Rapid Phenotypic Antibiotics Susceptibility Analysis by a 3D Printed Prototype

One of the most important public health concerns is the increase in antibiotic-resistant pathogens and corresponding treatment of associated infections. Addressing this challenge requires more efficient use of antibiotics, achievable by the use of evidence-based, effective antibiotics identified by antibiotic susceptibility testing (AST). However, the current standard method of phenotypic AST used for this purpose requires 48 h or more from sample collection to result. Until results are available, broad-spectrum antibiotics are used to avoid delaying treatment. The turnaround time must therefore be shortened in order for the results to be available before the second administration of antibiotics. The phenotypic electrochemical AST method presented here identifies effective antibiotics within 5-10 h after sampling. Spiked serum samples, including polymicrobial samples, with clinically relevant pathogens and respective concentrations commonly found in bloodstream infections (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa) are used. Direct loading of the test with diluted serum eliminates the need for a pre-culture, as required by existing methods. Furthermore, by combining several electrochemical measurement procedures with computational analysis, allowing the method to be used both online and offline, the AST achieves a sensitivity of 94.44% and a specificity of 95.83% considering each replicate individually.

RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter

Ovarian cancer is one of the most common gynaecological malignancies with poor prognosis and lack of effective treatment. The improvement of the situation of ovarian cancer urgently requires the exploration of its molecular mechanism to develop more effective molecular targeted drugs. In this study, the role of human ribosomal protein l35a (RPL35A) in ovarian cancer was explored in vitro and in vivo. Our data identified that RPL35A expression was abnormally elevated in ovarian cancer. Clinically, high expression of RPL35A predicted short survival and poor TNM staging in patients with ovarian cancer. Functionally, RPL35A knock down inhibited ovarian cancer cell proliferation and migration, enhanced apoptosis, while overexpression had the opposite effect. Mechanically, RPL35A promoted the direct binding of transcription factor YY1 to CTCF in ovarian cancer cells. Consistently, RPL35A regulated ovarian cancer progression depending on CTCF in vitro and in vivo. Furthermore, RPL35A affected the proliferation and apoptosis of ovarian cancer cells through PPAR signalling pathway. In conclusion, RPL35A drove ovarian cancer progression by promoting the binding of YY1 and CTCF promoter, and inhibiting this process may be an effective strategy for targeted therapy of this disease.

Remarkable Phenotypic Virulence Factors of Microsporum canis and Their Associated Genes: A Systematic Review

Microsporum canis is a widely distributed dermatophyte, which is among the main etiological agents of dermatophytosis in humans and domestic animals. This fungus invades, colonizes and nourishes itself on the keratinized tissues of the host through various virulence factors. This review will bring together the known information about the mechanisms, enzymes and their associated genes relevant to the pathogenesis processes of the fungus and will provide an overview of those virulence factors that should be better studied to establish effective methods of prevention and control of the disease. Public databases using the MeSH terms "Microsporum canis", "virulence factors" and each individual virulence factor were reviewed to enlist a series of articles, from where only original works in English and Spanish that included relevant information on the subject were selected. Out of the 147 articles obtained in the review, 46 were selected that reported virulence factors for M. canis in a period between 1988 and 2023. The rest of the articles were discarded because they did not contain information on the topic (67), some were written in different languages (3), and others were repeated in two or more databases (24) or were not original articles (7). The main virulence factors in M. canis are keratinases, fungilisins and subtilisins. However, less commonly reported are biofilms or dipeptidylpeptidases, among others, which have been little researched because they vary in expression or activity between strains and are not considered essential for the infection and survival of the fungus. Although it is known that they are truly involved in resistance, infection and metabolism, we recognize that their study could strengthen the knowledge of the pathogenesis of M. canis with the aim of achieving effective treatments, as well as the prevention and control of infection.

Identification of Chromoblastomycosis and Phaeohyphomycosis Agents through ITS-RFLP

Chromoblastomycosis (CBM) and phaeohyphomycosis (FEO) are infections caused by melanized filamentous fungal agents, primarily found in tropical and subtropical regions. Both infections pose significant challenges for the correct identification of the causative agent due to their morphological similarity, making conventional methods of morphological analysis highly subjective. Therefore, molecular techniques are necessary for the precise determination of these species. In this regard, this study aimed to contribute to a new methodology based on PCR-RFLP for the identification of agents causing CBM and FEO. Sequences from the Internal Transcribed Spacer (ITS) region were used to identify potential restriction enzyme sites in silico, followed by in vitro validation using the selected restriction enzymes. The obtained results were compared with species identification through morphological analyses and sequencing. The results demonstrated that the PCR-RFLP applied in this study accurately identified two major agents of chromoblastomycosis, Fonsecaea pedrosoi and Fonsecaea monophora, as well as Cladophialophora bantiana and Exophiala dermatitidis, both causative agents of phaeohyphomycosis. In this context, the proposed assay can complement current methods for identifying these species, aiding in diagnosis, and contributing to the proper management of these infections.

Clinical and genetic characterization of a Chinese family with pontocerebellar hypoplasia type 7

We report compound heterozygous variants in TOE1 in siblings of Chinese origin who presented with dyskinesia and intellectual disabilities. Our report provides further information regarding the etiology and pathogenesis of pontocerebellar hypoplasia type 7 syndrome (PCH7). Clinical manifestations were obtained, and genomic DNA was collected from family members. Whole-exome and Sanger sequencing were performed to identify associated genetic variants. Bioinformatics analysis was conducted to identify and characterize the pathogenicity of the heterozygous variants. Following long-term rehabilitation, both siblings showed minimal improvement, and their condition tended to progress. Whole-exome sequencing revealed two unreported heterozygous variants, NM_025077: c.C553T (p.R185W) and NM_025077: c.G562T (p.V188L), in the TOE1 gene mapped to 1p34.1. Sanger sequencing confirmed that the two variants in the proband and her brother were inherited from their parents. The NM_025077: c.C553T (p.R185W) variant was inherited from the father, and the NM_025077: c.G562T (p.V188L) variant was inherited from the mother. Although the two variants in the TOE1 gene have not been reported previously, they were associated with PCH7 based on integrated analysis. Thus, our report contributes to our knowledge regarding the etiology and phenotype of PCH 7.

Showing the limitations of available phenotypic assays to detect Burkholderia pseudomallei from clinical specimens in Nigeria

The genus Burkholderia comprises Gram-negative bacteria that are metabolically complex and versatile, often thriving in hostile settings. Burkholderia pseudomallei , the causative agent of melioidosis, is a prominent member of the genus and a clinical pathogen in tropical and sub-tropical regions. This pathogen is well known for its multidrug resistance and possible bioweapon potential. There is currently no report of the pathogen from clinical specimens in Nigeria, which might be due to misdiagnosis with phenotypic assays. This study aims to explore the accuracy of the use of phenotypic assays to diagnose B. pseudomallei in Nigeria. Two hundred and seventeen clinical samples and 28 Gram-negative clinical isolates were collected and analysed using Ashdown's selective agar and monoclonal antibody-based latex agglutination. Species-level identification was achieved using the analytical profile index (API) 20NE system. The susceptibility of the isolates to nine different antimicrobial agents was determined using the disc diffusion method. A total of seventy-four culture-positive isolates were obtained using Ashdown's selective agar. Twenty-two of these isolates were believed to be B. pseudomallei through the monoclonal antibody-based latex agglutination test and the API 20NE system subsequently identified 14 isolates as Burkholderia . The predominant Burkholderia species was B. cepacia with an isolation rate of 30.8 % (8/26). No isolate was distinctively identified as B. pseudomallei but five isolates were strongly suspected to be B. pseudomallei with similarity indices ranging from 81.9-91.3 %. Other bacterial species with definitive identity include Aeromonas sp., Sphingomonas sp. and Pseudomonas aeruginosa . The antibiotic susceptibility results revealed an overall resistance to amoxicillin-clavullanic acid of 71.4 %, to cefepime of 33.3 %, to trimethoprim-sulfamethoxazole of 38.1 %, to piperacillin-tazobactam of 33.3 %, to imipenem of 66.7 %, to doxycycline of 57.1% and to ceftazidime of 66.7 %. The highest intermediate resistance was observed for cefepime and piperacillin-tazobactam with a value of 66.7 % each, while there was no intermediate resistance for gentamicin, colistin and imipenem. Our findings, therefore, show that phenotypic assays alone are not sufficient in the diagnosis of melioidosis. Additionally, they provide robust support for present and future decisions to expand diagnostic capability for melioidosis beyond phenotypic assays in low-resource settings.

What's in a name? Characteristics of clinical biofilms

In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial species. Various mechanisms enable biofilm-associated bacteria to withstand antibiotics, including physical barriers, physiological adaptations, and changes in gene expression. Gene expression profiles in biofilms differ from individual cells but, there is little consensus among studies and so far, a 'biofilm signature transcriptome' has not been recognized. Additionally, the spatial and temporal variability within biofilms varies greatly depending on the system or environment. Despite all these variable conditions, which produce very diverse structures, they are all noted as biofilms. We discuss that clinical biofilms may differ from those grown in laboratories and found in the environment and discuss whether the characteristics that are commonly used to define and characterize biofilms have been shown in infectious biofilms. We emphasize that there is a need for a comprehensive understanding of the specific traits that are used to define bacteria in infections as clinical biofilms.

Phenotypic and genotypic antimicrobial resistance in Escherichia coli strains isolated from household dogs in Chile

Introduction

Antimicrobial resistance (AMR) is a major threat to animal and public health worldwide; consequently, several AMR surveillances programs have been implemented internationally in both human and veterinary medicine, including indicator bacteria such as Escherichia coli. However, companion animals are not typically included in these surveillance programs. Nevertheless, there have been reports of increasing levels of antimicrobial resistance in E. coli strains isolated from dogs worldwide. In Chile, there is limited information available on AMR in E. coli isolated from companion animals, which prevents the establishment of objective prevention and control measures.

Methods

For this reason, the aim of this study was to characterize the phenotypic and genotypic AMR of E. coli strains isolated from healthy household dogs in Chile. For this purpose, a multi-stage sampling was carried out in the Metropolitan Region of Chile, obtaining samples from 600 healthy dogs. These samples were processed using traditional bacteriology and molecular techniques to isolate E. coli strains. We assessed the minimal inhibitory concentration of 17 antimicrobials and conducted a search of six antimicrobial resistance genes, as well as class 1 and 2 integrons, in the isolated strains.

Results

Two-hundred and twenty-four strains of E. coli were recovered, and 96.9% (n = 217) showed resistance to at least one drug and only 3.1% (n = 7) were susceptible to all analyzed antimicrobials. Most strains were resistant to cefalexin (91.5%, n = 205, 1st-generation cephalosporin), followed by ampicillin (68.3%, n = 153) and cefpodoxime (31.3%, n = 70, 3rd-generation cephalosporin). Moreover, 24.1% (n = 54) tested positive for extended-spectrum-β-lactamases and 34.4% (n = 77) were multidrug resistant. As for the AMR genes, the most detected was qnrB (28.1%, n = 63), followed by blaCTX-M (22.3%, n = 50), and blaTEM-1 (19.6%, n = 44). Additionally, 16.1% (n = 36) harbored class 1 integrons. Our study shows that E. coli strains isolated from healthy household dogs exhibit resistance to several relevant drugs and also antimicrobial resistance genes considered critical for human health. These results can be used as a starting point for the prevention and control of antimicrobial resistance from companion animals. This background should be considered when formulating future resistance surveillance programs or control plans in which companion animals must be included.

Discovery of Potent, Dual-Inhibitors of Diacylglycerol Kinases Alpha and Zeta Guided by Phenotypic Optimization

We describe a phenotypic screening and optimization strategy to discover compounds that block intracellular checkpoint signaling in T-cells. We identified dual DGKα and ζ inhibitors notwithstanding the modest similarity between α and ζ relative to other DGK isoforms. Optimized compounds produced cytokine release and T-cell proliferation consistent with DGK inhibition and potentiated an immune response in human and mouse T-cells. Additionally, lead inhibitor BMS-502 demonstrated dose-dependent immune stimulation in the mouse OT-1 model, setting the stage for a drug discovery program.

In Vitro and In Vivo Drug-Response Profiling Using Patient-Derived High-Grade Glioma

BACKGROUND

Genomic profiling cannot solely predict the complexity of how tumor cells behave in their in vivo microenvironment and their susceptibility to therapies. The aim of the study was to establish a functional drug prediction model utilizing patient-derived GBM tumor samples for in vitro testing of drug efficacy followed by in vivo validation to overcome the disadvantages of a strict pharmacogenomics approach.

METHODS

High-throughput in vitro pharmacologic testing of patient-derived GBM tumors cultured as 3D organoids offered a cost-effective, clinically and phenotypically relevant model, inclusive of tumor plasticity and stroma. RNAseq analysis supplemented this 128-compound screening to predict more efficacious and patient-specific drug combinations with additional tumor stemness evaluated using flow cytometry. In vivo PDX mouse models rapidly validated (50 days) and determined mutational influence alongside of drug efficacy. We present a representative GBM case of three tumors resected at initial presentation, at first recurrence without any treatment, and at a second recurrence following radiation and chemotherapy, all from the same patient.

RESULTS

Molecular and in vitro screening helped identify effective drug targets against several pathways as well as synergistic drug combinations of cobimetinib and vemurafenib for this patient, supported in part by in vivo tumor growth assessment. Each tumor iteration showed significantly varying stemness and drug resistance.

CONCLUSIONS

Our integrative model utilizing molecular, in vitro, and in vivo approaches provides direct evidence of a patient's tumor response drifting with treatment and time, as demonstrated by dynamic changes in their tumor profile, which may affect how one would address that drift pharmacologically.

Antimicrobial susceptibility testing: An updated primer for clinicians in the era of antimicrobial resistance: Insights from the Society of Infectious Diseases Pharmacists

Antimicrobial susceptibility testing (AST) is a critical function of the clinical microbiology laboratory and is essential for optimizing care of patients with infectious diseases, monitoring antimicrobial resistance (AMR) trends, and informing public health initiatives. Several methods are available for performing AST including broth microdilution, agar dilution, and disk diffusion. Technological advances such as the development of commercial automated susceptibility testing platforms and the advent of rapid diagnostic tests have improved the rapidity, robustness, and clinical application of AST. Numerous accrediting and regulatory agencies are involved in the process of AST and setting and revising breakpoints, including the U.S. Food and Drug Administration and the Clinical and Laboratory Standards Institute. Challenges to optimizing AST include the emergence of new resistance mechanisms, the development of new antimicrobial agents, and generation of new data requiring updates and revisions to established methods and breakpoints. Together, the challenges in AST methods and their interpretation create important opportunities for well-informed clinicians to improve patient outcomes and provide value to antimicrobial stewardship programs, especially in the setting of rapidly changing and increasing AMR. Addressing AST challenges will involve continued development of new technologies along with collaboration between clinicians and the laboratory to facilitate optimal antimicrobial use, combat the increasing burden of AMR, and inform the development of novel antimicrobials. This updated primer serves to reinforce important principles of AST, and to provide guidance on their implementation and optimization.

Bacterial Persister Cells: Mechanisms of Formation, Control, and Eradication

Bacterial Persister Cells (BPCs) are quiescent, slow-growing or growth-arrested phenotypic variants of normal bacterial cells that are transiently tolerant to antibiotics. It seems that persister cells are the main cause of the recurrence of various chronic infections. Stress response (RpoS-mediated), Toxin-Antitoxin (TA) systems, inhibition of ATP production, Reactive Oxygen Species (ROS), efflux pumps, bacterial SOS response, cell-to-cell communication and stringent response (ppGpp- mediated) are the primary potential mechanisms for persistence cell formation. However, eradicating persistent cells is challenging as the specific molecular mechanisms that initiate their formation remain fuzzy and unknown. Here we reviewed and summarized the current understanding of how bacterial persister cells are formed, controlled, and destroyed.

Phenotypic characteristic of Staphylococcus aureus from subclinical mastitis in Etawah-crossbreed goats in Yogyakarta, Indonesia

Background and Aim

Subclinical mastitis (SCM) in Etawah-grade (PE) goats in Yogyakarta, Indonesia, is commonly due to Staphylococcus aureus. At present, S. aureus from SCM in PE goats in Yogyakarta has not been characterized. Therefore, this study aimed to phenotypically characterize S. aureus, which has been isolated from SCM of PE goats.

Materials and Methods

A total of 314 lactating PE goats were collected from 60 PE goat farms (e.g., Sleman, Bantul, and Kulonprogo) located in parts of Yogyakarta with an average age of 3-4 years old, three of which showed SCM based on the California mastitis test (CMT). Subclinical mastitis is confirmed in PE goats if CMT shows ++ or +++. Furthermore, S. aureus was detected by biochemical assays. Staphylococcus aureus could determine hemolysin (Hae), coagulase (Coa), clumping factor (Cf), and antibiotic susceptibility. Hemolytic bacteria were detected by culturing on blood agar plate, and Cf was detected by slide agglutination. The production of Coa was detected by tube coagulation. Staphylococcus aureus susceptibility was determined by antimicrobial agar diffusion using a paper disc.

Results

Phenotypically characterized S. aureus from PE goats with SCM in Yogyakarta, Indonesia, Coa-, Cf-, and Hae- were found to be resistant to erythromycin (ERYTHRO), ampicillin (AMP), penicillin (PEN-G), and sulfamethoxazole (SULFA).

Conclusion

The phenotypic characteristic of S. aureus, which was obtained from SCM in PE goats in Yogyakarta, consists of Coa, and Cf-. S. aureus cannot perform hemolysis of red blood cells. This phenotypic characteristic can prevent and control SCM in PE goats. Several antibiotics such as ERYTHRO, AMP, PEN-G, and SULFA were no longer effective for treating SCM in PE goats because S. aureus has developed its resistance to these antibiotics.

A Survey of Helicobacter pylori Antibiotic-Resistant Genotypes and Strain Lineages by Whole-Genome Sequencing in China

Antibiotic resistance is the most important factor leading to failed Helicobacter pylori eradication therapy, and personalized treatment based on antibiotic susceptibility is becoming increasingly important. To strengthen the understanding of antibiotic genotypic resistance of H. pylori and identify new antibiotic resistance loci, in this study, we identified phenotypic resistance information for 60 clinical isolates and compared the concordance of phenotypic and genotypic resistance using whole-genome sequencing (WGS). Clarithromycin and levofloxacin genotypic resistance was in almost perfect concordance with phenotypic resistance, with kappa coefficients of 0.867 and 0.833, respectively. All strains with the R16H/C mutation and truncation in rdxA were metronidazole resistant, with 100% specificity. For other genes of concern, at least one phenotypically sensitive strain had a previous mutation related to antibiotic resistance. Moreover, we found that the A1378G mutation of HP0399 and the A149G mutation of FabH might contribute to tetracycline resistance and multidrug resistance, respectively. Overall, the inference of resistance to clarithromycin and levofloxacin from genotypic resistance is reliable, and WGS has been very helpful in discovering novel H. pylori resistance loci. In addition, WGS has also enhanced our study of strain lineages, providing new ways to understand resistance information and mechanisms.

Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes

Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.

Phenotypic and Genotypic Characteristics of Uropathogenic Escherichia coli Isolates from Kenya

Introduction: Uropathogenic Escherichia coli (UPECs) are a significant cause of urinary tract infections (UTIs). In Kenya, UTIs are typically treated with β-lactam antibiotics without antibiotic susceptibility testing, which could accelerate antibiotic resistance among UPEC strains.

Aim: This study determined the occurrence of UPEC producing extended-spectrum β-lactamases (ESBLs), the genes conferring resistance to β-lactams, and the phylogenetic groups associated with ESBLs in Kenyan UPECs.

Methodology: Ninety-five UPEC isolates from six Kenyan hospitals were tested for ESBL and plasmid-mediated AmpC β-lactamase (pAmpC) production by combined disk diffusion and disk approximation tests, respectively. Real-time and conventional polymerase chain reactions (PCRs) were used to detect three ESBL and six pAmpC genes, respectively, and phylogenetic groups were assigned by a quadruplex PCR method.

Results: Twenty-four percent UPEC isolates were ESBL producers with bla_CTX-M (95.6%), bla_TEM (95.6%), and bla_SHV (21.7%) genes detected. Sixteen isolates had bla_CTX-M/TEM, whereas five had bla_{TEM/CTX-M/SHV}. A total of 5/23 ESBLs were cefoxitin resistant, but no AmpC genes were detected. The UPECs belonged predominantly to phylogenetic groups B2 (31/95; 32.6%) and D (30/95; 31.6%), while groups B2 and A had the most ESBL producers.

Conclusions: β-Lactam antibiotics have reduced utility for treating UTIs as a quarter of UPECs were ESBL producing. Single or multiple ESBL genes were present in UPECs, belonging primarily to phylogenetic groups B2 and A.

Beyond the Usual Suspects: Expanding on Mutations and Detection for Familial Hypercholesterolemia

Introduction: Familial hypercholesterolemia (FH) is a highly prevalent condition, predisposing individuals to premature cardiovascular disease and with a genetic basis more complex than initially thought. Advances in molecular technologies have provided novel insights into the role of next-generation-sequencing, the assessment and classification of newly found variants, the complex genotype-phenotype correlation, and the position of FH in the context of other dyslipidaemias.Areas covered: Understanding the scope of genetic determinants of FH has expanded substantially. This article reviews the current literature on the complexity that comes with this incremental knowledge and highlights the added value of genetic testing as an addition to phenotypic diagnosis of FH. Moreover, we discuss the broad genetic basis of FH, with a focus on the three main FH genes, but we also pay attention to polygenic hypercholesterolemia as well as minor and modulator genes involved in FH.Expert opinion: Both the availability and the need for genetic analysis of FH are on the rise as costs of sequencing continue to drop and new therapies require a genetic diagnosis for reimbursement. However, greater use of genetic testing requires more education of healthcare professionals, since molecular technologies will allow for rapid and accurate evaluation of large numbers of detected variants.

Genetic Parameters for First Lactation and Lifetime Traits of Nili-Ravi Buffaloes

The data on first lactation and lifetime performance records of 501 Nili-Ravi were collected for a period from 1983 to 2017 (35 years) maintained at ICAR-Central Institute for Research on Buffaloes, Sub-Campus, Nabha, Punjab. The data were analyzed to calculate heritability, genetic and phenotypic correlation for first lactation traits, viz., Age at First Calving (AFC), First Lactation Total Milk Yield (FLTMY), First Lactation Standard (305 days or less) Milk Yield (FLSMY), First Peak Milk Yield (FPY), First Lactation Length (FLL), First Dry Period (FDP), First Service Period (FSP) and First Calving Interval (FCI), Herd Life (HL), Productive Life (PL), Productive Days (PD), Unproductive Days (UD), Breeding Efficiency (BE), Total Lifetime Milk Yield (Total LTMY), Standard Lifetime Milk Yield (Standard LTMY), Milk Yield Per Day of Productive Life (MY/PL), Milk Yield Per Day of Productive Days (MY/PD), and Milk Yield Per Day of Herd Life (MY/HL). For estimation of variance component and heritability separately for each trait, the uni-trait animal model was equipped, whereas to estimate genetic and phenotypic correlations between traits, bi-trait animal models were fitted. The estimates of heritability for production and reproduction traits of Nili-Ravi were medium, i.e., 0.365 ± 0.087, 0.353 ± 0.071, 0.318 ± 0.082, 0.354 ± 0.076, and 0.362 ± 0.086 for FLSMY, FDP, FSP, FCI, and AFC, respectively. The estimates of heritability were low, i.e., 0.062 ± 0.088, 0.123 ± 0.090, 0.158 ± 0.090, 0.155 ± 0.091, and 0.129 ± 0.091 for HL, PL, PD, Total LTMY, and Standard LTMY and high, i.e., 0.669 ± 0.096 for BE. Genetic correlation for FLTMY was high with FLL (0.710 ± 0.103), and genetic correlation of FLTMY was high and positive with HL, Total LTMY, MY/PL, and MY/PD while low and positive with PL. Genetic correlation of AFC was low and negative with PL, PD, UD, BE, Total LTMY, Standard LTMY, MY/PL, and MY/PD and negative with MY/HL. Significant positive phenotypic association of FPY was seen with FLTMY, FLSMY, FLL, AFC, HL, Total LTMY, and Standard LTMY. Higher heritability of first lactation traits especially FPY suggests sufficient additive genetic variability, which can be exploited under selection and breeding policy in order to improve overall performance of Nili-Ravi buffaloes.

The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Phenotypic Drug Discovery

Phenotypic drug discovery has a long track record of delivering innovative drugs and has received renewed attention in the last few years. The promise of this approach, however, comes with several challenges that should be addressed to avoid wasting time and resources on drugs with undesired modes of action or, worse, false-positive hits. In this set of best practices, we go over the essential steps of phenotypic drug discovery and provide guidance on how to increase the chance of success in identifying validated and relevant chemical starting points for optimization: selecting the right assay, selecting the right compound screening library and developing appropriate hit validation assays. Then, we highlight the importance of initiating studies to determine the mode of action of the identified hits early and present the current state of the art.

Recent Advances in the Detection of Antibiotic and Multi-Drug Resistant Salmonella: An Update

Antibiotic and multi-drug resistant (MDR) Salmonella poses a significant threat to public health due to its ability to colonize animals (cold and warm-blooded) and contaminate freshwater supplies. Monitoring antibiotic resistant Salmonella is traditionally costly, involving the application of phenotypic and genotypic tests over several days. However, with the introduction of cheaper semi-automated devices in the last decade, strain detection and identification times have significantly fallen. This, in turn, has led to efficiently regulated food production systems and further reductions in food safety hazards. This review highlights current and emerging technologies used in the detection of antibiotic resistant and MDR Salmonella.

Novel mutation detection in craniosynostosis promotes characterization, identification, gene expression, tissue engineering and helps clinical practice and translational research

Introduction

Craniosynostosis (CS) syndrome is an autosomal dominant condition (ADC) classically combining with CS and nonsyndromic CS (NSCS) including digital anomalies of the hands and feet. The majority of cases caused by a heterozygous mutation (HM) in the third immunoglobulin-like domain (IgIII) of fibroblast growth factor receptor (FGFR) 2 mutations outside this region of the protein.

Material and Methods

We tried to find out the spectrum of genes involved in CS syndrome caused by the heterozygous missense mutation, the IgII and IgIII of FGFR2. FGFR3, FGFR4, TWIST, and MSX genes were performed and verified through the Indian population with CS children.

Results

We find out that at conserved linker region (LR), the changes occurred among the larger families. Independent genetic origins, but phenotypic similarities add to the evidence supporting the theory of selfish spermatogonial selective advantage for this rare gain-of-function FGFR2 mutation. Polygenic novel mutation in both syndromic and nonsyndromic cases of CS promotes the translational research and holds a great promise to reproduce the molecular-based therapy and treatment as well. In this article, we summarized that genes involved in CS as evidence-based approach for characterization, identification, gene expression, and tissue engineering. We also described other related genes and proteins for the CS involvement and improvement of the diseases progression.

Conclusion

HM again repeated the old story for both groups of syndromic CS and NSCS of Asian Indian children. Here, for the first time, we clearly reported that IgIII of FGFR2 mutations outside this region of the protein and tyrosine kinase (TK1 and TK2) responsible for both in molecular and cellular level for CS. It adds an evidence for future molecular targeting therapy to repair CS.

Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact

Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.

Phenotypic Detection of Carbapenem-Resistant Gram-Negative Bacilli from a Clinical Specimen in Sidama, Ethiopia: A Cross-Sectional Study

BACKGROUND

Carbapenem-resistant gram-negative bacteria are an emergent source of both community-acquired and healthcare-associated infection that poses a substantial hazard to public health. This study aimed to conclude the magnitude of carbapenem resistance gram-negative bacteria from a clinical specimen at Hawassa University Comprehensive Specialized Hospital.

METHODS

A hospital-based cross-sectional study was accompanied from February 13 to June 7, 2020, in which consecutive patients with 103 gram-negative bacteria were encompassed. The isolates included were 54 urine, 17 blood, 17 pusses, 4 cerebrospinal fluid (CSF), 3 aspirates, 3 effusions, 2 stools, 2 ear discharges, and 1 nasal swab. A semi-structured questionnaire was used to gather socio-demographic data from the attendant and clinical data from the patient's chart. Patients admitted in any wards and visited outpatients department were included for the study if gram-negative bacteria was identified for those who accepted the consent. A routine manual culture, Gram's staining and biochemical tests used to identify the bacteria. Antibiotic susceptibility was determined for twelve antibiotics including cotrimoxazole, ceftazidime, meropenem, gentamycin, chloramphenicol, ampicillin, ciprofloxacin, cefotaxime, cefuroxime, nitrofurantoin, piperacillin-tazobactam, and amikacin using the Kirby-Bauer disc diffusion method. Modified carbapenem inactivation (mCIM) method was used to determine carbapenem resistance using meropenem disk as per the recommendation of Clinical and Laboratory Standards Institute guideline. Statistical package for social science software version 21 was used for data entry and analysis. The odds ratio at 95% confidence interval (CI) and p-value <0.05 were taken as a statistically significant association.

RESULTS

Generally, 111 gram-negative bacteria were identified from 103 patients. Of 111 isolates, thirteen isolates (nine resistance and four intermediates) were identified in disk diffusion testing for meropenem. Of this, 10 isolates were carbapenemases producer with the overall rates of 9% in the Modified carbapenem inactivation method (mCIM). Pseudomonas spp. 3 (30.0%), E. coli, K. pneumonia, Acinetobacter spp. each two (20.0%), and K. oxytoca 1 (10.0%) were identified as carbapenemases positive. The rates of the multidrug, extensive, pan drug were 86.5, 43.3, and 1.8, respectively. Ampicillin 94 (97.9%), followed by cefuroxime 52 (91.2%), cefotaxime 94 (88.7%), cotrimoxazole 58 (88.1%), ceftazidime 40 (83.3%), ciprofloxacin 47 (77.1%), nitrofurantoin 35 (70.0%), gentamycin 71 (65.7%), with high level of resistance. However, piperacillin-tazobactam 41 (48.8%), chloramphenicol 25 (47.2%), meropenem 13 (11.7%), and amikacin 9 (8.5%) were with low rates of resistance. In this study, there were no variables statically associated with carbapenem resistance that is p > 0.05.

CONCLUSION

Our study showed that carbapenem-resistant gram-negative bacilli are 9% in the study area. Our finding signposts that ampicillin, cefuroxime, cefotaxime, cotrimoxazole, ceftazidime, ciprofloxacin, nitrofurantoin, and gentamycin with a high rate of resistance >50%. However, piperacillin-tazobactam, chloramphenicol, meropenem, and amikacin were at low rates of resistance. Therefore, a measure should be taken to contain carbapenem resistance gram-negative bacteria in the study area. Further, study with better method needs to be conducted to conclude the real scenario of carbapenem resistance.

Bispecific antibody target pair discovery by high-throughput phenotypic screening using in vitro combinatorial Fab libraries

Bispecific antibodies can uniquely influence cellular responses, but selecting target combinations for optimal functional activity remains challenging. Here we describe a high-throughput, combinatorial, phenotypic screening approach using a new bispecific antibody target discovery format, allowing screening of hundreds of target combinations. Simple in vitro mixing of Fab-fusion proteins from a diverse library enables the generation of thousands of screen-ready bispecific antibodies for high-throughput, biologically relevant assays. We identified an obligate bispecific co-targeting CD79a/b and CD22 as a potent inhibitor of human B cell activation from a short-term flow cytometry signaling assay. A long-term, high-content imaging assay identified anti-integrin bispecific inhibitors of human cell matrix accumulation targeting integrins β1 and β6 or αV and β1. In all cases, functional activity was conserved from the bispecific screening format to a therapeutically relevant format. We also introduce a broader type of mechanistic screen whereby functional modulation of different cell subsets in peripheral blood mononuclear cells was evaluated simultaneously. We identified bispecific antibodies capable of activating different T cell subsets of potential interest for applications in oncology or infectious disease, as well as bispecifics abrogating T cell activity of potential interest to autoimmune or inflammatory disease. The bispecific target pair discovery technology described herein offers access to new target biology and unique bispecific therapeutic opportunities in diverse disease indications.

Validation of a beef cattle maternal breeding objective based on a cross-sectional analysis of a large national cattle database

Despite the importance of validating any technology prior to recommendation for use, few studies exist in the scientific literature which have demonstrated the superior performance of high-ranking animals in a given total merit index; this is especially true for maternal cattle selection indexes. The objective of the present study was to demonstrate the impact of the Irish total merit maternal-based index and provide the benefits of using the Irish total merit maternal-based beef index as part of a breeding policy. The validation exercise was undertaken using 269,407 records (which included the cow's own records and her progeny records) from 92,300 females differing in a total merit index for maternal value; a comparison was also made with the Irish terminal index. Association analyses were undertaken within the framework of linear and threshold mixed models; the traits analyzed were fertility (e.g., calving interval), slaughter (e.g., harvest weight), live weight (e.g., weaning weight), and producer-recorded traits (e.g., docility). All traits were analyzed with the maternal index and terminal index fitted as covariate(s) separately. Depending on the independent variable analyzed, the other fixed effects included: parity of cow, heterosis and recombination loss of cow and/or progeny, gender of progeny, and the estimated breeding value of the sire; contemporary group was included as a random effect. The results demonstrate the effectiveness of using total merit indexes to improve performance in a whole range of different traits, despite the often antagonistic genetic correlations among traits that underpin the index. Cows excelling on the maternal index had less calving difficulty, superior fertility performance, lighter carcasses, and live weight, as well as being more easily managed. Additionally, progeny of higher maternal index cows were lighter at birth and more docile albeit with a small impact on slaughter traits. In contrast, higher terminal index cows had more calving difficulty, compromised fertility and had heavier carcasses themselves as well as their progeny. While the differences in phenotypic performance between groups on maternal index was, in most instances, relatively small, the benefits are: (1) expected to be greater when more genetically extreme groups of animals are evaluated and (2) expected to accumulate over time given the cumulative and permanent properties of breeding schemes.

[Phenotypic plasticity in insects]

Insects represent 85% of the animals. They have adapted to many environments and play a major role in ecosystems. Many insect species exhibit phenotypic plasticity. We here report on the mechanisms involved in phenotypic plasticity of different insects (aphids, migratory locust, map butterfly, honeybee) and also on the nutritional size plasticity in Drosophila and the plasticity of the wing eye-spots of the butterfly Bicyclus anynana. We also describe in more detail our work concerning the thermal plasticity of pigmentation in Drosophila. We have shown that the expression of the tan, yellow and Ddc genes, encoding enzymes of the melanin synthesis pathway, is modulated by temperature and that it is a consequence, at least in part, of the temperature-sensitive expression of the bab locus genes that repress them.

High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery

Esophageal adenocarcinoma (EAC) is a highly heterogeneous disease, dominated by large-scale genomic rearrangements and copy number alterations. Such characteristics have hampered conventional target-directed drug discovery and personalized medicine strategies, contributing to poor outcomes for patients. We describe the application of a high-content Cell Painting assay to profile the phenotypic response of 19,555 compounds across a panel of six EAC cell lines and two tissue-matched control lines. We built an automated high-content image analysis pipeline to identify compounds that selectively modified the phenotype of EAC cell lines. We further trained a machine-learning model to predict the mechanism of action of EAC selective compounds using phenotypic fingerprints from a library of reference compounds. We identified a number of phenotypic clusters enriched with similar pharmacological classes, including methotrexate and three other antimetabolites that are highly selective for EAC cell lines. We further identify a small number of hits from our diverse chemical library that show potent and selective activity for EAC cell lines and that do not cluster with the reference library of compounds, indicating they may be selectively targeting novel esophageal cancer biology. Overall, our results demonstrate that our EAC phenotypic screening platform can identify existing pharmacologic classes and novel compounds with selective activity for EAC cell phenotypes.

Aequorivita lutea sp. nov., a novel bacterium isolated from the estuarine sediment of the Pearl River in China, and transfer of Vitellibacter todarodis and Vitellibacter aquimaris to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov

A Gram-negative, aerobic, rod-shaped, non-motile by gliding bacterium was isolated from the estuarine sediment of the Pearl River in PR China and designated as strain q18^T. Colonies were circular, smooth and yellow on marine agar after 48 h cultivation. Salinity, temperature and pH for optimal growth were 5 % (NaCl), 30 °C and 7, respectively. The 16S rRNA gene sequence of the strain q18^T showed the highest similarity of 97.3 % to the type strain of Aequorivita echinoideorum CC-CZW007^T. 16S rRNA gene-based phylogenetic analysis indicated that strain q18^T grouped into the genus Aequorivita in the family Flavobacteriaceae of the phylum Bacteroidetes, and was distinct from all known species in the genus. Menaquinone (MK-6) was the main respiratory quinone detected in strain q18^T. The major fatty acids were iso-C_15 : 0 and iso-C_17 : 0 3-OH. The polar lipids of strain q18^T mainly comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and one unidentified polar lipid. The G+C content of the genome was ~42.8 mol%. The draft genome size of strain q18^T was 3.3 Mbp. The average nucleotide identity values were around 79.0 % between strain q18^T and reference Aequorivita strains. Based on the polyphasic analysis, strain q18^T was confirmed to represent a novel species of the genus Aequorivita, for which the name Aequorivita lutea sp. nov., is proposed. The type strain is q18^T (=CICC 24821^T=KCTC 72764 ^T). Further, based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, two species previously classified into the genus Vitellibacter, Vitellibacter todarodis Kim et al. 2018 and Vitellibacter aquimaris Thevarajoo et al. 2016, are transferred to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov. respectively.

Phenotypic synergy testing of ceftazidime-avibactam with aztreonam in a university hospital having high number of metallobetalactamase producing bacteria

BACKGROUND

Ceftazidime-avibactam combination with aztreonam and role of rapid synergy reporting has not been widely evaluated. Also the synergy correlation with various betalactamases has not been widely studied.

METHODS

We studied phenotypic synergy testings and molecular detection of betalactamases in our university hospital where we have large number of mellatobetalactmase producing bacteria. We tested two phenotypic synergy methods for ceftazidime-avibactam with aztreonam (Disc-E strip method, E strip-Agar method) for rapid reporting to clinicians (153 isolates). The treatment (colistin, ceftazidime-avibactam, ceftazidime-avibactam with aztreonam) was guided as indicated in the synergy testings. The resistance genes in bacteria were identified by polymerase chain reaction (PCR) and correlated with synergy results.

RESULTS

The highest synergy was seen in Klebsiella pneumoniae by Disc-E strip and E strip-Agar method (86% and 84% respectively). About 70% of Pseudomonas aeruginosa and 29% of Escherichia coli showed synergy. Molecular methods revealed multiple resistance gene combinations and bla _NDM (96%) was predominant gene in isolates showing synergy. Among isolates that were sensitive to ceftazidime-avibactam, the predominant genes were bla _OXA-48 and bla _IMP. Rapid laboratory reporting led to proper utilization of antibiotic combinations.

CONCLUSIONS

Ceftazidime-avibactam and aztreonam rapid synergy testing will be highly beneficial in treatment of infections by metallobetalactamase producing resistant bacteria, especially K. pneumoniae and P. aeruginosa.

Species Diversity of Dickeya and Pectobacterium Causing Potato Blackleg Disease in Pakistan

Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Pectobacterium atrosepticum. Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gapA gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (P. atrosepticum), SS28 (Pectobacterium polaris), SS70 (Dickeya dianthicola), SS90 (Pectobacterium parmentieri), SS95 (Pectobacterium punjabense), and SS96 (Pectobacterium versatile) were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA, and rplB). Phylogenetic analysis revealed considerable genetic diversity in the genus Pectobacterium. In silico DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference Pectobacterium and Dickeya strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: P. atrosepticum, P. versatile, P. parmentieri, P. polaris, P. punjabense, and D. dianthicola.

Carbapenem-Resistant but Cephalosporin-Susceptible Pseudomonas aeruginosa in Urinary Tract Infections: Opportunity for Colistin Sparing

This paper briefly reports the occurrence and epidemiology of carbapenem-resistant but cephalosporin-susceptible (Car-R/Ceph-S) Pseudomonas aeruginosa isolates from urinary tract infections (UTIs) in a tertiary-care hospital in the Southern Region of Hungary, and the phenotypic characterization of the possible resistance mechanisms in these isolates. Isolates and data were collected regarding P. aeruginosa UTIs corresponding to the period between 2008 and 2017. Susceptibility testing was performed using the Kirby–Bauer disk diffusion method; minimum inhibitory concentrations (MICs) of the isolates were determined using E-tests. The phenotypic detection of ampicillin C-type (AmpC) β-lactamases, efflux pump overexpression and carbapenemase production was also performed. P. aeruginosa represented n = 575 (2.72% ± 0.64%) from outpatient, and n = 1045 (5.43% ± 0.81%) from inpatient urinary samples, respectively. Based on the disk diffusion test, n = 359 (22.16%) were carbapenem-resistant; in addition to carbapenems, n = (64.34%) were also resistant to ciprofloxacin; n = (60.17%) to gentamicin/tobramycin; n = (58.51%) to levofloxacin; and n = (27.57%) to amikacin. From among the carbapenem-resistant isolates, n = 56 (15.59%) isolates were multidrug-resistant, while n = 16 (4.46%) were extensively drug-resistant. From among the Car-R/Ceph-S isolates (n = 57), overexpression of AmpC was observed in n = 7 cases (12.28%); carbapenemase production in n = 4 (7.02%); while overexpression of efflux pumps was present in n = 31 (54.39%) isolates. To spare last-resort agents, e.g., colistin, the use of broad-spectrum cephalosporins or safe, alternative agents should be considered in these infections.

Loss of phenotypic inheritance associated with ydcI mutation leads to increased frequency of small, slow persisters in Escherichia coli

Whenever a genetically homogenous population of bacterial cells is exposed to antibiotics, a tiny fraction of cells survives the treatment, the phenomenon known as bacterial persistence [G.L. Hobby et al., Exp. Biol. Med. 50, 281-285 (1942); J. Bigger, The Lancet 244, 497-500 (1944)]. Despite its biomedical relevance, the origin of the phenomenon is still unknown, and as a rare, phenotypically resistant subpopulation, persisters are notoriously hard to study and define. Using computerized tracking we show that persisters are small at birth and slowly replicating. We also determine that the high-persister mutant strain of Escherichia coli, HipQ, is associated with the phenotype of reduced phenotypic inheritance (RPI). We identify the gene responsible for RPI, ydcI, which encodes a transcription factor, and propose a mechanism whereby loss of phenotypic inheritance causes increased frequency of persisters. These results provide insight into the generation and maintenance of phenotypic variation and provide potential targets for the development of therapeutic strategies that tackle persistence in bacterial infections.

Effects of somatic cell score on milk yield and mid-infrared predicted composition and technological traits of Brown Swiss, Holstein Friesian, and Simmental cattle breeds

High milk somatic cell count (SCC) influences milk production and quality; however, very little is known about the effect of low SCC on milk quality, especially in terms of mineral content and coagulation properties. Thus, the present study aimed to investigate the effects of somatic cell score (SCS), calculated as log₂(SCC/100) + 3, on milk yield, composition (fat, crude protein, casein, lactose, milk urea nitrogen, protein fractions, and mineral contents), and coagulation properties of Brown Swiss, Holstein Friesian, and Simmental cows from multibreed herds. Milk composition and coagulation traits were predicted using mid-infrared spectroscopy. The data set comprised 95,591 observations of 6,940 cows in 313 multibreed herds, collected from January 2011 to December 2017. Observations were divided into 8 classes based on SCS. Statistical analysis was performed using a linear mixed model, which included breed, parity, stage of lactation, SCS class, and their interactions as fixed effects, and herd test day, cow, and residual as random effects. The probability that cows experienced SCS > 4.00 at 30 ± 5, 60 ± 5, or 90 ± 5 d after the observation test day was calculated for each SCS class, and odds ratios to the reference class (-1.00 < SCS ≤ 0.00) were reported. Results showed that the relationship between SCS and milk traits followed a third-order polynomial regression. The average loss of milk, fat, and crude protein yields were 0.43, 0.01, and 0.01 kg/d, respectively, for each SCS unit higher than 1.00. Very low SCS (<-1.00) had detrimental effects on milk yield and quality traits similar to or even stronger than high SCS (>4.00). Moreover, cows with SCS lower than -1.00 on a test day were about 7 times more likely to present high SCS within the following 90 ± 5 d than cows with SCS between -1.00 and 0.00. Breeds responded similarly to the increase of SCS, but the overall loss of fat and crude protein yields, and several minerals among Holstein Friesian were lower with increasing SCS. The best milk yield and quality were observed between SCS 0.00 and 1.00, but milk quality of Holstein Friesians started to decrease at lower SCS compared with milk quality of Brown Swiss and Simmental cows. Results suggest a breed-dependent optimum of SCS, and highlighted that very low SCS can be an indicator of udder health problems and, thus, may be used for early detection of mastitis.

Genetic characterization of White Fulani cattle in Nigeria: A comparative study

Objective

The objective of the present study was to evaluate heterozygosis in cattle population, and to characterize White Fulani breed by identifying DNA markers considering microsatellites.

Materials and Methods

A total of 41 cattle were randomly selected and used for sample (wool) collection for the characterization and identification of phenotypic traits of cattle in Nigeria. The DNA samples from the samples were prepared. Twelve microsatellite primers were used for the microsatellite analysis in the genomic DNA of cattle. The reinforced products were analyzed to determine polymorphic alleles and their frequencies.

Results

White Fulani is characterized by a high degree of genetic diversity. The microsatellites have multiple alleles and may show heterozygosity frequencies of at least 70%. White Fulani cows and their F1 descendants form a common cluster, to which the bulls of the Kuru and Red Boro breeds are adjacent. There is a clear differentiation of purebred populations of Tajik zebu-like cattle (Q = 98.7%) and a significant proportion of white Fulani (Q = 81.8%) from Nigeria. The microsatellite analysis of zebu of Nigeria allowed identifying a total of 80 alleles. In the KURU and PAX-KR-BOR rocks, 17 and 19 alleles were identified, respectively. In F1, 51 alleles were detected.

Conclusion

White Fulani cattle are characterized by a high degree of genetic diversities. This makes it a highly informative source in genetic analysis. The results can be applied in dealing with the conservation and sustainable applications of genetic resources in the Nigerian cattle population.

Systematic Review and Meta-analysis of Carbapenem Resistance of Acinetobacter baumannii in Iran

BACKGROUND

The prevalence of carbapenem resistance in Acinetobacter baumannii has been increasing worldwide, and therapeutic options are extremely limited. We performed a systematic review to evaluate the phenotypic and genotypic carbapenem resistance in A.baumannii reported in Iran.

METHODS

We systematically searched Pub Med, Web of Science Direct, and Google scholar databases to identify studies addressing the carbapenem resistance of A. baumannii. The selected papers were published between 2005 and 2016, but the sample collection period was between 2002 and 2016. To estimate the prevalence, the Der Simonian and Laird randomized models, a 95% confidence interval, was used. For the heterogeneity check, I2 test was used. The Egger test was used to check the propagation bias.

RESULTS

Analysis of data indicates that there was an increase in resistance to carbapenems from 4.5% in 2005 to a 100% prevalence rate in 2016 (65.4 (95% CI: 58.8 - 71.6).

CONCLUSION

According to the results of this study, the rate of resistance to carbapenem in A.baumannii has been increasing in Iran. The presence of carbapenem-resistant isolates is a major concern, because carbapenem is the main drug used against Multi Drug Resistant (MDR) isolates.

Phenotypic and morphometric differentiation of indigenous chickens from Kenya and other tropical countries augments perspectives for genetic resource improvement and conservation

Indigenous chickens at the Swahili coast and other traditional migratory corridors in Kenya represent important populations that are inconclusively characterized. Using a comprehensive dataset of Kenyan indigenous chickens and additional mined data of chickens from 8 African and 5 Asian countries, we performed univariate and multivariate assessments to uncover the underlying phenotypic and morphometric variability. Kenyan indigenous chickens expressed differentiation of several qualitative and quantitative traits, both among different counties in the Swahili coast, and among coastal, western, and northern migratory corridors. There was a substantial population stratification of these chickens, particularly distinctive clustering of chickens from Marsabit, Lamu, and Kilifi counties. The pooled dataset further clarified a closer phenotypic and morphometric proximity of chickens within different geographical regions. We additionally revealed a preponderance of bantam and rumpless traits to hot and humid locales, and feathered shanks to cooler regions. Currently, most chicken breeding programs in developing countries rely on phenotypic and morphometric properties. Hence, the high chicken diversity and population stratification observed in our study, possibly shaped by natural and artificial selective pressures, reveal opportunities for complementary phenotypic and genotypic assessments to identify resources for effective breed improvement and conservation strategies of indigenous chickens in the tropics.

Trajectories of Cognitive Function and Associated Phenotypic and Genotypic Factors in Breast Cancer

OBJECTIVES

This study identified women with unique trajectories of executive function, concentration, and visual working memory before and during adjuvant therapy for breast cancer, and examined phenotypic and genotypic predictors associated with subgroups.

SAMPLE & SETTING

399 postmenopausal women, of whom 288 were women with early-stage breast cancer and 111 were women without breast cancer, matched on age and years of education to the women with breast cancer, and all at an urban cancer center.

METHODS & VARIABLES

A repeated-measures design was used; assessments occurred before adjuvant therapy and every six months post-therapy initiation. Group-based trajectory modeling determined subgroups. Multinomial logistic regression identified phenotypic and genotypic characteristics.

RESULTS

Three executive function and concentration trajectory subgroups were identified.

IMPLICATIONS FOR NURSING

Advancing age, greater pretherapy fatigue, and poorer pretherapy cognitive function are associated with the low subgroups. DNA repair and oxidative stress mechanisms may be involved in the cognitive changes that women experience.

Current and Emerging Methods of Antibiotic Susceptibility Testing

Antibiotic susceptibility testing (AST) specifies effective antibiotic dosage and formulates a profile of empirical therapy for the proper management of an individual patient's health against deadly infections. Therefore, rapid diagnostic plays a pivotal role in the treatment of bacterial infection. In this article, the authors review the socio-economic burden and emergence of antibiotic resistance. An overview of the phenotypic, genotypic, and emerging techniques for AST has been provided and discussed, highlighting the advantages and limitations of each. The historical perspective on conventional methods that have paved the way for modern AST like disk diffusion, Epsilometer test (Etest), and microdilution, is presented. Several emerging methods, such as microfluidic-based optical and electrochemical AST have been critically evaluated. Finally, the challenges related with AST and its outlook in the future are presented.

First prospective comparison of genotypic versus phenotypic tropism assays in predicting virologic responses to maraviroc in a phase 3 study

Maraviroc (MVC, a CCR5 antagonist) is only fully active against CCR5 tropic [R5] HIV-1, and tropism testing is required prior to initiating treatment. The MODERN study prospectively compared genotypic (GTT) and phenotypic (Trofile®) tropism testing with treatment-naive HIV-1-infected participants randomized 1:1 to either GTT or Trofile tropism assessments. Participants with R5 virus were randomized 1:1 to receive darunavir/ritonavir (DRV/r) with either MVC or tenofovir/emtricitabine. Screening samples were also retrospectively tested using the alternative assay. Positive predictive values (PPVs) for each assay were estimated using both the observed MVC+DRV/r response rate (HIV-1 RNA <50 copies/mL at Week 48) and model-based response estimates. The observed MVC+DRV/r response rate was 146/181 (80.7%) for GTT versus 160/215 (74.4%) for Trofile, with a stratification adjusted difference of 6.6% (95% CI, -1.5% to 14.7%) in favor of GTT. The model-based PPV estimates (±standard error) were 80.5% (±2.38) and 78.0% (±2.35) for GTT and Trofile, respectively (difference, 2.5%; 95% CI, -2.0% to 7.0%). Most participants had R5 results using both assays (285/396; 72%) and, of those, 79.3% (226/285) had HIV-1 RNA <50 copies/mL at Week 48. Both the genotypic and phenotypic tropism assays evaluated can effectively predict treatment response to MVC.

Predominance of ST22-MRSA-IV Clone and Emergence of Clones for Methicillin-Resistant Staphylococcus aureus Clinical Isolates Collected from a Tertiary Teaching Hospital Over a Two-Year Period

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common nosocomial pathogens, causing mild to severe infections. This study aimed to determine the genotypic and phenotypic characteristics of clinical MRSA isolates collected from a teaching hospital from 2014 - 2015. These isolates were genotyped by multilocus sequence typing, staphylococcal cassette chromosomal mec (SCCmec) typing, virulence genes detection, and pulsed-field gel electrophoresis; they were phenotyped based on their antibiotics susceptibility profiles. The most prevalent sequence type was ST22. ST3547 was identified from a blood isolate from 2015. Three SCCmec types (III in 26.26%, IV in 70.71%, and V in 3.03% isolates) were detected. Agr type I, II, and III were also detected among the isolates. The most prevalent virulence genes found were hemolysin (100%) and intracellular adhesion (91.9%). At least one staphylococcal enterotoxin was detected in 83 (83.8%) isolates. All the isolates were susceptible to vancomycin (minimum inhibitory concentration ≤ 2 μg/mL). Statistical analysis revealed a significant increase in hypertension (p = 0.035), dyslipidemia and obesity (p = 0.046), and previous exposure to any quinolone (p = 0.010) cases over the two-year period. The emergence and circulation of community-associated MRSA variants were observed in our hospital.

Dyadobacter luticola sp. nov., isolated from a sewage sediment sample

A Gram-stain-negative, non-motile, aerobic bacterial strain, designated T17^T was isolated from a sample of sewage sediment from a Busan park (Republic of Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain T17^T had the highest 16S rRNA gene sequence similarity to Dyadobacter soli KCTC 22481^T (97.3 %), D.yadobacter fermentans DSM 18053^T (97.1 %) and D.yadobacter sediminis CGMCC 1.12895^T (97.1 %). The isolate exhibited relatively low levels of DNA-DNA relatedness with respect to D. soli KCTC 22481^T (28.2±3.6 %). The DNA G+C content was 49.1 mol%. The unique respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, five unidentified lipids, four aminolipids, two unidentified phospholipids and one glycophospholipid. The predominant cellular fatty acids (>5 % of total) were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 44.3 %), iso-C15 : 0 (15.7 %), C16 : 1ω5c (9.6 %), iso-C17 : 0 3-OH (9.3 %) and C16 : 0 (5.6 %). Moreover, physiological and biochemical characteristics distinguished strain T17^T from its related species, including temperature and pH ranges for growth, being positive for acetate hydrolysis, and being negative for acid produced from melibiose and rhamnose. The genotypic, chemotaxonomic and phenotypic data revealed that strain T17^T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter luticola sp. nov. is proposed. The type strain is T17^T (=KCTC 52981^T=CCTCC AB 2017091^T).

Phenotypic Detection of Carbapenemase-Producing Organisms from Clinical Isolates

The rapid spread of multidrug-resistant Gram-negative organisms constitutes one of the greatest challenges to global health. While Gram-negative organisms have developed several mechanisms to avert the bactericidal effects of commonly prescribed antibiotic agents, the increasing prevalence of carbapenemase-producing organisms (CPO) is particularly concerning given the rapid spread of mobile genetic elements containing carbapenemase genes, the limited treatment options for infections caused by these organisms, and the high mortality rates associated with CPO infections. Understanding if an organism is carbapenemase producing and, if so, the class of carbapenemase(s) produced has treatment implications, as some agents preferentially have activity against specific carbapenemases. Furthermore, CPO disseminate between patients with greater ease than non-CP-carbapenem-resistant organisms and warrant more intensive infection control measures than would be employed in the absence of carbapenemase production. Phenotypic assays currently used in clinical practice to detect CPO consist of the following: (i) growth-based assays which measure carbapenem resistance based on organism growth in the presence of a carbapenem antibiotic (e.g., modified Hodge test and modified carbapenem inactivation method), (ii) hydrolysis methods which detect carbapenem degradation products (e.g., Carba NP test and matrix-assisted laser desorption-ionization time of flight mass spectrometry), and (iii) lateral flow immunoassays which detect carbapenemase enzymes through the use of specific antibodies. Although there is no single phenotypic test that meets all specifications of the ideal test, as we describe in this review, there are a number of tests that are user-friendly, affordable, accurate, and feasible for implementation in clinical microbiology laboratories of all sizes.

Genetic and phenotypic characterization of the native rabbits in Middle Egypt

Aim:

Native rabbits in smallholder system are considered as important genetic resources, and the present study was aimed to study the genetic and phenotypic characterization and detection of the maternal origin of the native rabbit populations located at the Middle of Egypt.

Materials and Methods:

A survey of native rabbit populations was conducted in three governorates (Fayum [FY], Beni Suef [BN], and El Menia [MN]). The phenotypic characterization of rabbits included the profile body of the head, ears, eyes, neck, and legs and the coat colors. The blood samples were collected for genetic characterization based on mitochondrial (cytochrome b) and the microsatellite markers.

Results:

The phenotypic characterization of the body parts in the three populations was almost similar. The body weight of the mature rabbits in MN Government was significantly heaviest, and the measurements for the main body parts (body length, chest circumference, and abdominal girth) were the highest compared to the two populations. The results of mitochondrial (cytochrome b) analysis revealed that the rabbits from the three governments belonged to lineage A except one animal was recorded as lineage G from MN’s rabbit population. The results of the microsatellite markers revealed that the genetic diversity between the three populations showed genetic interferences; however, a closer genetic relationship was observed between BN and MN than FY. The majority of the genetic diversity was the individual variability.

Conclusion:

The mitochondrial lineage A is the major lineage in rabbit populations in the area of the Middle Egypt understudy. The genetic populations’ structure is the interferences among the three populations. A large-scale survey should be done on native rabbit populations for the sustainable management and conservation of the local breeds’ genetic resources.

Advanced Development of Primary Pancreatic Organoid Tumor Models for High-Throughput Phenotypic Drug Screening

Traditional high-throughput drug screening in oncology routinely relies on two-dimensional (2D) cell models, which inadequately recapitulate the physiologic context of cancer. Three-dimensional (3D) cell models are thought to better mimic the complexity of in vivo tumors. Numerous methods to culture 3D organoids have been described, but most are nonhomogeneous and expensive, and hence impractical for high-throughput screening (HTS) purposes. Here we describe an HTS-compatible method that enables the consistent production of organoids in standard flat-bottom 384- and 1536-well plates by combining the use of a cell-repellent surface with a bioprinting technology incorporating magnetic force. We validated this homogeneous process by evaluating the effects of well-characterized anticancer agents against four patient-derived pancreatic cancer KRAS mutant-associated primary cells, including cancer-associated fibroblasts. This technology was tested for its compatibility with HTS automation by completing a cytotoxicity pilot screen of ~3300 approved drugs. To highlight the benefits of the 3D format, we performed this pilot screen in parallel in both the 2D and 3D assays. These data indicate that this technique can be readily applied to support large-scale drug screening relying on clinically relevant, ex vivo 3D tumor models directly harvested from patients, an important milestone toward personalized medicine.

A systematic review and meta-analysis of genotypic methods for detecting antibiotic resistance in Helicobacter pylori

BACKGROUND

Antibiotic susceptibility testing is essential for tailored treatments to cure Helicobacter pylori (H. pylori) infection. However, phenotypic methods have some limitations.

OBJECTIVES

To evaluate the feasibility of genotypic detection methods compared with phenotypic detection methods using samples taken from H. pylori-infected patients.

METHODS

Literature searches were conducted in the following databases (from January 2000 to November 2016): PubMed, Embase, the Cochrane Library, and Web of Science. A meta-analysis and systematic review was performed for studies that compared genotypic methods with phenotypic methods for the detection of H. pylori antibiotic susceptibility.

RESULTS

This meta-analysis showed that the pooled sensitivity, specificity, and diagnostic odds ratio (DOR) for the A2142G/C and/or A2143G combination for the detection of clarithromycin resistance in the strain samples were 0.97 (95% CI: 0.94-0.99), 1.00 (95% CI: 0.99-1.00), and 13 742 (95% CI: 1708-110 554), respectively. The pooled sensitivity, specificity, and DOR for the A2142G/C and/or A2143G combination for the detection of clarithromycin resistance in biopsy samples were 0.96 (95% CI: 0.90-0.99), 0.96 (95% CI: 0.91-0.99), and 722 (95% CI: 117-4443), respectively. The summarized sensitivity, specificity, and DOR value for the ability of the genotypic methods to detect quinolone resistance in biopsy specimens were 0.97 (95% CI: 0.87-0.99), 0.99 (95% CI: 0.92-1.00), and 6042 (95% CI: 486-75 143), respectively.

CONCLUSION

The genotypic detection methods were reliable for the diagnosis of clarithromycin and quinolone resistance in the strain and biopsy specimens. The A2142G/C and/or A2143G combination had the best sensitivity and specificity for the detection of clarithromycin resistance.

Multicenter Evaluation of the Accelerate PhenoTest BC Kit for Rapid Identification and Phenotypic Antimicrobial Susceptibility Testing Using Morphokinetic Cellular Analysis

We describe results from a multicenter study evaluating the Accelerate Pheno system, a first of its kind diagnostic system that rapidly identifies common bloodstream pathogens from positive blood cultures within 90 min and determines bacterial phenotypic antimicrobial susceptibility testing (AST) results within ∼7 h. A combination of fresh clinical and seeded blood cultures were tested, and results from the Accelerate Pheno system were compared to Vitek 2 results for identification (ID) and broth microdilution or disk diffusion for AST. The Accelerate Pheno system accurately identified 14 common bacterial pathogens and two Candida spp. with sensitivities ranging from 94.6 to 100%. Of fresh positive blood cultures, 89% received a monomicrobial call with a positive predictive value of 97.3%. Six common Gram-positive cocci were evaluated for ID. Five were tested against eight antibiotics, two resistance phenotypes (methicillin-resistant Staphylococcus aureus and Staphylococcus spp. [MRSA/MRS]), and inducible clindamycin resistance (MLSb). From the 4,142 AST results, the overall essential agreement (EA) and categorical agreement (CA) were 97.6% and 97.9%, respectively. Overall very major error (VME), major error (ME), and minor error (mE) rates were 1.0%, 0.7%, and 1.3%, respectively. Eight species of Gram-negative rods were evaluated against 15 antibiotics. From the 6,331 AST results, overall EA and CA were 95.4% and 94.3%, respectively. Overall VME, ME, and mE rates were 0.5%, 0.9%, and 4.8%, respectively. The Accelerate Pheno system has the unique ability to identify and provide phenotypic MIC and categorical AST results in a few hours directly from positive blood culture bottles and support accurate antimicrobial adjustment.

The Slow March toward Rapid Phenotypic Antimicrobial Susceptibility Testing: Are We There Yet?

Antimicrobial susceptibility testing (AST) provides critical information for the management of patients with infections. The gold standard methods for assessing organism susceptibility are still based on growth and require incubation over relatively long periods of time. Until now, little progress has been made in developing rapid, growth-based, phenotypic AST systems. This commentary puts the recently FDA-cleared Accelerate PhenoTest (P. Pancholi et al., J Clin Microbiol 56:e01329-17, 2018, https://doi.org/10.1128/JCM.01329-17) in context by providing a historical perspective on attempts to accelerate phenotypic susceptibility results. In addition, some promising new innovations that promise to shorten the turnaround time for phenotypic AST will be briefly reviewed.

Deinococcus rufus sp. nov., isolated from soil near an iron factory

A Gram-stain-negative, non-motile, rod-shaped, red-pigmented strain, designated W37^T, was isolated from soil near an iron factory in Busan (Republic of Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W37^T was most closely related to Deinococcus yunweiensis YIM 007^T (98.3 %) and Deinococcus radioresistens 8A^T (96.3 %). The DNA-DNA relatedness between strain W37^T and D. yunweiensis YIM 007^T was 50.5 %. The predominant respiratory quinone was MK-8. The major polar lipids were an unidentified phosphoglycolipid, an unidentified aminophospholipid, four unidentified glycolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids (>5 %) of strain W37^T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and iso-C17 : 1ω9c. The DNA G+C content was 69.0 mol%. Moreover, the chemo-physical characteristics of strain W37^T clearly differed from those of related species, including ranges of growth temperature and pH, positive activity for 4-hydroxybenzoate and negative activity for cystine arylamidase. Phenotypic, chemotaxonomic and genotypic analyses indicated that strain W37^T represents a novel species of the genus Deinococcus, for which the name Deinococcus rufus sp. nov., is proposed. The type strain is W37^T (=KCTC 33913^T=CCTCC AB 2017081^T).

Phenotypic and Molecular Identification of Vancomycin Resistance in Clinical Staphylococcus Aureus Isolates in Osogbo, Nigeria

The use of vancomycin for treatment of serious infections caused by MRSA strains has resulted in emergence of vancomycin-resistant Staphylococcus aureus (VRSA) in clinical settings. Following our previous report of phenotypic VRSA in Nigeria, the current study attempts to determine the genetic basis underlying this resistance. Over a period of 6 months, non-duplicate clinical S. aureus isolates from 73 consecutive patients with infective conditions at Ladoke Akintola University of Technology Teaching Hospital, Osogbo were tested against a panel of eight selected antibiotics by disk diffusion test. The Epsilom test strip was used to determine vancomycin minimum inhibitory concentration (MIC) and polymerase chain reaction (PCR) assay to amplify nuc, mecA, vanA, and vanB genes. Of 73 isolates, 61 (83.6%) had MIC of ≤2 μg/ml, 11 (15.1%) had 4-8 μg/ml and 1 (1.4%) had 16 μg/ml. The mecA gene was detected in 5 (6.8%) isolates but none contained vanA or vanB genes. Both vancomycin-susceptible and intermediate isolates were resistant to multiple antibiotics, while the only vancomycin resistant isolate was resistant to all eight antibiotics. The result confirms the occurrence of phenotypic vancomycin intermediate-resistant S. aureus (VISA) and VRSA infections in Nigeria, but the molecular basis will require further investigation.

Phenotypic Detection of Extended Spectrum Beta lactamase and Carbapenemase Co-producing Clinical Isolates from Two Tertiary Hospitals in Kano, North West Nigeria

BACKGROUND

Continue rise in unprofessional use of antibiotics in our hospitals and communities is worrisome. A research study was therefore conducted to detect extended spectrum beta-lactamase (ESBL), carbapenemase, metallobeta lactamase and their co-production phenotypically from isolates obtained from patients admitted to or attending two tertiary hospitals in Kano, Nigeria.

METHOD

A total of 248 isolates of Escherichia coli and Klebsiella pneumoniaewere screened phenotypically for ESBL production and carbapenemase production according to CLS1 2012 breakpoints using double disk synergy test and modified Hodge test (MHT) respectively. Antibiotic susceptibility of the organisms was tested against colistin, tigecycline and 3 flouroquinolones.

RESULTS

The result shows that 58.0% of the isolates were ESBL producers with higher percentage in K. pneumoniae (62.9%). Further, about 40.3% and 36.6% of the isolates were resistant to meropenem and imipenem respectively. However, E. coli showed higher resistance to meropenem (47.1%) while K. pneumoniae showed higher resistance to imipenem (44.4%). Co-productions of carbapenemase and ESBL were observed in both E. coli and K. pneumoniae. Carbapenemase producing isolates were more obtained from uro-pathogens and wound isolates, with almost all the cases of co-production of the β lactamases occurring in urine and cathertips isolates. Overall susceptibilities of the isolates to colistin and tigecycline were 64.6and70.0% respectively, but isolates were less susceptible to flouroquinolones.

CONCLUSION

The finding of the study therefore indicates that carbapenem resistance is mediated by carbapenemase production and or overproduction of ESBL coupled with reduced porins. Co-production of carbapenemase, MBLs and ESBLs by some of the isolates is worrisome. Susceptibility to colistin and tigecycline was still promising, but increasing resistance to flouroquinolones has been observed.