Molecular Characterization and Antibiotic Susceptibility of Edwardsiella Tarda
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Uganda Journal of Agricultural Sciences ISSN: 1026 - 0919 (Print); 2410 - 6909 (Online) Volume 1 9 Number 1 (201 9 ) pp. 5 1 – 6 4 DOI: http://dx.doi.org/10.4314/ ujas .v1 9 i 1 . 5 © 201 9 National Agricultural Research Organisation https://www.ajol.info/index.php/ujas Licensed under a Creative Commons Attribution International Licence (4.0) (Available at www.ajol.info) Molecular C haracterization and Antibiotic S usceptibility of Edwardsiella tarda isolated from Farmed Nile Tilapia and African C atfish from Wakiso, Uganda M. Nantongo 1, 3, * , E. M. Mkupasi 1 , D. K. Byarugaba 2 , S. P . Wamala 2 , R. H. Mdegela 1 , J. K. Walakira 3 1 College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Tanzania . 2 College of Veterinary Medicine, Animal Science and Biosecur ity, Makerere University . 3 National Fisheries Resources Research Institute - NARO, Uganda. *Corresponding author. [email protected] Abstract. This study was conducted to isolate and characterize Edwardsiella tarda ( E. tarda ) and assess its antimicrobial susceptibility. The bacterium was isolated in Wakiso District, Uganda, from symptomatic and asymptomatic Nile tilapia and African catfish raised in earthen ponds, tanks and cages between September 2016 and February 2017. The bacterium was then identified using conventional biochemical tests and API 20E test kits and characterized by sequencing 16S rRNA gene. The a ntibiotic susceptibility of 16 drugs was established using the Kirby BeurDisc diffusion method. Eight E. tarda isolates were identified using conventional biochemical tests but only one iso late was confirmed to be E. tarda by PCR. Phylogenetic analysis indicated a distant relationship with other 16S rRNA gene sequences retrieved from the GenBank. Six virulence genes ( CitC , muk , gadB , katB , esaV , and fimA ) that enhance bacterial survival and pathogenesis in the host were detected. The isolate registered low levels of antibiotic resistance as it was resistant only to Oxacillin, Vancomycin and Penicillin, to whic h it is intrinsically resistant. This impl ies low antibiotic usage in aquaculture in the area . Despite its low occurrence, presence of virulent genes in E. tarda indicates its potential to affect fish and human health . Keywords : Aquaculture, Edwardsiella tarda , Phylogeny, Virulence Introduction Aquaculture in Uganda is increasing with a production of about 101659 tonnes (FAO, 2018). However, intensification of fish farming to meet the increasing fish demand is challenged with disease outbreaks (Bondad - Reantaso et al ., 2005). There is insufficient information on the type of fish pathogens affecting aquaculture systems in Uganda thus making management of disease outbreaks difficult. Fish diseases are known to cause economic losses, reduced growth and increased cost of production (Faruk et al ., 2004).Bacteria affect the health of both wild and Nantongo et al .: Molecular characterization and antibiotic susceptibility of Edwardsiella tarda farmed fish and Edwardsiella species are known pathogens affecting fish populations worldwide (Austin and Austin, 1987; Abowei & Briyai, 2011; Park et al ., 2012). Edwardsiella tard a is the causative agent of Edwardsiellosis in fish, characterized by systemic hemorrhagic septicemia, internal abscesses and skin lesions (Ewing et al ., 1965). The bacterium is opportunistic in nature, and disease outbreaks occur when poor environmental c onditions prevail like overcrowding, poor water quality conditions, high organic content and high temperature (Mohanty and Sahoo, 2007). These factors influence the production of substances such as haemolysin, siderophore, superoxide dismutase, extracellul ar products and intracellular components that contribute to E. tarda pathogenicity and also expression of the two protein secretion systems that are involved in E. tarda virulence (Hossain et al ., 2010; Guijarro et al ., 2015; Huicab - Pech et al ., 2016). Occu rrence of Edwardsiella species in farmed Nile tilapia and African catfish has been reported in Uganda but partially characterized to genus level (Walakira et al ., 2014). Its prevalence in aquaculture systems is reported to vary with ponds not exceeding 5% , and tanks ranging between 50 - 70% (Mohanty and Sahoo, 2007; Joh et al ., 2010). Edwardsiella tarda is also zoonotic causing gastroenteritis and skin lesions in humans (Park et al ., 2012). Edwardsiella tarda is a facultative intracellular pathogen but its pa thogenicity in host cells is not clearly understood (Xu and Zhang, 2014).However, its virulence factors are reported to enhance the bacterial survival, and pathogenesis in hosts. Therefore, identification of virulence - related genes is essential for explain ing the pathogenesis of this bacterium. M ethods and Materials Th e study was conducted in Wakiso District, central Uganda (0 ° 4 ˊ S, 32 ° 45 ˊ E) (Fig ure 1) . Figure 1 . Map of Uganda showing the location of Wakiso District 52 Uganda Journal of Agricultural Sciences 19 (1) F ish farming is one of the main economic activities in the district. Samples were collected from 17 active commercial and subsistence fish farms with ponds, tanks and cages. The study applied a cross - sectional study design. Fish farms were purposively selec ted, the inclusion criteria being history of disease outbreaks during the study period and willingness of the farmer to participate in the study. Simple random sampling technique was applied to select clinically healthy fish, whereas in case of disease occ urrence, sick fish were purposively selected from the culture system. Healthy and sick fish samples were collected and transported in sterile containers to the laboratory between September 2016 and February 2017. Necropsy on fish samples was conducted to examine external and internal lesions following procedures described by Noga (2010). Samples of organs (liver, spleen and kidney) and swabs from gills and skin were collected and subjected to bacteriological examination following methods described by Noga (2010) Samples were homogenized, inoculated on Xylose Lysine Desoxycholate (XLD) agar plates and incubated at 28 ° C for 36 hours after which they were examined for primary cultures. A well - differentiated single black colony was picked and sub cultured on XL D agar to produce a pure culture which were subjected to various biochemical tests. Identification of the bacterium was done using cultural and morphological characteristics, conventional biochemical tests and Analytical Profile Index (API 20E) system (Bio Merieux, France) according to manufacturer’s instructions and the biochemical profiles of the isolates from API 20E were determined. The isolates were preserved in cryovials containing Brain Heart Infusion broth and glycerol and then stored in the freezer at ˗ 4 ° C until further testing. Genomic DNA extraction was done using QIAamp DNA mini kit (Qiagen) following manufacturer’s instructions. DNA concentration was measured using NanoDrop ND - 1000 spectrophotometer (Thermo Fisher Scientific, Inc). The extracted DNA was preserved and stored at ˗ 20 ° C. The 16S rRNA gene was amplified by Polymerase Chain Reaction (PCR) using the 16S universal bacteria primers 27F (5’ - AGAGTTTGATCCTGGCTCAG - 3’) and 1492R (5’ - GGTTACCTTGTTACGACTT - 3’) with the expected amplicon size of 1465bp (Lane 1991) from Invitroge n, Thermo Fisher Scientific (Waltham, MA USA). Polymerase Chain Reaction was performed in a thermo cycler (iCycler from Bio - Rad, United States of America). Each PCR reaction was performed in a final volume of 25µl containing 2.5µl of 10× reaction buffer (5 0 mM KCl, 75 mM Tris - HCl (pH 9.0), 2mM MgCl 2 , 20mM (NH 4 ) 2 SO 4 ), 0.5µl 10 mM deoxyribonucleotide mix, 0.2µl of Taq DNA polymerase, 1µl 10 mM of each forward and reverse primer, 2µl of DNA template and 16.8µl of sterile ultrapure water. PCR conditions include d initial denaturation at 94 ° C for three minutes, followed by 30 cycles of amplification as follows; denaturation at 94 ° C for 30 seconds, annealing at 56 ° C for 30 seconds and extension at 72 ° C for two minutes. This was followed by a final extension step at 72 ° C for five minutes and left to stand at 4 ° C until collected for further analysis. The PCR products were analysed on 1% agarose gel (Ultrapure agarose from Invitrogen, Thermos Fisher Scientific) at 100Volts for 60 minutes. The amplified DNA on the gel was visualized using Safe Imager™ from Invitrogen and bands of interest excised using a scalpel blade for gel purification. ChemiDoc™ XRS Molecular image (Bio Rad) was used for viewing and capturing gel pictures. The purified PCR products were sequenced wi th 16S 27F and 16S 1492R universal bacteria primers by Sanger sequencing techniques at GATC Biotech, Germany using ABI genetic analyser . 53 Nantongo et al .: Molecular characterization and antibiotic susceptibility of Edwardsiella tarda Both the forward and reverse sequences of the 16S rRNA gene were edited in Bioedit to generate a consensus sequence. B asic Local Alignment Search Tool (BLAST) searches were carried out in GenBanks particularly the National Centre for Biotech Information (NCBI). Related sequences were obtained and multiple sequence alignments were performed using ClustalW algorithm. The al ignments were used to construct a phylogenetic tree using MEGA 7.0 (Kumar et al ., 2016) using the Neighbour - Joining method (Saitou and Nei, 1987). The gene sequences used in phylogenetic analysis are shown in Table 1. Table 1 . Isolates whose sequences were used in phylogenetic analysis SN