Identification of Antimicrobial Resistance Determinants in Aeromonas veronii Strain MS-17-88 Recovered From Channel Catfish (Ictalurus punctatus)

Aeromonas veronii is a Gram-negative species ubiquitous in different aquatic environments and capable of causing a variety of diseases to a broad host range. Aeromonas species have the capability to carry and acquire antimicrobial resistance (AMR) elements, and currently multi-drug resistant (MDR) Aeromonas isolates are commonly found across the world. A. veronii strain MS-17-88 is a MDR strain isolated from catfish in the southeastern United States. The present study was undertaken to uncover the mechanism of resistance in MDR A. veronii strain MS-17-88 through the detection of genomic features. To achieve this, genomic DNA was extracted, sequenced, and assembled. The A. veronii strain MS-17-88 genome comprised 5,178,226-bp with 58.6% G+C, and it encoded several AMR elements, including imiS, ampS, mcr-7.1, mcr-3, catB2, catB7, catB1, floR, vat(F), tet(34), tet(35), tet(E), dfrA3, and tetR. The phylogeny and resistance profile of a large collection of A. veronii strains, including MS-17-88, were evaluated. Phylogenetic analysis showed a close relationship between MS-17-88 and strain Ae5 isolated from fish in China and ARB3 strain isolated from pond water in Japan, indicating a common ancestor of these strains. Analysis of phage elements revealed 58 intact, 63 incomplete, and 15 questionable phage elements among the 53 A. veronii genomes. The average phage element number is 2.56 per genome, and strain MS-17-88 is one of two strains having the maximum number of identified prophage elements (6 elements each). The profile of resistance against various antibiotics across the 53 A. veronii genomes revealed the presence of tet(34), mcr-7.1, mcr-3, and dfrA3 in all genomes (100%). By comparison, sul1 and sul2 were detected in 7.5% and 1.8% of A. veronii genomes. Nearly 77% of strains carried tet(E), and 7.5% of strains carried floR. This result suggested a low abundance and prevalence of sulfonamide and florfenicol resistance genes compared with tetracycline resistance among A. veronii strains. Overall, the present study provides insights into the resistance patterns among 53 A. veronii genomes, which can inform therapeutic options for fish affected by A. veronii.


INTRODUCTION
Aeromonas species are Gram-negative rods in the family Aeromonadaceae. They are among the most common bacteria in aquatic environments and have been isolated from virtually all water source types including freshwater, estuarine environments, drinking waters, wastewaters, and sewage (Janda and Abbott, 2010). The disease caused by Aeromonas species affects a broad host range, including freshwater fish, amphibians, reptiles, and birds (Barony et al., 2015). Mesophilic Aeromonas species such as A. hydrophila, A. caviae, and A. veronii, are associated with several kinds of human infections, including gastroenteritis, wound infections, septicemia, and respiratory infections (Figueras, 2005;Igbinosa et al., 2012). A. veronii is one member of the genus Aeromonas, which is known for causing hemorrhagic septicemia in both wild and farmed fish such as channel catfish (Ictalurus punctatus) (Liu et al., 2016;Yang et al., 2017), snakehead (Ophiocephalus argus), whitefish (Coregonus clupeaformis) (Loch and Faisal, 2010), obscure puffer (Takifugu obscurus), Nile tilapia (Oreochromis niloticus) (Hassan et al., 2017), and common carp (Cyprinus carpio) (Sun et al., 2016). In recent years, an increasing number of Aeromonas species have become associated with disease of predominantly freshwater fish in most countries (Goni-Urriza et al., 2000), which results in causing severe outbreaks in different important aquaculture industries. Sulfonamides potentiated with trimethoprim or ormethoprim, oxytetracycline, florfenicol, and erythromycin are the most commonly used antimicrobial (AM) agents for treatment of Aeromonas-related diseases in global aquaculture (Serrano, 2005). Although the judicious use of AM-medicated feeds is important for treatment purposes when faced with outbreaks of bacterial infections (Okocha et al., 2018), a substantial number of reports suggest that indiscriminate use of AMs can foster selection pressure and enable development of multi-drug resistant (MDR) bacteria in aquatic environments (Arslan and Küçüksari, 2015). MDR in bacterial pathogens can result in therapeutic challenges for control of bacterial diseases (Marshall and Levy, 2011).
Over the past two decades, A. veronii has gained epidemiological and ecological importance by several research groups due to its potential as an opportunistic and primary pathogen for fish and the prevalence of MDR strains (Sanchez-Cespedes et al., 2008). Previous studies have reported the isolation of MDR A. veronii strains from different regions of the world such as Sri Lanka (Jagoda et al., 2017), China (Yang et al., 2017), and United States Tekedar et al., 2019). The resistance elements in Aeromonas species are often harbored in mobile genetic elements such as class 1 integrons, plasmids, IS elements, transposons, and genomic islands (Piotrowska and Popowska, 2015). These mobile elements can facilitate the spread of resistance among bacteria via transduction and conjugation (Sanchez-Cespedes et al., 2008;Hossain et al., 2013;Piotrowska and Popowska, 2015). Therefore, it is important to investigate the pattern of resistance, genetic relatedness, and mobile elements in Aeromonas species. High-throughput sequencing provides an opportunity to detect MDR bacteria, discover potential resistance mechanisms, and explore the mechanisms underlying resistance gene transfer (Liu et al., 2012).
The purpose of the current work was to uncover mechanisms of resistance in A. veronii strain MS-17-88, which was isolated from catfish in the southeastern U.S., and to assess the diversity, resistance profiles, and mobile elements in a large collection of A. veronii strains. Here we present the draft genome of A. veronii and results from a comparative analysis with 52 publicly available A. veronii genomes with a special emphasis on patterns of AMR genes and prophage elements distribution. To the best of our knowledge, no study has been published reporting a core-genome based phylogenetic relationship of sequenced A. veronii genomes, AMR profiles, and their mobilomes. Overall, our work provides a basis to understand the AMR profile for A. veronii in aquatic environments, which is an important step toward curtailing AMR spread and informing a treatment of disease caused by A. veronii.

Bacterial Strains and Data Source for Comparative Genome Analysis
A. veronii strain MS-17-88 was recovered from a diseased channel catfish in 2017 from the Aquatic Diagnostic Laboratory at the College of Veterinary Medicine, Mississippi State University. The isolate was confirmed phenotypically as A. veronii. A 20% glycerol stock culture was stored at −80 • C. A. veronii strain MS-17-88 was cultured in brain heart infusion (BHI) agar or broth (Difco) and incubated at 30 • C. Fifty-two A. veronii genomes were retrieved from the National Center for Biotechnology Information (NCBI) genomes database on October 9, 2018, including five complete genome sequences and forty-seven draft genome sequences (Table 1).

Phylogenetic Tree
A phylogenetic tree was constructed based on the complete core genome of A. veronii strain MS-17-88 and 52 A. veronii genomes to evaluate taxonomic positions. All publicly available A. veronii genome sequences (52 genomes) were downloaded from NCBI. Gene sets of the core genome were aligned using MUSCLE (Edgar, 2004) and concatenated. Concatenated alignment files were used as an input to compute a Kimura distance matrix, which was followed by using the concatenated files for the Neighbor-Joining algorithm as implemented in PHYLP (Felsenstein, 1989).

Subsystem Coverages and Genomes Structure Variation
A. veronii strain MS-17-88 and 52 A. veronii genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) for annotation, subsystem categorization, and comparison purposes (Aziz et al., 2008

Prophages
The presence of prophages in the 53 A. veronii genomes was determined using PHASTER (PHAge Search Tool Enhanced Release) (Arndt et al., 2016(Arndt et al., , 2019. Nucleotide sequences from 53 genomes were concatenated using Sequencher 5.4.5 to serve as an input file prior to submission to the PHASTER server. Results from PHASTER were arranged into three categories: score > 90 was considered intact phage element; a score between 70 and 90 was deemed questionable; and score < 70 was considered incomplete phage region (Arndt et al., 2019).

Comparative Analysis of Putative AMR Elements
The potential AMR genes and related elements for each genome were identified using ResFinder 3.1 (Zankari et al., 2012). ResFinder database was downloaded and used in CLC Workbench version 11.0.1 (CLC Bio) for the BLAST search. The contig files for each genome were concatenated, and concatenated nucleotide files were uploaded to CLC Workbench. A BLAST search was run with the following settings: 40% minimum identity and 40% minimum matching length. Resistance to β-lactam antibiotics in Aeromonas species is primarily mediated by β-lactamases, whose mode of action involves hydrolyzing the β-lactam ring. Many different βlactamases have been detected in Aeromonas species, such as TEM-, SHV-, OXA-, CMY-, and CTX-M-type β-lactamases. In the present study, ampS and imiS were detected in A. veronii stain 17-88. AmpS is a class 2d penicillinase and ImiS is a class 3 metallo-β-lactamase. The imiS gene has been detected in clinical isolates of A. veronii biovar sobria (Wu et al., 2012). MS-17-88 also harbors floR, which encodes a major facilitator superfamily efflux pump that exports florfenicol (Schwarz et al., 2004). Florfenicol is one among the three approved AMs for use in catfish aquaculture in the U.S (Bowker et al., 2010). Most fish pathogenic bacteria mediate florfenicol resistance through FloR (Dang et al., 2007;Gordon et al., 2008). Dissemination of florfenicol resistance among bacterial pathogens isolated from aquaculture can limit the efficacy of this agent as an important treatment option.

Phylogenetic Tree
The phylogenetic relationship between the A. veronii MS-17-88 genome and 52 other A. veronii genomes was assessed. The strains used in this analysis are from different countries and hosts, and they had distinct resistance profiles ( Table 1). The phylogenetic tree for the 53 A. veronii genomes was built from a core genome of 2,563 genes per genome (135,839 genes in total). The core has 2,538,377 bp per genome (134,533,981 bp in total). The phylogenetic tree showed that there are multiple highly conserved branches that are separated from the other A. veronii genomes. MDR A. veronii strain MS-17-88 from U.S. channel catfish, goldfish (Carassius auratus) MDR strain Ae5 from China, and A. veronii ARB3 from pond water in Japan were clustered together, which may indicate a common origin. Similarly, U.S. channel catfish isolate ML09-123 and China catfish isolate TH0426 were closely related, which also may suggest derivation from the same monophyletic origin despite their geographic disparity. Moreover, dairy cattle isolates and Greece surface sediment isolates (strain pamvotica) formed another closely related group. U.S. human isolates (strains AER 397, CECT 4257, and CCM 4359) and China pond sediment isolate B565 formed another clade. Lastly, U.S. surface water and Germany surface water isolates were closely related, and Greece fish isolates (strains 5.28.6, VCK, NS, and PDB) were clustered together. These data clearly suggest that the ecological niche is a more important factor contributing to relatedness among A. veronii isolates than geographical location. However, two isolates (CIP 107763 and VBF557) showed a distinct genetic relationship to the other isolates.
It has been postulated that a fish pathogenic Aeromonas hydrophila clonal group was transferred to the U.S. channel catfish aquaculture industry from China (Hossain et al., 2014). In the current study, we observed two different clonal groups of A. veronii that contain isolates from both U.S. and China. One clade has MDR A. veronii strain MS-17-88 from U.S. catfish aquaculture and MDR isolate Ae5 from goldfish in China, and another clade has U.S. channel catfish isolate ML09-123 and China catfish strain TH0426 (Figure 1).

Subsystems Coverage
The subsystems categorization based on RAST annotation is shown in Figure 2. SEED subsystem categorization analysis predicted 26 different categories for the evaluated A. veronii genomes. The most abundant systems are "amino acid and derivatives, " followed by "carbohydrates" and "protein metabolism." These subsystems are essential for bacteria to perform basic cellular processes and may indicate the potential ability of A. veronii to utilize different kinds of sugars and amino acids available in the environment . On the other hand, A. veronii genomes show remarkably low numbers of mobile genetic elements including phages, prophages, transposable elements, and plasmids. These mobile elements can mediate alteration of genotypes, and these findings may suggest that horizontal gene exchange may not contribute to A. veronii genomic variation as much as other species. Interestingly, U.S. catfish isolate strain MS-17-88 carries the most abundant subsystems (63 elements) associated with phages, prophages, transposable elements, and plasmids. Chinese catfish isolate strain TH0426 has the second largest number (52 elements) of phage and transposable elements. Therefore, these two strains (MS-17-88 and TH0426) may have acquired significant genome structure changes by gene acquisitions from mobile elements. It is notable that both strains were isolated from aquatic environments, and we speculate that the aquatic environment may be favorable for genetic exchange and horizontal gene acquisition.

Genome Structure Variation
Visualization of the alignment between A. veronii MS-17-88 and 52 other A. veronii genomes revealed that phage elements, transposons, and genomic islands comprise many of the MS-17-88-specific regions (Figure 3). This suggests that mobile elements, especially phages and transposons, play an important role in A. veronii genome variation. These mobile elements can result in genomic rearrangements and evolution through acquisition of novel virulence or antibiotic resistance genes which may result in emergence of new phenotypes (Brown-Jaque et al., 2015).

Prophages
Bacteriophages are responsible for loci rearrangements and deletions and are recognized as an important element in bacterial evolution (Tinsley et al., 2006). The vast majority of aquatic bacteria (about 70%) are infected with prophages (Chen et al., 2006). Of particular interest, bacteriophages can mediate horizontal gene transfer, including genes encoding virulence factors and antibiotic resistance (Colomer-Lluch et al., 2011). A higher number of phages may represent a concern because they can expand the pathogenicity of a bacterial strain or convert an avirulent strain into a virulent one (Canchaya et al., 2004). Even though phage elements may not be the main spreading factors of resistance elements, recent studies indicate that they can infrequently contribute to the dissemination of these elements (Allen et al., 2011;Enault et al., 2017). In Aeromonas, the transfer of resistance gene by phage elements has never been observed previously (Piotrowska and Popowska, 2015).
In the present study, we identified 58 intact, 63 incomplete, and 15 questionable phage elements among the 53 A. veronii genomes (Figure 4). The average phage element number is 2.56 per genome (136 identified phage elements/53 A. veronii strains). In a previous study, A. hydrophila genomes were found to harbor an average of 2.91 phage elements per genome (143 identified phage elements/49 A. hydrophila strains) (Awan et al., 2018). Almost all the strains carry one or more prophage elements, with the exceptions being strains FC951, CECT4486, and CCM7244, which do not carry any type of prophage. Strains MS-17-88 and TH0426 had the maximum number of identified prophage elements (6 elements per strain). The maximum number of complete prophage elements (5 complete phages) was present in strain MS-17-88 along with one incomplete phage element (Figure 4). The maximum number of incomplete prophage elements (4 incomplete phages) was present in strains TTU2014-108ASC and TTU2014-115AME. Strain MS-17-88 carries three different types of phage elements: vB_AbaM_ME3, phi018P, and RSA1. Interestingly, two of these phage elements (vB_AbaM_ME3 and RSA1) are not carried by any other evaluated A. veronii genomes, suggesting that this strain has been exposed to different environments and acquired unique phage elements. Phage vB_AbaM_ME3 was previously isolated from wastewater effluent using the propagating host Acinetobacter baumannii DSM 30007 (Kropinski et al., 2009). A. baumannii is a known nosocomial pathogen that causes pneumonia, urinary tract infection, and septicemia (Buttimer et al., 2016). Phage vB_AbaM_ME3 of A. baumannii has a size of 234,900 bp and 326 ORFs (Buttimer et al., 2016). The Myovirus-type phage RSA1 is relatively small (39 to 40 kb) and has lytic activity. It has restricted host range, mainly Ralstonia solanacearum, a soil-borne species pathogenic to many important crops (Yamada et al., 2007;Addy et al., 2019).
Interestingly, the MS-17-88 genome has four prophages sharing structural similarities with temperate Aeromo_phiO18P elements found in Aeromonas media isolated from a pond in Germany (Beilstein and Dreiseikelmann, 2008). The phiO18P phage type belongs to the Myoviridae phage family and consists of 33 kb. The phiO18P phage elements typically have 46 ORFs encoding proteins responsible for integration and regulation, replication, packaging, head and tail, and lysis (Beilstein and Dreiseikelmann, 2008). Unlike other prophage elements, Aeromo_phiO18P does not have a lytic phase; it replicates lysogenically by integrating its genome into the bacterial chromosome (Vincent et al., 2017). In some instances, the phageencoded genes are advantageous to the host bacteria (Dziewit and Radlinska, 2016). Aeromo_phiO18P shows significant similarity to the P2 phage family in Aeromonas salmonicida and Vibrio cholerae K139 genomes (Beilstein and Dreiseikelmann, 2008).
The present study documented 40 different types of phage elements across the 53 A. veronii genomes (Figure 5). Among these 40 phage elements, phage type "Aeromo_phiO18P" is the most abundant type in all the evaluated A. veronii genomes as well as the most abundant in strain MS-17-88. Strains CCM 4359 and XH.VA.1 carry five different phage elements. Incomplete Staphy_SPbeta_like phage element was detected in two strains . In our initial analysis of the MS-17-88 genome using PHASTER, we identified that the strain carries the floR gene inside incomplete phage element PHAGE_Staphy_SPbeta_like_NC_029119 (genome position 2631302-2644102), but later analysis with PHASTER showed that this may not be a true phage element. Further investigation of this region is warranted to determine whether a phage element mediated dissemination of the floR resistance gene (Garriss et al., 2009).

Comparative Analysis of Antibiotic Resistance Determinants
A comparative analysis of 87 AMR determinants and components was conducted to determine their distribution  among the 53 A. veronii strains. A. veronii MS-17-88 shared a common AMR gene composition with the other A. veronii genomes. Figure 6 shows the distribution of antibiotic resistance genes in each strain. All the A. veronii genomes carry tetracycline [tet(34) and tet(E)], and trimethoprim (dfrA3) resistance genes. Oxytetracycline, tetracycline, and trimethoprim/sulfamethoxazole have been extensively used in human clinical, veterinary, and agricultural sectors for decades. The linkage between AM use and resistance has been demonstrated for other bacteria in aquaculture ecosystems and other animal husbandry facilities (Verner-Jeffreys et al., 2009;Lagana et al., 2011;Tamminen et al., 2011). In addition to tet(34), tet(E), and dfrA3, A. veronii MS-17-88 genome carries colistin resistance genes (mcr-7.1 and mcr-3). There have been an increasing number of reports on the identification of mcr genes in many bacterial species globally (Stoesser et al., 2016;Elbediwi et al., 2019). A recent study reported that mcr-3 variants are more common in Aeromonas than in other bacterial species but aeromonads do not inherently carry the mcr-3 gene (Shen et al., 2018). However, it is speculated that Aeromonas isolates from the aquatic environment may be the major reservoir for the dissemination of mcr-3 genes to other  bacteria (Ling et al., 2017;Eichhorn et al., 2018). Furthermore, A. veronii MS-17-88 genome harbors a macrolide resistance gene vat(F) that encodes an acetyltransferase that acetylates class A streptogramins (Seoane and García Lobo, 2000). Six genes encoding resistance to β-lactamases were identified in A. veronii MS-17-88 genome including ampH and blaOXA-427 belong to class D beta-lactamase, ampS encoding a class 2d penicillinase and hydrolyzing mainly penicillins (Walsh et al., 1995), and cphA2, cphA8, and imiS encoding a class 3 metallo-β-lactamase and active mainly against carbapenems (Walsh et al., 1998).
Among the 53 A. veronii strains, AVNIH1 strain had resistance genes to almost all the antibiotic classes. This clinical strain was isolated from human stool, and the genome exhibits clear evidence of horizontal gene transfer (Hughes et al., 2016). In our analyses, we did not observe any pattern of antimicrobial resistance in specific bacterial host or sources. However, there was one exception: the highest number of AMR elements were observed in two human isolates (strain AVNIH from U.S.A; (Hughes et al., 2016) and ZJ12-3 from China; Shen et al., 2018), and one isolate from septicemic goldfish (strain Ae52 from Sri-Lanka; Jagoda et al., 2017). The use of antimicrobial agents in human medicine may be associated with these nosocomial trends (Hughes et al., 2016).
In regard to sulphonamide resistance, sul1 was detected in four strains (Ae52, ANIH1, Z2-7, and ZJ12-3) representing 7.5% of the A. veronii strains, and sul2 was present in one strain (Z2-7) representing 1.8%. This suggests that sul1 is the most frequent gene encoding sulfonamides resistance in A. veronii. Nearly all strains (100%) carried tet(34), and a significant proportion of strains carried tet(E) (20 strains; 37%). In contrast, tet(57) and tet(D) were detected in only one strain (ANIH1) (1.8%), and tet(A) was detected in two strains (Ae52 and ZJ12-3) (3.8%). floR gene conferring resistance to florfenicol and chloramphenicol was present in only four strains (MS-17-88, AVNIH1, Z2-7, and ZJ12-3) (7.5%). The prevalence of beta-lactam resistance genes in the 53 A. veronii genomes was as follows: ampH was detected in 41.5% of the strains, ampS was detected in 92.4% of the strains, imiH was detected in 13.2% of the strains, imiS was detected in 71.7% of the strains, blaCEPH-A3 was detected in 56.6% of the strains, blaOXA-427 was detected in 45.3% of the strains, cphA1 was detected in 17% of the strains, cphA2 was detected in 26.41% of the strains, cphA6 was detected in 13.2% of the strains, cphA7 was detected in 20.7% of the strains, and cphA8 was detected in 44% of the strains. Of the aminoglycoside resistance genes, aac(6 ′ )-Ic was the most prevalent (32%). Interestingly, A. veronii AVNIH1 and Ae52 strains carried multiple aminoglycoside-resistance genes. Several studies reported that the majority of Aeromonas species exhibit only a single aminoglycoside modifying gene (Dahanayake et al., 2019). However, Pseudomonas aeruginosa isolated from hospitals from Iran was reported to carry up to four aminoglycoside resistance genes (Perez-Vazquez et al., 2009).
In conclusion, we used genome sequencing to investigate genetic variation and AMR gene distribution in 53 A. veronii genomes. We found significant genetic differences and a high degree of genomic plasticity in the evaluated A. veronii genomes. Overall, the AMR gene frequency against sulfamethoxazole and florfenicol is low, while AMR genes against tetracycline are very high. Among tetracycline-resistant isolates, tet(34) and tet(E) were the most frequent AMR genes. Taken together, our results show that AMR genes are common and are distributed among A. veronii genomes; however, the frequency of most AMR genes in individual strains is still low. Identified phage elements may be useful for future development of an efficient and effective bio-treatment method to control bacterial diseases in aquaculture. The knowledge generated from this study can benefit our understanding of A. veronii evolution and provide insight into how A. veronii isolates are intrinsically resistant to multiple antimicrobials. In addition, A. veronii species are important considerations as potential sources for resistance determinants in the environment. Therefore, it is important to continue surveillance of resistance and genetic mechanisms of resistance in this species.

DATA AVAILABILITY STATEMENT
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article.

AUTHOR CONTRIBUTIONS
HT, ML, and HA designed and conceived the analysis and experiments. HT, MA, C-YH, AT, JB, and HA performed the experiments and analyzed the data. HT, ML, and HA wrote the manuscript. All authors read and approved the final manuscript.