Type II topoisomerase quinolone resistance-determining regions of Aeromonas caviae, A. hydrophila, and A. sobria complexes and mutations associated with quinolone resistance

Aeromonas caviae subsp. aquatica subsp. nov., a New Multidrug-Resistant Subspecies Isolated from a Drinking Water Storage Tank

The increasing prevalence and dissemination of multidrug-resistant bacteria represent a serious concern for public health. Aeromonas caviae is a pathogenic microorganism that causes a wide spectrum of diseases in fish and humans and is often associated with aquatic environments and isolated from foods and animals. Here, we present the isolation and characterization of the V15T strain isolated from a drinking water storage tank in Rio de Janeiro, Brazil. The V15T strain has a genome length of 4,443,347 bp with an average G + C content of 61.78% and a total of 4028 open reading frames. Its genome harbors eight types of antibiotic resistance genes (ARGs) involving resistance to beta-lactamases, macrolides, and quinolones. The presence of blaMOX-6, blaOXA-427/blaOXA-504, and mutations in parC were detected. In addition, other ARGs (macA, macB, opmH, and qnrA) and multidrug efflux pumps (such as MdtL), along with several resistance determinants and 106 genes encoding virulence factors, including adherence (polar and lateral flagella), secretion (T2SS, T6SS), toxin (hlyA), and stress adaptation (katG) systems, were observed. The genome sequence reported here provides insights into antibiotic resistance, biofilm formation, evolution, and virulence in Aeromonas strains, highlighting the need for more public health attention and the further monitoring of drinking water systems. Also, the results of physiological and phylogenetic data, average nucleotide identity (ANI) calculation, and digital DNA-DNA hybridization (dDDH) analysis support the inclusion of the strain V15T in the genus Aeromonas as a new subspecies with the proposed name Aeromonas caviae subsp. aquatica subsp. nov. (V15T = P53320T). This study highlights the genomic plasticity and pathogenic potential of Aeromonas within household drinking water systems, calling for the revision of water treatment protocols to address biofilm-mediated resistance and the implementation of routine genomic surveillance to mitigate public health risks.

Diagnostic low-dose X-ray radiation induces fluoroquinolone resistance in pathogenic bacteria

PURPOSE

The crisis of antibiotic resistance has been attributed to the overuse or misuse of these medications. However, exposure of bacteria to physical stresses such as X-ray radiation, can also lead to the development of resistance to antibiotics. The present study aimed to investigate the effect of exposure to diagnostic low-dose X-ray radiation on the bacterial response to antibiotics in two pathogenic bacteria, including the Gram-positive Staphylococcus aureus and Gram-negative Salmonella enteritidis.

METHODS

The bacterial strains were exposed to diagnostic X-ray doses of 5 and 10 mGy, which are equivalent to the doses delivered to patients during conventional radiography X-ray examinations in accordance with the European guidelines on quality criteria for diagnostic radiographic images. Following exposure to X-ray radiation, the samples were used to estimate bacterial growth dynamics and perform antibiotic susceptibility tests.

RESULTS

The results indicate that exposure to diagnostic low-dose X-ray radiation increased the number of viable bacterial colonies of both Staphylococcus aureus and Salmonella enteritidis and caused a significant change in bacterial susceptibility to antibiotics. For instance, in Staphylococcus aureus, the diameter of the inhibition zones for marbofloxacin decreased from 29.66 mm before irradiation to 7 mm after irradiation. A significant decrease in the inhibition zone was also observed for penicillin. In the case of Salmonella enteritidis, the diameter of the inhibition zone for marbofloxacin was 29 mm in unexposed bacteria but decreased to 15.66 mm after exposure to 10 mGy of X-ray radiation. Furthermore, a significant decrease in the inhibition zone was detected for amoxicillin and amoxicillin/clavulanic acid (AMC).

CONCLUSION

It is concluded that exposure to diagnostic X-ray radiation can significantly alter bacterial susceptibility to antibiotics. This irradiation decreased the effectiveness of fluoroquinolone and β-lactam antibiotics. Specifically, low-dose X-rays made Staphylococcus aureus resistant to marbofloxacin and increased its resistance to penicillin. Similarly, Salmonella Enteritidis became resistant to both marbofloxacin and enrofloxacin, and showed reduced sensitivity to amoxicillin and AMC.

Genetic characterization and virulence determinants of multidrug-resistant NDM-1-producing Aeromonas caviae

The emergence of carbapenemase significantly threatens public health. It is prevalent worldwide but rare in Aeromonas caviae. Unlike most bacterial species, A. caviae has two distinct flagella systems, which are closely related to biofilm formation. The ability to form biofilms on host tissues or inert surfaces constitutes an important cause of many persistent infections, which causes difficulties in clinical treatment. Here, we report on a multidrug-resistant (MDR) A. caviae carrying bla NDM-1 with a novel sequence type 1,416. The strong ability of biofilm formation of FAHZZU2447 was verified by a crystal violet assay. The resistome profile and location of the bla NDM-1 gene were determined by antimicrobial susceptibility testing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and Southern blot analysis. Moreover, the strain underwent whole-genome sequencing to identify its genomic characteristics. In addition, the bla NDM-1 gene was located on a ∼243 kb plasmid with genetic context IS1R-bla NDM-1-ble-trpF-dsbD-hp-sul1-qacE. Phylogenetic analysis indicated the transmission of A. caviae in China, Japan, and Thailand. Our study aimed to elucidate the genomic features of bla NDM-1-producing A. caviae, thereby clarifying the distribution of A. caviae worldwide and emphasizing the harmfulness of biofilm formation to the clinic. Further comprehensive surveillance of this species is needed to control further dissemination.

Antibiotic Resistance in the Finfish Aquaculture Industry: A Review

Significant challenges to worldwide sustainable food production continue to arise from environmental change and consistent population growth. In order to meet increasing demand, fish production industries are encouraged to maintain high growth densities and to rely on antibiotic intervention throughout all stages of development. The inappropriate administering of antibiotics over time introduces selective pressure, allowing the survival of resistant bacterial strains through adaptive pathways involving transferable nucleotide sequences (i.e., plasmids). This is one of the essential mechanisms of antibiotic resistance development in food production systems. This review article focuses on the main international regulations and governing the administering of antibiotics in finfish husbandry and summarizes recent data regarding the distribution of bacterial resistance in the finfish aquaculture food production chain. The second part of this review examines promising alternative approaches to finfish production, sustainable farming techniques, and vaccination that circumvents excessive antibiotic use, including new animal welfare measures. Then, we reflect on recent adaptations to increasingly interdisciplinary perspectives in the field and their greater alignment with the One Health initiative.

Plasmid-Mediated Fluoroquinolone Resistance Genes in Quinolone-Susceptible Aeromonas spp. Phenotypes Isolated From Recreational Surface Freshwater Reservoir

Aeromonas spp. are recognized as opportunistic pathogens causing diseases. Infections in humans can result mainly in gastrointestinal and wound diseases with or without progression to septicemia. Although Aeromonas spp. are not known uropathogens and they rarely cause urinary tract infection, we hypothesize that the presence of these bacteria in the water and the contact during, e.g., recreational and bathing activity can create the conditions for the colonization of the human body and may result to diseases in various locations, including the urinary tract. Our study presents the occurrence of aeromonad fluoroquinolone-susceptible phenotypes with the presence of plasmid-mediated fluoroquinolone resistance (PMQR) genes in a natural freshwater reservoir occasionally used for recreational activities. Sixty-nine isolates collected during the bathing period were identified by mass spectrometry and screened for the presence of fluoroquinolone-resistant phenotypes and genotypes. Fluoroquinolone susceptibility was determined as minimal inhibitory concentration values. PMQR qnr genes were detected by PCR. Isolates comprising eight species, namely, mainly Aeromonas veronii (50.7% isolates) and Aeromonas media (24.6% isolates) and rarely Aeromonas eucrenophila, Aeromonas caviae, Aeromonas bestiarum, Aeromonas ichthiosmia, and Aeromonas hydrophila, were selected. All isolates were phenotypically susceptible either to ciprofloxacin or levofloxacin. Unexpectedly, at least one to three of the PMQR genes were detected in 42.0% of the fluoroquinolone-susceptible Aeromonas spp. phenotypes. Mainly the qnrS (34.8% isolates) and qnrA (14.5% isolates) determinants were detected. In conclusion, the freshwater reservoir occasionally used for bathing was tainted with aeromonads, with a high occurrence of opportunistic pathogens such as A. veronii and A. media. MALDI‐TOF MS is a powerful technique for aeromonad identification. Our data reveals the mismatch phenomenon between fluoroquinolone-susceptible aeromonad phenotypes and the presence of plasmid-mediated qnr resistance genes. It suggests that phenotypically susceptible bacteria might be a potential source for the storage and transmission of these genes. The exposure during, e.g., a recreational activity may create the potential risk for causing infections, both diagnostically and therapeutically difficult, after expressing the resistance genes and quinolone-resistant strain selection.

Detection of S83V GyrA mutation in quinolone-resistant Shewanella algae using comparative genomics

BACKGROUND

Shewanella algae is a zoonotic pathogen that poses a serious health threat to immunocompromised hosts. Treatment of S. algae infections is challenging due to the pathogen's intrinsic resistance to a variety of β-lactam antibiotics. Therapeutic options have become further limited by the emergence of quinolone-resistant strains. Currently, there are few studies concerning the genetic and molecular mechanisms underlying acquired quinolones resistance in S. algae. qnrA was once proposed as the candidate gene related to quinolones resistance in S. algae. However, recent studies demonstrated qnrA are highly conservative and does not confer resistance to quinolones in S. algae.

METHODS

A total of 27 non-duplicated isolates of S. algae strains were examined. MICs of ciprofloxacin were determined using Vitek 2. Whole genome sequencing was performed using MiSeq platform. Comprehensive Antibiotic Resistance Database and ResFinder were used for annotation of quinolones resistance genes. Multiple sequence alignment by EMBOSS Clustal Omega were used to identified mutation in quinolone resistance-determining regions. To investigation of the alteration of protein structure induced by mutation, in silico molecular docking studies was conducted using Accryl Discovery studio visualizer.

RESULTS

All S. algae harbored the quinolone-resistance associated genes (qnrA, gyrA, gyrB, parC, and parE) regardless its resistance to ciprofloxacin. Comparison of these genomes identified a nonsynonymous mutation (S83V) in chromosome-encoded gyrase subunits (GyrA) in quinolone-resistant strain. We found this mutation disrupts the water-metal ion bridge, reduces the affinity of the quinolone-enzyme complex for the metal ions and therefore decrease the capability of quinolones to stabilize cleavage complexes.

CONCLUSIONS

The study provides insight into the quinolone resistance mechanisms in S. algae, which would be helpful for the evolution of antibiotic resistance in this bacterium.

Molecular Typing, Antibiogram and PCR-RFLP Based Detection of Aeromonas hydrophila Complex Isolated from Oreochromis niloticus

Motile Aeromonas septicemia is a common bacterial disease that affects Oreochromis niloticus and causes tremendous economic losses globally. In order to investigate the prevalence, molecular typing, antibiogram and the biodiversity of Aeromonas hydrophila complex, a total of 250 tilapia (Oreochromis niloticus) were collected randomly from 10 private tilapia farms (25 fish/farm) at El-Sharkia Governorate, Egypt. The collected fish were subjected to clinical and bacteriological examinations. The majority of infected fish displayed ulcerative necrosis, exophthalmia, and internal signs of hemorrhagic septicemia. The prevalence of A. hydrophia complex was 13.2%, where the liver was the most predominant affected organ (54.1%). Polymerase chain reaction (PCR) was used to verify the identification of A. hydrophila complex using one set of primers targeting gyrB as well as the detection of virulent genes (aerA, alt, and ahp). All isolates were positive for the gyrB-conserved gene and harbored aerA and alt virulence genes. However, none of those isolates were positive for the ahp gene. The antimicrobial sensitivity was carried out, where the recovered strains were completely sensitive to ciprofloxacin and highly resistant to amoxicillin. All retrieved strains showed the same phenotypic characteristics and were identical based on the restriction fragment length polymorphism (RFLP). Experimentally challenged fish presented a high mortality rate (76.67%) and showed typical signs as in naturally infected ones. In conclusion, the synergism of phenotypic and genotypic characterization is a valuable epidemiological tool for the diagnosis of A. hydrophila complex. RFLP is a fundamental tool for monitoring the biodiversity among all retrieved strains of A. hydrophia.

Prevalence and antibiotic sensitivity of bacteria isolated from imported ornamental fish in Italy: A translocation of resistant strains?

The rapid expansion of the ornamental aquaculture industry over the past decades has resulted in a concomitant increase in the use of antibiotics to combat infectious diseases. The aim of this study was to assess the possible role of ornamental fish in the translocation of antibiotic resistant bacteria, with possible consequences for aquarium and public health. We assessed the prevalence of bacterial infections and the antibiotic resistance profile of bacteria isolated from 134 ornamental fish imported into northwest Italy during two years of monitoring. Ornamental fish analyzed were imported mainly from Singapore (40%) and Israel (20%), followed by Thailand (13%), Sri Lanka (12%), Czech Republic (7%), Vietnam (5%) and Indonesia (3%). The most commonly imported fish were freshwater species, particularly those belonging to the Poeciliidae family. Bacteriological exam was positive in 68% of the fish examined. The most frequently isolated bacterium was Aeromonas sobria (37%). Bacteria showed resistance against lincomycin, ampicillin, oxytetracycline and tetracycline. Sensitivity was found for florfenicol, chloramphenicol, gentamicin, and trimethoprim/sulfamethoxazole. Odds ratio (OR) values were calculated as a measure of the association between antibiotic resistance of A. sobria and selected factors (country of origin, fish family and fish species), considering Thailand, Poeciliidae and Poecilia reticulata as control cases. Higher values were found for Vietnam (OR 5.6) and Xiphophorus helleri and X. maculatus (OR 3.0 and 3.7 respectively). Our findings underline the need to improve targeted surveillance of antimicrobial resistance and prevent the translocation of resistant or multi-resistant bacterial strains in ornamental fish, especially in fish imported from countries where surveillance is limited or lacking.

Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients

Fluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiont Aeromonas, a puzzling rise in Cp-resistant (Cpr) Aeromonas infections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonas isolates to exposure of the leech microbiota to very low levels of Cp (0.01 to 0.04 µg/ml), <1/100 of the clinical resistance breakpoint for Aeromonas Using competition experiments and comparative genomics of 37 strains, we determined the mechanisms of resistance in clinical and leech-derived Aeromonas isolates, traced their origin, and determined that the presence of merely 0.01 µg/ml Cp provides a strong competitive advantage for Cpr strains. Deep-sequencing the Cpr-conferring region of gyrA enabled tracing of the mutation-harboring Aeromonas population in archived gut samples, and an increase in the frequency of the Cpr-conferring mutation in 2011 coincides with the initial reports of CprAeromonas infections in patients receiving leech therapy.IMPORTANCE The role of subtherapeutic antimicrobial contamination in selecting for resistant strains has received increasing attention and is an important clinical matter. This study describes the relationship of resistant bacteria from the medicinal leech, Hirudo verbana, with patient infections following leech therapy. While our results highlight the need for alternative antibiotic therapies, the rise of Cpr bacteria demonstrates the importance of restricting the exposure of animals to antibiotics approved for veterinary use. The shift to a more resistant community and the dispersion of Cpr-conferring mechanisms via mobile elements occurred in a natural setting due to the presence of very low levels of fluoroquinolones, revealing the challenges of controlling the spread of antibiotic-resistant bacteria and highlighting the importance of a holistic approach in the management of antibiotic use.

Quinolone-resistant phenotype of Flavobacterium columnare isolates harbouring point mutations both in gyrA and parC but not in gyrB or parE

OBJECTIVES

The aim of this study was to determine mutations associated with a quinolone-resistant (QR) phenotype of Flavobacterium columnare isolates.

METHODS

The susceptibility of 53 F. columnare isolates to 11 antimicrobials, including 2 quinolones, was investigated by the disk diffusion method. Oxolinic acid (OXO) was subsequently chosen for minimum inhibitory concentration (MIC) assay. Sequence analysis of four genes within the quinolone resistance-determining regions (QRDRs) of OXO-resistant F. columnare compared with susceptible isolates was subsequently performed.

RESULTS

The disk diffusion assay revealed that the majority of isolates were susceptible to all tested antimicrobials. However, 14 and 8 isolates were resistant to the quinolone antibiotics OXO and nalidixic acid, respectively. No multidrug resistance was observed. The MIC assay revealed five additional isolates that were resistant to OXO (≥4μg/mL), making a total of 19 OXO-resistant isolates observed in this study. DNA sequencing identified missense mutations both in parC and gyrA but not in gyrB or parE in QR F. columnare isolates. Mutation in parC resulted in the change His87→Tyr. For gyrA, 15 isolates of Thai origin exhibited a change at residue Ser83 to either Phe, Tyr or Ala, whereas 3 Vietnamese isolates contained two mutation sites (Ser83→Phe and Asp87→Tyr).

CONCLUSION

This study is the first to reveal that QR phenotype F. columnare isolates harboured missense mutations both in parC and gyrA but not in gyrB or parE of the QRDRs.

Multidrug-Resistant Aeromonas veronii Recovered from Channel Catfish (Ictalurus punctatus) in China: Prevalence and Mechanisms of Fluoroquinolone Resistance

To emphasize the importance of the appropriate use of antibiotics in aquaculture systems, the prevalence of resistance to 25 antimicrobials was investigated in 42 Aeromonas veronii strains isolated from farm-raised channel catfish in China in 2006-2012. All experiments were based on minimal inhibitory concentrations (MICs), and susceptibility was assessed according to the Clinical and Laboratory Standards Institute. Some isolates displayed antibiotic resistance to the latest-generation fluoroquinolones (i.e., ciprofloxacin, levofloxacin, and norfloxacin) in vitro. Therefore, we screened for genes conferring resistance to fluoroquinolones and performed conjugation experiments to establish the resistance mechanisms. The antibiotic resistance rates were 14.29-21.42% to three kinds of fluoroquinolones: ciprofloxacin, levofloxacin, and norfloxacin. Among the 42 strains isolated, 15 carried the qnrS2 gene. The MICs of the fluoroquinolones in transconjugants with qnrS2 were more than fourfold higher compared with the recipient. Among the fluoroquinolone-resistant A. veronii strains, eight had point mutations in both gyrA codon 83 (Ser⁸³→Ile⁸³) and parC codon 87 (Ser⁸⁷→Ile⁸⁷). However, five isolates with point mutations in parC codon 52 remained susceptible to the three fluoroquinolones. In conclusion, the mechanisms of fluoroquinolone resistance in A. veronii isolates may be related to mutations in gyrA codon 83 and parC codon 87 and the presence of the qnrS2 gene.

Prevalence and characterization of plasmid-mediated quinolone resistance genes in Aeromonas spp. isolated from South African freshwater fish

An increasing incidence of multidrug-resistant Aeromonas spp., which are both fish and emerging opportunistic human pathogens, has been observed worldwide. Quinolone-resistant Aeromonas spp. isolates are increasingly being observed in clinical and environmental settings, and this has been attributed primarily to target gene alterations, efflux, and transferable quinolone resistance. Thirty-four Aeromonas spp., obtained from freshwater aquaculture systems, were screened for the presence of GyrA and ParC substitutions, efflux activity and the prevalence of plasmid-mediated quinolone resistance genes, qnr and aac-6'-Ib-cr. Although 44% of isolates were resistant to nalidixic acid, the majority were susceptible to ciprofloxacin and ofloxacin. The predominant GyrA substitution was Ser-83→Val among Aeromonas veronii isolates whilst Aeromonas hydrophila isolates displayed a Ser-83→Ile substitution, and Ser-80→Ile substitutions were observed in ParC. Minimum inhibitory concentrations of fluoro(quinolones) were determined in the presence and absence of the efflux pump inhibitor, phenylalanine-arginine β-naphthylamide (PAβN). Addition of PAβN had no effect on the levels of fluoro(quinolone) resistance observed for these isolates. Although no aac-6'-Ib-cr variant genes were identified, qnrB and qnrS were detected for 41% and 24% of isolates, respectively, by Southern hybridization and confirmed by PCR and sequencing. Quinolone resistance in these fish-associated Aeromonas isolates was related to mutations in the quinolone resistance determining regions of GyrA and ParC and presence of qnrB and qnrS. The presence of qnr alleles in Aeromonas spp. isolates may facilitate high-level fluoroquinolone resistance and potentially serve as reservoirs for the dissemination of qnr genes to other aquatic microbes.

Epidemiological cut-off values for Flavobacterium psychrophilum MIC data generated by a standard test protocol

Epidemiological cut-off values were developed for application to antibiotic susceptibility data for Flavobacterium psychrophilum generated by standard CLSI test protocols. The MIC values for ten antibiotic agents against Flavobacterium psychrophilum were determined in two laboratories. For five antibiotics, the data sets were of sufficient quality and quantity to allow the setting of valid epidemiological cut-off values. For these agents, the cut-off values, calculated by the application of the statistically based normalized resistance interpretation method, were ≤16 mg L(-1) for erythromycin, ≤2 mg L(-1) for florfenicol, ≤0.025 mg L(-1) for oxolinic acid (OXO), ≤0.125 mg L(-1) for oxytetracycline and ≤20 (1/19) mg L(-1) for trimethoprim/sulphamethoxazole. For ampicillin and amoxicillin, the majority of putative wild-type observations were 'off scale', and therefore, statistically valid cut-off values could not be calculated. For ormetoprim/sulphadimethoxine, the data were excessively diverse and a valid cut-off could not be determined. For flumequine, the putative wild-type data were extremely skewed, and for enrofloxacin, there was inadequate separation in the MIC values for putative wild-type and non-wild-type strains. It is argued that the adoption of OXO as a class representative for the quinolone group would be a valid method of determining susceptibilities to these agents.

Detection of antibiotic resistance, virulence gene determinants and biofilm formation in Aeromonas species isolated from cattle

This study aimed to assess the antibiogram of Aeromonas strains recovered from cattle faeces and the potential pathogenic status of the isolates. The antibiogram of the Aeromonas isolates demonstrated total resistance to clindamycin oxacillin, trimethoprim, novobiocin and ticarcillin. However, Aeromonas strains were sensitive to cefotaxime, oxytetracycline and tobramycin. The Aeromonas strains from Lovedale and Fort Cox farms were found to possess some virulence genes. The percentage distribution was aer 71.4%, ast 35.7%, fla 60.7%, lip 35.7% and hlyA 25% for Lovedale farm and aer 63.1%, alt 10.5%, ast 55.2%, fla 78.9%, lip 21% and hlyA 35.9% for Fort Cox farm. Class 1 integron was present in 27% of Aeromonas isolates; the bla TEM gene was present in 34.8%, while the blaP1 class A β-lactamase gene was detected in 12.1% of the isolates. Approximately 86% of the isolates formed a biofilm on microtitre plates. The presence of multiple antibiotic resistance and virulence genes in Aeromonas isolates from cattle faeces reveals the pathogenic and infectious importance of these isolates and is of great significance to public health. The possession of a biofilm-forming capability by such isolates may lead to difficulty during the management of infection related to Aeromonas species.

IncA/C plasmids harboured in serious multidrug-resistant Vibrio cholerae serogroup O139 strains in China

Vibrio cholerae serogroup O139 emerged in 1992 and is one of two major serogroups to have caused cholera epidemics. After 1998, serious multidrug-resistant (MDR) O139 strains quickly became common in China, showing a multidrug resistance profile to eight antibiotics. It is a great threat to public health, and elucidation of its mechanisms of resistance will provide a helpful guide for the clinical treatment and prevention of cholera. In this study, mega-plasmids from MDR V. cholerae O139 strains were identified by pulsed-field gel electrophoresis (PFGE) without enzyme digestion. One plasmid was isolated and sequenced, belonging to the IncA/C family. Ten antibiotic resistance genes were found in the MDR regions, including a blaTEM-20 gene, and these genes endowed the host with resistance to seven antibiotics. This kind of plasmid was positive in 71.2% (198/278) of toxigenic O139 strains, and the rate of plasmid positivity was consistent with the yearly change in MDR rates of these strains. This study reveals an important role of the IncA/C family plasmid in the spread of multiple antibiotic resistance of epidemic V. cholerae serogroup O139 strains, which has recombined with plasmids from different bacterial species and transferred among V. cholerae strains.

Lactococcus garvieae carries a chromosomally encoded pentapeptide repeat protein that confers reduced susceptibility to quinolones in Escherichia coli producing a cytotoxic effect

This study characterises a chromosomal gene of Lactococcus garvieae encoding a pentapeptide repeat protein designated as LgaQnr. This gene has been implicated in reduced susceptibility to quinolones in this bacterium, which is of relevance to both veterinary and human medicine. All of the L. garvieae isolates analysed were positive for the lgaqnr gene. The expression of lgaqnr in Escherichia coli reduced the susceptibility to quinolones, producing an adverse effect. The reduced susceptibility to ciprofloxacin was 16-fold in E. coli ATCC 25922 and 32-fold in E. coli DH10B, compared to the control strains. The minimum inhibitory concentration of nalidixic acid was also increased 4 or 5-fold. The effect of the expression of lgaqnr in E. coli was investigated by electron microscopy and was observed to affect the structure of the cell and the inner membrane of the recombinant cells.

Quinolone-resistant Escherichia coli isolated from birds of prey in Portugal are genetically distinct from those isolated from water environments and gulls in Portugal, Spain and Sweden

The influence of geographic distribution and type of habitat on the molecular epidemiology of ciprofloxacin resistant Escherichia coli was investigated. Ciprofloxacin resistant E. coli from wastewater, urban water with faecal contamination and faeces of gulls, pigeons and birds of prey, from Portugal, Spain and Sweden were compared based on multi-locus sequence typing (MLST) and quinolone resistance genetic determinants. Multi-locus sequence typing allowed the differentiation of E. coli lineages associated with birds of prey from those inhabiting gulls and waters. E. coli lineages of clinical relevance, such as the complex ST131, were detected in wastewater, streams and gulls in Portugal, Spain and Sweden. Quinolone resistance was due to gyrA and parC mutations, although distinct mutations were detected in birds of prey and in wastewater, streams and gulls isolates. These differences were correlated with specific MLST lineages, suggesting resistance inheritance. Among the plasmid-mediated quinolone resistance genes, only aac(6')-ib-cr and qnrS were detected in wastewater, streams and gulls isolates, but not in birds of prey. The horizontal transfer of the gene aac(6')-ib-cr could be inferred from its occurrence in different MLST lineages.

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.

Diversity and antibiotic resistance of Aeromonas spp. in drinking and waste water treatment plants

The taxonomic diversity and antibiotic resistance phenotypes of aeromonads were examined in samples from drinking and waste water treatment plants (surface, ground and disinfected water in a drinking water treatment plant, and raw and treated waste water) and tap water. Bacteria identification and intra-species variation were determined based on the analysis of the 16S rRNA, gyrB and cpn60 gene sequences. Resistance phenotypes were determined using the disc diffusion method. Aeromonas veronii prevailed in raw surface water, Aeromonas hydrophyla in ozonated water, and Aeromonas media and Aeromonas puntacta in waste water. No aeromonads were detected in ground water, after the chlorination tank or in tap water. Resistance to ceftazidime or meropenem was detected in isolates from the drinking water treatment plant and waste water isolates were intrinsically resistant to nalidixic acid. Most of the times, quinolone resistance was associated with the gyrA mutation in serine 83. The gene qnrS, but not the genes qnrA, B, C, D or qepA, was detected in both surface and waste water isolates. The gene aac(6')-ib-cr was detected in different waste water strains isolated in the presence of ciprofloxacin. Both quinolone resistance genes were detected only in the species A. media. This is the first study tracking antimicrobial resistance in aeromonads in drinking, tap and waste water and the importance of these bacteria as vectors of resistance in aquatic environments is discussed.

Molecular characterization of tetracycline- and quinolone-resistant Aeromonas salmonicida isolated in Korea

The antibiotic resistance of 16 Aeromonas (A.) salmonicida strains isolated from diseased fish and environmental samples in Korea from 2006 to 2009 were investigated in this study. Tetracycline or quinolone resistance was observed in eight and 16 of the isolates, respectively, based on the measured minimal inhibitory concentrations. Among the tetracycline-resistant strains, seven of the isolates harbored tetA gene and one isolate harbored tetE gene. Additionally, quinolone-resistance determining regions (QRDRs) consisting of the gyrA and parC genes were amplified and sequenced. Among the quinolone-resistant A. salmonicida strains, 15 harbored point mutations in the gyrA codon 83 which were responsible for the corresponding amino acid substitutions of Ser⁸³→Arg⁸³ or Ser⁸³→Asn⁸³. We detected no point mutations in other QRDRs, such as gyrA codons 87 and 92, and parC codons 80 and 84. Genetic similarity was assessed via pulsed-field gel electrophoresis, and the results indicated high clonality among the Korean antibiotic-resistant strains of A. salmonicida.

qnrVC-like gene located in a novel complex class 1 integron harboring the ISCR1 element in an Aeromonas punctata strain from an aquatic environment in Shandong Province, China

A qnrVC-like gene, qnrVC4, was found in a novel complex class 1 integron gene cassette array following the ISCR1 element and bla(PER-1) in a multidrug-resistant strain of the aquatic bacterium Aeromonas punctata. The deduced QnrVC4 protein sequence shares 45% to 81% amino acid identity with quinolone resistance determinants QnrB6, QnrA1, QnrS1, QnrC, QnrVC1, and QnrVC3. A Ser-83 to Ile amino acid substitution in gyrase A may be mainly responsible for ciprofloxacin resistance in this strain.

High prevalence of multidrug-tolerant bacteria and associated antimicrobial resistance genes isolated from ornamental fish and their carriage water

BACKGROUND

Antimicrobials are used to directly control bacterial infections in pet (ornamental) fish and are routinely added to the water these fish are shipped in to suppress the growth of potential pathogens during transport.

METHODOLOGY/PRINCIPAL FINDINGS

To assess the potential effects of this sustained selection pressure, 127 Aeromonas spp. isolated from warm and cold water ornamental fish species were screened for tolerance to 34 antimicrobials. Representative isolates were also examined for the presence of 54 resistance genes by a combination of miniaturized microarray and conventional PCR. Forty-seven of 94 Aeromonas spp. isolates recovered from tropical ornamental fish and their carriage water were tolerant to > or =15 antibiotics, representing seven or more different classes of antimicrobial. The quinolone and fluoroquinolone resistance gene, qnrS2, was detected at high frequency (37% tested recent isolates were positive by PCR). Class 1 integrons, IncA/C broad host range plasmids and a range of other antibiotic resistance genes, including floR, bla(TEM-1), tet(A), tet(D), tet(E), qacE2, sul1, and a number of different dihydrofolate reductase and aminoglycoside transferase coding genes were also detected in carriage water samples and bacterial isolates.

CONCLUSIONS

These data suggest that ornamental fish and their carriage water act as a reservoir for both multi-resistant bacteria and resistance genes.

Plasmid-mediated QnrS2 determinant in an Aeromonas caviae isolate recovered from a patient with diarrhoea

A qnrS2 gene was identified in an Aeromonas caviae isolate (MICs of ciprofloxacin, norfloxacin and ofloxacin >32 mg/L) from a stool sample collected from a patient with gastroenteritis. The analysis of the gyrA and parC genes revealed amino acid substitutions Ser83-Ile and Ser80-Thr, respectively. In addition, five out of 41 nalidixic acid-resistant Aeromonas isolates studied (26 identified as Aeromonas veronii bv sobria and 15 identified as A. caviae) showed ciprofloxacin resistance. The identification of plasmid-mediated qnr genes outside of the Enterobacteriaceae underlines a possible diffusion of these resistance determinants among Gram-negative rods. This emphasizes the importance of monitoring the emergence of these determinants as well as their dissemination among the Aeromonadaceae.

First gene cassettes of integrons as targets in finding adaptive genes in metagenomes

The first gene cassettes of integrons are involved in the last adaptation response to changing conditions and are also the most expressed. We propose a rapid method for the selection of clones carrying an integron first gene cassette that is useful for finding adaptive genes in environmental metagenomic libraries.

Spontaneous quinolone resistance in the zoonotic serovar of Vibrio vulnificus

This work demonstrates that Vibrio vulnificus biotype 2, serovar E, an eel pathogen able to infect humans, can become resistant to quinolone by specific mutations in gyrA (substitution of isoleucine for serine at position 83) and to some fluoroquinolones by additional mutations in parC (substitution of lysine for serine at position 85). Thus, to avoid the selection of resistant strains that are potentially pathogenic for humans, antibiotics other than quinolones must be used to treat vibriosis on farms.

Drug resistance mechanism of the fish-pathogenic bacterium Lactococcus garvieae

The minimum inhibitory concentrations (MICs) of 15 chemotherapeutic agents were tested against 146 Lactococcus garvieae strains isolated from 1999 to 2006 in Japan. The agents used included chloramphenicol, ciprofloxacin, erythromycin (EM), enoxacin, fleroxacin, florfenicol, kanamycin, lincomycin (LCM), norfloxacin, oxolinic acid, orbifloxacin, ofloxacin, benzylpenicillin, streptomycin and tetracycline (TC). Of the tested strains, 46 showed high levels of resistance to EM, LCM and TC. Twelve of these strains were detected to be carrying transferable R-plasmids using a conjugation experiment and, using Southern hybridization, were shown to have the same structure as the R-plasmid. The remaining 34 resistant strains had a similar DNA structure to that of the R-plasmid as confirmed by polymerase chain reaction (PCR) using primers designed from sites in the transferable R-plasmid. The EM and TC resistance genes were classified into the ermB and tetS groups using PCR. We also detected gyrA and/or parC mutants that are highly resistant to old and new generation quinolones. This study revealed that transferable R-plasmids encoding EM, LCM and TC are widely distributed and are conserved regardless of the area and/or time of collection.

Unexpected occurrence of plasmid-mediated quinolone resistance determinants in environmental Aeromonas spp

We searched for plasmid-mediated quinolone resistance determinants of the Qnr type in several water samples collected at diverse locations from the Seine River (Paris, France). The qnrS2 genes were identified from Aeromonas punctata subsp. punctata and A. media. The qnrS2 gene was located on IncU-type plasmids in both isolates, which resulted in increased MIC values of quinolones and fluoroquinolones, once they were transferred into Escherichia coli. The qnrS2 gene identified in A. punctata was part of novel genetic structure corresponding to a mobile insertion cassette element. This identification of plasmid-mediated qnr genes outside Enterobacteriaceae underlines a possible diffusion of those resistance determinants within gram-negative rods.

[Aeromonas spp. infections: retrospective study in Nîmes University Hospital, 1997-2004]

OBJECTIVE

Retrospective study of patients presenting Aeromonas spp. infections admitted to Nîmes hospital from January 1997 to December 2004.

PATIENTS AND METHOD

Aeromonas spp. infections were collected from the database of the bacteriology department. The Aeromonas species, suceptibility phenotype, epidemiological data, site and type (nosocomial or not) of infection, and evolution were collected from medical files.

RESULTS

Thirty infections were notified corresponding to 22 male and eight female of 50.6 years old (mean) and a mean stay duration of 31 days. Skin and soft tissues (50%), digestive tract (26.7%), bones and articulations (10%), blood stream (6.7%), urinary tract (3.3%) and lymph nodes (3.3%) were the sites of infection. Ten infections were nosocomial, four were associated with medical leeches. All strains were resistants to amoxicillin and amoxicillin- clavulanic acid, whereas resistance rate to other beta-lactams was under 10% and all were suceptible to fluoroquinolones and aminoglycosides. All patients received antibiotic treatment: 31% a single molecule, 69% an association and 62% needed a second line treatment. Strain was suceptible to the antibiotic in 78.5% of cases. Only one death occured not directly linked to Aeromonas infection.

DISCUSSION

Most of Aeromonas spp. infection sites were cutaneous and digestive. Nosocomial infections associated with medical leeches are not so uncommon and strict conditions of storage and administration are necessary. According to the susceptibility phenotype of our strains which is similar to literature data, a third generation cephalosporin or a fluoroquinolone should be used evenly associated with an aminoglycoside.

Role of the AheABC efflux pump in Aeromonas hydrophila intrinsic multidrug resistance

Gene inactivation and complementation experiments showed that the tripartite AheABC efflux pump of Aeromonas hydrophila extruded at least 13 substrates, including nine antibiotics. The use of phenylalanine-arginine-beta-naphthylamide (PAbetaN) revealed an additional system(s) contributing to intrinsic resistance. This is the first analysis of the role of multidrug efflux systems in Aeromonas spp.

Germline variations of the topoisomerase IIα gene as risk factors for primary gastric B-cell lymphoma

We investigated if germline variations of the Topoisomerase II alpha gene could predispose patients with chronic Helicobacter pylori infection to develop gastric lymphoma and conducted a mutation detection of the entire promoter region. Single marker and haplotype analysis did not reveal any associations with development of gastric lymphoma in general, histological grade or stage of disease (P>0.05). No genetic variations in the promotor region were found in 92 chromosomes of lymphoma patients and controls and linkage disequilibrium indicated a highly conserved genomic region. The results of our work exclude genetic variations as predisposing factors of primary gastric B-cell lymphoma development.

Detection of quinolone-resistance genes in Photobacterium damselae subsp. piscicida strains by targeting-induced local lesions in genomes

Quinolone-resistant strains of the fish-pathogenic bacterium, Photobacterium damselae subsp. piscicida are distributed widely in cultured yellowtail, Seriola quinqueradiata (Temminck & Schlegel), in Japan. The quinolone resistance-determining region (QRDR) was amplified with degenerate primers, followed by cassette ligation-mediated PCR. Open reading frames encoding proteins of 875 and 755 amino acid residues were detected in the gyrA and parC genes, respectively. Resistant strains of P. damselae subsp. piscicida carried a point mutation only in the gyrA QRDR leading to a Ser-to-Ile substitution at residue position 83. No amino acid alterations were discovered in the ParC sequence. A mutation in the gyrA gene was also detected in nalidixic acid-resistant mutants of strain SP96002 obtained from agar medium containing increased levels of quinolone. These results suggest that GyrA, as in other Gram-negative bacteria, is a target of quinolone in P. damselae subsp. piscicida. Furthermore, we attempted to detect a point mutation using targeting-induced local lesions in genomes (TILLING), which is a general strategy used for the detection of a variety of induced point mutations and naturally occurring polymorphisms. We developed a new detection method for the rapid and large-scale identification of quinolone-resistant strains of P. damselae subsp. piscicida using TILLING.

An unusually high level of quinolone resistance associated with type II topoisomerase mutations in quinolone resistance-determining regions of Aeromonas caviae isolated from diarrhoeal patients

We examined 158 strains belonging to different Aeromonas species isolated from hospitalized acute diarrhoea cases for susceptibility to quinolones. Compared to other species, a high percentage of the A. caviae strains were resistant to ciprofloxacin and norfloxacin. Based on MIC values, 6 A. caviae strains were selected and the nucleotide sequences for the quinolone-resistant-determining regions (QRDRs) of gyrA, gyrB and parC genes were analysed. In resistant strains, double mutations (Ser(83)-->Ile and Asp(87)-->Asn) and a single mutation (Ser(80)-->Ile) were detected in the QRDR of gyrA and parC, respectively.

Mechanisms of quinolone resistance and clonal relationship among Aeromonas salmonicida strains isolated from reared fish with furunculosis

The mechanisms of resistance to quinolone and epidemiological relationships among A. salmonicida strains isolated from diseased fish in French marine farms from 1998 to 2000 were investigated. The quinolone resistance-determining regions of the gyrA and parC genes of 12 clinical A. salmonicida isolates with different levels of quinolone susceptibility were sequenced. MICs were determined in the presence of the efflux pump inhibitor (EPI) Phe-Arg beta-naphthylamide and E(max) values (MIC without EPI/MIC in the presence of EPI) were calculated. Isolates fell into two classes: (i) those that had a wild-type gyrA gene with oxolinic acid MIC </= 0.5, flumequine MIC </= 1 and ciprofloxacin MIC </= 0.25 micro g ml(-1); and (ii) those that had a single mutation in gyrA encoding Asp-87 --> Asn with oxolinic acid MIC >/= 2, flumequine MIC >/= 4 and ciprofloxacin MIC >/= 0.125 micro g ml(-1). No mutations were found in parC. High E(max) values obtained for flumequine and oxolinic acid (up to 16 and 8, respectively, for the most resistant isolates of the two classes) indicated an important contribution of efflux to the resistance phenotype. Flumequine accumulation experiments confirmed that high E(max) values were associated with a much lower level of accumulation. PCR/RFLP assays conducted on 34 additional isolates showed the presence of a mutation at codon 87 of gyrA in nearly all the quinolone-resistant isolates. This finding, together with PFGE typing results, strongly suggests a common clonal origin of these quinolone-resistant isolates.

Analysis of the gyrA gene of clinical Yersinia ruckeri isolates with reduced susceptibility to quinolones

Antimicrobial susceptibility of seven clinical strains of Yersinia ruckeri representative of those isolated between 1994 and 2002 from a fish farm with endemic enteric redmouth disease was studied. All isolates displayed indistinguishable pulsed-field gel electrophoresis restriction patterns, indicating that they represented a single strain. However, considering both inhibition zone diameters (IZD) and MICs, the isolates recovered in 2001-2002 formed a separate cluster with lower levels of susceptibility to all the quinolones tested, especially nalidixic acid (NA) and oxolinic acid (OA), compared with the isolates recovered between 1994 and 1998. Analysis of the PCR product of the quinolone resistance-determining region of the gyrA gene from clinical isolates of Y. ruckeri with reduced susceptibility to OA and NA revealed a single amino acid substitution, Ser-83 to Arg-83 (Escherichia coli numbering). Identical substitution was observed in induced OA-resistant mutant strains, which displayed IZD and MICs of quinolones similar to those of the clinical isolates of Y. ruckeri with reduced susceptibility to these antimicrobial agents. These data indicate in that for Y. ruckeri, the substitution of Ser by Arg at position 83 of the gyrA gene is associated with reduced susceptibility to quinolones.

Detection and identification of ciprofloxacin-resistant Yersinia pestis by denaturing high-performance liquid chromatography

Denaturing high-performance liquid chromatography (DHPLC) has been used extensively to detect genetic variation. We used this method to detect and identify Yersinia pestis KIM5 ciprofloxacin-resistant isolates by analyzing the quinolone resistance-determining region (QRDR) of the gyrase A gene. Sequencing of the Y. pestis KIM5 strain gyrA QRDR from 55 ciprofloxacin-resistant isolates revealed five mutation types. We analyzed the gyrA QRDR by DHPLC to assess its ability to detect point mutations and to determine whether DHPLC peak profile analysis could be used as a molecular fingerprint. In addition to the five mutation types found in our ciprofloxacin-resistant isolates, several mutations in the QRDR were generated by site-directed mutagenesis and analyzed to further evaluate this method for the ability to detect QRDR mutations. Furthermore, a blind panel of 42 samples was analyzed by screening for two mutant types to evaluate the potential diagnostic value of this method. Our results showed that DHPLC is an efficient method for detecting mutations in genes that confer antibiotic resistance.