Population structure and antimicrobial susceptibility of Pseudomonas aeruginosa from animal infections in France

Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes

BACKGROUND

Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P. aeruginosa genomes remains an unsolved problem.

METHODS

We first curated the most comprehensive database yet of known P. aeruginosa AMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n = 1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of our P. aeruginosa AMR database, implemented in our AMR detection and prediction tool, ARDaP, was compared with three previously published in silico AMR gene detection or phenotype prediction tools-abritAMR, AMRFinderPlus, ResFinder-across both the Global Dataset and an analysis-naïve Validation Dataset (n = 102).

RESULTS

Our AMR database comprises 3639 mobile AMR genes and 728 chromosomal variants, including 75 previously unreported chromosomal AMR variants, 10 variants associated with unusual antimicrobial susceptibility, and 281 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder. ARDaP's superior performance was predominantly due to the inclusion of chromosomal AMR variants, which are generally not identified with most AMR identification tools.

CONCLUSIONS

Our ARDaP software and associated AMR variant database provides an accurate tool for predicting AMR phenotypes in P. aeruginosa, far surpassing the performance of current tools. Implementation of ARDaP for routine AMR prediction from P. aeruginosa genomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of the P. aeruginosa resistome, particularly the basis of colistin AMR.

Distribution of sequence types and antimicrobial resistance of clinical Pseudomonas aeruginosa isolates from dogs and cats visiting a veterinary teaching hospital in Thailand

BACKGROUND

Pseudomonas aeruginosa is an important opportunistic pathogen in dogs and cats and is resistant to several antimicrobial drugs; however, data on the clonal distribution of P. aeruginosa in veterinary hospital are limited. This study aimed to investigate the clonal dissemination and antimicrobial resistance of clinical P. aeruginosa in a veterinary teaching hospital in Thailand within a 1-year period. Minimum inhibitory concentration determination and whole genome sequencing were used for antimicrobial susceptibility analysis and genetic determination, respectively.

RESULTS

Forty-nine P. aeruginosa were isolated mostly from the skin, urinary tract, and ear canal of 39 dogs and 10 cats. These isolates belonged to 39 sequence types (STs) that included 9 strains of high-risk clones of ST235 (n = 2), ST244 (n = 2), ST274 (n = 2), ST277 (n = 1), ST308 (n = 1), and ST357 (n = 1). Overall antimicrobial resistance rate was low (< 25%), and no colistin-resistant strains were found. Two carbapenem-resistant strains belonging to ST235 and ST3405 were identified.

CONCLUSIONS

Clinical P. aeruginosa in dogs and cats represent STs diversity. High-risk clones and carbapenem-resistant strains are a public health concern. Nevertheless, this study was limited by a small number of isolates. Continuous monitoring is needed, particularly in large-scale settings with high numbers of P. aeruginosa, to restrict bacterial transfer from companion animal to humans in a veterinary hospital.

Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals

The importance of addressing the problem of biofilms in farm, wild, and companion animals lies in their pervasive impact on animal health and welfare. Biofilms, as resilient communities of microorganisms, pose a persistent challenge in causing infections and complicating treatment strategies. Recognizing and understanding the importance of mitigating biofilm formation is critical to ensuring the welfare of animals in a variety of settings, from farms to the wild and companion animals. Effectively addressing this issue not only improves the overall health of individual animals, but also contributes to the broader goals of sustainable agriculture, wildlife conservation, and responsible pet ownership. This review examines the current understanding of biofilm formation in animal diseases and elucidates the complex processes involved. Recognizing the limitations of traditional antibiotic treatments, mechanisms of resistance associated with biofilms are explored. The focus is on alternative therapeutic strategies to control biofilm, with illuminating case studies providing valuable context and practical insights. In conclusion, the review highlights the importance of exploring emerging approaches to mitigate biofilm formation in animals. It consolidates existing knowledge, highlights gaps in understanding, and encourages further research to address this critical facet of animal health. The comprehensive perspective provided by this review serves as a foundation for future investigations and interventions to improve the management of biofilm-associated infections in diverse animal populations.

Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings

Introduction

The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits.

Materials and methods

A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments.

Results

Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings.

Conclusion

FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates.

Determination of Antimicrobial Resistance and the Impact of Imipenem + Cilastatin Synergy with Tetracycline in Pseudomonas aeruginosa Isolates from Sepsis

Pseudomonas aeruginosa is among the most ubiquitous bacteria in the natural world, exhibiting metabolic and physiological versatility, which makes it highly adaptable. Imipenem + cilastatin and tetracycline are antibiotic combinations commonly used to treat infections caused by P. aeruginosa, including serious infections such as sepsis. In the context of bacterial infections, biofilm, formed by bacterial cells surrounded by extracellular substances forming a matrix, plays a pivotal role in the resistance of P. aeruginosa to antibiotics. This study aimed to characterize a representative panel of P. aeruginosa isolates from septicemias, assessing their susceptibility to various antibiotics, specifically, imipenem + cilastatin and tetracycline, and the impact of these treatments on biofilm formation. Results from antibiotic susceptibility tests revealed sensitivity in most isolates to six antibiotics, with four showing near or equal to 100% sensitivity. However, resistance was observed in some antibiotics, albeit at minimal levels. Notably, tetracycline showed a 100% resistance phenotype, while imipenem + cilastatin predominantly displayed an intermediate phenotype (85.72%), with some resistance (38.1%). Microdilution susceptibility testing identified effective combinations against different isolates. Regarding biofilm formation, P. aeruginosa demonstrated the ability to produce biofilms. The staining of microtiter plates confirmed that specific concentrations of imipenem + cilastatin and tetracycline could inhibit biofilm production. A significant proportion of isolates exhibited resistance to aminoglycoside antibiotics because of the presence of modifying genes (aac(3)-II and aac(3)-III), reducing their effectiveness. This study also explored various resistance genes, unveiling diverse resistance mechanisms among P. aeruginosa isolates. Several virulence genes were detected, including the las quorum-sensing system genes (lasI and lasR) in a significant proportion of isolates, contributing to virulence factor activation. However, genes related to the type IV pili (T4P) system (pilB and pilA) were found in limited isolates. In conclusion, this comprehensive study sheds light on the intricate dynamics of P. aeruginosa, a remarkably adaptable bacterium with a widespread presence in the natural world. Our findings provide valuable insights into the ongoing battle against P. aeruginosa infections, highlighting the need for tailored antibiotic therapies and innovative approaches to combat biofilm-related resistance.

Pseudomonas spp. in Canine Otitis Externa

Canine otitis externa (OE) is a commonly diagnosed condition seen in veterinary practice worldwide. In this review, we discuss the mechanisms of the disease, with a particular focus on the biological characteristics of Pseudomonas aeruginosa and the impact that antibiotic resistance has on successful recovery from OE. We also consider potential alternatives to antimicrobial chemotherapy for the treatment of recalcitrant infections. P. aeruginosa is not a typical constituent of the canine ear microbiota, but is frequently isolated from cases of chronic OE, and the nature of this pathogen often makes treatment difficult. Biofilm formation is identified in 40-95% of P. aeruginosa from cases of OE and intrinsic and acquired antibiotic resistance, especially resistance to clinically important antibiotics, highlights the need for alternative treatments. The role of other virulence factors in OE remains relatively unexplored and further work is needed. The studies described in this work highlight several potential alternative treatments, including the use of bacteriophages. This review provides a summary of the aetiology of OE with particular reference to the dysbiosis that leads to colonisation by P. aeruginosa and highlights the need for novel treatments for the future management of P. aeruginosa otitis.

Antimicrobial resistance and genotyping of Pseudomonas aeruginosa isolated from the ear canals of dogs in Japan

The strong bond between dogs and their owners creates a close association that could result in the transfer of antibiotic-resistant bacteria from canines to humans, potentially leading to the spread of antimicrobial resistance genes. Pseudomonas aeruginosa, a common causative agent of persistent ear infections in dogs, is often resistant to multiple antibiotics. Assessing the antimicrobial resistance profile and genotype of P. aeruginosa is crucial for the appropriate use of veterinary pharmaceuticals. However, in recent years, few studies have been conducted on this bacterium in Japan. We determined the antimicrobial resistance profile and genotype of P. aeruginosa isolated from the ear canal of dogs in Japan in 2020. Analysis of antimicrobial resistance using disk diffusion tests indicated a high frequency of resistance to most antimicrobial agents. Particularly, 29 isolates from the ear canals of the 29 affected dogs (100%) were resistant to cefovecin, cefpodoxime, and florfenicol; however, they were susceptible to cefepime and piperacillin/tazobactam. Only 3.4, 10.3, and 10.3% of the isolates were resistant to ceftazidime, tobramycin, and gentamicin, respectively. Furthermore, upon analyzing the population structure using multilocus sequence typing, a considerably large clonal complex was not observed in the tested isolates. Three isolates, namely ST3881, ST1646, and ST532, were clonally related to the clinically isolated sequence types in Japan (such as ST1831, ST1413, ST1812, and ST1849), which is indicative of dog-to-human transmission. Considering the variation in antibiotic resistance compared to that reported by previous studies and the potential risk of dog-to-human transmission, we believe that the survey for antimicrobial resistance profile and population structure should be continued regularly. However, the prevalence of multidrug-resistant P. aeruginosa in dogs in Japan is not a crisis.

The Impact of the Virulence of Pseudomonas aeruginosa Isolated from Dogs

Pseudomonas aeruginosa is a pathogenic bacterium that can cause serious infections in both humans and animals, including dogs. Treatment of this bacterium is challenging because some strains have developed multi-drug resistance. This study aimed to evaluate the antimicrobial resistance patterns and biofilm production of clinical isolates of P. aeruginosa obtained from dogs. The study found that resistance to various β-lactam antimicrobials was widespread, with cefovecin and ceftiofur showing resistance in 74% and 59% of the isolates tested, respectively. Among the aminoglycosides, all strains showed susceptibility to amikacin and tobramycin, while gentamicin resistance was observed in 7% of the tested isolates. Furthermore, all isolates carried the oprD gene, which is essential in governing the entry of antibiotics into bacterial cells. The study also investigated the presence of virulence genes and found that all isolates carried exoS, exoA, exoT, exoY, aprA, algD, and plcH genes. This study compared P. aeruginosa resistance patterns worldwide, emphasizing regional understanding and responsible antibiotic use to prevent multi-drug resistance from emerging. In general, the results of this study emphasize the importance of the continued monitoring of antimicrobial resistance in veterinary medicine.

Fosfomycin Resistance in Bacteria Isolated from Companion Animals (Dogs and Cats)

Fosfomycin is an old antibacterial agent, which is currently used mainly in human medicine, in uncomplicated Urinary Tract Infections (UTIs). The purpose of this review is to investigate the presence and the characteristics of Fosfomycin resistance in bacteria isolated from canine or feline samples, estimate the possible causes of the dissemination of associated strains in pets, and underline the requirements of prospective relevant studies. Preferred Reporting Items for Systematic Reviews (PRISMA) guidelines were used for the search of current literature in two databases. A total of 33 articles were finally included in the review. Relevant data were tracked down, assembled, and compared. Referring to the geographical distribution, Northeast Asia was the main area of origin of the studies. E. coli was the predominant species detected, followed by other Enterobacteriaceae, Staphylococci, and Pseudomonas spp. FosA and fosA3 were the more frequently encountered Antimicrobial Resistance Genes (ARGs) in the related Gram-negative isolates, while fosB was regularly encountered in Gram-positive ones. The majority of the strains were multidrug-resistant (MDR) and co-carried resistance genes against several classes of antibiotics and especially β-Lactams, such as bla_CTX-M and mecA. These results demonstrate the fact that the cause of the spreading of Fosfomycin-resistant bacteria among pets could be the extended use of other antibacterial agents, that promote the prevalence of MDR, epidemic strains among an animal population. Through the circulation of these strains into a community, a public health issue could arise. Further research is essential though, for the comprehensive consideration of the issue, as the current data are limited.

Antimicrobial activity and chemical profile of wood vinegar from eucalyptus (Eucalyptus urophylla x Eucalyptus grandis - clone I144) and bamboo (Bambusa vulgaris)

Microbial resistance to drugs is a public health problem; therefore, there is a search for alternatives to replace conventional products with natural agents. One of the potential antimicrobial agents is wood vinegar derived from the carbonization of lignocellulosic raw materials. The objectives of the present work were to evaluate the antibacterial and antifungal action of two kinds of wood vinegar (WV), one of Eucalyptus urograndis wood and another of Bambusa vulgaris biomass, and determine their chemical profile. The antimicrobial effect was assessed against Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enteritidis, Escherichia coli, Streptococcus agalactiae, and Candida albicans. The minimum inhibitory concentration and the minimum bactericidal and fungicidal concentrations were determined. Micrographs of the microorganisms before and after exposure to both kinds of wood vinegar were obtained by scanning electron microscopy. The chemical profile of the eucalyptus and bamboo vinegar was carried out by gas chromatography and mass spectrometry (GC/MS). Both types of WV presented significant antimicrobial activity, with the bamboo one having a higher efficiency. Both studied pyroligneous extracts seem promising for developing natural antimicrobials due to their efficiency against pathogens. GC/MS analyses demonstrated that the chemical profiles of both kinds of WV were similar but with some significant differences. The major component of the eucalyptus vinegar was furfural (17.2%), while the bamboo WV was phenol (15.3%). Several compounds in both WVs have proven antimicrobial activity, such as acetic acid, furfural, phenol, cresols, guaiacol, and xylenols. Together, they are the major in the chemical composition of the organic fraction of both WVs. Bamboo vinegar had a more expressive content of organic acids. Micrographs of microorganisms taken after exposure to both kinds of wood vinegar displayed several cell modifications. The potential of both types of wood vinegar as a basis for natural antimicrobial products seems feasible due to their proven effect on inhibiting the microorganisms' growth assessed in this experiment.

Comparative Genomics of Pseudomonas aeruginosa Strains Isolated from Different Ecological Niches

The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. bla_OXA-488 (a variant of bla_OXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.

Molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital environment

This study aimed to investigate sites for colonization and molecular epidemiology of antimicrobial-resistant Pseudomonas aeruginosa in a veterinary teaching hospital. Bacterial specimens from surface and liquid samples (n = 165) located in five rooms were collected three times every 2 months, and antimicrobial susceptibility was subsequently determined by minimum inhibitory concentrations. The genomes of resistant strains were further analyzed using whole-genome sequencing. Among 19 P. aeruginosa isolates (11.5%, 19/165), sinks were the most frequent colonization site (53.3%), followed by rubber tubes (44.4%), and anesthesia-breathing circuit (33.3%). The highest resistance to gentamicin (47.4%), followed by piperacillin/tazobactam (36.8%), levofloxacin (36.8%), and ciprofloxacin (36.8%), was observed from 19 P. aeruginosa isolates, of which 10 were resistant strains. Of these 10 antimicrobial-resistant isolates, five were multidrug-resistant isolates, including carbapenem. From the multilocus sequence typing (MLST) analysis, five sequence types (STs), including a high-risk clone of human ST235 (n = 3), and ST244 (n = 3), ST606 (n = 2), ST485 (n = 1), and ST3405 (n = 1) were identified in resistant strains. Multiresistant genes were identified consistent with STs, except ST235. The MLST approach and single nucleotide polymorphism analysis revealed a link between resistant strains from ward rooms and those from examination, wound care, and operating rooms. The improvement of routine cleaning, especially of sink environments, and the continued monitoring of antimicrobial resistance of P. aeruginosa in veterinary hospitals are necessary to prevent the spread of resistant clones and ensure infection control.

Synthesis, characterization, DFT, antioxidant, antibacterial, pharmacokinetics and inhibition of SARS-CoV-2 main protease of some heterocyclic hydrazones

Three hydrazone derivatives have been synthesized using condensation reaction of 4-hydrazinylbenzoic acid with three aromatic aldehydes namely: thiophene-2-carbaldehyde, thiophene-3-carbaldehyde and 2-furaldehyde in ethanol at 78 °C reflux. The synthesized molecules have been characterized using spectroscopic and physicochemical methods including UV-Vis, IR, ¹H NMR, ¹³C NMR, ¹⁵N NMR and melting point determination. Optimized molecular structures, UV-Vis and IR spectra modeling, the reactivity, the stability and some quantum chemical parameters of the synthesized molecules were modeled utilizing density functional theory (DFT). The obtained theoretical results were found in good agreement with the experimental results. On the other hand, the antioxidant and antibacterial activities of the molecules under study were evaluated to better understand the associated mechanisms of action specifically. Also, predicted ADME-T and pharmacokinetic parameters indicated that these compounds showed good oral bioavailability. Finally, molecular docking has been used to predict the inhibitory activity of the studied hydrazone derivatives on the SARS-CoV-2 main protease (Mpro).

Pseudomonas aeruginosa biofilm dispersion by the mouse antimicrobial peptide CRAMP

Pseudomonas aeruginosa (P. aeruginosa) is a known bacterium that produces biofilms and causes severe infection. Furthermore, P. aeruginosa biofilms are extremely difficult to eradicate, leading to the development of chronic and antibiotic-resistant infections. Our previous study showed that a cathelicidin-related antimicrobial peptide (CRAMP) inhibits the formation of P. aeruginosa biofilms and markedly reduces the biomass of preformed biofilms, while the mechanism of eradicating bacterial biofilms remains elusive. Therefore, in this study, the potential mechanism by which CRAMP eradicates P. aeruginosa biofilms was investigated through an integrative analysis of transcriptomic, proteomic, and metabolomic data. The omics data revealed CRAMP functioned against P. aeruginosa biofilms by different pathways, including the Pseudomonas quinolone signal (PQS) system, cyclic dimeric guanosine monophosphate (c-di-GMP) signalling pathway, and synthesis pathways of exopolysaccharides and rhamnolipid. Moreover, a total of 2914 differential transcripts, 785 differential proteins, and 280 differential metabolites were identified. A series of phenotypic validation tests demonstrated that CRAMP reduced the c-di-GMP level with a decrease in exopolysaccharides, especially alginate, in P. aeruginosa PAO1 biofilm cells, improved bacterial flagellar motility, and increased the rhamnolipid content, contributing to the dispersion of biofilms. Our study provides new insight into the development of CRAMP as a potentially effective antibiofilm dispersant.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Pseudomonas aeruginosa in dogs and cats

Pseudomonas aeruginosa (P. aeruginosa) was identified among the most relevant antimicrobial‐resistant (AMR) bacteria in the EU for dogs and cats in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR P. aeruginosa can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33–90% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2, 3 and 4 (Categories A, B, C and D; 0–5%, 1–5%, 5–33% and 5–33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Section 5 (Category E, 33–90% probability of meeting the criteria). The animal species to be listed for AMR P. aeruginosa according to Article 8 criteria are mainly dogs and cats.

Molecular Detection and Phylogenetic Analysis of Pseudomonas aeruginosa Isolated from Some Infected and Healthy Ruminants in Basrah, Iraq

Although P. aeruginosa is an environmental organism, it is infrequently found on the skin, mucous membranes, and in the feces of some healthy animals (wild, companion, or farm animals). P. aeruginosa produces a variety of toxins and enzymes which promote tissue invasion and damage. P. aeruginosa demonstrated resistance to several antimicrobial agents. It is of significant importance in both animal and human medicine. The present study aimed to isolate and diagnose P. aeruginosa isolates from some ruminants, cow and sheep, from different regions of Basrah, Iraq. A total of 200 samples were taken from infected and healthy ruminants, as well as the environment surrounding the animal in Basrah, Iraq. The identification of Pseudomonas aeruginosa was performed by conventional and molecular methods using the 16S rRNA gene and aroE gene by polymerase chain reaction (PCR). The recorded data pointed out that P. aeruginosa was successfully isolated from infected animals (cows and sheep) with total percentages of 46% and 22%, respectively. These percentages were obtained at 8% and 4% from healthy cows and sheep, respectively. The percentages of isolation of the environment surrounding cows and sheep were 40% and 32%, respectively. A higher percentage of infection was observed in the eye, skin, and wound swabs of cows. Healthy cows and sheep gave only three isolates of P. aeruginosa, while the environmental swabs recorded 18 isolates. Bacterial isolates were identified by culture methods and Vitek- 2. To confirm the diagnosis more accurately at the level of the species, the molecular confirmation was performed by PCR amplification of genus and species with 16S rRNA gene sequences. The results pointed out that all 10 selected isolates gave positive results, and the gene size was ≈ 1500 bp. New strains were recorded in GenBank/NCBI, and the phylogenetic tree was constructed. The isolates fall in three clads. Molecular confirmation of other isolates in this study (42 isolates) was carried out by PCR amplification of aroE gene. All PCR products of these isolates were amplified≈ 495 pb on agarose gel electrophoresis.

Genomic and Metabolic Characteristics of the Pathogenicity in Pseudomonas aeruginosa

In recent years, the effectiveness of antimicrobials in the treatment of Pseudomonas aeruginosa infections has gradually decreased. This pathogen can be observed in several clinical cases, such as pneumonia, urinary tract infections, sepsis, in immunocompromised hosts, such as neutropenic cancer, burns, and AIDS patients. Furthermore, Pseudomonas aeruginosa causes diseases in both livestock and pets. The highly flexible and versatile genome of P. aeruginosa allows it to have a high rate of pathogenicity. The numerous secreted virulence factors, resulting from its numerous secretion systems, the multi-resistance to different classes of antibiotics, and the ability to produce biofilms are pathogenicity factors that cause numerous problems in the fight against P. aeruginosa infections and that must be better understood for an effective treatment. Infections by P. aeruginosa represent, therefore, a major health problem and, as resistance genes can be disseminated between the microbiotas associated with humans, animals, and the environment, this issue needs be addressed on the basis of an One Health approach. This review intends to bring together and describe in detail the molecular and metabolic pathways in P. aeruginosa's pathogenesis, to contribute for the development of a more targeted therapy against this pathogen.

Occurrence of Pseudomonas spp. in Raw Vegetables: Molecular and Phenotypical Analysis of Their Antimicrobial Resistance and Virulence-Related Traits

Pseudomonas is characterized by its great capacity to colonize different ecological niches, but also by its antimicrobial resistance and pathogenicity, causing human, animal, or plant diseases. Raw and undercooked food is a potential carrier of foodborne disease. The aim of this study was to determine the occurrence of Pseudomonas spp. among raw vegetables, analysing their antimicrobial resistance, virulence, and molecular typing. A total of 163 Pseudomonas spp. isolates (12 different species) were recovered from 77 of the 145 analysed samples (53.1%) and were classified into 139 different pulsed-field gel electrophoresis patterns. Low antimicrobial resistance levels, but one multidrug-resistant isolate, were found. Among the 37 recovered P. aeruginosa strains, 28 sequence-types and nine serotypes were detected. Eleven OprD patterns and an insertion sequence (ISPa1635) truncating the oprD gene of one imipenem-resistant strain were found. Ten virulotypes were observed, including four exoU-positive and thirty-one exoS-positive strains. The lasR gene was absent in three ST155 strains and was truncated by different insertion sequences (ISPre2, IS1411, and ISPst7) in other three strains. High biofilm, motility, pigment, elastase, and rhamnolipid production were detected. Our study demonstrated a low occurrence of P. aeruginosa (18%) and low antimicrobial resistance, but a high number of virulence-related traits in these P. aeruginosa strains, highlighting their pathological importance.

Prevalence of multidrug resistance in Pseudomonas spp. isolated from wild bird feces in an urban aquatic environment

Antimicrobial resistance (AMR) has been detected in the microbiota of wildlife, yet little is known about the origin and impact within the ecosystem. Due to the shortage of nonepizootic surveillance, there is limited understanding of the natural prevalence and circulation of AMR bacteria in the wild animal population, including avian species. In this surveillance study, feces from wild birds in proximity to the River Cam, Cambridge, England, were collected and Pseudomonas spp. were isolated. Of the 115 samples collected, 24 (20.9%; 95% CI, 12.6%‒29.2%) harbored Pseudomonas spp. of which 18 (75%; 95% CI, 58%‒92%) had a multiple antibiotic resistance (MAR) index greater than 0.2. No Pseudomonas spp. isolate in this study was pansusceptible. Resistance was found among the 24 isolates against ciprofloxacin (87.5%; 95% CI, 74.3%‒100%) and cefepime (83.3%; 95% CI, 68.4%‒98.2%), both of which are extensively used to treat opportunistic Pseudomonas spp. infections. The prevalence of Pseudomonas spp. in the wild bird feces sampled during this study is greater than previous, similar studies. Additionally, their multidrug resistance profile provides insight into the potential risk for ecosystem contamination. It further highlights the importance of a One Health approach, including ongoing surveillance efforts that help to develop the understanding of how wildlife, including avifauna, may contribute and disperse AMR across the ecosystem.

Occurrence, virulence, carbapenem resistance, susceptibility to disinfectants and public health hazard of Pseudomonas aeruginosa isolated from animals, humans and environment in intensive farms

AIMS

This work aimed to determine the occurrence, virulence, antibiogram, carbapenem resistance genes and susceptibility to disinfectants of Pseudomonas aeruginosa isolated from animals, environment and workers in intensive farms.

METHODS AND RESULTS

A total of 610 samples from intensive beef cattle and sheep farms in Kafr El Sheikh Governorate, Egypt were screened for the presence of P. aeruginosa using bacteriological assays. The isolates were characterized by PCR and tested for susceptibility to antibiotics using disk diffusion method and disinfectants by quantitative suspension test. In all, 60 P. aeruginosa isolates were recovered in this study and all isolates harboured at least one of the virulence genes tested. Human P. aeruginosa isolates were highly resistant to cephalosporins, fluroquinolones, aminoglycosides, carbapenems and penicillins+β-lactamase inhibitors than non-human isolates. Colistin resistance was higher in non-human than human P. aeruginosa isolates, whereas low resistance to aztreonam was observed in non-human and human isolates. Carbapenem-resistant P. aeruginosa (CRPA) strains were recovered from workers (56.5%), sheep (8.3%) and cattle (8.3%). All CRPA harboured at least one of the carbapenem resistance genes tested and most of them showed multidrug resistance (MDR) or extensive drug resistance (XDR) phenotypes. Glutaraldehyde 1% and hydrogen peroxide 3% eliminated P. aeruginosa completely in the absence and presence of organic matter within short contact time compared with other disinfectants.

CONCLUSIONS

This study reported the occurrence of CRPA in animals and workers in intensive farms. Glutaraldehyde and hydrogen peroxide were the most effective disinfectants against P. aeruginosa.

SIGNIFICANCE AND IMPACT OF THE STUDY

The occurrence of CRPA in intensive livestock farms is a serious challenge that threatens animal and human health and increases the risk of P. aeruginosa infection in the community. Therefore, it is vital to control the spread of CRPA by banning or restricting the use of antibiotics and applying proper cleaning and disinfection protocols in livestock farms.

Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis

Intense genome sequencing of Pseudomonas aeruginosa isolates from cystic fibrosis (CF) airways has shown inefficient eradication of the infecting bacteria, as well as previously undocumented patient-to-patient transmission of adapted clones. However, genome sequencing has limited potential as a predictor of chronic infection and of the adaptive state during infection, and thus there is increasing interest in linking phenotypic traits to the genome sequences. Phenotypic information ranges from genome-wide transcriptomic analysis of patient samples to determination of more specific traits associated with metabolic changes, stress responses, antibiotic resistance and tolerance, biofilm formation and slow growth. Environmental conditions in the CF lung shape both genetic and phenotypic changes of P. aeruginosa during infection. In this Review, we discuss the adaptive and evolutionary trajectories that lead to early diversification and late convergence, which enable P. aeruginosa to succeed in this niche, and we point out how knowledge of these biological features may be used to guide diagnosis and therapy.

Occurrence, antimicrobial susceptibility, and pathogenic factors of Pseudomonas aeruginosa in canine clinical samples

Background and Aim:

Pseudomonas aeruginosa is a relevant opportunistic and difficult to treat pathogen due to its widespread environmental diffusion, intrinsic resistance to many classes of antimicrobials, high ability to acquire additional resistance mechanisms, and wide range of pathogenic factors. The present study aimed to investigate the prevalence of P. aeruginosa in canine clinical samples, the antimicrobial susceptibility against antipseudomonal antibiotics, and the presence of extracellular pathogenic factors of the isolates, as well as their ability to produce biofilm.

Materials and Methods:

Overall, 300 clinical specimens from dogs with pyoderma or abscesses (n=58), otitis (n=59), and suspected bladder infection (n=183) were analyzed by standard bacteriological methods. P. aeruginosa isolates were tested for their antimicrobial susceptibility by disk and gradient diffusion methods to determine the minimum inhibitory concentrations. The ability of the isolates to produce biofilm was investigated by a microtiter plate assay, while virulence genes coding for elastase (lasB), exotoxin A (toxA), alkaline protease (aprA), hemolytic phospholipase C (plcH), and exoenzyme S (ExoS) were detected by polymerase chain reaction method.

Results:

A total of 24 isolates of P. aeruginosa were found in clinical specimens (urine n=3, skin/soft tissue n=6, and ear canal n=15). No resistance was found to ceftazidime, gentamicin, aztreonam, and imipenem (IMI), while low levels of resistance were found to enrofloxacin (ENR) (4.2%) and piperacillin-tazobactam (8.3%). However, 41.7% and 29.2% of the isolates showed intermediate susceptibility to ENR and IMI, respectively. Disk and gradient diffusion methods showed high concordance. The majority of the isolates revealed a weak (33.3%) or intermediate (45.8%) ability to form biofilm, while the strong biofilm producers (20.8%) derived exclusively from the ear canal samples. All isolates (100%) were positive for lasB, aprA, and plcH genes, while exoS and toxA were amplified in 21 (87.5%) and 22 (91.7%) isolates, respectively.

Conclusion:

In the present study, P. aeruginosa isolates from canine clinical samples were characterized by low levels of antimicrobial resistance against antipseudomonal drugs. However, the high presence of isolates with intermediate susceptibility for some categories of antibiotics, including carbapenems which are not authorized for veterinary use, could represent an early warning signal. Moreover, the presence of isolates with strong ability to produce biofilm represents a challenge for the interpretation of the antimicrobial susceptibility profile. In addition, the high prevalence of the extracellular pathogenic factors was indicative of the potential virulence of the isolates.

Antimicrobial resistance and virulence of Pseudomonas spp. among healthy animals: concern about exolysin ExlA detection

Pseudomonas is a ubiquitous genus that also causes human, animal and plant diseases. Most studies have focused on clinical P. aeruginosa strains from humans, but they are scarce on animal strains. This study was aimed to determine the occurrence of Pseudomonas spp. among faecal samples of healthy animals, and to analyse their antimicrobial resistance, and pathogenicity. Among 704 animal faecal samples analysed, 133 Pseudomonas spp. isolates (23 species) were recovered from 46 samples (6.5%), and classified in 75 different PFGE patterns. Low antimicrobial resistance levels were found, being the highest to aztreonam (50.3%). Five sequence-types (ST1648, ST1711, ST2096, ST2194, ST2252), two serotypes (O:3, O:6), and three virulotypes (analysing 15 virulence and quorum-sensing genes) were observed among the 9 P. aeruginosa strains. Type-3-Secretion System genes were absent in the six O:3-serotype strains that additionally showed high cytotoxicity and produced higher biofilm biomass, phenazine pigments and motility than PAO1 control strain. In these six strains, the exlAB locus, and other virulence genotypes (e.g. RGP69 pathogenicity island) exclusive of PA7 outliers were detected by whole genome sequencing. This is the first description of the presence of the ExlA exolysin in P. aeruginosa from healthy animals, highlighting their pathological importance.

ESKAPE Bacteria and Extended-Spectrum-β-Lactamase-Producing Escherichia coli Isolated from Wastewater and Process Water from German Poultry Slaughterhouses

The wastewater of livestock slaughterhouses is considered a source of antimicrobial-resistant bacteria with clinical relevance and may thus be important for their dissemination into the environment. To get an overview of their occurrence and characteristics, we investigated process water (n = 50) from delivery and unclean areas as well as wastewater (n = 32) from the in-house wastewater treatment plants (WWTPs) of two German poultry slaughterhouses (slaughterhouses S1 and S2). The samples were screened for ESKAPE bacteria (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp.) and Escherichia coli Their antimicrobial resistance phenotypes and the presence of extended-spectrum-β-lactamase (ESBL), carbapenemase, and mobilizable colistin resistance genes were determined. Selected ESKAPE bacteria were epidemiologically classified using different molecular typing techniques. At least one of the target species was detected in 87.5% (n = 28/32) of the wastewater samples and 86.0% (n = 43/50) of the process water samples. The vast majority of the recovered isolates (94.9%, n = 448/472) was represented by E. coli (39.4%), the A. calcoaceticus-A. baumannii (ACB) complex (32.4%), S. aureus (12.3%), and K. pneumoniae (10.8%), which were widely distributed in the delivery and unclean areas of the individual slaughterhouses, including their wastewater effluents. Enterobacter spp., Enterococcus spp., and P. aeruginosa were less abundant and made up 5.1% of the isolates. Phenotypic and genotypic analyses revealed that the recovered isolates exhibited diverse resistance phenotypes and β-lactamase genes. In conclusion, wastewater effluents from the investigated poultry slaughterhouses exhibited clinically relevant bacteria (E. coli, methicillin-resistant S. aureus, K. pneumoniae, and species of the ACB and Enterobacter cloacae complexes) that contribute to the dissemination of clinically relevant resistances (i.e., blaCTX-M or blaSHV and mcr-1) in the environment.IMPORTANCE Bacteria from livestock may be opportunistic pathogens and carriers of clinically relevant resistance genes, as many antimicrobials are used in both veterinary and human medicine. They may be released into the environment from wastewater treatment plants (WWTPs), which are influenced by wastewater from slaughterhouses, thereby endangering public health. Moreover, process water that accumulates during the slaughtering of poultry is an important reservoir for livestock-associated multidrug-resistant bacteria and may serve as a vector of transmission to occupationally exposed slaughterhouse employees. Mitigation solutions aimed at the reduction of the bacterial discharge into the production water circuit as well as interventions against their further transmission and dissemination need to be elaborated. Furthermore, the efficacy of in-house WWTPs needs to be questioned. Reliable data on the occurrence and diversity of clinically relevant bacteria within the slaughtering production chain and in the WWTP effluents in Germany will help to assess their impact on public and environmental health.

Molecular Characteristics of GES-Type Carbapenemase-Producing Pseudomonas aeruginosa Clinical Isolates from Long-Term Care Facilities and General Hospitals in South Korea

Since carbapenems have been used for the treatment of infections in medical settings, multidrug-resistant Pseudomonas aeruginosa containing resistance for carbapenems has become a major cause of nosocomial infections worldwide. Information on carbapenemase-producing P. aeruginosa isolates at community hospitals, including long-term care facilities and general hospitals, has rarely been reported in South Korea. The aims of this study were to describe the characteristics of seven carbapenemase-producing P. aeruginosa isolates recovered from two long-term care facilities in South Korea. The carbapenemase genes were identified by PCR and sequencing. Strain typing was assessed by pulsed field gel electrophoresis and multilocus sequence typing (MLST) analysis. Isolates with a genomic island and class I integron surrounding bla_GES-type were confirmed by the PCR mapping method. Of seven GES-type carbapenemase-producing P. aeruginosa isolates, the bla_GES-24 gene was detected in six isolates, and the bla_GES-5 gene was detected in one isolate. The epidemiological relatedness of the seven isolates carrying bla_GES-24 and bla_GES-5 showed >81% similarity. Five isolates carrying bla_GES-24 were sequence type 155 (ST155) by MLST, followed by one ST244 isolate carrying bla_GES-24 and one ST308 isolate carrying bla_GES-5. bla_GES-type genes were embedded in two different class I integrons in a genomic island-15-like region. Our results indicate the possible spread of carbapenemase-producing P. aeruginosa and present a current threat of antimicrobial resistance in community hospitals.

Carbapenem-resistant Pseudomonas Aeruginosa Originating from Farm Animals and People in Egypt

Introduction

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) has become the leading cause of health care-associated infections. Treatment is difficult due to the lack of an effective antimicrobial therapy, and mortality is high. This study investigated the occurrence of CRPA in farm animals (buffaloes and cattle), livestock drinking water, and humans in Egypt.

Material and Methods

A total of 180 samples were examined: 50 faecal each from buffaloes and cattle, 30 of livestock drinking water, and 50 stool from humans. The samples were cultured on cetrimide agar and the plates were incubated aerobically at 37°C for 24 h. The isolates were examined for the presence of the bla_KPC, bla_OXA-48, and bla_NDM carbapenemase-encoding genes using PCR and investigated for the exotoxin A (toxA) gene. The toxA gene from carbapenem- group resistant isolates was phylogenetically analysed.

Results

P. aeruginosa was isolated from buffaloes, cattle, drinking water, and humans, with occurrences of 40%, 34%, 10%, and 20%, respectively. Carbapenem resistance genes were found in 60%, 59%, 67%, and 70% in buffalo, cattle, water and human samples, respectively. The toxA gene was detected in 80% of samples. The phylogenetic analysis showed that cattle and water sequences were in one cluster and more related to each other than to human isolates.

Conclusion

Occurrence of CRPA among farm animals, drinking water, and humans was high, reflecting the environmental origin of P. aeruginosa and highlighting contaminated water as a potential transmitter of CRPA to livestock and next to humans.

Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes

Pseudomonas aeruginosa is a highly versatile, antibiotic-resistant Gram-negative bacterium known for causing opportunistic infections and contamination of industrial products. Despite extensive genomic analysis of clinical P. aeruginosa strains, no genomes exist for preservative-tolerant industrial strains. A unique collection of 69 industrial isolates was assembled and compared to clinical and environmental strains; 16 genetically distinct industrial strains were subjected to array tube genotyping, multilocus sequence typing and whole-genome sequencing. The industrial strains possessed high preservative tolerance and were dispersed widely across P. aeruginosa as a species, but recurrence of strains from the same lineage within specific industrial products and locations was identified. The industrial P. aeruginosa genomes (mean=7.0 Mb) were significantly larger than those of previously sequenced environmental (mean=6.5 Mb; n=19) and clinical (mean=6.6 Mb; n=66) strains. Complete sequencing of the P. aeruginosa industrial strain RW109, which encoded the largest genome (7.75 Mb), revealed a multireplicon structure including a megaplasmid (555 265 bp) and large plasmid (151 612 bp). The RW109 megaplasmid represented an emerging plasmid family conserved in seven industrial and two clinical P. aeruginosa strains, and associated with extremely stress-resilient phenotypes, including antimicrobial resistance and solvent tolerance. Here, by defining the detailed phylogenomics of P. aeruginosa industrial strains, we show that they uniquely possess multireplicon, megaplasmid-bearing genomes, and significantly greater genomic content worthy of further study.

Antimicrobial resistance in bacteria isolated from diseased horses in France

BACKGROUND

Horses are one of the potential reservoirs of antimicrobial resistance (AMR) determinants that could be transferred to human subjects.

OBJECTIVE

To describe the AMR patterns of major bacteria isolated from diseased horses in France.

STUDY DESIGN

Retrospective observational study.

METHODS

Data collected between 2012 and 2016 by RESAPATH, the French national surveillance network for AMR, were analysed. Only antimicrobials relevant in veterinary and human medicine for the isolated bacteria were considered. Mono- and multidrug resistance were calculated. The resistance proportions of major equine diseases were assessed and compared. Where data permitted, resistance trends were investigated using nonlinear analysis (generalised additive models).

RESULTS

A total of 12,695 antibiograms were analysed. The five most frequently isolated bacteria were Streptococcus spp., Escherichia coli, Pseudomonas spp., Staphylococcus aureus, Pantoea spp. and Klebsiella spp. The highest proportions of resistance to gentamicin were found for S. aureus (22.1%) and Pseudomonas spp. (26.9%). Klebsiella spp. and E. coli had the highest proportions of resistance to trimethoprim-sulfamethoxazole (15.5 and 26.2%, respectively). Proportions of resistance to tetracycline were among the highest for all the bacteria considered. Resistance to third-generation cephalosporins was below 10% for all Enterobacteriaceae. The highest proportions of multidrug resistance (22.5%) were found among S. aureus isolates, which is worrying given their zoonotic potential. From 2012 to 2016, resistance proportions decreased in Pseudomonas spp. isolates, but remained the same for S. aureus. For Streptococcus spp. and E. coli, resistance proportions to trimethoprim-sulfamethoxazole increased.

MAIN LIMITATIONS

Since antibiograms are not systematic analyses, any selection bias could impact the results.

CONCLUSIONS

Such studies are essential to estimate the magnitude of the potential threat of AMR to public health, to design efficient control strategies and to measure their effectiveness. These findings may also guide the initial empirical treatment of horse diseases.

Cultivable microbiota and pulmonary lesions in polymicrobial bovine pneumonia

In the present study, the spectrum of bacterial pathogens in the nasal shedding during disease process and in pneumonic lungs of dead animals was studied. A total of 288 clinical samples from cattle and buffaloes comprising of nasal swabs, blood, tracheal swabs, heart blood and lung tissue samples were collected from diseased (n = 190) and dead animals (n = 98). The recovered bacterial isolates were characterized by biochemical reactions, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI TOF-MS) and the 16S rRNA sequence analysis. The predominant bacterial isolates associated were Pasteurella multocida, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus. The emerging pathogens causing bovine pneumonia identified were Leclercia spp., Stenotrophononas maltophila and Staphylococcus sciuri. Bacteriological examination of pneumonic lungs samples revealed 96.9% samples to be positive for polymicrobial isolation. Macroscopical lesions of lungs exhibited various stages and types of pneumonia with variable degree of haemorrhages, oedema and emphysema. Histopathologically, the fibrinous bronchopneumonia was observed to be the most frequent lesions seen in bovine pneumonia. Multi-drug resistance (MDR) was observed in 10% of P. multocida isolates. The resistance was seen for penicillin, cephalosporins and fluoroquinolones. Multi-drug resistance was seen in 90% of the E.coli tested. K. pneumoniae, E. hormaechei, E. cloacae, P. putida and Leclercia spp. identified were found to be multi-drug resistant. Understanding the etiological diversity of bacterial pathogens of bovine pneumonia may provide information for the better choice of therapeutics and health management.

Epidemiology and molecular characterization of the antimicrobial resistance of Pseudomonas aeruginosa in Chinese mink infected by hemorrhagic pneumonia

Hemorrhagic pneumonia in mink is a fatal disease caused by Pseudomonas aeruginosa. Very little is known about P. aeruginosa in relation to genotype and the mechanisms underlying antimicrobial resistance in mink. A total of 110 P. aeruginosa samples were collected from mink from Chinese mink farms between 2007 and 2015. Samples underwent molecular genotyping using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST), antimicrobial susceptibility and its mechanism were investigated at the molecular level. The PFGE identified 73 unique types and 15 clusters, while MLST identified 43 (7 new) sequence types (ST) and 12 sequence type clonal complexes (STCC). Sequence types and PFGE showed persistence of endemic clones in cities Wendeng (Shandong, China) and Dalian (Liaoning, China), even in different timelines. The MLST also revealed the gene correlation of the mink P. aeruginosa across different time and place. The ST1058 (n = 14), ST882 (n = 11), and ST2442 (n = 10) were the predominant types, among which ST1058 was the only one found both in Shandong province and Dalian (Liaoning, China). The MLST for P. aeruginosa infection in mink was highly associated with that in humans and other animals, implying possible transmission events. A small proportion of mink exhibited drug resistance to P. aeruginosa (9/69, 13%) with resistance predominantly to fluoroquinolone, aminoglycoside, and β-lactamase. Eight strains had mutations in the quinolone-resistance determining regions (QRDR). High proportions (65%; 72/110) of the fosA gene and 2 types of glpt deletion for fosmycin were detected. Furthermore, in the whole genome sequence of one multidrug resistant strain, we identified 27 genes that conferred resistance to 14 types of drugs.

Biofilm-forming ability and infection potential of Pseudomonas aeruginosa strains isolated from animals and humans

Pseudomonas aeruginosa has been amongst the top 10 'superbugs' worldwide and is causing infections with poor outcomes in both humans and animals. From 202 P. aeruginosa isolates (n = 121 animal and n = 81 human), 40 were selected on the basis of biofilm-forming ability and were comparatively characterized in terms of virulence determinants to the type strain P. aeruginosa PAO1. Biofilm formation, pyocyanin and hemolysin production, and bacterial motility patterns were compared with the ability to kill human cell line A549 in vitro. On average, there was no significant difference between levels of animal and human cytotoxicity, while human isolates produced higher amounts of pyocyanin, hemolysins and showed increased swimming ability. Non-parametric statistical analysis identified the highest positive correlation between hemolysis and the swarming ability. For the first time an ensemble machine learning approach used on the in vitro virulence data determined the highest relative predictive importance of the submerged biofilm formation for the cytotoxicity, as an indicator of the infection ability. The findings from the in vitro study were validated in vivo using zebrafish (Danio rerio) embryos. This study highlighted no major differences between P. aeruginosa species isolated from animal and human infections and the importance of pyocyanin production in cytotoxicity and infection ability.

Pseudomonas aeruginosa Isolates from Spanish Children: Occurrence in Faecal Samples, Antimicrobial Resistance, Virulence, and Molecular Typing

Pseudomonas aeruginosa is a major opportunistic human pathogen, responsible for nosocomial infections and infections in patients with impaired immune systems. Little data exist about the faecal colonisation by P. aeruginosa isolates in healthy humans. The occurrence, antimicrobial resistance phenotype, virulence genotype, and genetic lineages of P. aeruginosa from faecal samples of children from two different Spanish regions were characterised. Seventy-two P. aeruginosa were isolated from 1,443 faecal samples. Low antimicrobial resistance levels were detected: ceftazidime (8%), cefepime (7%), aztreonam (7%), gentamicin (3%), ciprofloxacin (1%), and imipenem (1%); susceptibility to meropenem, amikacin, tobramycin, levofloxacin, and colistin. Four multidrug-resistant strains were found. Important differences were detected between both geographical regions. Forty-one sequence types were detected among the 48 tested strains. Virulence and quorum sensing genes were analysed and 13 virulotypes were detected, being 26 exoU-positive strains. Alteration in protein OprD showed eight different patterns. The unique imipenem-resistant strain showed a premature stop codon in OprD. Intestinal colonisation by P. aeruginosa, mainly by international clones (as ST244, ST253, and ST274), is an important factor for the systemic infections development and the environmental dissemination. Periodic active surveillance is useful to identify these community human reservoirs and to control the evolution of antibiotic resistance and virulence activity.

Antimicrobial Resistance in Acinetobacter spp. and Pseudomonas spp

The nonfermenting bacteria belonging to Acinetobacter spp. and Pseudomonas spp. are capable of colonizing both humans and animals and can also be opportunistic pathogens. More specifically, the species Acinetobacter baumannii and Pseudomonas aeruginosa have been recurrently reported as multidrug-resistant and even pandrug-resistant in clinical isolates. Both species were categorized among the ESKAPE pathogens, ESKAPE standing for Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , A. baumannii , P. aeruginosa , and Enterobacter species. These six pathogens are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. A. baumannii and P. aeruginosa are both intrinsically resistant to many antibiotics due to complementary mechanisms, the main ones being the low permeability of their outer membrane, the production of the AmpC beta-lactamase, and the production of several efflux systems belonging to the resistance-nodulation-cell division family. In addition, they are both capable of acquiring multiple resistance determinants, such as beta-lactamases or carbapenemases. Even if such enzymes have rarely been identified in bacteria of animal origin, they may sooner or later spread to this reservoir. The goal of this article is to give an overview of the resistance phenotypes described in these pathogens and to provide a comprehensive analysis of all data that have been reported on Acinetobacter spp. and Pseudomonas spp. from animal hosts.

Pseudomonas aeruginosa variants obtained from veterinary clinical samples reveal a role for cyclic di-GMP in biofilm formation and colony morphology

Overuse of antibiotics is contributing to an emerging antimicrobial resistance crisis. To better understand how bacteria adapt tolerance and resist antibiotic treatment, Pseudomonas aeruginosa isolates obtained from infection sites sampled from companion animals were collected and evaluated for phenotypic differences. Selected pairs of clonal isolates were obtained from individual infection samples and were assessed for antibiotic susceptibility, cyclic di-GMP levels, biofilm production, motility and genetic-relatedness. A total of 18 samples from equine, feline and canine origin were characterized. A sample from canine otitis media produced a phenotypically heterogeneous pair of P. aeruginosa isolates, 42121A and 42121B, which during growth on culture medium respectively exhibited hyper dye-binding small colony morphology and wild-type phenotypes. Antibiotic susceptibility to gentamicin and ciprofloxacin also differed between this pair of clonal isolates. Sequence analysis of gyrA, a gene known to be involved in ciprofloxacin resistance, indicated that 42121A and 42121B both contained mutations that confer ciprofloxacin resistance, but this did not explain the differences in ciprofloxacin resistance that were observed. Cyclic di-GMP levels also varied between this pair of isolates and were shown to contribute to the observed colony morphology variation and ability to form a biofilm. Our results demonstrate the role of cyclic di-GMP in generating the observed morphological phenotypes that are known to contribute to biofilm-mediated antibiotic tolerance. The generation of phenotypic diversity may go unnoticed during standard diagnostic evaluation, which potentially impacts the therapeutic strategy chosen to treat the corresponding infection and may contribute to the spread of antibiotic resistance.

Resistance of Animal Strains of Pseudomonas aeruginosa to Carbapenems

Carbapenems are major antibiotics reserved to human medicine. This study aimed to investigate the mechanisms of carbapenem resistance of a selection of Pseudomonas aeruginosa veterinary strains from the French network Resapath. Thirty (5.7%) imipenem and/or meropenem non-susceptible P. aeruginosa of canine (n = 24), feline (n = 5), or bovine (n = 1) origin were identified in a large collection of 527 veterinary strains gathered by the Resapath. These resistant isolates belonged to 25 MultiLocus Sequence Types (MLST), of which 17 (68%) are shared with clinical (human) strains, such as high risk clones ST233 and ST395. Interestingly, none of the veterinary strains produced a carbapenemase, and only six of them (20%) harbored deletions or insertion sequence (IS) disrupting the porin OprD gene. The remaining 24 strains contained mutations or IS in various loci resulting in down-regulation of gene oprD coupled with upregulation of efflux system CzcCBA (n = 3; activation of sensor kinase CzcS ± CopS), MexEF-OprN (n = 4; alteration of oxido reductase MexS), MexXY (n = 8; activation of two-component system ParRS), or MexAB-OprM (n = 12; alteration of regulator MexR, NalC ± NalD). Two efflux pumps were co-produced simultaneously in three mutants. Finally, in 11 out of 12 strains displaying an intact porin OprD, derepression of MexAB-OprM accounted for a decreased susceptibility to meropenem relative to imipenem. Though not treated by carbapenems, animals thus represent a reservoir of multidrug resistant P. aeruginosa strains potentially able to contaminate fragile outpatients.

Bacteria from Animals as a Pool of Antimicrobial Resistance Genes

Antimicrobial agents are used in both veterinary and human medicine. The intensive use of antimicrobials in animals may promote the fixation of antimicrobial resistance genes in bacteria, which may be zoonotic or capable to transfer these genes to human-adapted pathogens or to human gut microbiota via direct contact, food or the environment. This review summarizes the current knowledge of the use of antimicrobial agents in animal health and explores the role of bacteria from animals as a pool of antimicrobial resistance genes for human bacteria. This review focused in relevant examples within the ESC(K)APE (Enterococcus faecium, Staphylococcus aureus, Clostridium difficile (Klebsiella pneumoniae), Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae) group of bacterial pathogens that are the leading cause of nosocomial infections throughout the world.

Activity of AMP2041 against human and animal multidrug resistant Pseudomonas aeruginosa clinical isolates

Background

Antimicrobial resistance is a growing threat to public health. Pseudomonas aeruginosa is a relevant pathogen causing human and animal infections, frequently displaying high levels of resistance to commonly used antimicrobials. The increasing difficulty to develop new effective antibiotics have discouraged investment in this area and only a few new antibiotics are currently under development. An approach to overcome antibiotic resistance could be based on antimicrobial peptides since they offer advantages over currently used microbicides.

Methods

The antimicrobial activity of the synthetic peptide AMP2041 was evaluated against 49 P. aeruginosa clinical strains with high levels of antimicrobial resistance, isolated from humans (n = 19) and animals (n = 30). In vitro activity was evaluated by a microdilution assay for lethal dose 90% (LD₉₀), while the activity over time was performed by time-kill assay with 12.5 µg/ml of AMP2014. Evidences for a direct membrane damage were investigated on P. aeruginosa ATCC 27853 reference strain, on animal isolate PA-VET 38 and on human isolate PA-H 24 by propidium iodide and on P. aeruginosa ATCC 27853 by scanning electron microscopy.

Results

AMP2041 showed a dose-dependent activity, with a mean (SEM) LD₉₀ of 1.69 and 3.3 µg/ml for animal and human strains, respectively. AMP2041 showed microbicidal activity on P. aeruginosa isolates from a patient with cystic fibrosis (CF) and resistance increased from first infection isolate (LD₉₀ = 0.3 μg/ml) to the mucoid phenotype (LD₉₀ = 10.4 μg/ml). The time-kill assay showed a time-dependent bactericidal effect of AMP2041 and LD₉₀ was reached within 20 min for all the strains. The stain-dead assay showed an increasing of membrane permeabilization and SEM analysis revealed holes, dents and bursts throughout bacterial cell wall after 30 min of incubation with AMP2041.

Conclusions

The obtained results assessed for the first time the good antimicrobial activity of AMP2041 on P. aeruginosa strains of human origin, including those deriving from a CF patient. We confirmed the excellent antimicrobial activity of AMP2041 on P. aeruginosa strains derived from dog otitis. We also assessed that AMP2041 antimicrobial activity is linked to changes of the P. aeruginosa cell wall morphology and to the increasing of membrane permeability.

Antimicrobial resistance and genomic rep-PCR fingerprints of Pseudomonas aeruginosa strains from animals on the background of the global population structure

Background

Pseudomonas aeruginosa is an important human opportunistic pathogen responsible for fatal nosocomial infections worldwide, and has emerged as a relevant animal pathogen. Treatment options are dramatically decreasing, due to antimicrobial resistance and the microorganism’s large versatile genome.

Antimicrobial resistance profiles, serotype frequency and genomic profile of unrelated P. aeruginosa isolates of veterinary origin (n = 73), including domesticated, farm, zoo and wild animals mainly from Portugal were studied. The genomic profile, determined by DiversiLab system (Rep-PCR-based technique), was compared with the P. aeruginosa global population structure to evaluate their relatedness.

Results

Around 40% of the isolates expressed serotypes O6 (20.5%) and O1 (17.8%). A total of 46.6% of isolates was susceptible to all antimicrobials tested. Isolates obtained from most animals were non-multidrug resistant (86.3%), whereas 11% were multidrug resistant, MDR (non-susceptible to at least one agent in ≥ three antimicrobial categories), and 2.7% extensively drug resistant, XDR (non-susceptible to at least one agent in all but two or fewer antimicrobial categories). Resistance percentages were as follows: amikacin (0.0%), aztreonam (41.1%), cefepime (9.6%), ceftazidime (2.7%), ciprofloxacin (15.1%), colistin (0.0%), gentamicin (12.3%), imipenem (1.4%), meropenem (1.4%), piperacillin + tazobactam (12.3%), ticarcillin (16.4%), ticarcillin + clavulanic acid (17.8%), and tobramycin (1.4%).

Animal isolates form a population with a non-clonal epidemic structure indistinguishable from the global P. aeruginosa population structure, where no specific ‘animal clonal lineage’ was detected.

Conclusions

Serotypes O6 and O1 were the most frequent. Serotype frequency and antimicrobial resistance patterns found in P. aeruginosa from animals were as expected for this species. This study confirms earlier results that P. aeruginosa has a non-clonal population structure, and shows that P. aeruginosa population from animals is homogeneously scattered and indistinguishable from the global population structure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-0977-8) contains supplementary material, which is available to authorized users.

Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing

As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin–antitoxin (T–A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.

Antibiotic susceptibility pattern and analysis of plasmid profiles of Pseudomonas aeruginosa from human, animal and plant sources

Multidrug resistant organisms (MDROs) constitute a major public health threat globally. Clinical isolates of Pseudomonas aeruginosa remains one of the most studied MDROs however there is paucity of information regarding the susceptibility of its animal and plants isolates to antipseudomonas drug in Nigeria. From a total of 252 samples consisting of plants, animals and clinical samples, 54, 24 and 22 P. aeruginosa were isolated from vegetables, animals and clinical sources respectively. All the isolates were identified by standard biochemical methods. Antimicrobial susceptibility testing (AST) of the 100 P. aeruginosa isolates against 7 antipseudomonal drugs was carried out by disk diffusion method, the phenotypic detection of ESBL was done by double disk synergy test (DDST) while plasmid extraction on 20 selected isolates based on their resistance to 2 or more classes of antibiotics was carried out by alkaline lysis method and analysed with Lambda DNA/Hind lll marker respectively. The AST results revealed highest resistance of 91 and 55 % to ceftazidime and carbenicillin respectively while highest susceptibilities of 99 % for piperacillin–tazobactam and imipenem were recorded in overall assay. Fifteen out of 100 isolates specifically (10) from vegetables, (3) clinical and (2) poultry isolates showed synergy towards the beta-lactamase inhibitor indicating production of ESBL by DDST method. Detection of plasmids was among vegetable (n = 4), poultry (n = 4), cow (n = 3) and clinical isolates (n = 1). Plasmid profile for the selected isolates revealed 6 of the strains had one plasmids each while 5 strains possessed 2–4 plasmids and 1 strain had 5 plasmids. The sizes of the plasmid range from <1 to ≥23kbp. Detection of ESBL and Plasmids among the investigated isolates is suggestive of multiple interplay of resistance mechanism among the isolates. Plants and animal isolates of P. aeruginosa harbouring multiple mechanisms of resistance is of concern due to the danger it poses on the public health.

Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection

We report the 6,498,072-bp complete genome sequence of Pseudomonas aeruginosa PA1, which was isolated from a patient with a respiratory tract infection in Chongqing, People's Republic of China. Whole-genome sequencing was performed using single-molecule real-time (SMRT) technology, and de novo assembly revealed a single contig with 396-fold sequence coverage.