Prevalence and characterisation of Salmonella Waycross and Salmonella enterica subsp. salamae in Nile perch (Lates niloticus) of Lake Victoria, Tanzania

The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems

With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.

Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh

Wet markets in low-and middle-income countries are often reported to have inadequate sanitation resulting in fecal contamination of sold produce. Consumption of contaminated wet market-sourced foods has been linked to individual illness and disease outbreaks. This pilot study, conducted in two major wet markets in Dhaka city, Bangladesh during a 4-month period in 2021 aimed to assess the occurrence and characteristics of Escherichia coli and non-typhoidal Salmonella spp. (NTS) from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon). Fifty-four individuals of each species were collected. The identity of the bacterial isolates was confirmed by PCR and their susceptibility toward 15 antimicrobials was tested by disk diffusion. The whole genome of 15 E. coli and nine Salmonella spp. were sequenced using Oxford Nanopore Technology. E. coli was present in 60-74% of tilapia muscle tissue and 41-44% of shrimp muscle tissue. Salmonella spp. was found in skin (29%) and gills (26%) of tilapia, and occasionally in muscle and intestinal samples of shrimp. The E. coli had several Multilocus sequence typing and serotypes and limited antimicrobial resistance (AMR) determinants, such as point mutations on glpT and pmrB. One E. coli (BD17) from tilapia carried resistance genes for beta-lactams, quinolones, and tetracycline. All the E. coli belonged to commensal phylogroups B1 and A and showed no Shiga-toxin and other virulence genes, confirming their commensal non-pathogenic status. Among the Salmonella isolates, five belonged to Kentucky serovar and had similar AMR genes and phenotypic resistance patterns. Three strains of this serovar were ST198, often associated with human disease, carried the same resistance genes, and were genetically related to strains from the region. The two undetermined sequence types of S. Kentucky were distantly related and positioned in a separate phylogenetic clade. Two Brunei serovar isolates, one Augustenborg isolate, and one Hartford isolate showed different resistance profiles. This study revealed high fecal contamination levels in tilapia and shrimp sold at two main wet markets in Dhaka. Together with the occurrence of Salmonella spp., including S. Kentucky ST198, a well-known human pathogen, these results stress the need to improve hygienic practices and sanitation standards at markets to improve food safety and protect consumer health.

Salmonella Salamae and S. Waycross isolated from Nile perch in Lake Victoria show limited human pathogenic potential

Non-enterica subspecies of Salmonella enterica are rarely associated with human infections. Paradoxically, food safety legislations consider the entire genus Salmonella as pathogenic to humans. Globally, large amounts of seafoods are rejected and wasted due to findings of Salmonella. To inform better food safety decisions, we investigated the pathogenicity of Salmonella Salamae 42:r- and Salmonella Waycross isolated from Nile perch from Lake Victoria. Genome-wide analysis revealed absence of significant virulence determinants including on key Salmonella pathogenicity islands in both serovars. In epithelial cells, S. Salamae showed a weak invasion ability that was lower than the invH mutant of S. Typhimiurium used as negative control. Similarly, S. Salamae could not replicate inside macrophages. Moreover, intracellular replication in S. Waycross strains was significantly lower compared to the wild type S. Typhimurium. Our findings suggest a low pathogenicity of S. Salamae reinforcing the existing literature that non-enterica subspecies are avirulent. We propose that food legislations and actions taken on findings of Salmonella are revisited to avoid wasting valuable sea- and other foods.

Salmonella in the processing line of farmed Tambatinga (Colossoma macropomum x Piaractus brachypomus) in Mato Grosso, Brazil: serotypes of occurrence and antimicrobial profile

The objective of this study was to evaluate the dispersion dynamics and antimicrobial resistance profiles of Salmonella in the processing of Tambatinga (Colossoma macropomum x Piaractus brachypomus). Thirty fish were monitored during four processing stages (reception, first wash, evisceration, and prepackage area) in a fish slaughterhouse. One hundred and twenty fish surface samples were collected and tested through bacteriological analysis, PCR, serotyping, and antimicrobial resistance profile (disk-diffusion). Of these samples, 7.5% (9/120) were positive for Salmonella, with 0.83% being observed in the pre-packaging phase, indicating a low occurrence at this stage. All the analyzed stages were positive for Salmonella, with the prevalent serovars being Ndolo, Mbandaka, Typhimurium, Rough, and O:16. All strains were sensitive to various antimicrobials. Improvements in microbiological control during all processing stages should be implemented to ensure a Salmonella-free product.

Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania

Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by bla_CTX–M and bla_TEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried bla_CTX–M–15 and bla_TEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.

Assessment of a novel nanostructured flocculant with elevated flocculation and antimicrobial activity

In this work, a novel process involving the preparation of nanochitosan-grafted flocculants (CPAM-g-NCS) to treat low turbid and salmonella suspensions simultaneously was introduced. Nanotechnology was employed to enhance the adsorption-adhesion and sterilization abilities of dual-functional flocculants. The monomers of chitosan, acrylamide, methacryloyl ethyl trimethyl ammonium chloride, and sodium tripolyphosphate were utilized for flocculants copolymerization. Then, using fourier-transform infrared spectroscopy, nuclear magnetic resonance hydrogen spectrum, and thermogravimetric and differential scanning calorimetry analysis, the successful synthesis of CPAM-g-NCS was verified. Scanning electron microscopy and size analysis suggested that nanostructured flocculants with irregular morphology and nanocolloids of 60.44 nm were formed. CPAM-g-NCS was applied to treat a series of simulated low turbid and salmonella suspensions. The simulation results showed that the minimum residual turbidity of 1.97 NTU and optical density of 0.16 (initial 0.89) can be achieved at dosages of 2.5 and 8.75 mg L^-1, respectively, which were superior to conventional organics flocculants. Mechanistic studies suggested that the excellent adsorption property, and large numbers of quaternary ammonium and amino groups of nanoflocculants contributed to the superior flocculation and antibacterial performance of CPAM-g-NCS.