Limited performance of MALDI-TOF for identification of fish Aeromonas isolates at species level

Technical specifications for a EU-wide baseline survey of antimicrobial resistance in bacteria from aquaculture animals

The European Commission requested scientific and technical assistance in the preparation of a EU-wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system.

Use of Matrix-Assisted and Laser Desorption/Ionization Time-of-Flight Technology in the Identification of Aeromonas Strains Isolated from Retail Sushi and Sashimi

The genus Aeromonas includes well-known pathogenic species for fishes and humans that are widely distributed in the aquatic environment and foods. Nowadays, one of the main issues related to wild Aeromonas isolates is their identification at the species level, which is challenging using classical microbiological and biomolecular methods. This study aims to test MALDI-TOF MS technology in the identification of Aeromonas strains isolated from n. 60 retail sushi and sashimi boxes using an implemented version of the SARAMIS software V4.12. A total of 43 certified Aeromonas strains were used to implement the SARAMIS database by importing the spectra obtained from their identification. The original SARAMIS version (V4.12) failed to recognize 62.79% of the certified strains, while the herein-implemented version (V4.12plus) allowed the identification of all the certified strains at least to the genus level with a match of no less than 85%. Regarding the sushi and sashimi samples, Aeromonas spp. was detected in n. 18 (30%) boxes. A total of 127 colonies were identified at the species level, with A. salmonicida detected as the most prevalent species, followed by A. bestiarum and A. caviae. Based on the results of the present study, we could speculate that MALDI-TOF technology could be a useful tool both for the food industry to monitor product contamination and for clinical purposes to make diagnoses effectively and quickly.

Acrylamide exposure induces growth retardation, neurotoxicity, stress, and immune/antioxidant disruption in Nile tilapia (Oreochromis niloticus): The alleviative effects of Chlorella vulgaris diets

This study looked at the toxic impacts of water-born acrylamide (ACR) on Nile tilapia (Oreochromis niloticus) in terms of behaviors, growth, immune/antioxidant parameters and their regulating genes, biochemical indices, tissue architecture, and resistance to Aeromonas hydrophila. As well as the probable ameliorative effect of Chlorella vulgaris (CV) microalgae as a feed additive against ACR exposure was studied. The 96-h lethal concentration 50 of ACR was investigated and found to be 34.67 mg/L for O. niloticus. For the chronic exposure study, a total of 180 healthy O. niloticus (24.33 ± 0.03 g) were allocated into four groups in tri-replicates (15 fish/replicate), C (control) and ACR groups were fed a basal diet and exposed to 0 and 1/10 of 96-h LC50 of ACR (3.46 mg/L), respectively. ACR+ CV5 and ACR+ CV10 groups were fed basal diets with 5 % and 10 % CV supplements, respectively and exposed to 1/10 of 96-h LC50 of ACR for 60 days. After the exposure trial (60 days) the experimental groups were challenged with A. hydrophila. The findings demonstrated that ACR exposure induced growth retardation (P˂0.01) (lower final body weight, body weight gain, specific growth rate, feed intake, protein efficiency ratio, final body length, and condition factor as well as higher feed conversion ratio). A substantial decrease in the immune/antioxidant parameters (P˂0.05) (lysozyme, serum bactericidal activity %, superoxide dismutase, and reduced glutathione) and neurotransmitter (acetylcholine esterase) (P˂0.01) was noticed with ACR exposure. A substantial increase (P˂0.01) in the serum levels of hepato-renal indicators, lipid peroxidation biomarker, and cortisol was noticed as a result of ACR exposure. ACR exposure resulted in up-regulation (P˂0.05) of the pro-inflammatory cytokines and down-regulation (P˂0.05) of the antioxidant-related gene expression. Furthermore, the hepatic, renal, brain, and splenic tissues were badly affected by ACR exposure. ACR-exposed fish were more sensitive to A. hydrophila infection and recorded the lowest survival rate (P˂0.01). Feeding the ACR-exposed fish with CV diets significantly improved the growth and immune/antioxidant status, as well as modulating the hepatorenal functions, stress, and neurotransmitter level compared to the exposed-non fed fish. In addition, modulation of the pro-inflammatory and antioxidant-related gene expression was noticed by CV supplementation. Dietary CV improved the tissue architecture and increased the resistance to A. hydrophila challenge in the ACR-exposed fish. Noteworthy, the inclusion of 10 % CV produced better results than 5 %. Overall, CV diets could be added as a feed supplement in the O. niloticus diet to boost the fish's health, productivity, and resistance to A. hydrophila challenge during ACR exposure.

Characterization of Aeromonas Isolates from Ornamental Fish: Species, Virulence Genes, and Antimicrobial Susceptibility

This study aimed to characterize 300 Aeromonas spp. strains isolated from 123 ornamental fish of 32 different species presenting with septicemia, skin lesions, and/or eye lesions. Within the 300 strains, 53.0% were identified as A. veronii, 41.3% as A. hydrophila, and 5.7% as A. caviae. Among the six virulence genes investigated, the most frequent were act (90.3%) and aer (79.3%). More than 50% of A. hydrophila strains were positive for all the studied genes. A total of 30 virulence profiles were identified, with the five main profiles identified comprising 75% of strains. Only five strains were negative for all genes and were identified as A. caviae and A. veronii. The antimicrobial susceptibility profile was performed for 234 strains, with sulfonamides presenting more than 50% of the resistance rates. Susceptibility was observed mainly for cephalosporins, aminoglycosides, chloramphenicol and piperacillin-tazobactam. Multidrug resistance was detected in 82.5% of the studied strains, including A. caviae with 100% multidrug resistance, and A. hydrophila with 90.9% multidrug resistance. The SE-AFLP analysis resulted in 66 genotypes of A. hydrophila, 118 genotypes of A. veronii, and 14 genotypes of A. caviae, demonstrating the greater heterogeneity of A. veronii and A. caviae. However, no direct correlation was observed between the genotypes and the strains' origins or virulence and resistance profiles.

Genotypic Comparison of Pasteurella multocida from Healthy Animals at Entry to the Feedlots with That and from Bovine Respiratory Disease-Affected Animals during the Fattening Period

The aim of this study was to investigate the possible genotypic differences between commensal Pasteurella multocida isolates from apparently healthy animals (AHA) at the time of entry to feedlots and those from BRD-affected animals (BRD-AA). A total of 20 batches of beef calves in seven feedlots were followed-up during the fattening period. P. multocida was isolated from 28.1% of AHA and 22.9% of BRD-AA. All isolates belonged to the A: L3 genotype. Most isolates from clinical cases (81.0%) grouped into a PFGE cluster were significantly associated with BRD cases (OR, 24.9; 95% CI, 6.4-96.2). The whole genomes of 14 isolates representative of the pulsotypes most frequently detected in BRD-AA and AHA were sequenced and compared with 53 bovine genomes belonging to the identified ST13, ST79, and ST80 genotypes for a global comparison. No differences were found in the virulence-associated gene content between sequence types (STs) globally or between BRD-AA and AHA isolates in this study. Significantly, ST79 isolates harbored ARGs, conferring resistance to different antimicrobials, including macrolides and tetracyclines, which are commonly used for the treatment of BRD. Two Spanish ST79 isolates carried an ICE highly similar to ICE Tn7407, which was recently detected in Germany, suggesting that ST79 P. multocida isolates in Europe and North America may be associated with different ICEs.

Accurate Identification and Virulence Detection of Aeromonas: a Single-Center Retrospective Study on the Clinical Features and Outcomes Associated with Aeromonas Bacteremia in Southwestern China

In this study, Aeromonas spp. were re-identified, and the clinical aspects associated with Aeromonas bacteremia, as well as drug resistance and virulence genes, were elucidated. A total of 188 isolates were classified into 7 Aeromonas spp. using housekeeping gene sequencing, which was the standard to assess the accuracy of the VITEK MALDI-TOF system and the VITEK2 Compact system. The VITEK MS system and housekeeping gene sequencing had a 39.89% clear coincidence rate, whereas the VITEK2 Compact system and the standard had a 2.13% coincidence rate. Aeromonas bacteremia was associated with septic shock, hematologic malignancy, and post-hepatitic cirrhosis. Hematological malignancy, hypoproteinemia, systemic steroid use, central venous catheterization, and virulence genes act and ast were linked to poor outcomes. Aeromonas bacteremia had a 37.5% mortality rate; however, differences in mortality rates among Aeromonas spp. were observed. According to the broth microdilution method, over 90% of isolates were sensitive to most antimicrobials, except ceftriaxone (83.33%) and imipenem (83.33%). Polymerase chain reaction and DNA sequencing verified the presence of drug resistance genes; bla_CphA was detected in 3 isolates, while bla_NDM-1 was found in one isolate. In summary, common methods for identifying Aeromonas spp. are ineffective. Immunocompromised patients have a higher risk of infection and mortality. Furthermore, carbapenem resistance is a serious problem.

BruSIC: a novel selective medium for the primary isolation of Brucella in veterinary samples

Brucellosis, a re-emerging zoonotic infection, threatens animal welfare and public health with serious economic consequences. A definitive diagnosis requires Brucella isolation by culturing field specimens in specific media. This study aimed to (i) assess the effectivity of recommended Farrell's médium (FM) and CITA medium (CM) for the isolation of four Brucella melitensis strains (16M, Rev1, and the 16MΔwzm and Rev1Δwzm in-frame deletion mutants) with variable susceptibility to polymyxins; (ii) develop a Brucella selective medium (BSM) suitable for these strains; (iii) test BSM, FM, and CM with other Brucella species; and (iv) develop an improved selective culture medium (BruSIC) for all brucellae, including B. abortus bv1. The four B. melitensis strains were strongly inhibited in FM and (except Rev1) CM. Since Rev1Δwzm's CM inhibition was due to a synergistic effect of colistin and vancomycin, we formulated BSM with half the concentrations of both antibiotics, achieving a similar growth of B. melitensis to blood agar base (BAB) and an inhibition of contaminant microorganisms comparable to CM; CM performance was surpassed by BSM for the primary isolation of B. melitensis when tested in 1,789 real sheep samples. For other brucellae, BSM and CM were more inhibitory than FM for B. abortus bv1 when using plates immediately after preparation but not after ≥4 weeks of storage. To address this, we developed the improved solid medium BruSIC by replacing the calf serum in BSM with activated charcoal. BruSIC yielded faster colony growth than BSM and CM and similar CFU numbers than BAB (including for B. ovis in BAB-Serum) and inhibited accompanying microorganisms in sheep and cow samples as effectively as BSM. IMPORTANCE Farrell's medium (FM) and CITA medium (CM), recommended for Brucella isolation in animal samples, are inhibitory for certain strains. A reformulated Brucella selective medium (BSM), containing half the CM vancomycin and colistin concentrations, improved the isolation of B. melitensis, but not Brucella abortus bv1. A novel Brucella selective culture medium (BruSIC), in which calf serum is replaced by activated charcoal, retains the selectivity and improves the productivity of BSM and CM. BruSIC allows the growth of all brucellae faster than in CM or BSM, and at CFU number equivalent to BAB supplemented by calf serum, including B. abortus bv1 and the serum-dependent Brucella ovis. Due to its performance and reduced cost, BruSIC represents an added-value alternative to the existing selective culture media for these bacteria.

Detection and Antimicrobial Resistance of Enterobacteriaceae other than Escherichia Coli in Raccoons from the Madrid Region of Spain

Introduction

Raccoons are an invasive alien species widely distributed in the Madrid region of Spain. These animals can carry a variety of enteric bacteria with associated antimicrobial resistance, which can infect humans and livestock. However, to our knowledge, the presence of non-E. coli Enterobacteriaceae in raccoons has not been previously studied.

Material and Methods

We conducted a study to examine the species distribution of Enterobacteriaceae isolates other than E. coli, as well as their antimicrobial resistance, in the faeces of 83 raccoons in the Madrid region.

Results

We detected 12 Enterobacteriaceae isolates other than E. coli belonging to seven different species: Citrobacter freundii (1 isolate), Citrobacter gillenii (3 isolates), Citrobacter murliniae (1 isolate), Citrobacter portucalensis (2 isolates), Enterobacter hormaechei subsp. hoffmannii (1 isolate), Hafnia paralvei (2 isolates) and Raoultella ornithinolytica (2 isolates). These isolates were found in 7 of the 83 (8.4%) animals studied. To our knowledge, this study is the first report of the presence of non-E. coli Enterobacteriaceae in raccoon faeces. All isolates but one were resistant to at least one of the 14 antimicrobials tested. Resistance to ampicillin (83.3%), amoxicillinclavulanic acid (50%) and cefoxitin (33.3%) was the most frequent.

Conclusion

Our study indicates that raccoons are a potential source of infection with Enterobacteriaceae other than E. coli for humans and livestock in the Madrid region.

Comparison of MALDI-TOF mass spectrometry and rpoB gene sequencing for the identification of clinical isolates of Aeromonas spp

Aeromonas spp., widely present in rivers and soil, cause mild gastroenteritis, severe septicemia, and soft tissue infections in humans. Treatment of these infections require accurate identification of pathogenic Aeromonas spp. However, identification at the species level using conventional methods is highly challenging. In this study, we aimed to compare the accuracy of two different approaches developed for bacterial identification: (i) housekeeping gene sequencing (rpoB) in conjunction with phylogenetic analysis and (ii) matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS) (MALDI Biotyper and VITEK MS), for differentiating Aeromonas spp. We analyzed 58 Aeromonas isolates recovered from patients at different medical institutions in Japan using both identification methods. The rpoB sequencing method was the most accurate, identifying all Aeromonas isolates at the species level. Meanwhile, the MALDI Biotyper system correctly identified 53 (91.4%) isolates at the genus level and an additional 30 (51.7%) at the species level. The VITEK MS system correctly identified 58 (100%) isolates at the genus level and an additional 34 (58.6%) at the species level. Thus, MALDI Biotyper and VITEK MS accurately identified isolates at the genus level, but differences were found in the accuracy of identification of species. However, the low cost and ease of analysis make MALDI-TOF MS-based methods strong candidates for use in clinical laboratories that require easy-to-use identification methods.

•

Mass spectrometry (MS)-based methods evaluated for Aeromonas spp. identification.

•

Housekeeping gene rpoB sequencing most accurately identified Aeromonas species.

•

MALDI Biotyper and VITEK MS differed in accuracy depending on the species.

•

Database extension will help improve identification accuracy of MS-based methods.

Diversity and antimicrobial susceptibility profiles of Aeromonas spp. isolated from diseased freshwater fishes in Thailand

Motile Aeromonas septicemia (MAS), a disease caused by Aeromonas spp., is recognized as a major disease in freshwater aquaculture. This study aimed to investigate the distribution and diversity of Aeromonas spp. and their antimicrobial susceptibility patterns. A total of 86 isolates of Aeromonas spp. were recovered from diseased freshwater fishes from 13 farms in Thailand. All isolates were identified using biochemical characteristics, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), polymerase chain reaction assays, and the gyrB gene sequence analysis. The result of MALDI-TOF MS showed 100% (86 isolates) accuracy at genus-level identification, and 88.4% (76 isolates) accuracy at species-level identification. Six species of Aeromonas were confirmed through nucleotide sequencing and phylogenetic analysis of the gyrB gene Aeromonas veronii (72.1%), Aeromonas jandaei (11.6%), Aeromonas schubertii (9.3%), Aeromonas diversa (3.5%), Aeromonas hydrophila (2.3%), and Aeromonas punctata (1.2%). Antimicrobial susceptibility tests for all isolates revealed resistance against amoxicillin (99%), ampicillin (98%), oxolinic acid (81.4%), oxytetracycline (77%), trimethoprim-sulfamethoxazole (24%), and enrofloxacin (21%). The multiple antibiotic resistance (MAR) index varied between 0.14 and 0.86, with MAR values more than 0.2 in 99% of isolates. Furthermore, four diverse multidrug-resistant (MDR) patterns were found among Aeromonas isolates. Our finding show that A. veronii is the most abundant species in Thai cultured freshwater fish with the highest MDR patterns.

Nocardiosis in Free-Ranging Cetaceans from the Central-Eastern Atlantic Ocean and Contiguous Mediterranean Sea

We report the pathologic features of nocardiosis in five free-ranging delphinids from the Canary Islands and Andalusia, namely four striped dolphins (Stenella coerulealba) and one bottlenose dolphin (Tursiops truncatus). All animals had a multiorgan (disseminated) pattern of infection involving suppurative to pyogranulomatous and thromboembolic lesions in two or more organs. Most affected organs were (by decreasing order) lung, pulmonary lymph nodes, liver, kidney, adrenal glands, and central nervous system. Typical intralesional and intravascular branched and filamentous bacteria were highlighted by Grocott's methenamine silver and Gram stains. Bacterial analysis including 16S rRNA gene sequencing identified Nocardia farcinica in two striped dolphins and Nocardia otitidiscaviarum in one striped dolphin and the bottlenose dolphin. All dolphins tested (n = 4) for cetacean morbillivirus were negative; one dolphin had concurrent cutaneous herpesvirosis. These results provide the first record of N. otitidiscaviarum in cetaceans, the first account of N. farcinica in free-ranging dolphins, and confirmation of nocardiosis in central eastern Atlantic Ocean. These results expand the known geographic range of nocardiosis in cetaceans.

Application of Modified Carbapenem Inactivation Method and Its Derivative Tests for the Detection of Carbapenemase-Producing Aeromonas

PURPOSE

Infection and transmission of carbapenem-resistant Aeromonas is a serious threat to public health. Rapid and accurate detection carbapenem-resistant of these organisms is essential for reasonable treatment and infection control. This study aimed to find a simple and effective method to detect carbapenem-resistant phenotype in Aeromonas.

METHODS

A total of 131 clinical preserved Aeromonas strains were used in this study. The carbapenemase genes were detected by PCR. Modified carbapenem inactivation method (mCIM) in conjunction with EDTA-modified carbapenem inactivation method (eCIM) and simplified carbapenem inactivation method (sCIM) were performed to detect carbapenemases. We also designed a simple method, carbapenem inactivation method using supernatant (CIM-s), to detect the carbapenemase activity in the medium.

RESULTS

Of the 131 Aeromonas strains, 79 contained carbapenemase genes, including 68 blaCphA , 6 blaKPC-2 , 2 blaNDM-1 and 3 blaKPC-2+CphA . However, routine antibiotic susceptibility testing could not completely identify carbapenemase-producing Aeromonas. In phenotypic assays, the sensitivity and specificity of mCIM were 100%. The combined mCIM and eCIM could distinguish serine carbapenemase and metallo-β-carbapenemases except co-producing organisms. The sensitivity and specificity of sCIM were 92.4% and 100%, respectively, which could not detect CphA totally. CIM-s results indicate that these carbapenemases could secrete into the medium to perform their hydrolytic activities and had a sensitivity and specificity of 97.5% and 100%, respectively.

CONCLUSION

The combination of mCIM and eCIM can effectively detect and distinguish different types of carbapenemase in Aeromonas, and could be used as an important supplement approach to the antibiotic susceptibility testing.

Virulence and Antimicrobial Resistance Pattern of Aeromonas spp. Colonizing European Pond Turtles Emys orbicularis and Their Natural Environment. First Study from Poland

The aim of the study was to isolate and identify species belonging to the Aeromonas genus and evaluate the antimicrobial resistance and virulence patterns of isolates colonizing European pond turtles (Emys orbicularis) from natural environment of Eastern Poland. In total, 74 turtles and 15 samples of water from their natural environment were examined. More than 40 strains were isolated and identified: A. bestiarum (n = 1), A. hydrophila (n = 13), A. allosaccharophila (n = 2), A. salmonicida (n = 3), and A. veronii (n = 23). The highest incidence of resistance was noted for ampicillin (100%) and sulfamethoxazole (62.0%), followed by erythromycin and colistin (both 40.5%). Moreover, eight strains were intermediately resistant to meropenem (19%). Most Aeromonas isolates were found to possess more than one virulence gene among fla, aer, hlyA, act, ela, alt, and ast. We showed that the population of free-living European pond turtles was highly colonized by Aeromonas spp. Such strains may be an infectious agent not only for the population of turtles but also for other species of animals inhabiting their natural environment. Moreover, the undesirable properties of water quality caused by the presence of drug-resistant aeromonads could have a negative impact on human health.

Evaluation of three sample preparation methods for the identification of clinical strains by using two MALDI-TOF MS systems

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the microbial identification, especially in the clinical microbiology laboratories. However, although numerous studies on the identification of microorganisms by MALDI-TOF MS have been reported previously, few studies focused on the effect of pretreatment on identification. Due to the sensitivity of MALDI-TOF MS, different preparation methods will lead to changes in microbial protein fingerprints. In this study, for evaluating a more appropriate preparation method for the clinical microbiology identification, we analyzed the performance of three sample preparation methods on two different MALDI-TOF MS systems. A total of 321 clinical isolates, 127 species, were employed in the comparative study of three different sample preparation methods including the direct colony transfer method (DCTM), the on-target extraction method (OTEM), and the in-tube extraction method (ITEM) compatible with MALDI-TOF MS. All isolates were tested on the Microflex LT and Autof ms1000 devices. The spectra were analyzed using the Bruker biotyper and the Autof ms1000 systems. The results were confirmed by 16/18S rRNA sequencing. Results reveal that the accuracies of isolates identification by Bruker biotyper successfully identified 83.8%, 96.0%, and 95.3% after performing the DCTM, OTEM, and ITEM, respectively, while the Autof ms1000 identified 97.5%, 100%, and 99.7%. These data suggested that the identification rates are comparable among the three preparation methods using the Autof ms1000 and Bruker microflex LT systems but the OTEM is more suitable and necessary for clinical application, owing to its key advantages of simplicity and accuracy.

Main bacterial species causing clinical disease in ornamental freshwater fish in Brazil

Bacterial diseases are common in ornamental fish, more frequently associated with ubiquitous bacteria from the aquarium environment. The disease can lead to fish mortality and cause high economic losses if not rapidly controlled. The aim of this study was to identify the main causative bacterial agents of infection in ornamental fish with different clinical signs. A total of 126 freshwater fish, from 12 families and 38 species, with clinical signs were collected in a wholesaler in São Paulo, SP, Brazil. Samples were taken from the eye, skin ulcers, kidneys, and gills, plated on MacConkey, CHROMagar Orientation, and blood agar and incubated under aerobic and anaerobic conditions. Bacterial identification was performed by MALDI-TOF mass spectrometry. From the 126 studied animals, 112 were positive for bacterial isolation. Among the positive animals, 32.1% presented infection caused by a single bacterial species, while in the remaining 67.9%, two to six different bacterial species were identified. A total of 259 bacterial strains were obtained and classified among 46 bacterial species. The species of higher frequency were Aeromonas veronii (26.3%), Aeromonas hydrophilla (16.2%), Shewanella putrefaciens (7.3%), Citrobacter freundii (8.1%), Vibrio albensis (5.8%), and Klebsiella pneumoniae (4.2%). MALDI-TOF MS showed to be a rapid method for diagnosis of bacterial disease outbreaks in ornamental fish establishments.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for Identification of Bacterial Isolates From Horses

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is used for bacterial identification by analyzing the spectra of isolates and comparing them against a database of reference spectra; it is known for its rapidity and accuracy. Although MALDI-TOF MS is used for identification of bacterial isolates from animals, not all animal pathogens are identified correctly. In this study, we used a commercial MALDI-TOF MS identification system to examine 3724 bacterial isolates from horses and their environments. Isolates that could not be identified with MALDI-TOF MS were identified by 16S rRNA gene sequence taxonomic analysis. MALDI-TOF MS could identify 86.2% of the isolates from horses to the species level, showing that this method could be successfully applied for bacterial identification in horses. However, some species known to be equine pathogenic agents including Taylorella equigenitalis and Rhodococcus equi were difficult to identify with MALDI-TOF MS, which might be the result of an inadequate reference database. Some Prevotella, Staphylococcus, and Streptococcus isolates, which could not be identified with either MALDI-TOF MS or 16S rRNA gene sequencing analysis, formed clusters in the 16S rRNA phylogenic tree, and might be unknown species isolated from horses. Adding the spectra of isolates identified in this study to an in-house database might make MALDI-TOF MS a more useful tool for identifying equine isolates.

High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains

Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.

A Case of Aeromonas trota in an Immunocompromised Patient with Diarrhea

According to recent literature, 95.4% of the Aeromonas strains associated with human clinical cases correspond to four species: Aeromonas caviae, Aeromonas dhakensis, Aeromonas veronii and Aeromonas hydrophila. However, other less prevalent species such as Aeromonas trota, are also described from clinical samples. Based on its low incidence, the latter species can be regarded as rare and it is the only Aeromonas species susceptible to ampicillin. From the taxonomic point of view, A. trota is considered a synonym of the species Aeromonas enteropelogenes. The objective of this study is to present a new clinical case associated with A. trota in order to increase the knowledge about this species. The strain was recovered from the feces of a 69-year-old patient with a diarrheal syndrome and peritoneal psammocarcinoma. The preliminary identification as Aeromonas sp. was obtained with the API 20E, but it was characterized as Aeromonas jandei and also as Aeromonas enteropelogenes with different scores with the matrix-assisted laser desorption ionization time of flight (MALDI-TOF). Based on the sequence of the rpoD gene, it was confirmed to be A. trota. The antimicrobial resistance pattern showed that the strain was susceptible to ampicillin, penicillins in combination with beta-lactamase inhibitors, quinolones, carbapenems, aminoglycosides and cephalosporins, except cephalothin. In conclusion, the recognition of an Aeromonas strain susceptible to ampicillin should alert the clinical microbiologist of the possible involvement of this rare species. Furthermore, the MALDI-TOF database should be updated indicating that the species A. enteropelogenes, is a synonym of A. trota.

Low Cassette Variability in Class 2 and Class 1 Integrons of Aeromonas spp. Isolated from Environmental Samples

Integrons are prokaryotic genetic elements known to carry and exchange antibiotic resistance gene cassettes through a site-specific recombinase called integrase. In this work, 107 Aeromonas isolates from environmental origin, including fish, water, and sediments, were investigated for the presence of integrons. Using specific primers for Class 1, 2 and 3 integrases, only Class 1 and Class 2 integrons were detected. Detection of Class 2 integrases and their associated variable regions required two rounds of polymerase chain reaction (PCR). Sequencing of the intI2 amplicons confirmed them as integrase-derived products. Class 1 integrons were detected in 26 out of 107 isolates. PCR amplification of the variable regions associated to these integrons revealed an outstanding homogeneity, 25 of them having variable regions with an identical dfrA12-orfF-aadA2 cassette array and one integron carrying only the dfrA16 cassette. To assess clone diversity, chromosomal DNA from isolates was subjected to enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), which discarded clonality in all instances. Class 2 integrons were surprisingly more prevalent than Class1 integrons, being detected in 60 out of 107 isolates. Forty-six of them showed a unique ERIC profile, while the remaining 14 strains displayed profiles that could be grouped in five different patterns. Cassette arrangements of all Class 2 variable regions were those described as the most prevalent (dfrA1-sat2-aadA1). A rather startling result of this work is the sensitivity to trimethoprim, streptomycin, and streptothricin of most strains, despite the presence of the cognate resistance genes. To know the integron distribution in environmental Aeromonas species, a phylogenetic reconstruction was done using rpoD/gyrB or rpoD/gyrA gene sequences. Isolates bearing these elements corresponded to Aeromonas hydrophila, Aeromonas veronii, Aeromonas salmonicida, Aeromonas dhakensis, Aeromonas sanarellii, Aeromonas taiwanensis, Aeromonas media, Aeromonas caviae, Aeromonas jandaei, and Aeromonas sp. This work revealed an unusual high incidence of Class 2 integrons and a low variability of cassette arrangements in environmental Aeromonas species.

An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity

The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.

Potentially human-virulent Vibrio vulnificus isolates from diseased great pompano (Trachinotus goodei)

Vibrio vulnificus is an opportunistic human pathogen responsible for the majority of seafood-associated deaths worldwide and is also a relevant fish pathogen for the aquaculture industry. In addition to infections in aquatic livestock, V. vulnificus also represents a risk to aquarium animals. For the first time, this work describes an important mortality outbreak in Trachinotus goodei in a zoo aquarium, with the isolation of Vibrio vulnificus (Vv) from the internal organs of the diseased fish. The isolates were identified by MALDI-TOF MS, serotyped and characterized by pulsed-field gel electrophoresis (PFGE). Although the isolates from great pompanos did not belong to pathovar piscis (formerly biotype 2) or to any of the fish-related serovars, they all had identical phenotypes, antimicrobial susceptibility profiles and PFGE patterns, which together with their isolation in pure culture from internal organs is strongly indicative of their clinical significance. Moreover, Vv isolates harboured important genetic markers of human virulence potential: they had the clinical variant of the vcg gene, gave the 338 bp DNA amplification product of the pilF gene and resisted the bactericidal activity of human serum. All these results strongly suggest that these Vv isolates should be considered potentially virulent for humans. These results extend the range of fish species affected by V. vulnificus, confirm the threat that this pathogen represents to aquatic animals and highlight the risk that this bacterial pathogen poses to human health.

Evaluation of MALDI-TOF MS and an expanded custom reference spectra database for the identification and differentiation of Taylorella equigenitalis and Taylorella asinigenitalis

Misidentification between Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), and Taylorella asinigenitalis is observed by the gold standard culture method. The performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for Taylorella species identification was evaluated using 85 T. equigenitalis and 28 T. asinigenitalis strains selected on the basis of multilocus sequence typing data. Seven of the T. equigenitalis and 9 of the T. asinigenitalis strains were used to generate in-house reference spectra to expand the existing commercial Bruker database. Two bacterial incubation times and 3 different sample preparation procedures were compared. Overall, we demonstrated the usefulness of MALDI-TOF MS as a differential diagnostic tool for CEM; however, commercial spectra databases should be expanded with T. asinigenitalis reference spectra to achieve the expected performance. Moreover, direct spotting of 48-h colonies was not only the most efficient protocol but also the easiest to implement in a clinical setting.

Proteomic characterization and discrimination of Aeromonas species recovered from meat and water samples with a spotlight on the antimicrobial resistance of Aeromonas hydrophila

Aeromonas is recognized as a human pathogen following ingestion of contaminated food and water. One major problem in Aeromonas identification is that certain species are phenotypically very similar. The antimicrobial resistance is another significant challenge worldwide. We therefore aimed to use mass spectrometry technology for identification and discrimination of Aeromonas species and to screen the antimicrobial resistance of Aeromonas hydrophila (A. hydrophila). A total of 150 chicken meat and water samples were cultured, and then, the isolates were identified biochemically by the Vitek^® 2 Compact system. Proteomic identification was performed by MALDI‐TOF MS and confirmed by a microchannel fluidics electrophoresis assay. Principal component analysis (PCA) and single‐peak analysis created by MALDI were also used to discriminate the Aeromonas species. The antimicrobial resistance of the A. hydrophila isolates was determined by Vitek^® 2 AST cards. In total, 43 samples were positive for Aeromonas and comprised 22 A. hydrophila, 12 Aeromonas caviae (A. caviae), and 9 Aeromonas sobria (A. sobria) isolates. Thirty‐nine out of 43 (90.69%) Aeromonas isolates were identified by the Vitek^® 2 Compact system, whereas 100% of the Aeromonas isolates were correctly identified by MALDI‐TOF MS with a score value ≥2.00. PCA successfully separated A. hydrophila, A. caviae and A. sobria isolates into two groups. Single‐peak analysis revealed four discriminating peaks that separated A. hydrophila from A. caviae and A. sobria isolates. The resistance of A. hydrophila to antibiotics was 95.46% for ampicillin, 50% for cefotaxime, 45.45% for norfloxacin and pefloxacin, 36.36% for ceftazidime and ciprofloxacin, 31.81% for ofloxacin and 27.27% for nalidixic acid and tobramycin. In conclusion, chicken meat and water were tainted with Aeromonas spp., with a high occurrence of A. hydrophila. MALDI‐TOF MS is a powerful technique for characterizing aeromonads at the genus and species levels. Future studies should investigate the resistance of A. hydrophila to various antimicrobial agents.