scholarly journals Distribution of Biofilm-associated Genes among Acinetobacter baumannii by in-silico PCR

2021 ◽  
pp. 140-149
Author(s):  
A. Aldrin Joshua ◽  
A. S. Smiline Girija ◽  
P. Sankar Ganesh ◽  
J. Vijayashree Priyadharsini
Keyword(s):  
Acinetobacter Baumannii ◽  
In Silico ◽  
Target Genes ◽  
Multidrug Resistant ◽  
Pcr Analysis ◽  
Evolutionary Analysis ◽  
Ompa Gene ◽  
Clinical Strains ◽  
Tract Infections ◽  
In Silico Pcr

Background: Acinetobacter baumannii is a coccobacillus that is Gram negative, non motile, non fermentative and oxidase negative. It is the most common and successful nosocomial pathogen recognised by WHO. This dreadful pathogen causes urinary tract infections, ventilator associated pneumonia (VAP), bacteremia, etc., These infections are most common in hospital wards especially Intensive Care Unit (ICU). The infections are due to biofilm formation by the virulent genes of A. baumannii, and the common biofilm-associated genes of A. baumannii were bap, csuE, fimH, epsA, bfmS, ptk, pgaB, ompA, blaPER-1. Among these, bap, epsA and ompA genes are highly prevalent among the clinical strains of A. baumannii. Aim:  To detect the three vital biofilm-associated genes of A. baumannii by in-silico PCR analysis. Materials and Methods: 19 isolates of A. baumannii were selected and 3 target genes, namely epsA, ompA and bap gene were used for the amplification process through in-silico PCR simulation tools. Evolutionary analysis was done for the ompA gene. Results: The epsA gene was expressed in 10.52% of the total strains selected with the highest occurrence of ompA gene as 57.89%. bap gene was not observed from the study strains included. From evolutionary analysis based on ompA distributed strains, the Acinetobacter baumannii SDF and Acinetobacter baumannii BJAB0715 might be the parental strains where the evolution of strains would have started. Through successive generations, the Acinetobacter baumannii MDR-ZJ06 and Acinetobacter baumannii TYTH-1 had become the multidrug resistant strains present in the environment. Conclusion: The findings of the study confirms the distribution of epsA and ompA genes among the 19 different strains of A. baumannii. The study suggests periodical monitoring of biofilm based virulence genes among the clinical strains and to curtail the A. baumannii infections.

scholarly journals Distribution of Four Biofilm Associated Gene among A. baumannii by in Silico-PCR

2021 ◽  
pp. 317-324
Author(s):  
J. D. Monesh Babu ◽  
A. S. Smiline Girija ◽  
P. Sankar Ganesh ◽  
J. Vijayashree Priyadharsini
Keyword(s):  
Acinetobacter Baumannii ◽  
In Silico ◽  
Biofilm Formation ◽  
Experimental Validation ◽  
Pcr Amplification ◽  
Opportunistic Pathogen ◽  
Clinical Strains ◽  
Oral Biofilms ◽  
Different Strains ◽  
In Silico Pcr

Background: A.baumannii is an opportunistic pathogen known for its efficient biofilm formation that is attributed for its virulence. Acinetobacter baumannii is an inhabitant of oral biofilms as well. Many gene operons are involved in the biofilm formation that need to be monitored frequently. Aim: The aim of the present study was to detect the distribution of four biofilm associated genes among A.baumannii. Materials and Methods: Four biofilm forming genes viz., bfms, ptk, pgaB, and fimH of A.baumannii were selected. Forward and reverse primers of those four genes were used for in-silico PCR amplification. 19 strains of A.baumannii set as default on the server were chosen and the amplicon bands were observed Results: The present investigation documents the distribution of four vital biofilm associated gene among 19 different strains of A.baumannii among which bfms was distributed at a higher frequency followed by pgaB and ptk Conclusion: The finding of the study suggests the presence of pgaB, bfms, ptk among the 19 different strains of A.baumannii. However further experimental validation must be done to frequently monitor the presence of the genes among the clinical strains of A.baumannii.

scholarly journals Plasmid Derived AmpC Genotypes among the Multidrug Resistant Enterobacteriaceae Strains Isolated from Urine Samples in Southern India

2021 ◽  
Author(s):  
P Ronni Mol ◽  
Ganesan Shanthi ◽  
Khalid Bindayna
Keyword(s):  
Clinical Laboratory ◽  
Multidrug Resistant ◽  
Cross Sectional Study ◽  
Urine Samples ◽  
Pcr Analysis ◽  
Genotype Distribution ◽  
Cross Sectional ◽  
Beta Lactamases ◽  
Hospital Infection Control ◽  
Tract Infections

Introduction: The most common pathogens causing Urinary Tract Infections (UTI) in community and hospital settings are Enterobacteriaceae. Antibiotic resistance is a major problem worldwide because of an increase in the use of antibiotics. Production of Extended Spectrum Beta-Lactamases (ESBLs) and AmpC beta-lactamases is the most common cause of resistance among Enterobacteriaceae (AmpC). Initially, AmpC β-lactamases received less attention globally, but now it has become a rising problem. Detection of AmpC β-lactamases expressing microbes is a requirement for addressing surveillance, for problems of hospital infection control, and for choosing optimal antimicrobial therapy. Aim: To study the genotype distribution of plasmid mediated AmpC β-lactamase produced in Enterobacteriaceaestrains isolated from urine samples. Materials and Methods: A cross-sectional study based on clinical laboratory surveillance was conducted from July 2019 to February 2020. Sixty Enterobacteriaceae isolates were identified by standard biochemical reactions. AmpC screening were done by cefoxitin disk diffusion and confirmed by an inhibitor-based assay using boronic acid. The presence of six plasmid mediated AmpC genes was determined by multiplex Polymerase Chain Reaction (PCR). Statistical Package for the Social Science (SPSS) version 20.0 was used to obtain descriptive data. Results: Among 60 Enterobacteriaceae isolates, 23 (38.3%) were cefoxitin-resistant isolates which contain Escherichia colistrain (n=17) while the remaining samples consist ofKlebsiella pneumoniae (n=5) and Proteus mirabilis strains (n=1). AmpC β-lactamase production was phenotypically confirmed in 12(20%) isolates and genotypically confirmed by PCR analysis in 16(26.6%) of all the urine isolates. In the present study, 3(13%), 2 (8.6%) of cefoxitin resistant isolates harboured the DHA, EBC gene and 1(4.3%) each harboured FOX and CIT gene, and 9(39.1%) harboured a combination of the genes. Conclusion: The present study suggested the predominant existence of plasmid mediated AmpC producers in Multi-Drug Resistant (MDR) Escherichia coli and Klebsiella pneumoniae. We suggest continuous surveillance is important to effectively control the spread of these strains and for optimal clinical outcome.

scholarly journals Draft Genome Sequences of Two Carbapenemase-Producing Acinetobacter baumannii Clinical Strains Isolated from Albanian and Togolese Patients

2017 ◽  
Vol 5 (20) ◽  
Author(s):  
Mohamed M. H. Abdelbary ◽  
Guy Prod’hom ◽  
Gilbert Greub ◽  
Laurence Senn ◽  
Dominique S. Blanc
Keyword(s):  
Acinetobacter Baumannii ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
University Hospital ◽  
Genome Sequences ◽  
Content Type ◽  
Clinical Strains

ABSTRACT We report here the draft genome sequences of two multidrug-resistant Acinetobacter baumannii clinical strains, H31499 and H31506, which were isolated at the Lausanne University Hospital in 2015 from an Albanian and a Togolese patient, respectively.

scholarly journals KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping

2019 ◽  
Vol 35 (17) ◽  
pp. 3187-3190 ◽  
Author(s):  
Alsamman M Alsamman ◽  
Shafik D Ibrahim ◽  
Aladdin Hamwieh
Keyword(s):  
High Throughput ◽  
In Silico ◽  
Genetic Maps ◽  
Supplementary Information ◽  
Pcr Analysis ◽  
Analysis Tool ◽  
Data Types ◽  
Kasp Assay ◽  
In Silico Pcr

Abstract Motivation Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool. Results To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results. Availability and implementation Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon). Supplementary information Supplementary data are available at Bioinformatics online.

Antibiotic Resistance and Phylogenetic Characterization of Acinetobacter baumannii Strains Isolated from Commercial Raw Meat in Switzerland

2014 ◽  
Vol 77 (11) ◽  
pp. 1976-1981 ◽  
Author(s):  
AGNESE LUPO ◽  
DEBORA VOGT ◽  
SALOME N. SEIFFERT ◽  
ANDREA ENDIMIANI ◽  
VINCENT PERRETEN
Keyword(s):  
Acinetobacter Baumannii ◽  
Antibiotic Susceptibility ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Fourth Generation ◽  
Pcr Analysis ◽  
Resistant Bacteria ◽  
Human Pathogens ◽  
Raw Meat ◽  
Phylogenetic Characterization

The spread of antibiotic-resistant bacteria through food has become a major public health concern because some important human pathogens may be transferred via the food chain. Acinetobacter baumannii is one of the most life-threatening gram-negative pathogens; multidrug-resistant (MDR) clones of A. baumannii are spreading worldwide, causing outbreaks in hospitals. However, the role of raw meat as a reservoir of A. baumannii remains unexplored. In this study, we describe for the first time the antibiotic susceptibility and fingerprint (repetitive extragenic palindromic PCR [rep-PCR] profile and sequence types [STs]) of A. baumannii strains found in raw meat retailed in Switzerland. Our results indicate that A. baumannii was present in 62 (25.0%) of 248 (CI 95%: 19.7 to 30.9%) meat samples analyzed between November 2012 and May 2013, with those derived from poultry being the most contaminated (48.0% [CI 95%: 37.8 to 58.3%]). Thirty-nine strains were further tested for antibiotic susceptibility and clonality. Strains were frequently not susceptible (intermediate and/or resistant) to third- and fourth-generation cephalosporins for human use (i.e., ceftriaxone [65%], cefotaxime [32%], ceftazidime [5%], and cefepime [2.5%]). Resistance to piperacillin-tazobactam, ciprofloxacin, colistin, and tetracycline was sporadically observed (2.5, 2.5, 5, and 5%, respectively), whereas resistance to carbapenems was not found. The strains were genetically very diverse from each other and belonged to 29 different STs, forming 12 singletons and 6 clonal complexes (CCs), of which 3 were new (CC277, CC360, and CC347). Rep-PCR analysis further distinguished some strains of the same ST. Moreover, some A. baumannii strains from meat belonged to the clonal complexes CC32 and CC79, similar to the MDR isolates responsible for human infections. In conclusion, our findings suggest that raw meat represents a reservoir of MDR A. baumannii and may serve as a vector for the spread of these pathogens into both community and hospital settings.

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