Detection of the floR gene in a diversity of florfenicol resistant Gram-negative bacilli from freshwater salmon farms in Chile

Detection of florfenicol resistance in opportunistic Acinetobacter spp. infections in rural Thailand

Florfenicol (Ff) is an antimicrobial agent belonging to the class amphenicol used for the treatment of bacterial infections in livestock, poultry, and aquaculture (animal farming). It inhibits protein synthesis. Ff is an analog of chloramphenicol, an amphenicol compound on the WHO essential medicine list that is used for the treatment of human infections. Due to the extensive usage of Ff in animal farming, zoonotic pathogens have developed resistance to this antimicrobial agent. There are numerous reports of resistance genes from organisms infecting or colonizing animals found in human pathogens, suggesting a possible exchange of genetic materials. One of these genes is floR, a gene that encodes for an efflux pump that removes Ff from bacterial cells, conferring resistance against amphenicol, and is often associated with mobile genetic elements and other resistant determinants. In this study, we analyzed bacterial isolates recovered in rural Thailand from patients and environmental samples collected for disease monitoring. Whole genome sequencing was carried out for all the samples collected. Speciation and genome annotation was performed revealing the presence of the floR gene in the bacterial genome. The minimum inhibitory concentration (MIC) was determined for Ff and chloramphenicol. Chromosomal and phylogenetic analyses were performed to investigate the acquisition pattern of the floR gene. The presence of a conserved floR gene in unrelated Acinetobacter spp. isolated from human bacterial infections and environmental samples was observed, suggesting multiple and independent inter-species genetic exchange of drug-resistant determinants. The floR was found to be in the variable region containing various mobile genetic elements and other antibiotic resistance determinants; however, no evidence of HGT could be found. The floR gene identified in this study is chromosomal for all isolates. The study highlights a plausible impact of antimicrobials used in veterinary settings on human health. Ff shares cross-resistance with chloramphenicol, which is still in use in several countries. Furthermore, by selecting for floR-resistance genes, we may be selecting for and facilitating the zoonotic and reverse zoonotic exchange of other flanking resistance markers between human and animal pathogens or commensals with detrimental public health consequences.

A review on the antibiotic florfenicol: Occurrence, environmental fate, effects, and health risks

Florfenicol, as a replacement for chloramphenicol, can tightly bind to the A site of the 23S rRNA in the 50S subunit of the 70S ribosome, thereby inhibiting protein synthesis and bacterial proliferation. Due to the widespread use in aquaculture and veterinary medicine, florfenicol has been detected in the aquatic environment worldwide. Concerns over the effects and health risks of florfenicol on target and non-target organisms have been raised in recent years. Although the ecotoxicity of florfenicol has been widely reported in different species, no attempt has been made to review the current research progress of florfenicol toxicity, hormesis, and its health risks posed to biota. In this study, a comprehensive literature review was conducted to summarize the effects of florfenicol on various organisms including bacteria, algae, invertebrates, fishes, birds, and mammals. The generation of antibiotic resistant bacteria and spread antibiotic resistant genes, closely associated with hormesis, are pressing environmental health issues stemming from overuse or misuse of antibiotics including florfenicol. Exposure to florfenicol at μg/L-mg/L induced hormetic effects in several algal species, and chromoplasts might serve as a target for florfenicol-induced effects; however, the underlying molecular mechanisms are completely lacking. Exposure to high levels (mg/L) of florfenicol modified the xenobiotic metabolism, antioxidant systems, and energy metabolism, resulting in hepatotoxicity, renal toxicity, immunotoxicity, developmental toxicity, reproductive toxicity, obesogenic effects, and hormesis in different animal species. Mitochondria and the associated energy metabolism are suggested to be the primary targets for florfenicol toxicity in animals, albeit further in-depth investigations are warranted for revealing the long-term effects (e.g., whole-life-cycle impacts, multigenerational effects) of florfenicol, especially at environmental levels, and the underlying mechanisms. This will facilitate the evaluation of potential hormetic effects and construction of adverse outcome pathways for environmental risk assessment and regulation of florfenicol.

An update on the prevalence of colistin and carbapenem-resistant Gram-negative bacteria in aquaculture: an emerging threat to public health

Aquaculture has been recognized as a hotspot for the emergence and spread of antimicrobial resistance genes conferring resistance to clinically important antibiotics. This review gives insights into studies investigating the prevalence of colistin and carbapenem resistance (CCR) among Gram-negative bacilli in aquaculture. Overall, a high incidence of CCR has been reported in aquatic farms in several countries, with CCR being more prevalent among opportunistic human pathogens such as Acinetobacter nosocomialis, Shewanella algae, Photobacterium damselae, Vibrio spp., Aeromonas spp., as well as members of Enterobacteriaceae family. A high proportion of isolates in these studies exhibited wide-spectrum profiles of antimicrobial resistance, highlighting their multidrug-resistance properties (MDR). Several mobile colistin resistance genes (including, mcr-1, mcr-1.1, mcr-2, mcr-2.1, mcr-3, mcr-3.1, mcr-4.1, mcr-4.3, mcr-5.1, mcr-6.1, mcr-7.1, mcr-8.1, and mcr-10.1) and carbapenemase encoding genes (including, blaOXA-48, blaOXA-55, blaNDM, blaKPC, blaIMI, blaAIM, blaVIM, and blaIMP) have been detected in aquatic farms in different countries. The majority of these were carried on MDR Incompatibility (Inc) plasmids including IncA/C, and IncX4, which have been associated with a wide host range of different sources. Thus, there is a risk for the possible spread of resistance genes between fish, their environments, and humans. These findings highlight the need to monitor and regulate the usage of antimicrobials in aquaculture. A multisectoral and transdisciplinary (One Health) approach is urgently needed to reduce the spread of resistant bacteria and/or resistance genes originating in aquaculture and avoid their global reach.

Tentative Epidemiological Cut-Off Values and Distribution of Resistance Genes in Aquatic Pseudomonas Species Isolated from Rainbow Trout

Epidemiological cut-off value (ECV) analysis for commonly used antimicrobials in aquaculture have not been established for many aquatic pathogens, including Pseudomonas. This study was the first to examine the categorization of 92 aquatic Pseudomonas isolates by calculating seven antimicrobials ECVs using two analytical methods: normalized resistance interpretation and ECOFFinder. Pseudomonas spp. isolates had decreased sensitivity to all antimicrobials examined except for doxycycline and ciprofloxacin. The PCR analysis of the 91 isolates of Pseudomonas spp. detected the tetracycline genes are predominant with the count of 41 genes, including tetA, tetC, tetD, tetM, tetS and tetH, following sulfonamide genes are in 21 isolates including sul1 and sul2, floR gene in 15 isolates and ermA gene in three isolates. Our findings provide an understanding of the antimicrobial categorization of Pseudomonas species, which are significant groups, subgroups, and species for aquaculture due to insufficiently defined breakpoints or cut-off values reported in CLSI and/or EUCAST.

A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S)

While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.

Antibiotic Resistance Properties among Pseudomonas spp. Associated with Salmon Processing Environments

Continuous monitoring of antimicrobial resistance in bacteria along the food chain is crucial for the assessment of human health risks. Uncritical use of antibiotics in farming over years can be one of the main reasons for increased antibiotic resistance in bacteria. In this study, we aimed to classify 222 presumptive Pseudomonas isolates originating from a salmon processing environment, and to examine the phenotypic and genotypic antibiotic resistance profiles of these isolates. Of all the analyzed isolates 68% belonged to Pseudomonas, and the most abundant species were Pseudomonas fluorescens, Pseudomonas azotoformans, Pseudomonas gessardii, Pseudomonas libanesis, Pseudomonas lundensis, Pseudomonas cedrina and Pseudomonas extremaustralis based on sequencing of the rpoD gene. As many as 27% of Pseudomonas isolates could not be classified to species level. Phenotypic susceptibility analysis by disc diffusion method revealed a high level of resistance towards the antibiotics ampicillin, amoxicillin, cefotaxime, ceftriaxone, imipenem, and the fish farming relevant antibiotics florfenicol and oxolinic acid among the Pseudomonas isolates. Whole genome sequencing and subsequent analysis of AMR determinants by ResFinder and CARD revealed that no isolates harbored any acquired resistance determinants, but all isolates carried variants of genes known from P. aeruginosa to be involved in multidrug efflux pump systems.

Microbiota composition and susceptibility to florfenicol and oxytetracycline of bacterial isolates from mussels (Mytilus spp.) reared on different years and distance from salmon farms

Chilean aquaculture mainly produces salmonids and molluscs. Salmonid production has been questioned by its excessive use of antimicrobials. This study aimed to investigate the bacterial microbiota composition of Mytilus spp. cultivated near salmonid farms and to determine the minimum inhibitory concentration (MIC) to florfenicol and oxytetracycline of its culturable bacteria. Seven Mytilus farming sites classified according to their proximity to salmon farms as close (CSF) or distant (DSF) were sampled in two years. We analyzed Mytilus microbiota composition through culture-independent methods, and isolated culturable bacteria, and identified those isolates with MIC values ≥ 64 μg mL^-1 to florfenicol or oxytetracycline. Results revealed that the alpha diversity was affected by sampling year but not by Mytilus farming site location or its interaction. Nevertheless, in 2018, we observed a significant negative correlation between the alpha diversity of Mytilus microbiota in each farm sites and the tonnes of florfenicol reported for each phytosanitary management area. We detected significant differences in beta diversity and relative abundance of specific bacterial taxa in Mytilus microbiota depending on the proximity to salmon farms and years. A higher proportion of isolates with MIC values ≥ 64 μg mL^-1 to both antibiotics was detected in 2019 compared to 2018, but not significant differences were detected according to Mytilus farming site location. However, in 2019, isolates from CSF sites showed higher MIC values for both antibiotics than those from DSF. Bacterial genera corresponding to isolates with MIC values ≥ 64 μg mL^-1 represented a low proportion of Mytilus microbiota identified with the culture-independent approach, reflecting the need to implement new methodologies in the study of antimicrobial resistance. These results suggest that the proximity to salmonid farms and sampling year influence the Mytilus microbiota and MIC values of their bacterial isolates; however, other environmental variables should be considered in further studies.

New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods

Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe River and Bohai Bay. Our results showed that accumulated DNA yields after five extractions were 1.8–3.1 times higher than that by single DNA extractions. High-throughput sequencing showed that insufficient DNA extraction could generate PCR bias and skew community structure characterization in sediment. The relative abundances of some pathogenic bacteria, such as Enterobacteriales, Lactobacillales, and Streptomycetales, were significantly different between single and successive DNA extraction samples. In addition, real-time fluorescent quantitative PCR (qPCR) showed that ARGs, intI1, and 16S rRNA gene abundance strongly increased with increasing extraction cycles. Among the measured ARGs, sulfonamide resistance genes and multidrug resistance genes were dominant subtypes in the study region. Nevertheless, different subtypes of ARGs did not respond equally to the additional extraction cycles; some continued to have linear growth trends, and some tended to level off. Additionally, more correlations between ARGs and bacterial communities were observed in the successive DNA extraction samples than in the single DNA extraction samples. It is suggested that 3–4 additional extraction cycles are required in future studies when extracting DNA from sediment samples. Taken together, our results highlight that performing successive DNA extractions on sediment samples optimizes the extractable DNA yield and can lead to a better picture of the abundance of ARGs and their potential hosts in sediments.

The Gene Regulatory Roles of Herbal Extracts on the Growth, Immune System, and Reproduction of Fish

The crucial need for safe and healthy aquatic animals obligates researchers in aquaculture to investigate alternative and beneficial additives. Medicinal herbals and their extracts are compromised with diverse effects on the performances of aquatic animals. These compounds can affect growth performance and stimulate the immune system when used in fish diet. In addition, the use of medicinal herbs and their extracts can reduce oxidative stress induced by several stressors during fish culture. Correspondingly, aquatic animals could gain increased resistance against infectious pathogens and environmental stressors. Nevertheless, the exact mode of action where these additives can affect aquatic animals' performances is still not well documented. Understanding the mechanistic role of herbal supplements and their derivatives is a vital tool to develop further the strategies and application of these additives for feasible and sustainable aquaculture. Gene-related studies have clarified the detailed information on the herbal supplements' mode of action when administered orally in aquafeed. Several review articles have presented the potential roles of medicinal herbs on the performances of aquatic animals. However, this review article discusses the outputs of studies conducted on aquatic animals fed dietary, medicinal herbs, focusing on the gene expression related to growth and immune performances. Furthermore, a particular focus is directed to the expected influence of herbal supplements on the reproduction of aquatic animals.

Fecal indicators, pathogens, antibiotic resistance genes, and ecotoxicity in Galveston Bay after Hurricane Harvey

Unprecedented rainfall after Hurricane Harvey caused a catastrophic flood in the southern coast of Texas, and flushed significant floodwater and sediments into Galveston Bay, the largest estuary along the Texas Gulf Coast. This study investigated the immediate and long-term (6 months post-Harvey) fecal indicators, pathogenic bacteria, antibiotic resistance genes (ARGs), and ecotoxicity in the Galveston Bay. Dramatic decrease of salinity profile to zero, increased levels of fecal indicator bacteria and pathogenic bacteria, and detection of various ARGs were observed in the water and sediment samples collected 2 weeks post-Harvey. High levels of Bla_TEM and cytotoxicity measured by yeast bioluminescent assay (BLYR) were also observed especially near the river mouths. While Vibrio spp. was dominant in water, much higher abundance of fecal indicator bacteria and pathogen were detected in the sediments. A decreasing trend of Bla_TEM and cytotoxicity was observed in March 2018 samples, suggesting the Bay has returned to its pre-hurricane conditions 6 months post-Harvey. Interestingly, the abundance of fecal indicator bacteria and pathogens were shifted dramatically according to high-streamflow and low-streamflow seasons in the Bay. The data are useful to construct the model of risk assessment in coastal estuaries system and predict the effects of extreme flooding events in the future.

Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss)

The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistance genes and resistant bacterial hazards. However, scant research has been devoted to the possible sources of diversity in fresh fillet bacterial ecosystems (farm environment including rivers and practices, and factory environment). In this study bacterial communities and the antibiotic resistance genes of fresh rainbow trout fillet were described using amplicon sequencing of the V3-V4 region of the 16S rRNA gene and high-throughput qPCR assay. The antibiotic residues were quantified using liquid chromatography/mass spectrometry methods. A total of 56 fillets (composed of muscle and skin tissue) from fish raised on two farms on the same river were collected and processed under either factory or laboratory sterile filleting conditions. We observed a core-bacterial community profile on the fresh rainbow trout fillets, but the processing conditions of the fillets has a great influence on their mean bacterial load (3.38 ± 1.01 log CFU/g vs 2.29 ± 0.72 log CFU/g) and on the inter-individual diversity of the bacterial community. The bacterial communities were dominated by Gamma- and Alpha-proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The most prevalent genera were Pseudomonas, Escherichia-Shigella, Chryseobacterium, and Carnobacterium. Of the 73 antibiotic residues searched, only oxytetracycline residues were detected in 13/56 fillets, all below the European Union maximum residue limit (6.40–40.20 μg/kg). Of the 248 antibiotic resistance genes searched, 11 were found to be present in at least 20% of the fish population (tetracycline resistance genes tetM and tetV, β-lactam resistance genes bla_DHA and bla_ACC, macrolide resistance gene mphA, vancomycin resistance genes vanTG and vanWG and multidrug-resistance genes mdtE, mexF, vgaB and msrA) at relatively low abundances calculated proportionally to the 16S rRNA gene.

Molecular analysis of florfenicol-resistant bacteria isolated from drinking water distribution systems in Southwestern Nigeria

OBJECTIVES

Use of chloramphenicol or its veterinary analogue florfenicol can selectively favour antibiotic-resistant bacteria. Understanding how resistance is mobilised and disseminated among pathogens is vital in knowing how different bacterial taxa might serve as reservoirs of these genes for pathogenic bacteria.

METHODS

Bacterial isolates (n=30) were selected on the basis of multidrug resistance and resistance to florfenicol from among 296 bacteria originally isolated from drinking water distribution systems in Southwestern Nigeria. Bacterial identification, minimum inhibitory concentration (MIC) determination for florfenicol, PCR detection of florfenicol resistance genes (floR, fexA and cfx) and sequence analysis were employed to characterise the isolates.

RESULTS

According to sequence data (16S rDNA, v2-v3 region), 30strains were selected, includingPseudomonas spp. (43.3%), Serratia spp. (13.3%), Proteus spp. (26.7%), Acinetobacter spp. (13.3%) and Providencia rettgeri (3.3%). MICs ranged between >16μg/mL and >1024μg/mL. floR was the only resistance gene detected (11/30; 36.7%). The majority of floR-positive isolates (8/11; 72.7%) were Proteus spp. All floR sequences shared 100% identity and 1-2 synonymous substitutions relative to other published sequences.

CONCLUSIONS

floR-positive strains in this study were originally selected randomly without antibiotics. Finding floR in four genera without selective enrichment is consistent with widespread distribution of this resistance trait in drinking water systems in Nigeria. Further work is needed to determine whether human and veterinary antibiotic use practices in Nigeria are contributing to proliferation of this important antibiotic resistance trait and to determine whether the presence of floR-producing strains is compromising human and animal health.

Comparison of Stomaching versus Rinsing for Recovering Bacterial Communities from Rainbow Trout (Oncorhynchus mykiss) Fillets

ABSTRACT

The use of high-throughput methods allows a better characterization of food-related bacterial communities. However, such methods require large amounts of high-quality bacterial DNA, which may be a challenge when dealing with a complex matrix that has a low concentration of bacteria, such as fresh fish fillets. Therefore, the choice of method used to recover bacteria from a food matrix in a cost-effective way is critical, yet little information is available on the performance of commonly used methods. We assessed the recovery capacity of two such methods: stomaching and mechanical rinsing. The efficiency of the methods was evaluated through quantitative recovery and compatibility with end-point quantitative PCR (qPCR). Fresh rainbow trout (Oncorhynchus mykiss) fillets were inoculated with a bacterial marker, Brochothrix thermosphacta, at different concentrations (7.52 to 1.52 log CFU/g). The fillets were processed by one of the two methods, and the recovery of the marker in the suspensions was assessed by plate counting and qPCR targeting B. thermosphacta-rpoC. The same analyses were performed on six noninoculated fresh fillets. Stomaching and mechanical rinsing allowed efficient and repeatable recovery of the bacterial communities from the 42 inoculated fillets. No significant differences in recovery ratios were observed between the marker enumerated in the inoculation suspensions and in the corresponding recovery suspensions after rinsing and stomaching. However, the stomaching method allowed too many particles to pass through the filters bag, making necessary a limiting supplementary filtration step. As a consequence, only the rinsing recovery method allowed proper PCR quantification of the inoculated B. thermosphacta. The mean recovered bacterial level of the fillets was approximately 3 log CFU/g. It seems more relevant and cost-effective to recover the endogenous bacterial microbiota of a fish fillet structure using the rinsing method rather than the stomaching method.

HIGHLIGHTS

Analysis of Resistance to Florfenicol and the Related Mechanism of Dissemination in Different Animal-Derived Bacteria

Bacterial resistance to antibiotics has become an important concern for public health. This study was aimed to investigate the characteristics and the distribution of the florfenicol-related resistance genes in bacteria isolated from four farms. A total of 106 florfenicol-resistant Gram-negative bacilli were examined for florfenicol-related resistance genes, and the positive isolates were further characterized. The antimicrobial sensitivity results showed that most of them (100, 94.33%) belonged to multidrug resistance Enterobacteriaceae. About 91.51% of the strains carried floR gene, while 4.72% carried cfr gene. According to the pulsed-field gel electrophoresis results, 34 Escherichia coli were subdivided into 22 profiles, the genetic similarity coefficient of which ranged from 80.3 to 98.0%. The multilocus sequence typing (MLST) results revealed 17 sequence types (STs), with ST10 being the most prevalent. The genome sequencing result showed that the Proteus vulgaris G32 genome consists of a 4.06-Mb chromosome, a 177,911-bp plasmid (pG32-177), and a 51,686-bp plasmid (pG32-51). A floR located in a drug-resistant region on the chromosome of P. vulgaris G32 was with IS91 family transposase, and the other floR gene on the plasmid pG32-177 was with an ISCR2 insertion sequence. The cfr gene was located on the pG32-51 flanked by IS26 element and TnpA26. This study suggested that the mobile genetic elements played an important role in the replication of resistance genes and the horizontal resistance gene transfer.

Live Feeds Used in the Larval Culture of Red Cusk Eel, Genypterus chilensis, Carry High Levels of Antimicrobial-Resistant Bacteria and Antibiotic-Resistance Genes (ARGs)

Simple Summary

The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibiotics, mainly florfenicol. In this study, the role of live prey (rotifers and the brine shrimp Artemia franciscana) used to feed fish larvae as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis was investigated. Samples of live feeds were collected during the larval growth period and their bacterial contents were determined. High levels of potentially opportunistic pathogens, such as Vibrio spp., as well as florfenicol-resistant bacteria, were detected. Sixty-five florfenicol-resistant isolates were recovered from these cultures and identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%), which exhibited a high incidence of co-resistance to the antibiotics streptomycin, oxytetracycline, co-trimoxazole, and kanamycin. The majority of them carried the florfenicol-resistance encoding genes floR and fexA. The high prevalence of antibiotic-resistant bacteria and the associated genetic elements in live feed administered to reared fish larvae requires the prompt implementation of efficient management strategies to prevent future therapy failures in fish larval cultures and the spread of antibiotic-resistant bacteria to associated aquatic environments.

Abstract

The culture of red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibacterials. The main aim of this study was to evaluate the role of live feed as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis. Samples of rotifer and Artemia cultures used as live feed were collected during the larval growth period and culturable bacterial counts were performed using a spread plate method. Rotifer and Artemia cultures exhibited high levels of resistant bacteria (8.03 × 10⁴ to 1.79 × 10⁷ CFU/g and 1.47 × 10⁶ to 3.50 × 10⁸ CFU/g, respectively). Sixty-five florfenicol-resistant isolates were identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%) using 16S rRNA gene sequence analysis. A high incidence of resistance to streptomycin (93.8%), oxytetracycline (89.2%), co-trimoxazole (84.6%), and kanamycin (73.8%) was exhibited by resistant isolates. A high proportion of isolates (76.9%) carried the florfenicol-resistance encoding genes floR and fexA, as well as plasmid DNA (75.0%). The high prevalence of multiresistant bacteria in live feed increases the incidence of the resistant microbiota in reared fish larvae, thus proper monitoring and management strategies for live feed cultures appear to be a priority for preventing future therapy failures in fish larval cultures.

Acinetobacter baumannii Efflux Pumps and Antibiotic Resistance

Acinetobacter baumannii is a nosocomial pathogen and gram-negative coccobacillus that is responsible for opportunistic infections, pneumonia, and infections of the urinary tract, bloodstream, skin, and soft tissue. This bacterium poses a major public health problem due to inducing resistance to several drugs, isolates, multidrug treatment, and occasionally pan drugs. Drug resistance is not only a major concern caused by A. baumannii but also is considered as the main challenge in many other pathogens. Several factors such as the efflux pump are associated with antibiotic resistance, biofilm production, and genetic mutations. In this review, A. baumannii is introduced in then some of the practical works conducted on the existing efflux pump are reviewed. The importance of the efflux pump is considered in this paper in relation to the antibiotic resistance and mechanisms developed for the inhibition of these pumps as well.

Characterization of Mechanisms Lowering Susceptibility to Flumequine among Bacteria Isolated from Chilean Salmonid Farms

Despite their great importance for human therapy, quinolones are still used in Chilean salmon farming, with flumequine and oxolinic acid currently approved for use in this industry. The aim of this study was to improve our knowledge of the mechanisms conferring low susceptibility or resistance to quinolones among bacteria recovered from Chilean salmon farms. Sixty-five isolates exhibiting resistance, reduced susceptibility, or susceptibility to flumequine recovered from salmon farms were identified by their 16S rRNA genes, detecting a high predominance of species belonging to the Pseudomonas genus (52%). The minimum inhibitory concentrations (MIC) of flumequine in the absence and presence of the efflux pump inhibitor (EPI) Phe-Arg-β-naphthylamide and resistance patterns of isolates were determined by a microdilution broth and disk diffusion assays, respectively, observing MIC values ranging from 0.25 to >64 µg/mL and a high level of multi-resistance (96%), mostly showing resistance to florfenicol and oxytetracycline. Furthermore, mechanisms conferring low susceptibility to quinolones mediated by efflux pump activity, quinolone target mutations, or horizontally acquired resistance genes (qepA, oqxA, aac(6′)-lb-cr, qnr) were investigated. Among isolates exhibiting resistance to flumequine (≥16 µg/mL), the occurrence of chromosomal mutations in target protein GyrA appears to be unusual (three out of 15), contrasting with the high incidence of mutations in GyrB (14 out of 17). Bacterial isolates showing resistance or reduced susceptibility to quinolones mediated by efflux pumps appear to be highly prevalent (49 isolates, 75%), thus suggesting a major role of intrinsic resistance mediated by active efflux.

In Vitro Susceptibility and Florfenicol Resistance in Citrobacter Isolates and Whole-Genome Analysis of Multidrug-Resistant Citrobacter freundii

The genus Citrobacter is an opportunistic pathogen causing infections in animals, and the published data for its resistance to florfenicol are scarce. In this study, we investigated the antimicrobial susceptibility and molecular characteristics of florfenicol resistance genes among Citrobacter isolates from animal and relevant environmental samples and conducted a comparative analysis of a multidrug-resistant Citrobacter freundii strain isolated from a rabbit. Among 20 Citrobacter strains isolated from animal samples, resistance was most commonly observed to ampicillin (100%), tetracycline (75%), streptomycin (65%), florfenicol (60%), chloramphenicol (60%), and aztreonam (50%), while all the strains found in environmental samples were resistant to few antibiotics. The florfenicol resistance gene floR was detected in 12 isolates (48%, 12/25) from animal samples, and all of the floR-positive isolates were resistant to florfenicol with minimum inhibitory concentration (MIC) values ≥256 μg/mL. Sequencing and comparative analysis of the plasmids from a multidrug-resistant C. freundii isolate named R47 showed that the floR-containing region in the plasmid pR47-54 was a truncated transposon-like structure and could be found on both plasmids and chromosomes of bacteria of either animal or human origin. Furthermore, a range of antimicrobial and metal resistance genes associated with mobile genetic elements could be identified in pR47-54 and the other plasmid pR47-309 of C. freundii R47. These results provide in-depth views into the phenotypic and molecular characteristics of Citrobacter isolates recovered from animal and relevant environmental samples, as well as highlight the role horizontal gene transfer plays in the dissemination of plasmid-encoded resistance genes.

Comparative genomics analysis of Raoultella planticola S25 isolated from duck in China, with florfenicol resistance

To characterize the florfenicol resistance gene and analyze the structure of the resistance gene-related sequence of an Raoultella planticola strain S25 isolated from a duck fecal sample from a farm in South China. Molecular cloning was performed to clone the resistance genes such as mdfA, floR and so on, and the minimum inhibitory concentrations (MICs) were quantified to determine the resistance levels generated by the cloned genes and the related strains. Sequencing and comparative genomics methods were used to analyze the structure of the resistance gene-related sequence. The result showed that the genome of R. planticola S25 consists of a 5.47 Mb chromosome encoding 4962 predicted coding sequence (CDS) and a 68,566 bp plasmid, pS25-68, encoding 84 ORFs. The plasmid sharing the greatest sequence identity with the floR-carrying plasmid pS25-68 is plasmid1 in Klebsiella pneumoniae strain blaNDM-1, which was isolated from a patient in Canada. The mdfA1 gene encoded on the chromosome generated resistance to florfenicol in addition to chloramphenicol. Comparative genomic analysis of the floR-related transposon-like fragment of pS25-68 showed that an approximately 3 kb sequence encoding IS91-virD2-floR-lysR was conserved and presented in the majority of the sequences (84.5 %, 169/200) collected from the database. The results of this work demonstrated that horizontal transfer of the florfenicol resistance gene floR occurred widely between the bacteria of different species and with different origins and that additional florfenicol resistance genes may be present in the bacterial population.

Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile

Point sources such as wastewater treatment plants, terrestrial agriculture, and aquaculture may release antibiotic residues, antibiotic resistant bacteria, and antibiotic resistance genes (ARGs) into aquatic ecosystems. However, there is a lack of quantitative studies attributing environmental ARG abundance to specific sources. The goal of this study was to evaluate the role of freshwater trout farms in the release and dissemination of ARGs into the environment. Sediment samples upstream and downstream from five rainbow trout farms were collected over time in southern Chile. A microfluidic quantitative polymerase chain reaction approach was used to quantify an ARG array covering different mechanisms of resistance, and data were analyzed using principal component analysis (PCA) and linear mixed regression models. Surveys were also conducted to obtain information about management practices, including antibiotic use, at the farms. Florfenicol and oxytetracycline were used at these farms, although at different rates. A total of 93 samples were analyzed. In the PCA, , , , , (A), (B), (C), (W), and grouped together. A statistically significant increase in abundance of , , , and several genes was found downstream from the farms compared with upstream sites, and retention ponds had the highest ARG abundance at each site. Antibiotic resistance gene levels returned to baseline at an average distance of 132.7 m downstream from the farms. Although results from this study indicate an influence of trout farms on the presence of ARGs in the immediate environment, the extent of their contribution to ARG dissemination is unknown and deserves further investigation.

Occurrence of Transferable Integrons and sul and dfr Genes Among Sulfonamide-and/or Trimethoprim-Resistant Bacteria Isolated From Chilean Salmonid Farms

Salmon farming industry in Chile currently uses a significant quantity of antimicrobials to control bacterial pathologies. The main aims of this study were to investigate the presence of transferable sulfonamide- and trimethoprim-resistance genes, sul and dfr, and their association with integrons among bacteria associated to Chilean salmon farming. For this purpose, 91 Gram-negative strains resistant to sulfisoxazole and/or trimethoprim recovered from various sources of seven Chilean salmonid farms and mainly identified as belonging to the Pseudomonas genus (81.0%) were studied. Patterns of antimicrobial resistance of strains showed a high incidence of resistance to florfenicol (98.9%), erythromycin (95.6%), furazolidone (90.1%) and amoxicillin (98.0%), whereas strains exhibited minimum inhibitory concentrations (MIC₉₀) values of sulfisoxazole and trimethoprim of >4,096 and >2,048 μg mL⁻¹, respectively. Strains were studied for their carriage of these genes by polymerase chain reaction, using specific primers, and 28 strains (30.8%) were found to carry at least one type of sul gene, mainly associated to a class 1 integron (17 strains), and identified by 16S rRNA gene sequencing as mainly belonging to the Pseudomonas genus (21 strains). Of these, 22 strains carried the sul1 gene, 3 strains carried the sul2 gene, and 3 strains carried both the sul1 and sul2 genes. Among these, 19 strains also carried the class 1 integron-integrase gene intI1, whereas the dfrA1, dfrA12 and dfrA14 genes were detected, mostly not inserted in the class 1 integron. Otherwise, the sul3 and intI2 genes were not found. In addition, the capability to transfer by conjugation these resistance determinants was evaluated in 22 selected strains, and sul and dfr genes were successfully transferred by 10 assayed strains, mainly mediated by a 10 kb plasmid, with a frequency of transfer of 1.4 × 10⁻⁵ to 8.4 × 10⁻³ transconjugant per recipient cell, and exhibiting a co-transference of resistance to florfenicol and oxytetracycline, currently the most used in Chilean salmon industry, suggesting an antibacterial co-selection phenomenon. This is the first report of the characterization and transferability of integrons as well as sul and dfr genes among bacteria associated to Chilean salmon farms, evidencing a relevant role of this environment as a reservoir of these genes.

Spread of the florfenicol resistance floR gene among clinical Klebsiella pneumoniae isolates in China

Background

Florfenicol is a derivative of chloramphenicol that is used only for the treatment of animal diseases. A key resistance gene for florfenicol, floR, can spread among bacteria of the same and different species or genera through horizontal gene transfer. To analyze the potential transmission of resistance genes between animal and human pathogens, we investigated floR in Klebsiella pneumoniae isolates from patient samples. floR in human pathogens may originate from animal pathogens and would reflect the risk to human health of using antimicrobial agents in animals.

Methods

PCR was used to identify floR-positive strains. The floR genes were cloned, and the minimum inhibitory concentrations (MICs) were determined to assess the relative resistance levels of the genes and strains. Sequencing and comparative genomics methods were used to analyze floR gene-related sequence structure as well as the molecular mechanism of resistance dissemination.

Results

Of the strains evaluated, 20.42% (67/328) were resistant to florfenicol, and 86.96% (20/23) of the floR-positive strains demonstrated high resistance to florfenicol with MICs ≥512 μg/mL. Conjugation experiments showed that transferrable plasmids carried the floR gene in three isolates. Sequencing analysis of a plasmid approximately 125 kb in size (pKP18-125) indicated that the floR gene was flanked by multiple copies of mobile genetic elements. Comparative genomics analysis of a 9-kb transposon-like fragment of pKP18-125 showed that an approximately 2-kb sequence encoding lysR-floR-virD2 was conserved in the majority (79.01%, 83/105) of floR sequences collected from NCBI nucleotide database. Interestingly, the most similar sequence was a 7-kb fragment of plasmid pEC012 from an Escherichia coli strain isolated from a chicken.

Conclusions

Identified on a transferable plasmid in the human pathogen K. pneumoniae, the floR gene may be disseminated through horizontal gene transfer from animal pathogens. Studies on the molecular mechanism of resistance gene dissemination in different bacterial species of animal origin could provide useful information for preventing or controlling the spread of resistance between animal and human pathogens.

Extended antibiotic treatment in salmon farms select multiresistant gut bacteria with a high prevalence of antibiotic resistance genes

The high use of antibiotics for the treatment of bacterial diseases is one of the main problems in the mass production of animal protein. Salmon farming in Chile is a clear example of the above statement, where more than 5,500 tonnes of antibiotics have been used over the last 10 years. This has caused a great impact both at the production level and on the environment; however, there are still few works in relation to it. In order to demonstrate the impact of the high use of antibiotics on fish gut microbiota, we have selected four salmon farms presenting a similar amount of fish of the Atlantic salmon species (Salmo salar), ranging from 4,500 to 6,000 tonnes. All of these farms used treatments with high doses of antibiotics. Thus, 15 healthy fish were selected and euthanised in order to isolate the bacteria resistant to the antibiotics oxytetracycline and florfenicol from the gut microbiota. In total, 47 bacterial isolates resistant to florfenicol and 44 resistant to oxytetracycline were isolated, among which isolates with Minimum Inhibitory Concentrations (MIC) exceeding 2048 μg/mL for florfenicol and 1024 μg/mL for oxytetracycline were found. In addition, another six different antibiotics were tested in order to demonstrate the multiresistance phenomenon. In this regard, six isolates of 91 showed elevated resistance values for the eight tested antibiotics, including florfenicol and oxytetracycline, were found. These bacteria were called “super-resistant” bacteria. This phenotypic resistance was verified at a genotypic level since most isolates showed antibiotic resistance genes (ARGs) to florfenicol and oxytetracycline. Specifically, 77% of antibiotic resistant bacteria showed at least one gene resistant to florfenicol and 89% showed at least one gene resistant to oxytetracycline. In the present study, it was demonstrated that the high use of the antibiotics florfenicol and oxytetracycline has, as a consequence, the selection of multiresistant bacteria in the gut microbiota of farmed fish of the Salmo salar species at the seawater stage. Also, the phenotypic resistance of these bacteria can be correlated with the presence of antibiotic resistance genes.

Antimicrobial activity of trans-cinnamic acid and commonly used antibiotics against important fish pathogens and nonpathogenic isolates

AIMS

Antibiotics and several other chemicals have been used to prevent fish diseases. However, this situation results in economic loss for the companies in the aquaculture industry and most importantly it pollutes the environment. Cinnamic acid is a naturally occurring aromatic acid and is considered to be safe for human consumption. Therefore, in this study, the antibacterial activity of trans-cinnamic acid and commonly used antibiotics, namely chloramphenicol, vancomycin, streptomycin and erythromycin, were tested against 32 bacteria, including fish pathogens, nonpathogenic isolates and collection strains.

METHODS AND RESULTS

Trans-cinnamic acid was applied against the bacteria using the disc diffusion and microdilution method under in vitro conditions. Antibiotics were also tested under similar conditions against all tested bacteria using the disc diffusion method. The results show that among 32 bacterial strains trans-cinnamic acid exhibited potent inhibitory effect on the Gram-negative fish pathogen Aeromonas sobria. In addition, a moderate inhibition of trans-cinnamic acid of fish pathogens Aeromonas salmonicida, Vibrio (Listonella) anguillarum, Vibrio crassostreae and Yersinia ruckeri was also observed for trans-cinnamic acid in our study. On the contrary, the majority of nonpathogenic intestinal isolates were resistant to trans-cinnamic acid.

CONCLUSIONS

To the best of our knowledge, this is the first report on the antimicrobial activity of trans-cinnamic acid on 24 of the studied bacteria isolated from fish. In conclusion, trans-cinnamic acid can be used as an environmentally friendly alternative additive to prevent and control primarily A. sobria, as well as other pathogenic bacteria such as A. salmonicida, V. anguillarum, V. crassostreae and Y. ruckeri.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that trans-cinnamic acid may present an environmentally friendly alternative therapeutic agent against A. sobria infections in the aquaculture industry.

Current Status of the Use of Antibiotics and the Antimicrobial Resistance in the Chilean Salmon Farms

The Chilean salmon industry has undergone a rapid development making the country the world's second largest producer of farmed salmon, but this growth has been accompanied by an intensive use of antibiotics. This overuse has become so significant that Chilean salmon aquaculture currently has one of the highest rates of antibiotic consumption per ton of harvested fish in the world. This review has focused on discussing use of antibiotics and current status of scientific knowledge regarding to incidence of antimicrobial resistance and associated genes in the Chilean salmonid farms. Over recent years there has been a consistent increase in the amount of antimicrobials used by Chilean salmonid farms, from 143.2 tons in 2010 to 382.5 tons in 2016. During 2016, Chilean companies utilized approximately 0.53 kg of antibiotics per ton of harvested salmon, 363.4 tons (95%) were used in marine farms, and 19.1 tons (5%) in freshwater farms dedicated to smolt production. Florfenicol and oxytetracycline were by far the most frequently used antibiotics during 2016 (82.5 and 16.8%, respectively), mainly being used to treat Piscirickettsia salmonis, currently considered the main bacterial threat to this industry. However, the increasing development of this industry in Chile, as well as the intensive use of antimicrobials, has not been accompanied by the necessary scientific research needed to understand the impact of the intensive use of antibiotics in this industry. Over the last two decades several studies assessing antimicrobial resistance and the resistome in the freshwater and marine environment impacted by salmon farming have been conducted, but information on the ecological and environmental consequences of antibiotic use in fish farming is still scarce. In addition, studies reporting the antimicrobial susceptibility of bacterial pathogens, mainly P. salmonis, have been developed, but a high number of these studies were aimed at setting their epidemiological cut-off values. In conclusion, further studies are urgently required, mainly focused on understanding the evolution and epidemiology of resistance genes in Chilean salmonid farming, and to investigate the feasibility of a link between these genes among bacteria from salmonid farms and human and fish pathogens.

Acquisition of resistance to carbapenem and macrolide-mediated quorum sensing inhibition by Pseudomonas aeruginosa via ICETn4371 6385

Pseudomonas aeruginosa can cause life-threatening infections in immunocompromised patients. The first-line agents to treat P. aeruginosa infections are carbapenems. However, the emergence of carbapenem-resistant P. aeruginosa strains greatly compromised the effectiveness of carbapenem treatment, which makes the surveillance on their spreading and transmission important. Here we characterized the full-length genomes of two carbapenem-resistant P. aeruginosa clinical isolates that are capable of producing New Delhi metallo-β-lactamase-1 (NDM-1). We show that bla_NDM-1 is carried by a novel integrative and conjugative element (ICE) ICE_Tn43716385, which also carries the macrolide resistance gene msr(E) and the florfenicol resistance gene floR. By exogenously expressing msr(E) in P. aeruginosa laboratory strains, we show that Msr(E) can abolish azithromycin-mediated quorum sensing inhibition in vitro and anti-Pseudomonas effect in vivo. We conclude that ICEs are important in transmitting carbapenem resistance, and that anti-virulence treatment of P. aeruginosa infections using sub-inhibitory concentrations of macrolides can be challenged by horizontal gene transfer.

Yichen Ding et al. identify a novel integrative and conjugative element that confers Pseudomonas aeruginosa with resistance to carbapenem, the last-resort drug for susceptable Gram-negative bacterial infections. This study also shows how antivirulence treatment for P. aeruginosainfections can be challenged by horizontal gene transfer.

Current Status of the Use of Antibiotics and the Antimicrobial Resistance in the Chilean Salmon Farms

The Chilean salmon industry has undergone a rapid development making the country the world's second largest producer of farmed salmon, but this growth has been accompanied by an intensive use of antibiotics. This overuse has become so significant that Chilean salmon aquaculture currently has one of the highest rates of antibiotic consumption per ton of harvested fish in the world. This review has focused on discussing use of antibiotics and current status of scientific knowledge regarding to incidence of antimicrobial resistance and associated genes in the Chilean salmonid farms. Over recent years there has been a consistent increase in the amount of antimicrobials used by Chilean salmonid farms, from 143.2 tons in 2010 to 382.5 tons in 2016. During 2016, Chilean companies utilized approximately 0.53 kg of antibiotics per ton of harvested salmon, 363.4 tons (95%) were used in marine farms, and 19.1 tons (5%) in freshwater farms dedicated to smolt production. Florfenicol and oxytetracycline were by far the most frequently used antibiotics during 2016 (82.5 and 16.8%, respectively), mainly being used to treat Piscirickettsia salmonis, currently considered the main bacterial threat to this industry. However, the increasing development of this industry in Chile, as well as the intensive use of antimicrobials, has not been accompanied by the necessary scientific research needed to understand the impact of the intensive use of antibiotics in this industry. Over the last two decades several studies assessing antimicrobial resistance and the resistome in the freshwater and marine environment impacted by salmon farming have been conducted, but information on the ecological and environmental consequences of antibiotic use in fish farming is still scarce. In addition, studies reporting the antimicrobial susceptibility of bacterial pathogens, mainly P. salmonis, have been developed, but a high number of these studies were aimed at setting their epidemiological cut-off values. In conclusion, further studies are urgently required, mainly focused on understanding the evolution and epidemiology of resistance genes in Chilean salmonid farming, and to investigate the feasibility of a link between these genes among bacteria from salmonid farms and human and fish pathogens.

Impact of point sources on antibiotic resistance genes in the natural environment: a systematic review of the evidence

There is a growing concern about the role of the environment in the dissemination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this systematic review, we summarize evidence for increases of ARG in the natural environment associated with potential sources of ARB and ARG such as agricultural facilities and wastewater treatment plants. A total of 5247 citations were identified, including studies that ascertained both ARG and ARB outcomes. All studies were screened for relevance to the question and methodology. This paper summarizes the evidence only for those studies with ARG outcomes (n= 24). Sixteen studies were at high (n= 3) or at unclear (n= 13) risk of bias in the estimation of source effects due to lack of information or failure to control for confounders. Statistical methods were used in nine studies; three studies assessed the effect of multiple sources using modeling approaches, and none reported effect measures. Most studies reported higher ARG concentration downstream/near the source, but heterogeneous findings hindered making any sound conclusions. To quantify increases of ARG in the environment due to specific point sources, there is a need for studies that emphasize analytic or design control of confounding, and that provide effect measure estimates.

ISCR2 is associated with the dissemination of multiple resistance genes among Vibrio spp. and Pseudoalteromonas spp. isolated from farmed fish

58 multiresistant strains representing diverse genera were isolated from farmed fish in an aquaculture facility. Resistant rates of strains harboring ISCR2, an insertion sequence type element, were higher than those in which this element was absent. Full genome sequencing of a Vibrio isolate containing ISCR2 confirmed that it is associated with multiple resistance genes, many of which are of clinical relevance. We describe the structural variation within ISCR2, and its distribution throughout multiple diverse aquatic genera, including Vibrio, Shewenalla, Pseudoalteromonas and Psychrobacter, suggesting the potential role of ISCR2 in disseminating antibiotic resistance. We also observe, and experimentally verify, a novel macrolide resistance gene that is also associated with ISCR2.

Antimicrobial Compounds from Eukaryotic Microalgae against Human Pathogens and Diseases in Aquaculture

The search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. In this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. In this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human pathogens but also about their potential to limit microbial infections in aquaculture. An alternative to conventional antibiotics is needed as the microbial resistance to these drugs is increasing in humans and animals. Furthermore, using natural antibiotics for livestock could meet the consumer demand to avoid chemicals in food, would support a sustainable aquaculture and present the advantage of being environmentally friendly. Using natural and renewable microalgal compounds is still in its early days, but considering the important research development and rapid improvement in culture, extraction and purification processes, the valorization of microalgae will surely extend in the future.

Comprehensive antibiotic susceptibility profiling of Chilean Piscirickettsia salmonis field isolates

Antibiotics have been extensively used against infections produced by Piscirickettsia salmonis, a fish pathogen and causative agent of piscirickettsiosis and one of the major concerns for the Chilean salmon industry. Therefore, the emergence of resistant phenotypes is to be expected. With the aim of obtaining a landscape of the antimicrobial resistance of P. salmonis in Chile, the susceptibility profiles for quinolones, florfenicol and oxytetracycline (OTC) of 292 field isolates derived from main rearing areas, different hosts and collected over 5 years were assessed. The results allowed for the determination of epidemiological cut-off values that were used to characterize the pathogen population. This work represents the first large-scale field study addressing the antimicrobial susceptibility of P. salmonis, providing evidence of the existence of resistant types with a high incidence of resistance to quinolones. Remarkably, despite the amounts and frequency of therapies, our results disclosed that the issue of resistance to florfenicol and OTC is still in the onset.

Contamination of sulfonamide antibiotics and sulfamethazine-resistant bacteria in the downstream and estuarine areas of Jiulong River in Southeast China

Surface water samples from downstream and estuarine areas of Jiulong River were collected in August 2011 and May 2012 for detecting sulfonamide antibiotic residues and isolating sulfamethazine-resistant bacteria. Sulfamethazine was detected in all samples in May 2012 at an average concentration of 78.3 ng L(-1), which was the highest among the nine sulfonamide antibiotics determined. Sulfamethazine-resistant bacteria (SRB) were screened using antibiotic-containing agar plates. The SRB average abundance in the samples was 3.69 × 10(4) and 2.17 × 10(3) CFUs mL(-1) in August 2011 and May 2012, respectively, and was positively correlated to sulfamethazine concentration in May 2012. The 16S rRNA gene sequencing of all the 121 SRB isolates revealed high diversity. Furthermore, the SRB isolates exhibited multidrug resistance, with 48.7% showing resistance to at least three antibiotics. The abundance and persistence of highly diverse SRB and their multidrug resistance are likely to demonstrate the transferable pressure from coastal environments on public health.

Scallop larvae hatcheries as source of bacteria carrying genes encoding for non-enzymatic phenicol resistance

The main aim of the study was to evaluate the role of scallop hatcheries as source of the floR and cmlA genes. A number of 133 and 121 florfenicol-resistant strains were isolated from scallop larval cultures prior to their transfer to seawater and from effluent samples from 2 commercial hatcheries and identified by 16S rRNA gene sequence analysis, observing a predominance of the Pseudomonas, Pseudoalteromonas and Halomonas genera and exhibiting an important incidence of co-resistance to streptomycin, oxytetracycline and co-trimoxazole. A high percentage of strains from both hatcheries carried the floR gene (68.4% and 89.3% of strains), whereas a lower carriage of the cmlA gene was detected (27.1% and 54.5% of strains). The high prevalence of floR-carrying bacteria in reared scallop larvae and hatchery effluents contributes to enrich the marine resistome in marine environments, prompting the need of a continuous surveillance of these genes in the mariculture environments.

Antimicrobial resistance and antimicrobial resistance genes in marine bacteria from salmon aquaculture and non-aquaculture sites

Antimicrobial resistance (AR) detected by disc diffusion and antimicrobial resistance genes detected by DNA hybridization and polymerase chain reaction with amplicon sequencing were studied in 124 marine bacterial isolates from a Chilean salmon aquaculture site and 76 from a site without aquaculture 8 km distant. Resistance to one or more antimicrobials was present in 81% of the isolates regardless of site. Resistance to tetracycline was most commonly encoded by tetA and tetG; to trimethoprim, by dfrA1, dfrA5 and dfrA12; to sulfamethizole, by sul1 and sul2; to amoxicillin, by blaTEM ; and to streptomycin, by strA-strB. Integron integrase intl1 was detected in 14 sul1-positive isolates, associated with aad9 gene cassettes in two from the aquaculture site. intl2 Integrase was only detected in three dfrA1-positive isolates from the aquaculture site and was not associated with gene cassettes in any. Of nine isolates tested for conjugation, two from the aquaculture site transferred AR determinants to Escherichia coli. High levels of AR in marine sediments from aquaculture and non-aquaculture sites suggest that dispersion of the large amounts of antimicrobials used in Chilean salmon aquaculture has created selective pressure in areas of the marine environment far removed from the initial site of use of these agents.

Antimicrobial resistance among Enterobacteriaceae in South America: history, current dissemination status and associated socioeconomic factors

South America exhibits some of the higher rates of antimicrobial resistance in Enterobactericeae worldwide. This continent includes 12 independent countries with huge socioeconomic differences, where the ample access to antimicrobials, including counterfeit ones, coexists with ineffective health systems and sanitation problems, favoring the emergence and dissemination of resistant strains. This work presents a literature review concerning the evolution and current status of antimicrobial resistance threats found among Enterobacteriaceae in South America. Resistance to β-lactams, fluoroquinolones and aminoglycosides was emphasized along with description of key epidemiological studies that highlight the success of specific resistance determinants in different parts of the continent. In addition, a discussion regarding political and socioeconomic factors possibly related to the dissemination of antimicrobial resistant strains in clinical settings and at the community is presented. Finally, in order to assess the possible sources of resistant bacteria, we compile the current knowledge about the occurrence of antimicrobial resistance in isolates in South American' food, food-producing animals and off-hospitals environments. By addressing that intensive intercontinental commerce and tourism neutralizes the protective effect of geographic barriers, we provide arguments reinforcing that globally integrated efforts are needed to decelerate the emergence and dissemination of antimicrobial resistant strains.

Role of shellfish hatchery as a reservoir of antimicrobial resistant bacteria

The main aim of this study was to determine the occurrence of resistant bacteria in florfenicol-treated and untreated scallop larval cultures from a commercial hatchery and to characterize some selected florfenicol-resistant strains. Larval cultures from untreated and treated rearing tanks exhibited percentages of copiotrophic bacteria resistant to florfenicol ranging from 0.03% to 10.67% and 0.49-18.34%, respectively, whereas florfenicol resistance among oligotrophic bacteria varied from 1.44% to 35.50% and 3.62-95.71%, from untreated and treated larvae, respectively. Florfenicol resistant microbiota from reared scallop larvae mainly belonged to the Pseudomonas and Pseudoalteromonas genus and were mainly resistant to florfenicol, chloramphenicol, streptomycin and co-trimoxazole. This is the first study reporting antimicrobial resistant bacteria associated to a shellfish hatchery and the results suggest that a continuous surveillance of antimicrobial resistance even in absence of antibacterial therapy is urgently required to evaluate potential undesirable consequences on the surrounding environments.

Mechanisms of antimicrobial resistance in finfish aquaculture environments

Consumer demand for affordable fish drives the ever-growing global aquaculture industry. The intensification and expansion of culture conditions in the production of several finfish species has been coupled with an increase in bacterial fish disease and the need for treatment with antimicrobials. Understanding the molecular mechanisms of antimicrobial resistance prevalent in aquaculture environments is important to design effective disease treatment strategies, to prioritize the use and registration of antimicrobials for aquaculture use, and to assess and minimize potential risks to public health. In this brief article we provide an overview of the molecular mechanisms of antimicrobial resistance in genes found in finfish aquaculture environments and highlight specific research that should provide the basis of sound, science-based policies for the use of antimicrobials in aquaculture.

Food and human gut as reservoirs of transferable antibiotic resistance encoding genes

The increase and spread of antibiotic resistance (AR) over the past decade in human pathogens has become a worldwide health concern. Recent genomic and metagenomic studies in humans, animals, in food and in the environment have led to the discovery of a huge reservoir of AR genes called the resistome that could be mobilized and transferred from these sources to human pathogens. AR is a natural phenomenon developed by bacteria to protect antibiotic-producing bacteria from their own products and also to increase their survival in highly competitive microbial environments. Although antibiotics are used extensively in humans and animals, there is also considerable usage of antibiotics in agriculture, especially in animal feeds and aquaculture. The aim of this review is to give an overview of the sources of AR and the use of antibiotics in these reservoirs as selectors for emergence of AR bacteria in humans via the food chain.

Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health

The worldwide growth of aquaculture has been accompanied by a rapid increase in therapeutic and prophylactic usage of antimicrobials including those important in human therapeutics. Approximately 80% of antimicrobials used in aquaculture enter the environment with their activity intact where they select for bacteria whose resistance arises from mutations or more importantly, from mobile genetic elements containing multiple resistance determinants transmissible to other bacteria. Such selection alters biodiversity in aquatic environments and the normal flora of fish and shellfish. The commonality of the mobilome (the total of all mobile genetic elements in a genome) between aquatic and terrestrial bacteria together with the presence of residual antimicrobials, biofilms, and high concentrations of bacteriophages where the aquatic environment may also be contaminated with pathogens of human and animal origin can stimulate exchange of genetic information between aquatic and terrestrial bacteria. Several recently found genetic elements and resistance determinants for quinolones, tetracyclines, and β-lactamases are shared between aquatic bacteria, fish pathogens, and human pathogens, and appear to have originated in aquatic bacteria. Excessive use of antimicrobials in aquaculture can thus potentially negatively impact animal and human health as well as the aquatic environment and should be better assessed and regulated.

Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies

The environment, and especially freshwater, constitutes a reactor where the evolution and the rise of new resistances occur. In water bodies such as waste water effluents, lakes, and rivers or streams, bacteria from different sources, e.g., urban, industrial, and agricultural waste, probably selected by intensive antibiotic usage, are collected and mixed with environmental species. This may cause two effects on the development of antibiotic resistances: first, the contamination of water by antibiotics or other pollutants lead to the rise of resistances due to selection processes, for instance, of strains over-expressing broad range defensive mechanisms, such as efflux pumps. Second, since environmental species are provided with intrinsic antibiotic resistance mechanisms, the mixture with allochthonous species is likely to cause genetic exchange. In this context, the role of phages and integrons for the spread of resistance mechanisms appears significant. Allochthonous species could acquire new resistances from environmental donors and introduce the newly acquired resistance mechanisms into the clinics. This is illustrated by clinically relevant resistance mechanisms, such as the fluoroquinolones resistance genes qnr. Freshwater appears to play an important role in the emergence and in the spread of antibiotic resistances, highlighting the necessity for strategies of water quality improvement. We assume that further knowledge is needed to better understand the role of the environment as reservoir of antibiotic resistances and to elucidate the link between environmental pollution by anthropogenic pressures and emergence of antibiotic resistances. Only an integrated vision of these two aspects can provide elements to assess the risk of spread of antibiotic resistances via water bodies and suggest, in this context, solutions for this urgent health issue.

Detection of aacA-aphD, qacEδ1, marA, floR, and tetA genes from multidrug-resistant bacteria: Comparative analysis of real-time multiplex PCR assays using EvaGreen(®) and SYBR(®) Green I dyes

We have developed multiplex real-time PCR assays that utilize DNA-intercalating dyes, SYBR Green I (SG) and EvaGreen (EG), with two primer sets (set 1=qacEδ1, tetA and aacA-aphD; set 2=tetA, marA, and floR) to simultaneously amplify the qacEδ1, tetA, aacA-aphD, marA, and floR genes. Validity of the multiplex PCR assays was confirmed by testing 83 bacterial isolates, including Staphylococcus aureus (28 isolates), Enterococcus spp. (17 isolates), Salmonella enterica serovar Typhimurium (8 isolates), Citrobacter spp. (9 isolates), Escherichia coli (14 isolates) and Aeromonas veronii (7 isolates), and performing sequence analysis of representative PCR products. Agarose gel analysis revealed the presence of correct size PCR products, and the differences in their thermal melting (T(m)) curves were used to distinguish various PCR products. Although T(m) peaks of different amplicons after EG-based singleplex and multiplex PCR assays were resolved nicely, only one or two peaks were seen for SG-bound amplicons. EG-based multiplex real-time PCR assays provided better peak resolution. There was a good correlation with a better linear relationship between the C(t) and log input DNA concentration for the set 1 and set 2 genes in EG-based assays (R(EG)(2)=0.9813and0.9803) than in SG-based assays (R(SG)(2)=0.5276and0.6255). The sensitivities of detection were 2.5-25fg and 25-250fg of template DNA in EG and SG-based singleplex and multiplex PCR assays, respectively. The assays, which could be completed in less than 45min, offer sensitive and rapid detection of qacEδ1, aacA-aphD, marA, floR, and tetA genes from a diverse group of multiple antibiotic-resistant bacterial strains.