Distinct Biotypes Research Articles

Biotypes of functional brain engagement during emotion processing differentiate heterogeneity in internalizing symptoms and interpersonal violence histories among adolescent girls

Youth exposed to early life interpersonal violence (IPV) demonstrate heterogeneous clinical symptoms. Studies based on univariate methods suggest that neurocircuitry related to emotion processing explains heterogeneity in internalizing symptoms. Here, we use a multivariate, data-driven method of identifying distinct functional brain activation profiles (i.e., “biotypes”) and test whether these biotypes differentiate internalizing symptoms among IPV-exposed youth. 114 adolescent girls (n = 38 with no IPV exposure or psychopathology; n = 76 with IPV exposure and heterogeneous internalizing symptoms), aged 11–17, completed an emotion processing task during fMRI. To identify distinct biotypes of brain engagement profiles, data-driven clustering analysis was applied to patterns of voxel activation, constrained within a mask of distributed regions implicated in emotion processing. Resulting biotypes (BT1-3) were compared on measures of IPV exposure and internalizing symptoms, as well as symptom reduction during Trauma-Focused Cognitive Behavioral Therapy (TF-CBT) among a subset of participants (n = 21). Cluster analyses identified three biotypes, differentiated by engagement of medial prefrontal, anterior insula, hippocampus, parietal, and ventral visual cortex during emotion processing. BT1 exhibited low levels of IPV exposure and internalizing symptoms. BT2 exhibited elevated levels of IPV, except sexual assault, and demonstrated moderate severity across internalizing symptom domains. BT3 exhibited elevated severity across all IPV and internalizing symptom domains. Greater symptom reduction during TF-CBT was associated with increased pre-to post-treatment changes in similarity with BT1. These results demonstrate distinct profiles of emotion processing neurocircuitry that differentiate heterogeneity in internalizing symptoms in IPV-exposed adolescent girls.

Genetic variation and possible origins of weedy rice found in California.

Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.

DNA-aided identification of Culex mosquitoes (Diptera: Culicidae) reveals unexpected diversity in underground cavities in Austria

Subterranean cavities serve as resting places and hibernation shelters for mosquitoes. In Europe, members of the genus Culex are often the most abundant insects on cave walls. Culex pipiens L., the common house mosquito, exists in two physically very similar, yet genetically and ecologically distinct biotypes (or forms, ‘f.’), namely Cx. pipiens f. pipiens and Cx. pipiens f. molestus. Autogeny and stenogamy of the latter form have been interpreted as adaptations to underground habitats. The epigean occurrence of the two biotypes and their hybrids was recently examined in Eastern Austria, but the hypogean distribution of the Cx. pipiens complex and morphologically similar non-members such as Cx. torrentium is unknown. Considering the key role of Culex mosquitoes in the epidemiology of certain zoonotic pathogens, the general paucity of data on species composition and relative abundance in subterranean shelters appears unfortunate.For a first pertinent investigation in Austria, we collected mosquitoes in four eastern federal states. Based on analyses of the ACE2 gene and the CQ11 microsatellite locus, 150 female and three male mosquitoes of the genus Culex, two females of the genus Culiseta and a single female of the genus Anopheles were determined to species level or below. In our catches, Cx. pipiens f. pipiens exceeded the apparent abundance of the purportedly cave-adapted Cx. pipiens f. molestus many times over. Records of Cx. hortensis and Cx. territans, two species rarely collected in Austria, lead us to infer that underground habitats host a higher diversity of culicine mosquitoes than previously thought.

Adaptive Identification of Cortical and Subcortical Imaging Markers of Early Life Stress and Posttraumatic Stress Disorder.

Posttraumatic stress disorder (PTSD) is a heterogeneous condition associated with a range of brain imaging abnormalities. Early life stress (ELS) contributes to this heterogeneity, but we do not know how a history of ELS influences traditionally defined brain signatures of PTSD. Here, we used a novel machine learning method - evolving partitions to improve classification (EPIC) - to identify shared and unique structural neuroimaging markers of ELS and PTSD in 97 combat-exposed military veterans. We used EPIC with repeated cross-validation (CV) to determine how combinations of cortical thickness, surface area, and subcortical brain volumes could contribute to classification of PTSD (n=40) versus controls (n=57), and classification of ELS within the PTSD (ELS+ n=16; ELS- n=24) and control groups (ELS+ n=16; ELS- n=41). Additional inputs included intracranial volume, age, sex, adult trauma, and depression. On average, EPIC classified PTSD with 69% accuracy (SD=5%), and ELS with 64% accuracy in the PTSD group (SD=10%), and 62% accuracy in controls (SD=6%). EPIC selected unique sets of individual features that classified each group with 75-85% accuracy in post hoc analyses; combinations of regions marginally improved classification from the individual atlas-defined brain regions. Across analyses, surface area in the right posterior cingulate was the only variable that was repeatedly selected as an important feature for classification of PTSD and ELS. EPIC revealed unique patterns of features that distinguished PTSD and ELS in this sample of combat-exposed military veterans, which may represent distinct biotypes of stress-related neuropathology.

Addressing heterogeneity (and homogeneity) in treatment mechanisms in depression and the potential to develop diagnostic and predictive biomarkers.

It has been 10 years since machine learning was first applied to neuroimaging data in psychiatric disorders to identify diagnostic and prognostic markers at the level of the individual. Proof of concept findings in major depression have since been extended in international samples and are beginning to include hundreds of samples from multisite data. Neuroimaging provides the unique capability to detect an acute depressive state in major depression, while we would not expect perfect classification with current diagnostic criteria which are based solely on clinical features. We review developments and the potential impact of heterogeneity, as well as homogeneity, on classification for diagnosis and prediction of clinical outcome. It is likely that there are distinct biotypes which comprise the disorder and which predict clinical outcome. Neuroimaging-based biotypes could aid in identifying the illness in individuals who are unable to recognise their illness and perhaps to identify the treatment resistant form early in the course of the illness. We propose that heterogeneous symptom profiles can arise from a limited number of neural biotypes and that apparently heterogeneous clinical outcomes include a common baseline predictor and common mechanism of treatment. Baseline predictors of clinical outcome reflect factors which indicate the general likelihood of response as well as those which are selective for a particular form of treatment. Irrespective of the mechanism, the capacity for response will moderate the outcome, which includes inherent models of interpersonal relationships that could be associated with genetic risk load and represented by patterns of functional and structural neural correlates as a predictive biomarker. We propose that methods which directly address heterogeneity are essential and that a synergistic combination could bring together data-driven inductive and symptom-based deductive approaches. Through this iterative process, major depression can develop from being syndrome characterized by a collection of symptoms to a disease with an identifiable pathophysiology.

Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells

ABSTRACTLong non-coding RNAs have emerged as an important regulatory layer in biological systems. Of the various types of lncRNAs, one class (designated as divergent RNAs/XH), which is in head-to-head overlap with the coding genes, has emerged as a critical biotype that regulates development and cellular differentiation. This work aimed to analyze previously published data on differential expression, epigenetic and network analysis in order to demonstrate the association of divergent lncRNAs, a specific biotype with the differentiation of human neural progenitor cells (hNPCs). We have analyzed various available RNAseq databases that address the neuronal and astrocytic differentiation of hNPCs and identified differentially expressed lncRNAs (DELs) during cell-fate determination. Key DELs identified from the databases were experimentally verified by us in our in-vitro hNPC differentiation system. We also analyzed the change in promoter activity using ChIP-seq datasets of the histone markers H3K4me3 (activation) and H3K27me3 (inactivation) of these DELs. Additionally, we explored the change in the euchromatinization state of DELs (by analyzing DNase-seq data) during lineage-specific differentiation of hNPCs and performed their network analysis. We were able to identify differences between neuronal and astrocytic differentiation of hNPCs at the level of divergent DELs epigenetic markers, DNAase hypersensitive sites and gene expression network. Divergent lncRNAs are more involved in neuronal rather than astrocytic differentiation, while the sense downstream lncRNA biotype appears to be more involved in astrocytic differentiation. By studying the lncRNA involvement of distinct biotypes, we have been able to indicate the preferential role of a particular biotype during lineage-specific differentiation.

Differences in escape behavior between pea aphid biotypes reflect their host plants’ palatability to mammalian herbivores

Phytophagous insects have evolved traits that help them avoid predation risks, traits that may be affected by characteristics of the host plant. Since most phytophagous insects have narrow host ranges, we expect differences in risk avoidance between plant-specialized populations of several closely related insect lineages. To test this hypothesis, we used the pea aphid (Acyrthosiphon pisum), which forms a complex of about 15 biotypes, each adapted to one or a few species of legume plants (Fabaceae). We examined the differences in defensive behaviors of 38 clones from 13 distinct plant-specialized biotypes of pea aphids. We exposed mature aphids to simulated breath of a mammalian herbivore, a cue that causes part of the aphids in a colony to immediately drop off the plant to avoid incidental ingestion during mammal feeding. Dropping tendency varied substantially between biotypes (15–93% average rates). Dropping rates of a certain biotype of aphid reflected their host’s palatability to mammalian herbivores, with ∼80–90% rates in fodder and pasture plants and ∼15–40% dropping in inedible plants. The dropping tendency showed no correlation with walking ability (tarsal & body length), nor with the tendency to escape in response to the alarm pheromone released by conspecifics in response to arthropod enemies. The specialization on a specific host plant brings with it particular selective pressures, and it seems that the palatability of the plants to mammals promotes behavioral divergence between biotypes, reinforcing diversification through ecological divergence.

Attention Impairments and the 'Inattention Biotype' in Major Depressive Disorder

Background. Attention impairments are an under-investigated symptom and diagnostic criterion of Major Depressive Disorder (MDD) that predicts poorer prognoses. Despite the centrality of attention for a variety of critical cognitive functions, we lack a detailed characterization of attention impairments and their neural signatures in MDD patients. Methods. We advance a deep multi-modal characterization of selective attention impairments in MDD patients. Multi-modal data were acquired on 1008 MDD patients and 336 healthy controls who took part in a biomarker study known as the international Study to Predict Optimized Treatment for Depression (iSPOT-D), of whom of 15% also underwent functional magnetic resonance imaging (MRI). Our characterization is anchored in a behavioral marker of attention impairments, and validated by independent measures of neural circuit dysfunction (fMRI), oscillatory neural activity (EEG), and clinical symptom features. Outcomes. Our results show that attention impairments in MDD are associated with hypo-connectivity of the fronto-parietal attention network, particularly in females and older adults. These attention impairments are associated with decreased alpha (8-13 Hz) power at rest and are unrelated to insomnia, excessive worrying, or symptom severity. Interpretation. Attention impairments in MDD patients represent a distinct biotype of depressed individuals that is specific, cohesive, and observable across multiple units of analysis. These attention impairments are associated with circuit dysfunction in a canonical attention network as well as low oscillatory power in the alpha frequency band. Our results provide a target for the development of more precise therapeutics to address dysfunction in top-down attentional control. Funding: L.M.W was supported by a National Institutes of Health grants (R01MH101496 and UH2AG052163). A.S.K. is supported by the National Defense Science and Engineering Graduate (NDSEG) fellowship, the Stanford Center for Mind, Brain, and Computation (MBC) traineeship, and the Stanford Neurosciences PhD Program. T.M.B is supported by the National Institute of Mental Health (K23-MH113708). Declaration of Interest: Over the past three years L.M.W has scientific advisory board fees from Psyberguide of the One Mind Institute and consultancy from Humana and Blackthorn Therapeutics for projects not related to this work.

146. Diagnosis and Biotype Comparisons Across the Psychosis Spectrum: Investigating White Matter Microstructural Differences From the Bipolar-Schizophrenia Network on Intermediate Phenotypes (B-SNIP) Study Using Free-Water Imaging

In order to classify individuals across the psychosis spectrum, the B-SNIP consortium identified three neurobiologically distinct biotypes, independent of clinical phenomenology. To externally validate the Biotype model, we used free-water fractional volume (FW) and free-water corrected fractional anisotropy (FAT) to compare white matter differences across brain-based biotypes and clinical categorization.

Identification of Distinct Psychosis Biotypes Using Brain-Based Biomarkers.

(Reprinted with permission from American Journal of Psychiatry 2016; 173:373-384).

Brain-behavior patterns define a dimensional biotype in medication-naïve adults with attention-deficit hyperactivity disorder.

Childhood-onset attention-deficit hyperactivity disorder (ADHD) in adults is clinically heterogeneous and commonly presents with different patterns of cognitive deficits. It is unclear if this clinical heterogeneity expresses a dimensional or categorical difference in ADHD. We first studied differences in functional connectivity in multi-echo resting-state functional magnetic resonance imaging (rs-fMRI) acquired from 80 medication-naïve adults with ADHD and 123 matched healthy controls. We then used canonical correlation analysis (CCA) to identify latent relationships between symptoms and patterns of altered functional connectivity (dimensional biotype) in patients. Clustering methods were implemented to test if the individual associations between resting-state brain connectivity and symptoms reflected a non-overlapping categorical biotype. Adults with ADHD showed stronger functional connectivity compared to healthy controls, predominantly between the default-mode, cingulo-opercular and subcortical networks. CCA identified a single mode of brain-symptom co-variation, corresponding to an ADHD dimensional biotype. This dimensional biotype is characterized by a unique combination of altered connectivity correlating with symptoms of hyperactivity-impulsivity, inattention, and intelligence. Clustering analyses did not support the existence of distinct categorical biotypes of adult ADHD. Overall, our data advance a novel finding that the reduced functional segregation between default-mode and cognitive control networks supports a clinically important dimensional biotype of childhood-onset adult ADHD. Despite the heterogeneity of its presentation, our work suggests that childhood-onset adult ADHD is a single disorder characterized by dimensional brain-symptom mediators.

Gene Phenotypes: The Role Can't Be Ignored in Etiology of Dental Caries

Gene Phenotypes: The Role Can't Be Ignored in Etiology of Dental Caries

The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana.

Nearly half of child pneumonia deaths occur in sub-Saharan Africa. Microbial communities in the nasopharynx are a reservoir for pneumonia pathogens and remain poorly described in African children. Nasopharyngeal swabs were collected from children with pneumonia (N = 204), children with upper respiratory infection symptoms (N = 55) and healthy children (N = 60) in Botswana between April 2012 and April 2014. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used partitioning around medoids to cluster samples into microbiota biotypes. We then used multivariable logistic regression to examine whether microbiota biotypes were associated with pneumonia and upper respiratory infection symptoms. Mean ages of children with pneumonia, children with upper respiratory infection symptoms and healthy children were 8.2, 11.4 and 8.0 months, respectively. Clustering of nasopharyngeal microbiota identified 5 distinct biotypes: Corynebacterium/Dolosigranulum-dominant (23%), Haemophilus-dominant (11%), Moraxella-dominant (24%), Staphylococcus-dominant (13%) and Streptococcus-dominant (28%). The Haemophilus-dominant [odds ratio (OR): 13.55; 95% confidence interval (CI): 2.10-87.26], the Staphylococcus-dominant (OR: 8.27; 95% CI: 2.13-32.14) and the Streptococcus-dominant (OR: 39.97; 95% CI: 6.63-241.00) biotypes were associated with pneumonia. The Moraxella-dominant (OR: 3.71; 95% CI: 1.09-12.64) and Streptococcus-dominant (OR: 12.26; 95% CI: 1.81-83.06) biotypes were associated with upper respiratory infection symptoms. In children with pneumonia, HIV infection was associated with a lower relative abundance of Dolosigranulum (P = 0.03). Pneumonia and upper respiratory infection symptoms are associated with distinct nasopharyngeal microbiota biotypes in African children. A lower abundance of the commensal genus Dolosigranulum may contribute to the higher pneumonia risk of HIV-infected children.

Modelling West Nile virus transmission risk in Europe: effect of temperature and mosquito biotypes on the basic reproduction number

West Nile virus (WNV) is a mosquito-borne flavivirus which has caused repeated outbreaks in humans in southern and central Europe, but thus far not in northern Europe. The main mosquito vector for WNV, Culex pipiens, consists of two behaviourally distinct biotypes, pipiens and molestus, which can form hybrids. Differences between biotypes, such as vector competence and host preference, could be important in determining the risk of WNV outbreaks. Risks for WNV establishment can be modelled with basic reproduction number (R0) models. However, existing R0 models have not differentiated between biotypes. The aim of this study was, therefore, to explore the role of temperature-dependent and biotype-specific effects on the risk of WNV establishment in Europe. We developed an R0 model with temperature-dependent and biotype-specific parameters, and calculated R0 values using the next-generation matrix for several scenarios relevant for Europe. In addition, elasticity analysis was done to investigate the contribution of each biotype to R0. Global warming and increased mosquito-to-host ratios can possibly result in more intense WNV circulation in birds and spill-over to humans in northern Europe. Different contributions of the Cx. pipiens biotypes to R0 shows the importance of including biotype-specific parameters in models for reliable WNV risk assessments.

Iodometric and Molecular Detection of ESBL Production Among Clinical Isolates of E. coli Fingerprinted by ERIC-PCR: The First Egyptian Report Declares the Emergence of E. coli O25b-ST131clone Harboring blaGES.

The extensive use of β-lactam antibiotics has led to emergence and spread of extended-spectrum β-lactamases (ESBLs). This study was conducted to investigate the prevalence of 7 different ESBL genes (blaTEM, blaSHV, blaCTX-M, blaVEB, blaPER, blaGES, and blaOXA-10) and O25b-ST131 high-risk clone among 61 clinical isolates of Escherichia coli. Also, one broad-spectrum β-lactamase (blaOXA-1) was investigated. This study was also constructed to evaluate iodometric overlay method in detection of ESBL production. Phenotypic identification of E. coli isolates using API 20E revealed 18 distinct biotypes. DNA fingerprinting using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) differentiated all isolates into 2 main phylogenetic groups with 60 distinct genetic profiles. Elevated values of minimal inhibitory concentration (MIC)50 and MIC90 for third- and fourth-generation cephalosporins were observed. Phenotypic tests revealed that 85.24% of isolates were ESBL producers. The incidence rates of blaTEM, blaSHV, blaCTX-M, blaGES, blaOXA-1, and blaOXA-10 among E. coli ESBL producer phenotype were 69.23%, 25%, 96.15%, 3.85%, 11.54%, and 48%, respectively. On the other hand, blaVEB and blaPER were not detected. Sequencing of blaTEM and blaSHV revealed that blaTEM-214 and blaSHV-11 were the most prevalent variants. Group characterization of blaCTX-M revealed that blaCTX-M-1 was the most prevalent group of blaCTX-M family. It was found that 30.77% of E. coli ESBL producers belonged to O25b-ST131 clone harboring blaCTX-M-15. This study concluded that iodometric overlay method was 100% sensitive in detection of ESBL production. To our knowledge, this is the first Egyptian study that declares the emergence of E. coli O25b-ST131 harboring blaGES.

Vector competence of northern European Culex pipiens biotypes and hybrids for West Nile virus is differentially affected by temperature.

BackgroundOutbreaks of West Nile virus (WNV) have not occurred in northern Europe despite nearby circulation of WNV in the southern part of the continent. The main vector for WNV, the mosquito Culex (Cx.) pipiens, consists of two behaviorally distinct biotypes, pipiens and molestus, which can form hybrids. Although temperature has been shown to influence vector competence of Cx. pipiens for WNV and biotypes are differentially susceptible towards infection, the interaction between the two has not been elucidated.MethodsWe determined vector competence of the Cx. pipiens biotypes and hybrids, after 14 days of incubation at 18, 23 and 28 °C. Mosquitoes were orally infected by providing an infectious blood meal or by injecting WNV directly in the thorax. Infection and transmission rates were determined by testing the bodies and saliva for WNV presence. In addition, titers of mosquitoes with WNV-positive bodies and saliva samples were determined.ResultsOrally infected biotype pipiens and hybrids showed significantly increased transmission rates with higher temperatures, up to 32 and 14 %, respectively. In contrast, the molestus biotype had an overall transmission rate of 10 %, which did not increase with temperature. All mosquitoes that were infected via WNV injections had (close to) 100 % infection and transmission rates, suggesting an important role of the mosquito midgut barrier. We found no effect of increasing temperature on viral titers.ConclusionsTemperature differentially affected vector competence of the Cx. pipiens biotypes. This shows the importance of accounting for biotype-by-temperature interactions, which influence the outcomes of vector competence studies. Vector competence studies with Cx. pipiens mosquitoes differentiated to the biotype level are essential for proper WNV risk assessments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-016-1677-0) contains supplementary material, which is available to authorized users.

Reproduction and Population Dynamics as Biotypic Markers of Russian Wheat Aphid Diuraphis noxia (Kurdjumov).

Russian wheat aphid Diuraphis noxia (Kurdjumov) is widely established in wheat-growing countries where it causes significant economic losses. The development and use of Russian wheat aphid (RWA)-resistant wheat varieties has been constrained by the variation in resident RWA populations and the evolution of virulent biotypes. An experiment was set up at the Kenya Agricultural and Livestock Research Organization (KALRO), Njoro, to characterize RWA populations based on phenotypic characteristics of reproduction, development and population dynamics. RWA populations from the regions of Eldoret, Mau Narok and Njoro were used in the study. A factorial experiment was set up in randomized complete block design replicated eleven times. A single day-old nymph was placed on a new, fully-open leaf in a 0.5 cm-diameter clear plastic straw leaf cage and observed daily for its entire lifetime. The results showed that there were variations in aphid lifespan, reproductive longevity and aphid fecundity between populations, indicating that the phenotypic markers used to determine biotypes were good enough to show distinct biotypes among populations of the RWA in Kenya. Further, the study concluded that the use of phenotypic life and reproductive markers was a valid way of characterizing biotypes of RWA worldwide.

Identification of Distinct Psychosis Biotypes Using Brain-Based Biomarkers.

Clinical phenomenology remains the primary means for classifying psychoses despite considerable evidence that this method incompletely captures biologically meaningful differentiations. Rather than relying on clinical diagnoses as the gold standard, this project drew on neurobiological heterogeneity among psychosis cases to delineate subgroups independent of their phenomenological manifestations. A large biomarker panel (neuropsychological, stop signal, saccadic control, and auditory stimulation paradigms) characterizing diverse aspects of brain function was collected on individuals with schizophrenia, schizoaffective disorder, and bipolar disorder with psychosis (N=711), their first-degree relatives (N=883), and demographically comparable healthy subjects (N=278). Biomarker variance across paradigms was exploited to create nine integrated variables that were used to capture neurobiological variance among the psychosis cases. Data on external validating measures (social functioning, structural magnetic resonance imaging, family biomarkers, and clinical information) were collected. Multivariate taxometric analyses identified three neurobiologically distinct psychosis biotypes that did not respect clinical diagnosis boundaries. The same analysis procedure using clinical DSM diagnoses as the criteria was best described by a single severity continuum (schizophrenia worse than schizoaffective disorder worse than bipolar psychosis); this was not the case for biotypes. The external validating measures supported the distinctiveness of these subgroups compared with clinical diagnosis, highlighting a possible advantage of neurobiological versus clinical categorization schemes for differentiating psychotic disorders. These data illustrate how multiple pathways may lead to clinically similar psychosis manifestations, and they provide explanations for the marked heterogeneity observed across laboratories on the same biomarker variables when DSM diagnoses are used as the gold standard.

Detection of Multidrug Resistance Genes in Pseudomonas aeruginosa Isolated from Bovine Mastitic Milk

A total of 270 milk samples were collected from private and governmental cow`s farms (200 samples from mastitic cows and 70 from apparently healthy cows). The samples were collected from different provinces (130 samples from Dakahlia, 66 samples from Sharkia and 74 samples from Damieta). Twenty isolates ofP. aeruginosawere isolated from 270 total milk samples in a percentage of 7.4. Damietta providence showed high percentage P. aeruginosaisolates 8.1% followed by Sharkia providence and Dakhlia providence (7.6% and 6.9% respectively). Biochemical identification provided 16 distinct biotypes. Isolates that used galactose, mannose, manitol, displayed a green pigment and ? hemolysis belonged to the more frequent biotype (80%). Most isolates showed multidrug resistance to antibiotic disc used (17 types) the rate of resistance ranged from 25%-100%. In Quinolone group, 85% of isolates were resistant to nalidixic acid and in flouroquinolne group, the resistance was ofloxacin enrofloxacin, followed by ciprofloxacin, and (95%, 85% and 80% respectively). In aminoglycosides group, 70% of isolates were resistance to neomycin followed by amikacin (65%) and gentamycin (50%). In polypeptides and sulphonamides groups, all isolates were resistance to colstin sulfate and sulfa methaxozoletrimethoprim, while in ?-lactamspencillin, macrolide, tetracycline and chloramphenicol groups, 95% of isolates were resistance to ampicillin, Erythromycin, tetracycline and chloramphenicol repectively. In lincomides group, 85% of isolates were resistance to both lincomycin and Clindamycin.On the other hand, in ?-lactams (Cephalosporine)group, the resistance was only 30% to cefadroxil and 25% to and cephalothin. The detection of ?-lactams multidrug resistance genes using multiplex PCR in 20 isolates was observed where 10 % of isolates (2 isolates) harbour LAT-1 to LAT4, CMY-2 to CMY-7, BIL-1 genes; 4 isolates (20%) harbour MIR-IT ATC-1 and all is dolates harbour DHA-1, DHA-3 genes. The Detection of flouroquinolone multidrug resistance genes in 20 P. aeruginosaisolates using singplex PCR, where 6 isolates harbored ParC gene and all isolates harbored gyrA gene.

Widespread distribution of CTX-M and plasmid-mediated AmpC β-lactamases in Escherichia coli from Brazilian chicken meat.

The dissemination of plasmid-mediated antimicrobial resistance genes may pose a substantial public health risk. In the present work, the occurrences of blaCTX-M and plasmid-mediated ampC and qnr genes were investigated in Escherichia coli from 16 chicken carcasses produced by four commercial brands in Brazil. Of the brands tested, three were exporters, including one of organic chicken. Our study assessed 136 E. coli isolates that were grouped into 77 distinct biotypes defined by their origin, resistance profiling, the presence of β-lactamase and plasmid-mediated quinolone resistance genes and enterobacterial repetitive intergenic consensus-polimerase chain reaction typing. The blaCTX-M-15, blaCTX-M-2 and blaCTX-M-8 genes were detected in one, 17 and eight different biotypes, respectively (45 isolates). Twenty-one biotypes (46 isolates) harboured blaCMY-2. Additionally, blaCMY-2 was identified in isolates that also carried either blaCTX-M-2 or blaCTX-M-8. The qnrB and/or qnrS genes occurred in isolates carrying each of the four types of β-lactamase determinants detected and also in oxyimino-cephalosporin-susceptible strains. Plasmid-mediated extended-spectrum β-lactamase (ESBL) and AmpC determinants were identified in carcasses from the four brands tested. Notably, this is the first description of blaCTX-M-15 genes in meat or food-producing animals from South America. The blaCTX-M-8, blaCTX-M-15 and blaCMY-2 genes were transferable in conjugation experiments. The findings of the present study indicate that plasmid-mediated ESBL and AmpC-encoding genes are widely distributed in Brazilian chicken meat.