R) against three or more drugs
Table 9 Phenotypes of multi-drug resistant isolates from RTE food commodities
Table 10 Antimicrobial susceptibility profile of Klebsiella pneumoniae RTE-E3 and Citrobacter freundii RTE-E5 strain against 20 antibiotics
Table 11 Comparison of major genomic features between Klebsiella pneumoniae RTE-E3 strain and type strain K. pneumoniae
Table 12 Comparison of major genomic features between Citrobacter freundii RTE-E5 strain and type strain C. freundii
Table 13 A summary of the AMR genes annotated in the Klebsiella pneumoniae RTE-E3 genome and corresponding AMR genes of K. pneumoniae genome along with resistance phenotype
Table 14 A summary of the AMR genes annotated in the Citrobacter freundii RTE-E5 genome and corresponding AMR genes of C. freundii genome along with resistance phenotype

List of Figures
Figure 1 Map showing the geographic locations throughout Bangladesh, including the three major cities where the RTE food samples used in this study were collected: Dhaka, Chittagong, and Coxsbazar
Figure 2 Representative images of fermented milk products: dahi-1 (A), chanar-Misti (B), paneer (C), and baghabari ghee (D) obtained from Dhaka, Bangladesh and borhani (E), Sandesh (F), dahi-2 (G), and dahi-3 (H) obtained from Halal shop in Tokyo, Japan respectively

Figure 3 Composition of the bacterial (A and C) and fungal (B and D) microbiota at phylum to genus levels in dahi, chanar-Misti based on 16S rDNA (V4) or ITS region, respectively, characterized by amplicon sequencing with MySeq system
Figure 4 Composition of the bacterial (E and F) and fungal (G and H) microbiota at phylum to genus levels in paneer, borhani based on 16S rDNA (V4) or ITS region, respectively, characterized by amplicon sequencing with MySeq system
Figure 5 Heat map showing the relative abundance of identified OTUs (filtered by 0.1% counts of whole OTUs) of the bacteria (A) and fungi (B) in the fermented Bangladeshi milk products. The numbers are the reads of identified OTUs in each sample
Figure 6 The inhibition zone of Enterobacteriaceae, Staphylococci and Bacilli isolates
Figure 7 Numbers of isolates from DHL agar (A and D), mannitol salt (MS) agar (B and E), and NGKG agar (C and F) plates showing no clear zone (NCZ: red-column), resistance (R: dark-yellow column), and intermediate resistance (IR: light-yellow column) against antibiotics. CFFX: ciprofloxacin, ABPC: ampicillin, FOM: fosfomycin, OFLX: ofloxacin, TC: tetracycline, GM: gentamicin, VCM: vancomycin, LVFX: levofloxacin, ST: trimethoprim-sulfamethoxazole, CP: chloramphenicol, CFX: cefoxitin
Figure 8 Changes in Klebsiella pneumoniae RTE-E3 viable counts in six models of common ready-to-eat foods including fuska (open circles), chotpoti (closed circles), egg chop (open triangles), cream bun (closed triangles), betel leaves (open squares), and basil seed juice (closed squares) stored at 30 °C for 72 h. Values are presented as the mean ± standard deviation (n = 3). The numbers stated above the time points reflect the mean log CFU/g from three replicates. CFU, colony forming unit
Figure 9 Changes in Citrobacter freundii RTE-E5 viable counts in six models of common ready-to-eat foods including fuska (open circles), chotpoti (closed circles), egg chop (open triangles), cream bun (closed triangles), betel leaves (open squares), and basil seed juice (closed squares) stored at 30 °C for 72 h. Values are presented as the mean ± standard deviation (n = 3). The numbers stated above the time points reflect the mean log CFU/g from three replicates. CFU, colony forming unit
Figure 10 The inhibition zone of Enterobacteriaceae, Staphylococci, and Bacilli isolates
Figure 11 Changes in Klebsiella pneumoniae RTE-E3 viable counts in six models of common ready-to-eat foods including fuska (open circles), chotpoti (closed circles), egg chop (open triangles), cream bun (closed triangles), betel leaves (open squares), and basil seed juice (closed squares) stored at 30 °C for 72 h. Values are presented as the mean ± standard deviation (n = 3). The numbers stated above the time points reflect the mean log CFU/g from three replicates. CFU, colony forming unit.
Figure 12 Changes in C. freundii RTE-E5 viable counts in six models of common ready-to-eat foods including fuska (open circles), chotpoti (closed circles), egg chop (open triangles), cream bun (closed triangles), betel leaves (open squares), and basil seed juice (closed squares) stored at 30 °C for 72 h. Values are presented as the mean ± standard deviation (n = 3). The numbers stated above the time points reflect the mean log CFU/g from three replicates. CFU, colony forming unit.
Figure 13 A circular graphical display of the distribution of the genome annotations of Klebsiella pneumoniae RTE-E3 strain. The components described from the outer to inner rings include: contigs, CDS on the forward strand, CDS on the reverse strand, RNA genes, CDS with homology to known antimicrobial resistance genes, CDS with homology to know virulence factors, GC content, and GC skew. The colours of the CDSs on the forward and reverse strand indicate the subsystem that these genes belong to.
Figure 14 A circular graphical display of the distribution of the genome annotations of Citrobacter freundii RTE-E5 strain. The components described from the outer to inner rings include: contigs, CDS on the forward strand, CDS on the reverse strand, RNA genes, CDS with homology to known antimicrobial resistance genes, CDS with homology to know virulence factors, GC content, and GC skew. The colours of the CDSs on the forward and reverse strand indicate the subsystem that these genes belong to. CDS, coding sequence
Figure 15 Comparative genome map of Klebsiella pneumoniae strain RTE-E3 (DDBJ accession no. AP025034) and four multi-drug-resistant K. pneumoniae strains (1084, CP003785; HS11286, CP003200; Kj-K1, CP032163; CG43, CP006648) generated using Blast Ring Image Generator using the RTE-E3 genome as a reference
Figure 16 Comparative genome map of Citrobacter freundii RTE-E5 (DDBJ accession no. AP025035) and four multi-drug-resistant C. freundii strains (B38, CP016762; HM38, NZ_CP024672; L75, NZ_CP047307; ZY198, NZ_CP055247) generated using Blast Ring Image Generator using the RTE-E3 genome as a referenceFigure 17 Genome map of Klebsiella pneumoniae RTE-E3 strain generated using CG view server showing the virulence factor genes (up to 90% identity to known virulence factors) annotated in the RTE-E3 genome
Figure 18 Genome map of Citrobacter freundii RTE-E5 strain generated using CG view server showing the virulence factor genes (up to 95% identity to known virulence factors) annotated in the RTE-E5 genom

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