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226800.9976Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS. BACKGROUND: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS). METHODS: A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis. RESULTS: A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL(B) and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL(B) and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples. CONCLUSION: High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL(B) and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.202134866919
222010.9975Rapid detection and molecular survey of blaVIM, blaIMP and blaNDM genes among clinical isolates of Acinetobacter baumannii using new multiplex real-time PCR and melting curve analysis. BACKGROUND: Acinetobacter baumannii is a cosmopolitan bacterium that is frequently reported from hospitalized patients, especially those patients who admitted in the intensive care unit. Recently, multiplex real-time PCR has been introduced for rapid detection of the resistance genes in clinical isolates of bacteria. The current study aimed to develop and evaluate multiplex real-time PCR to detect common resistance genes among clinical isolates of A. baumannii. RESULTS: Multiplex real-time PCR based on melting curve analysis showed different T(m) corresponding to the amplified fragment consisted of 83.5 °C, 93.3 °C and 89.3 °C for blaIMP, blaVIM and blaNDM, respectively. Results of multiplex real-time PCR showed that the prevalence of blaIMP, blaVIM and blaNDM among the clinical isolates of A. baumannii were 5/128(3.9%), 9/128(7.03%) and 0/128(0%), respectively. Multiplex real-time PCR was able to simultaneously identify the resistance genes, while showed 100% concordance with the results of conventional PCR. CONCLUSIONS: The current study showed that blaVIM, was the most prevalent MBL gene among the clinical isolates of A. baumannii while no amplification of blaNDM was seen. Multiplex real-time PCR can be sensitive and reliable technique for rapid detection of resistance genes in clinical isolates.201931182026
217520.9975Drug-resistant genes carried by Acinetobacter baumanii isolated from patients with lower respiratory tract infection. BACKGROUND: Acinetobacter baumanii (A. baumanii ) remains an important microbial pathogen resulting in nosocomial acquired infections with significant morbidity and mortality. The mechanism by which nosocomial bacteria, like A. baumanii, attain multidrug resistance to antibiotics is of considerable interest. The aim in this study was to investigate the spread status of antibiotic resistance genes, such as multiple β-lactamase genes and aminoglycoside-modifying enzyme genes, from A. baumanii strains isolated from patients with lower respiratory tract infections (LRTIs). METHODS: Two thousand six hundred and ninety-eight sputum or the bronchoalveolar lavage samples from inpatients with LRTIs were collected in 21 hospitals in the mainland of China from November 2007 to February 2009. All samples were routinely inoculated. The isolated bacterial strains and their susceptibility were analyzed via VITEK-2 expert system. Several kinds of antibiotic resistant genes were further differentiated via polymerase chain reaction and sequencing methods. RESULTS: Totally, 39 A. baumanii strains were isolated from 2698 sputum or bronchoalveolar lavage samples. There was not only a high resistant rate of the isolated A. baumanii strains to ampicillin and first- and second-generation cephalosporins (94.87%, 100% and 97.44%, respectively), but also to the third-generation cephalosporins (ceftriaxone at 92.31%, ceftazidine at 51.28%) and imipenem (43.59%) as well. The lowest antibiotic resistance rate of 20.51% was found to amikacin. The OXA-23 gene was identified in 17 strains of A. baumanii, and the AmpC gene in 23 strains. The TEM-1 gene was carried in 15 strains. PER-1 and SHV-2 genes were detected in two different strains. Aminoglycoside-modifying enzyme gene aac-3-Ia was found in 23 strains, and the aac-6'-Ib gene in 19 strains. aac-3-Ia and aac-6'-Ib genes hibernated in three A. baumanii strains that showed no drug-resistant phenotype. CONCLUSIONS: A. baumanii can carry multiple drug-resistant genes at the same time and result in multi-drug resistance. Aminoglycoside-modifying enzyme genes could be hibernating in aminoglycoside sensitive strains without expressing their phenotype.201021034630
234730.9974Multiple drug resistance of Listeria monocytogenes isolated from aborted women by using serological and molecular techniques in Diwaniyah city/Iraq. BACKGROUND AND OBJECTIVES: The study was sought to detect the effect of Listeria monocytogenes on pregnant Iraqi women at Al-Diwaniya hospitals and determination of virulence genes and antimicrobial susceptibility of isolates. MATERIALS AND METHODS: 360 specimens including blood, urine, vaginal and endocervical were collected from 90 patients with spontaneous abortions. Blood samples were displayed to immunological study and remaining specimens were subjected to bacteriological diagnosis. PCR was used to determine the virulence factors and antimicrobial resistance genes. RESULTS: Fifteen positive samples (16.6%) of patients and thirteen isolates (14.5%) from patients were recognized based on ELISA and PCR assay respectively. The general isolation of L. monocytogenes strains in cases of abortive women was 13/270 (4.8%). L. monocytogenes strains were highly virulent because of presence of virulence factors associated genes, namely actA, hlyA, plcA and prfA in all strains. Multiple drug resistance (MAR) index values of 15.4% of isolates were >0.2. CONCLUSION: It is necessary for conducting susceptibility testing and to select the suitable antibiotics and avoid the effects of these bacteria in pregnant women.202032994901
146140.9974Phenotypic and Genetic Characterization of Carbapenemase and ESBLs Producing Gram-negative Bacteria (GNB) Isolated from Patients with Cystic Fibrosis (CF) in Tehran Hospitals. BACKGROUND: Cystic Fibrosis (CF) is an autosomal recessive genetic disorder in white populations caused by mutation in a gene that encodes Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. Since frequent respiratory tract infections are the major problem in patients with CF, obligation to identify the causative bacteria and determining their antibiotic resistance pattern is crucial. The purpose of this project was to detect Gram-negative bacteria (GNB) isolated from sputa of CF patients and to determine their antibiotic resistance pattern. MATERIALS AND METHODS: The sputum of 52 CF patients, treated as inpatients at hospitals in Tehran, was obtained between November 2011 and June 2012. Samples cultured in selective and non-selective media and GNB recognized by biochemical tests. Antimicrobial susceptibility testing to cephalosporins, aminoglycosides and carbapenems was performed by disk diffusion method and MICs of them were measured. For phenotypic detection of carbapenemase and ESBLs production, the Modified Hodge test, double disk synergy test and the combined disk methods were performed. Subsequently, the genes encoding the extended spectrum beta-lactamases (blaPER, blaCTX-M) and carbapenemases (blaIMP-1, blaGES, blaKPC, blaNDM, blaVIM-1, blaVIM-2, blaSPM, blaSIM) in Gram negative bacteria were targeted among the resistant isolates by using PCR. PFGE was used to determine any genetic relationship among the Pseudomonas aeruginosa isolated from these patients. RESULTS: Fifty five GNB were isolated from 52 sputum samples including Pseudomonas aeruginosa, Klebsiella ozaenae, Alcaligenes xylosoxidans, Achromobacter denitrificans, Klebsiella pneumonia and Stenotrophomonas maltophilia. The rates of resistance to different antibiotic were as follows: cefixime (%80), ceftriaxone (%43), ceftazidime (%45) and meropenem (%7). The prevalence of genes encoding the ESBLs and Carbapenemases among the the phenotypically positive strains were as follows: blaCTX-M (19), blaIMP-1 (2), blaVIM-1 (2) and blaVIM-2 (3) genes respectively. No other genes were detected. PFGE analysis revealed 8 genotypes. Six isolates had mutually 3 similar patterns. CONCLUSION: This study showed the existence of important ESBLs and carbapenemases genes among the GNB isolated from patients with CF. Continuous surveillance of ESBLs and Carbapenemases, also identification of their types, in bacteria isolated from these patients have an important clinical impact, since, it can often provide valuable information for effective infection control measures and for the choice of appropriate antimicrobial therapy.201424596716
148950.9974Direct detection of mecA, bla(SHV) , bla(CTX)(-M) , bla(TEM) and bla(OXA) genes from positive blood culture bottles by multiplex-touchdown PCR assay. Methicillin-resistant staphylococci (MRS) and ESBL(Extended-Spectrum β-Lactamase)-producing bacteria are the most important resistant pathogens in sepsis. In this study, a new multiplex-touchdown PCR method (MT-PCR) was developed to detect rapidly and simultaneously the presence of mecA, bla(SHV) , bla(CTX)(-M) , bla(TEM) and bla(OXA) genes from positive blood culture bottles. The technique showed a sensitivity of 10(3 ) CFU ml(-1) for mecA detection and of 10(2)  CFU ml(-1) for other genes, and 100% specificity in the detection of all genes. All genes were detected in the spiked blood culture bottles artificially contaminated with reference strains. Three methicillin-resistant S. aureus (MRSA), two methicillin-resistant S. epidermidis (MRSE) and 32 ESBL-producing bacteria, were isolated from the clinical blood culture specimens in 48 h by standard microbiological procedures. The corresponding genes were detected directly in the three MRSA, two MRSE and 29 ESBL-producing bacteria from the clinical blood culture specimens in 4 h by MT-PCR assay. None of the bla(SHV) , bla(CTX)(-M) , bla(TEM) and bla(OXA) genes were detected in three other bottles with ESBL-producing bacteria because of other ESBL genotypes in the pathogens. Likewise, all bottles proven negative by culture remained negative by PCR. The proposed method was rapid, sensitive and specific, and was able to directly detect the genes of MRS and ESBL-producing bacteria from the blood culture bottles. SIGNIFICANCE AND IMPACT OF THE STUDY: Many studies on the development of PCR for the detection of resistance genes have already been published, including multiplex PCR methods. However, cross-amplification reactions can be a major concern in multiplex PCR methods. In this study, we developed a highly sensitive and specific multiplex-touchdown PCR assay for simultaneous detection of mecA, bla(SHV) , bla(CTX)(-M) , bla(TEM) and bla(OXA) genes from positive blood culture bottles, cross-amplification was absent and false-positive results were not obtained.201727699804
220260.9974EVALUATION THE PREVALENCE OF MULTIDRUG RESISTANCE BACTERIA AMONG IRAQI PATIENTS AND ITS ASSOCIATION WITH PATIENTS' PREDICTIVE FACTORS: A CROSS-SECTIONAL STUDY. OBJECTIVE: The aim: The study aimed to evaluate the prevalence of multidrug resistance bacteria (MDR),, it's types and explore the patient's predictive factors associated with it. PATIENTS AND METHODS: Materials and methods: The study was a cross-sectional observational study conducted in a microbiology lab in AL-Zahraa Teaching Hospital and Alsader Medical City, in Najaf Province, Iraq. The participants included patients presented with different kinds of infections and caused by organisms isolated from different sources. The patients had positive growth media were 304 out of total 475 patients. RESULTS: Results: The data extraction sheet included the laboratory culture and sensitivity report and patient sociodemographic factors and risk factors. The study displayed an extremely high prevalence of MDR bacteria 88% and the prevalence of extensive drug resistance (XDR) was 23%, whereas Pan-drug resistance (PDR) prevalence was 2%. Specifically, Methicillin resistance Staphylococcus Aureus (MRSA) was detected in 73% of the total patients infected with Staph. Bacteria. The prevalence of Extended spectrum beta-lactamases (ESBLs) was reached to 56% among the patients infected with Enterobacteria, while carbap¬enem resistance (CR) was recorded in 25% of the patients infected with different kinds of bacteria. Only education level was significantly associated with the prevalence of MDR. Patients with (college/post-graduate) education were associated with a low incidence of MDR. CONCLUSION: Conclusions: A very high prevalence of multidrug resistance bacteria was noted in patients with a bacterial infection. Among all patients' characters, only higher education was associated with lower incidence.202337326087
222170.9974Rapid detection of blaKPC carbapenemase genes by real-time PCR. Carbapenem resistance among Enterobacteriaceae is an emerging problem worldwide. Klebsiella pneumoniae carbapenemase (bla(KPC)) enzymes are among the most common beta-lactamases described. In this study, we report the development and validation of a real-time PCR (q-PCR) assay for the detection of bla(KPC) genes using TaqMan chemistry. The q-PCR amplification of bla(KPC) DNA was linear over 7 log dilutions (r(2) = 0.999; slope, 3.54), and the amplification efficiency was 91.6%. The q-PCR detection limit was 1 CFU, and there was no cross-reaction with DNA extracted from several multidrug-resistant bacteria. Perianal/rectal swabs (n = 187) collected in duplicate from 128 patients admitted to Sheba Medical Center surgical intensive care units were evaluated for the presence of carbapenem-resistant bacteria by culturing on MacConkey agar-plus-carbapenem disks and for bla(KPC) genes by q-PCR. Carbapenem-resistant organisms, all K. pneumoniae, were isolated from 47 (25.1%) of the 187 samples collected, while bla(KPC) genes were detected in 54 (28.9%) of the patient samples extracted by the NucliSENS easyMAG system. Of these, seven samples were positive for bla(KPC) genes by q-PCR but negative for carbapenem resistance by culture, while all samples in which no carbapenem-resistant bacteria were detected by culture also tested negative by q-PCR. Thus, the sensitivity and specificity of the q-PCR assay after extraction by the NucliSENS easyMAG system were 100% and 95%, respectively. Similar values were obtained after DNA extraction by the Roche MagNA Pure LC instrument: 97.9% sensitivity and 96.4% specificity. Overall, the bla(KPC) q-PCR assay appears to be highly sensitive and specific. The utilization of q-PCR will shorten the time to bla(KPC) detection from 24 h to 4 h and will help in rapidly isolating colonized or infected patients and assigning them to cohorts.200818614657
219180.9974Microbial profile, antimicrobial resistance, and molecular characterization of diabetic foot infections in a university hospital. INTRODUCTION: Diabetic foot infections (DFIs) are among the most severe complications of diabetes. The aim of this study was to determine the etiological pathogens of DFIs in different Wagner's and IDSA/IWGDF grades, and to assess their antimicrobial susceptibility pattern together with molecular characterization of antibiotic resistance genes. METHODS: A prospective study was conducted on 120 DFI patients at Main Alexandria University Hospital, Egypt. The aerobic and anaerobic etiological pathogens were determined using semi-quantitative culture and PCR respectively. The antimicrobial susceptibility pattern was done according to Clinical Laboratory Standards Institute guidelines. Detection of carbapenemases and class-1 integron genes was carried out by polymerase chain reaction (PCR). RESULTS: A total of 178 (124 aerobic, 54 anaerobic) pathogens were identified from patients with DFI, with an average of 1.82 isolates/subject. Among aerobic pathogens, Gram-negative predominated (98/124; 79%), of which Pseudomonas spp. and Proteus spp. were the most common. MRSA constituted more than 50% of Gram-positive isolates. Polymicrobial infection was found in 42 (42.9%) subjects. The proportion of Gram-negative bacteria and anaerobes increased with increased DFI grades and severity. Multidrug and extensively drug resistant isolates were observed in 86 patients (87.7%). PCR identified carbapenemases genes in 14 (11.7%) and class 1 integron in 28 (23.3%) DFI cases. Vancomycin, teicoplanin, linezolid were the most effective antimicrobial agents against Gram-positive pathogens, while colistin, imipenem, meropenem, and piperacillin-tazobactam were effective against Gram-negative pathogens. CONCLUSIONS: Multidrug and extensively drug resistant Gram-negative bacteria were the dominant pathogens among all DFI severity grades. However, the proportion of Gram-positive bacteria decreased with the severity of infection. The clinical role of our relatively high rate of anaerobes should be investigated. The results found in this study could be beneficial for designing future empiric antimicrobial protocols in relation to the severity of DFIs.202133898340
213990.9974Study of Some Resistance Genes in Clinical Proteus mirabilis. Proteus mirabilis belongs to the family Enterobacteriaceae and is capable of transforming in shape from rod to elongated and swarming motility by flagella. It is an opportunity for bacteria and can cause different clinical diseases. Therefore, this study aimed to assay and detect a sequence of genes that encode for antibiotic resistance in multidrug resistance clinical isolates of Proteus mirabilis, including blaTEM, aac(6')-Ib, qnrA, IntI2, IntI1 and secondly to investigate the relationship in the phylogenetic tree among these genes in Iraq comparison with global strains in NCBI. The study included the identifying of 500 clinical samples depending on morphological and biochemical tests and confirming Proteus mirabilis diagnosis by the VITEK-2 Compact system. The confirmed isolates of Proteus mirabilis were 95 clinical isolates (19%). Antibiotic susceptibility test of all these isolates was done using twelve antibiotics tested using Amoxicillin, Aztreonam, Imipenem, Cefoxitin, Amikacin, Ceftazidem, Ciprofloxacin, Nalidixic acid, Gentamicin, Sulphamethazol-trimethoprim, Cefotaxime, Amoxicillin-clavulanic acid. The results showed that multidrug resistance Proteus mirabilis isolates contained the genes in different levels as follow blaTEM gene (90%), aac(6')-Ib gene (80%) ,IntI1 gene (100%), IntI2 gene (80%). These genes were sequenced and detected phylogenetic relationships among these genes and global genes were documented in NCBI. The results showed that some Iraqi isolates contain genetic variation compared to global strains. Therefore, this variation was detected and registered in NCBI of all five antibiotic resistance genes mentioned above and accepted under accession numbers of aacIb gene (LC613168.1), blaTEM gene (LC613166.1), IntI1 gene (LC613169.1), IntI2 gene (LC613170.1).202237274906
1481100.9974Molecular versus conventional assay for diagnosis of hospital-acquired pneumonia in critically ill patients: a single center experience. PURPOSE: Lower respiratory tract infections are reported as one of top five causes of mortality and morbidity in the world. A bacterial etiology is often involved in HAP, most frequently from multidrug resistant gram-negative bacteria, and fast accurate diagnosis of etiologic agent(s) of LRTI is essential for an appropriate management. The aim of this retrospective study was to evaluate the analytical performance of Biofire Filmarray Pneumonia Plus for bacteria detection in bronchoalveolar lavage samples and the concordance of bacterial loads between BFPP and cultural gold standard methods. METHODS: A total of 111 BAL samples were obtained from 111 consecutive patients admitted to Intensive Care Unit of "Renato Dulbecco" Teaching Hospital of Catanzaro, from March 2023 to March 2024. RESULTS: Compared to conventional methods, BFPP showed a sensitivity of 99 % and a specificity of 64 %. The agreement between the two methods was assessed by calculating PPA and NPA, being 89 % and 95 %, respectively. The most common bacterial species identified at BFPP was Klebsiella pneumoniae, followed by Acinetobacter calcaceuticus-baumanii complex, Staphylococcus aureus and Pseudomonas aeruginosa. Bacterial load (CFU/ml) in relation to copy number detected by molecular analysis showed the best performance for value ≥10(6) copie/mL. About molecular mechanisms of resistance in comparison to phenotypic profiles, the highest level of performance was observed for presence of KPC genes, all isolates showing resistance to carbapenems, followed by OXA-48 like and NDM. CONCLUSION: The high concordance reported in this study between the identification of resistance genes and phenotypic indication can lead to an appropriate, fast and tailored antibiotic therapy.202540513663
2173110.9973Antimicrobial susceptibility and integrons detection among extended-spectrum β-lactamase producing Enterobacteriaceae isolates in patients with urinary tract infection. BACKGROUND: Integrons are bacterial mobile genetic components responsible for mediating the antibiotic resistance process by carrying and spreading antimicrobial resistance genes among bacteria through horizontal gene transfer. OBJECTIVES: This cross-sectional hospital-based study aimed to find the prevalence of antibiotic resistance patterns and to detect integrons classes (I, II, and III) among bacterial isolates in patients with urinary tract infections (UTI) in Sulaimani, Iraq. PATIENTS AND METHODS: Mid-stream urine samples (no. = 400) were collected from patients with UTI at three different Hospitals from Sulaimani, Iraq, between September 2021 to January 2022. Urine samples were cultured on various agar media, and grown bacteria were isolated. Antibiotic susceptibility test (AST) and an extended-spectrum β-lactamase (ESBL) screen were done for isolated bacteria. Then, integrons classes were screened using conventional PCR with gene sequencing and uploaded to the National Center for Biotechnology Information (NCBI). RESULTS: The frequency rate of Enterobacteriaceae was 67.03% among positive urine cultures. E. coli (no. = 86) and Klebsiella pneumoniae (no. = 32) isolates were identified. The most sensitive antibiotics were the carbapenem group (85.3%) and nitrofurantoin (NFN) (64.2%), while the most resistant antibiotics were nalidixic acid (NA) and 3(rd) generation cephalosporin. The occurrence rate of ESBL was 56.6% with a predominance of class I integron (54.2%), then class II (15.8%) and no positive record for class III integron were observed. CONCLUSION: Most bacterial isolates from patients with UTI produced class I and II integrons genes with favourable ESBL properties.202337283901
1471120.9973Antimicrobial Resistance Pattern and Genetic Characteristics of ESBL and Carbapenemase-producing Escherichia coli at a Tertiary Care Hospital in Bangladesh. Uropathogenic Escherichia coli is frequently resistant to different antibiotic leading to a critical condition of the patients. The purpose of the present study was to see antibiotic resistance pattern and genetic characteristics of ESBL and Carbapenemase-producing Escherichia coli. This cross sectional study was conducted in the Department of Microbiology at Mymensingh Medical College, Mymensingh, Bangladesh from October 2014 to December 2015. Patients presented with clinically diagnosed urinary tract infection at any age with both sexes who attended in the OPD of Mymensingh Medical College Hospital and the Doctors Diagnostic Centre in Mymensingh, Bangladesh was selected as study population. Non duplicate clinical isolates from urine were collected in full aseptic precaution for culture of bacteria. Escherichia coli were confirmed by PCR Stargetingadk. Antimicrobial susceptibility was measured by broth microdilution test. Minimum inhibitory concentrations against 18 antimicrobial agents were measured. Beta-lactamase genes were detected by multiplex PCR. For all the isolates showing resistance to imipenem and/or meropenem, presence of carbapenemase genes was confirmed by multiplex/uniplex PCR using primers. A total of 233 non-duplicate clinical isolates of Escherichia coli were collected from patients of which dominant phylogenetic group was B2 which was 78(33.5%) isolates of which 71 isolates were B2a and 7 isolates were B2b. Furthermore, Group A was in 29.6% isolates and Group D was in 26.6% isolates. E. coli showed significantly higher resistance rates to piperacillin, cephalosporins, and some other antimicrobials. Meropenem-resistance was detected in 8.2% of E. coli. The detection rate of blaTEM was 41.6% in E. coli. Carbapenemase genes were detected in 9(3.9%) isolates of E. coli and identified as genes encoding NDM-1, -5, and 7 and OXA-181. All the blaNDM-positive E. coli isolates carried also blaCTX-M-15, except for a group B1 isolate. E. coli is significantly higher resistance rates to piperacillin, cephalosporins, and some other antimicrobials and possesses different ESBL and carbapenemase genes.202031915333
2234130.9973Clinical relevance of molecular identification of microorganisms and detection of antimicrobial resistance genes in bloodstream infections of paediatric cancer patients. BACKGROUND: Bloodstream infections (BSIs) are the major cause of mortality in cancer patients. Molecular techniques are used for rapid diagnosis of BSI, allowing early therapy and improving survival. We aimed to establish whether real-time quantitative polymerase chain reaction (qPCR) could improve early diagnosis and therapy in paediatric cancer patients, and describe the predominant pathogens of BSI and their antimicrobial susceptibility. METHODS: Blood samples were processed by the BACTEC system and microbial identification and susceptibility tests were performed by the Phoenix system. All samples were screened by multiplex 16 s rDNA qPCR. Seventeen species were evaluated using sex-specific TaqMan probes and resistance genes blaSHV, blaTEM, blaCTX, blaKPC, blaIMP, blaSPM, blaVIM, vanA, vanB and mecA were screened by SYBR Green reactions. Therapeutic efficacy was evaluated at the time of positive blood culture and at final phenotypic identification and antimicrobial susceptibility results. RESULTS: We analyzed 69 episodes of BSI from 64 patients. Gram-positive bacteria were identified in 61 % of the samples, Gram-negative bacteria in 32 % and fungi in 7 %. There was 78.2 % of agreement between the phenotypic and molecular methods in final species identification. The mecA gene was detected in 81.4 % of Staphylococcus spp., and 91.6 % were concordant with the phenotypic method. Detection of vanA gene was 100 % concordant. The concordance for Gram-negative susceptibilities was 71.4 % for Enterobacteriaceae and 50 % for Pseudomonas aeruginosa. Therapy was more frequently inadequate in patients who died, and the molecular test was concordant with the phenotypic susceptibility test in 50 %. CONCLUSIONS: qPCR has potential indication for early identification of pathogens and antimicrobial resistance genes from BSI in paediatric cancer patients and may improve antimicrobial therapy.201627585633
2172140.9973Detection of blaPER-1 & blaOxa10 among imipenem resistant isolates of Pseudomonas aeruginosa isolated from burn patients hospitalized in Shiraz Burn Hospital. BACKGROUND AND OBJECTIVES: Pseudomonas aeruginosa is one of the most important Gram negative opportunistic bacteria which causes infection among burn patients. Resistance to the antibiotics in this group of bacteria is increased due to the activity of extended spectrum β-lactamase (ESBLs) genes. In the current study, we investigated the prevalence of two genes (blaPER-1 & blaOxa10 ) related β-lactamase genes among imipenem resistance clinical isolates of P. aeruginosa in hospitalized patients. MATERIALS AND METHODS: From May 2010 to March 2011, 270 P. aeruginosa isolated from hospitalized burned patients' wounds in Shiraz Burn Hospital, were tested for Imipenem resistance by disk diffusion method. Presence of ESBLs exo-enzyme, blaPER-1 and blaOxa10 genes were also evaluated in the resistant isolate. RESULTS: 210 (77.7%) of 270 P. aeruginosa isolates were resistant to imipenem. blaPER-1 and blaOxa10 were detected among 168 (80.0%) of imipenem resistant isolates. Furthermore, 160 (76.2%) of them had blaOxa10 gene and 84 (40.0%) of them had blaPER-1 while 63 (30.0%) resistant isolates contained both genes simultaneously. CONCLUSION: This study showed a high prevalence of blaPER-1 and blaOxa10 genes in hospitalized burn patients in south west of Iran. Therefore, it's highly recommended to perform such tests routinely to evaluate the resistance pattern in order to better antibiotic selection in the burned patients.201526644867
1462150.9973Phenotypic 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.202032628575
2153160.9973Molecular Characterization and Epidemiology of Antibiotic Resistance Genes of β-Lactamase Producing Bacterial Pathogens Causing Septicemia from Tertiary Care Hospitals. Septicemia is a systematic inflammatory response and can be a consequence of abdominal, urinary tract and lung infections. Keeping in view the importance of Gram-negative bacteria as one of the leading causes of septicemia, the current study was designed with the aim to determine the antibiotic susceptibility pattern, the molecular basis for antibiotic resistance and the mutations in selected genes of bacterial isolates. In this study, clinical samples (n = 3389) were collected from potentially infected male (n = 1898) and female (n = 1491) patients. A total of 443 (13.07%) patients were found to be positive for bacterial growth, of whom 181 (40.8%) were Gram-positive and 262 (59.1%) were Gram-negative. The infected patients included 238 males, who made up 12.5% of the total number tested, and 205 females, who made up 13.7%. The identification of bacterial isolates revealed that 184 patients (41.5%) were infected with Escherichia coli and 78 (17.6%) with Pseudomonas aeruginosa. The clinical isolates were identified using Gram staining biochemical tests and were confirmed using polymerase chain reaction (PCR), with specific primers for E. coli (USP) and P. aeruginosa (oprL). Most of the isolates were resistant to aztreonam (ATM), cefotaxime (CTX), ampicillin (AMP) and trimethoprim/sulfamethoxazole (SXT), and were sensitive to tigecycline (TGC), meropenem (MEM) and imipenem (IPM), as revealed by high minimum inhibitory concentration (MIC) values. Among the antibiotic-resistant bacteria, 126 (28.4%) samples were positive for ESBL, 105 (23.7%) for AmpC β-lactamases and 45 (10.1%) for MBL. The sequencing and mutational analysis of antibiotic resistance genes revealed mutations in TEM, SHV and AAC genes. We conclude that antibiotic resistance is increasing; this requires the attention of health authorities and clinicians for proper management of the disease burden.202336978484
1490170.9973Rapid detection of Gram-negative bacteria and their drug resistance genes from positive blood cultures using an automated microarray assay. We evaluated the performance of the Verigene Gram-negative blood culture (BC-GN) assay (CE-IVD version) for identification of Gram-negative (GN) bacteria and detection of resistance genes. A total of 163 GN organisms (72 characterized strains and 91 clinical isolates from 86 patients) were tested; among the clinical isolates, 86 (94.5%) isolates were included in the BC-GN panel. For identification, the agreement was 98.6% (146/148, 95% confidence interval [CI], 92.1-100) and 70% (7/10, 95% CI, 53.5-100) for monomicrobial and polymicrobial cultures, respectively. Of the 48 resistance genes harbored by 43 characterized strains, all were correctly detected. Of the 19 clinical isolates harboring resistance genes, 1 CTX-M-producing Escherichia coli isolated in polymicrobial culture was not detected. Overall, BC-GN assay provides acceptable accuracy for rapid identification of Gram-negative bacteria and detection of resistance genes, compared with routine laboratory methods despite that it has limitations in the number of genus/species and resistance gene included in the panel and it shows lower sensitivity in polymicrobial cultures.201525591999
2349180.9973DETECTION OF MECA AND NUC GENES OF MULTI-DRUG RESISTANT STAPHYLOCOCCUS AUREUS ISOLATED FROM DIFFERENT CLINICAL SAMPLES. BACKGROUND: During this study, six isolates of multiple antibiotic resistant Staphylococcus aureus bacteria were obtained from different clinical specimens (burn swabs, urinary tract infections, wound swabs): three isolates from burns, two isolates from urinary tract infections, and one isolate from wound swabs. They were obtained from private laboratories in Baghdad from 1/1/2023 to 3/15/2023. METHOD: The diagnosis of these isolates was confirmed using the Vitek2 device. A susceptibility test was conducted on ten antibiotics, and S. aureus bacteria showed resistance to most antibiotics, polymerase chain reaction was done to mecA and Nuc gene by conventional PCR. RESULTS: The results of the molecular detection of the MecA gene showed that all isolates of multi-drug-resistant S. aureus possess this gene. In contrast, the results of the molecular detection of the nuc gene showed that only isolates No. 1 and No. 4 carry this gene, while the rest of the isolates do not carry this gene. CONCLUSION: S. aureus are resistant to antibiotics because they possess resistance genes such as the mecA gene.202439724880
1469190.9973Investigation of Bacterial Infections and Antibiotic Resistance Patterns Among Clinical Isolates in the Center of Iran. Introduction: Bacterial infection is a considerable problem in hospitals. Thus, this study was executed to appraise the rampancy of bacterial infections, antimicrobial susceptibility patterns, and molecular characterization of isolates among patients in Bafgh Hospital in Yazd, Iran, in 2020. Methods: In the current study, we surveyed 103 isolates of 400 clinical specimens from early March 2020 to September 2020 in Bafgh Hospital. We assessed phenotypic traits and antibiotic resistance with standard microbiological methods. Phenotypic methods were also performed to identify extended-spectrum beta-lactamases (ESBLs) in Gram-negative bacilli, inducible clindamycin resistance, and methicillin resistance in Staphylococcus according to CLSI guidelines. Molecular identification of isolates was done by conventional PCR 16S rRNA gene sequencing. Furthermore, we investigated the prevalence of resistant genes including bla (TEM), bla (PER-2), bla (CTX-M), bla (SHV), and bla (VEB-1) in Gram-negative bacteria and the mecA gene in staphylococcal species. Results: From 400 different clinical specimens, 103 isolates of Gram-positive and Gram-negative bacteria were isolated. Based on phenotypic and molecular methods, most common isolates were Escherichia coli (53 isolates), followed by Klebsiella spp. (18 isolates), and Staphylococcus aureus (16 isolates). The highest resistance was found in Gram-positive bacteria to erythromycin (66.67%) and penicillin (55.56%), while considering Gram-negative bacteria, the most resistant was cefixime (49.41%) and trimethoprim-sulfamethoxazole (47.05%). In addition, out of 16 S. aureus isolates, 62.5% and 17.65% were resistant to methicillin and clindamycin, respectively. Among 83 Gram-negative isolates, 22.89% were ESBL-positive. The prevalence of bla (SHV), bla (PER2), bla (TEM), bla (CTX-M), and bla (VEB-1) genes was 78.31%, 59.03%, 40.96%, 30.12%, and 0%, respectively. Conclusions: The outbreak of bacterial infections is relatively high in hospitals. Recognizing risk agents for bacterial infections and restricting the administration of multidrug-resistant antibiotics is a substantial measure that must be taken to prevent patient mortality.202540822981