Potential impact of a microarray-based nucleic acid assay for rapid detection of Gram-negative bacteria and resistance markers in positive blood cultures. - Related Documents




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148701.0000Potential impact of a microarray-based nucleic acid assay for rapid detection of Gram-negative bacteria and resistance markers in positive blood cultures. We evaluated the Verigene Gram-negative blood culture (BC-GN) test, a microarray that detects Gram-negative bacteria and several resistance genes. A total of 102 positive blood cultures were tested, and the BC-GN test correctly identified 97.9% of the isolates within its panel. Resistance genes (CTX-M, KPC, VIM, and OXA genes) were detected in 29.8% of the isolates, with positive predictive values of 95.8% (95% confidence interval [CI], 87.7% to 98.9%) in Enterobacteriaceae and 100% (95% CI, 75.9% to 100%) in Pseudomonas aeruginosa and negative predictive values of 100% (95% CI, 93.9% to 100%) and 78.6% (95% CI, 51.0% to 93.6%), respectively.201424478405
148810.9999Evaluation of an automated rapid diagnostic assay for detection of Gram-negative bacteria and their drug-resistance genes in positive blood cultures. We evaluated the performance of the Verigene Gram-Negative Blood Culture Nucleic Acid Test (BC-GN; Nanosphere, Northbrook, IL, USA), an automated multiplex assay for rapid identification of positive blood cultures caused by 9 Gram-negative bacteria (GNB) and for detection of 9 genes associated with β-lactam resistance. The BC-GN assay can be performed directly from positive blood cultures with 5 minutes of hands-on and 2 hours of run time per sample. A total of 397 GNB positive blood cultures were analyzed using the BC-GN assay. Of the 397 samples, 295 were simulated samples prepared by inoculating GNB into blood culture bottles, and the remaining were clinical samples from 102 patients with positive blood cultures. Aliquots of the positive blood cultures were tested by the BC-GN assay. The results of bacterial identification between the BC-GN assay and standard laboratory methods were as follows: Acinetobacter spp. (39 isolates for the BC-GN assay/39 for the standard methods), Citrobacter spp. (7/7), Escherichia coli (87/87), Klebsiella oxytoca (13/13), and Proteus spp. (11/11); Enterobacter spp. (29/30); Klebsiella pneumoniae (62/72); Pseudomonas aeruginosa (124/125); and Serratia marcescens (18/21); respectively. From the 102 clinical samples, 104 bacterial species were identified with the BC-GN assay, whereas 110 were identified with the standard methods. The BC-GN assay also detected all β-lactam resistance genes tested (233 genes), including 54 bla(CTX-M), 119 bla(IMP), 8 bla(KPC), 16 bla(NDM), 24 bla(OXA-23), 1 bla(OXA-24/40), 1 bla(OXA-48), 4 bla(OXA-58), and 6 blaVIM. The data shows that the BC-GN assay provides rapid detection of GNB and β-lactam resistance genes in positive blood cultures and has the potential to contributing to optimal patient management by earlier detection of major antimicrobial resistance genes.201424705449
149020.9998Rapid 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
149130.9997Evaluation of an expanded antibiotic resistance gene panel on prediction of antimicrobial susceptibility results for Gram-negative bacteria in blood cultures. The QIAstat-Dx BCID Panels (RUO) ("QIAstat," QIAGEN, Hilden, Germany) for identification of 13 Gram-negative bacteria and 18 antimicrobial resistance (AMR) gene groups was evaluated. The study was conducted in two phases; in phase 1, analytical performance was evaluated against 154 challenge isolates against whole genome sequencing data. In this phase, sensitivity and specificity of organism identification calls were 153/154 (99.3%) and 1,748/1,749 (99.8%), respectively. For AMR genes, sensitivity was 434/435 (99.8%) and specificity was 2,334/2,337 (99.9%). One false-negative bla(IMP), one false-positive bla(CTX-M), and two false-positive aac-6'-lb detections were noted in this challenge set of organisms. In phase 2, 101 clinical blood culture isolates of Gram-negative rods were evaluated by the multiplexed PCR versus reference broth microdilution, for the ability of identification combined with AMR genes to predict final susceptibility results. Negative predictive values were 92.8% for ampicillin resistance (100% for Escherichia coli), 93.4% for ceftriaxone, 97.4% for ceftazidime, and 98.7% for cefepime. In constrast, negative predictive values for current standard of care (identification plus detection of bla(CTX-M)) ranged from 56.5% to 88.8%. This study demonstrated additive value of additional beta-lactamase genes for bacteria isolated from blood cultures. IMPORTANCE: Prediction of Gram-negative bacteria resistance through detection of resistance genes is complex. This study evaluated a novel, direct-from-blood or bacterial isolate multiplexed PCR for the detection of 17 resistance genes, and evaluated the prediction of antimicrobial susceptibility.202439297627
125240.9997Fluoroquinolone resistance in bacterial isolates from ocular infections: Trend in antibiotic susceptibility patterns between 2005-2020. PURPOSE: To assess the fluoroquinolone resistance pattern and trends among bacterial isolates from ocular infections over a 16-year period and explore alternative antibiotics in fluoroquinolone-resistant strains. METHODS: In this retrospective, longitudinal study, the microbiology laboratory records of patients with different ocular infections diagnosed at an eye institute in central India from 2005-2020 were reviewed to determine the pattern of fluoroquinolone (ciprofloxacin, ofloxacin, gatifloxacin, and moxifloxacin) resistance. Antibiotic susceptibility testing was done using the Kirby-Bauer disc diffusion method. RESULTS: In 725 Gram-positive bacteria, the resistance of ciprofloxacin, ofloxacin, gatifloxacin, and moxifloxacin was 55.9% (95% confidence interval [CI]: 52.2 - 59.6), 42.7% (95% CI: 39.0 - 46.4), 47.6% (95% CI: 43.9 - 51.3), and 45.6% (95% CI: 41.7-49.5), respectively. In 266 Gram-negative bacteria, the resistance of ciprofloxacin, ofloxacin, gatifloxacin, and moxifloxacin was 57.9% (95% CI: 51.9 - 63.9), 56.0% (95% CI: 49.7 - 62.1), 59.9% (95% CI: 53.8 - 66.0), and 74.3% (95% CI: 68.3 - 80.2), respectively. A declining trend in resistance to ciprofloxacin (P < 0.001), ofloxacin (P < 0.001), and moxifloxacin (P < 0.001) was seen in Gram-positive bacteria, whereas a reduction in resistance to only moxifloxacin (P = 0.04) was seen in Gram-negative bacteria. In fluoroquinolone-resistant Gram-positive bacteria, cefuroxime exhibited the highest susceptibility, whereas in fluoroquinolone-resistant Gram-negative bacteria, colistin exhibited the highest susceptibility. CONCLUSION: Fluoroquinolone resistance was high among bacteria from ocular infections in central India, but a declining trend in resistance to some of the fluoroquinolones was observed in recent times. Cefuroxime and colistin emerged as alternatives in fluoroquinolone-resistant Gram-positive and Gram-negative bacterial infections, respectively.202236453351
147950.9997BioFire FilmArray BCID2 versus VITEK-2 System in Determining Microbial Etiology and Antibiotic-Resistant Genes of Pathogens Recovered from Central Line-Associated Bloodstream Infections. Central line-associated bloodstream infection (CLABSI) is among the most serious hospital acquired infections. Therefore, the rapid detection of the causative microorganism is of crucial importance to allow for the appropriate antimicrobial therapy. In the present study, we analyzed the clinical performance of the BioFire FilmArray Blood Culture Identification 2 (BCID2) panel in the identification of 33 microbial species and 10 antibiotic resistance genes in comparison to the VITEK-2 system. A total of 104 blood specimens were included. The FilmArray BCID2 results were concordant with the VITEK-2 system in 69/97 specimens (71.1%). Non-concordance was either due to the detection of more pathogens by the FilmArray BCID2 23/28 (82%) or microbial species were misidentified 5/28 (18%). Hence, in comparison to the VITEK-2 system, the FilmArray BCID2 panel showed an overall sensitivity of 75.8% (95% CI, 66-83%) and an overall specificity of 98% (95% CI, 97-98.8%) in detecting microbial species. For the resistance genes, the FilmArray BCID was able to detect the presence of blaCTX-M gene in 23 Gram-negative isolates, blaNDM and blaOXA-48- like genes in 14 and 13 isolates, respectively. The mecA and mecC genes were found in 23 Staphylococcus species, while mecA, mecC and MREJ genes were found in 4 Staphylococcus aureus isolates. The sensitivity and specificity for detecting resistance genes by the FilmArray BCID2 was 90% (95% CI, 81.4-95%) and 99.6% (95% CI, 99-100%), respectively. As concluded, the present study emphasizes the high sensitivity and specificity of the FilmArray BCID2 in the rapid and reliable detection of different bacteria and fungi from positive blood culture bottles, as well as the accurate detection of various antibiotic resistance markers.202236358274
146760.9996Detection of bla (CTX-M15) and bla (OXA-48) genes in Gram-negative isolates from neonatal sepsis in central of Iran. BACKGROUND AND OBJECTIVES: The aim of this study was to determine the prevalence of neonatal sepsis with a focus on antibiotic resistance and the frequency of the bla (CTX-M-15) and bla (OXA-48) genes in Gram-negative isolates. MATERIALS AND METHODS: A total of 108 Umbilical Cord Blood (UCB) and 153 peripheral blood samples were cultured via BACTEC from May 2017 to June 2018. The bacterial isolates were identified using phenotypic and genotypic analyses. The antibiotic susceptibility profile of the isolates was determined by disk diffusion. PCR was used to determine the frequency of β-lactamase genes. RESULTS: Among the 153 infants, 21 (13.7%) proved positive for sepsis. Escherichia coli, Staphylococcus epidermidis and Klebsiella pneumoniae were the most frequent isolates in the peripheral blood cultures. E. coli and Stenotrophomonas maltophilia were isolated from two UCB cultures. The highest resistance among the Gram-positive strains was to cefixime, ceftriaxone, cefotaxime and clindamycin. In the Gram-negative bacteria the highest rates of resistance were to ampicillin (91.7%). The frequency of bla (OXA-48) and bla (CTX-M-15) genes was 25% and 50%, respectively. CONCLUSION: The high antibiotic resistance among the isolates reveals the importance of monitoring antibiotic consumption and improving control standards in the health care system, especially in neonatal wards.201931719958
148970.9996Direct 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
222080.9996Rapid 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
145090.9996The Spread of Insertion Sequences Element and Transposons in Carbapenem Resistant Acinetobacter baumannii in a Hospital Setting in Southwestern Iran. BACKGROUND: Acinetobacter baumannii is one of the most important hospital pathogenic bacteria that cause infectious diseases. The present study aimed to determine the frequency of carbapenem resistance genes in association with transposable elements and molecular typing of carbapenem-resistant A. baumannii bacteria collected from patients in Shiraz, Iran. MATERIALS AND METHODS: A total of 170 carbapenem-resistant A. baumannii isolates were obtained from different clinical specimens in two hospitals. The minimum inhibitory concentrations (MIC) of imipenem were determined and the prevalence of OXA Carbapenemases, Metallo-β-lactamases genes, insertion sequences (IS) elements, and transposons were evaluated by the polymerase chain reaction (PCR) method. Finally, molecular typing of the isolates was performed by the Enterobacterial Repetitive Intergenic Consensus-PCR method. RESULTS: The MICs ranged from 16 to 1,024 µg/mL for imipenem-resistant A. baumannii isolates. Out of the 170 carbapenem resistant A. baumannii isolates, bla(OXA-24-like) (94, 55.3%) followed by bla(OXA-23-like) (71, 41.7%) were predominant. In addition, A. baumannii isolates carried bla(VIM) (71, 41.7%), bla(GES) (32, 18.8%), bla(SPM) (4, 2.3%), and bla(KPC) (1, 0.6%). Moreover, ISAba1 (94.2%) and Tn2009 (39.2%) were the most frequent transposable elements. Furthermore, (71, 44.0%) and (161, 94.7%) of the ISAba1 of the isolates were associated with bla(OXA-23) and bla(OXA-51) genes, respectively. Besides (3, 1.7%), (1, 0.6%) and (5, 2.9%) of bla(OXA-23) were associated with IS18, ISAba4, and ISAba2, respectively. Considering an 80.0% cut off, clusters and four singletons were detected. CONCLUSION: According to the results, transposable elements played an important role in the development of resistance genes and resistance to carbapenems. The results also indicated carbapenem-resistant A. baumannii bacteria as a public health concern.202235706082
2176100.9996Evaluation of phenotypic and genotypic patterns of aminoglycoside resistance in the Gram-negative bacteria isolates collected from pediatric and general hospitals. The purpose of the current study was to evaluate the phenotypic and genotypic patterns of aminoglycoside resistance among the Gram-negative bacteria (GNB) isolates collected from pediatric and general hospitals in Iran. A total of 836 clinical isolates of GNB were collected from pediatric and general hospitals from January 2018 to the end of December 2019. The identification of bacterial isolates was performed by conventional biochemical tests. Susceptibility to aminoglycosides was evaluated by the disk diffusion method (DDM). The frequency of genes encoding aminoglycoside-modifying enzymes (AMEs) was screened by the PCR method via specific primers. Among all pediatric and general hospitals, the predominant GNB isolates were Acinetobacter spp. (n = 327) and Escherichia coli (n = 144). However, E. coli (n = 20/144; 13.9%) had the highest frequency in clinical samples collected from pediatrics. The DDM results showed that 64.3% of all GNB were resistant to all of the tested aminoglycoside agents. Acinetobacter spp. and Klebsiella pneumoniae with 93.6%, Pseudomonas aeruginosa with 93.4%, and Enterobacter spp. with 86.5% exhibited very high levels of resistance to gentamicin. Amikacin was the most effective antibiotic against E. coli isolates. In total, the results showed that the aac (6')-Ib gene with 59% had the highest frequency among genes encoding AMEs in GNB. The frequency of the surveyed aminoglycoside-modifying enzyme genes among all GNB was found as follows: aph (3')-VIe (48.7%), aadA15 (38.6%), aph (3')-Ia (31.3%), aph (3')-II (14.4%), and aph (6) (2.6%). The obtained data demonstrated that the phenotypic and genotypic aminoglycoside resistance among GNB was quite high and it is possible that the resistance genes may frequently spread among clinical isolates of GNB.202235119565
1478110.9996Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections. The FilmArray Blood Culture Identification 2 panel (BCID2; bioMérieux) is a fully automated PCR-based assay for identifying bacteria, fungi, and bacterial resistance markers in positive blood cultures (BC) in about 1 h. In this multicenter study, we evaluated the performance of the BCID2 panel for pathogen detection in positive BC. Conventional culture and BCID2 were performed in parallel at four tertiary-care hospitals. We included 152 positive BC-130 monomicrobial and 22 polymicrobial cultures-in this analysis. The BCID2 assay correctly identified 90% (88/98) of Gram-negative and 89% (70/79) of Gram-positive bacteria. Five bacterial isolates targeted by the BCID2 panel and recovered from five positive BC, including three polymicrobial cultures, were missed by the BCID2 assay. Fifteen isolates were off-panel organisms, accounting for 8% (15/182) of the isolates obtained from BC. The mean positive percent agreement between the BCID2 assay and standard culture was 97% (95% confidence interval, 95 to 99%), with agreement ranging from 67% for Candida albicans to 100% for 17 targets included in the BCID2 panel. BCID2 also identified the bla(CTX-M) gene in seven BC, including one for which no extended-spectrum β-lactamase (ESBL)-producing isolate was obtained in culture. However, it failed to detect ESBL-encoding genes in three BC. Two of the 18 mecA/C genes detected by the BCID2 were not confirmed. No carbapenemase, mecA/C, or MREJ targets were detected. The median turnaround time was significantly shorter for BCID2 than for culture. The BCID2 panel may facilitate faster pathogen identification in bloodstream infections. IMPORTANCE Rapid molecular diagnosis combining the identification of pathogens and the detection of antibiotic resistance genes from positive blood cultures (BC) can improve the outcome for patients with bloodstream infections. The FilmArray BCID2 panel, an updated version of the original BCID, can detect 11 Gram-positive bacteria, 15 Gram-negative bacteria, 7 fungal pathogens, and 10 antimicrobial resistance genes directly from a positive BC. Here, we evaluated the real-life microbiological performance of the BCID2 assay in comparison to the results of standard methods used in routine practice at four tertiary care hospitals.202336519852
1454120.9996OCCURRENCE OF AMINOGLYCOSIDES RESISTANCE GENES ACC(6)-IB AND ACC(3)-II AMONG GRAM-NEGATIVE ISOLATES CAUSING URINARY TRACT INFECTION IN PEDIATRIC PATIENTS, NAJAF, IRAQ. OBJECTIVE: The aim: The aim of the study was to detect the antimicrobial susceptibility patterns and frequency of aminoglycosides resistance genes of Gram-negative bacteria isolated from pediatric patient with UTI. PATIENTS AND METHODS: Materials and methods: The study has been performed with a total of 500 urine specimens collected from pediatric patients under the age of 18 year suspected with UTI, admitted to hospitals in Al-Najaf province/Iraq during the period from November 2018 to March 2019. RESULTS: Results: A total of 500 urine specimens had been tested, 120 (24%) had signifficant bacteriuria, while there 380 (76%) had non-signi!cant bacteriuria. Escherichia coli represent about 70 (68.2%) followed by followed by 23 (22.5%) K. pneumoniae, 5 (4.9%) P. aeruginosa, 2 (1.9%) Proteus spp., 1 (0.9%) Enterobacter spp. and 1 (0.9%) Oligella uratolytic. The antimicrobial susceptibility profile of 102 Gram-negative isolates, revealed that 59 (58%) were multidrug resistant (MDR) and 38(37%) were extensive drug resistant (XDR). The PCR results of aminoglycosides resistance showing that 23 (74.1%) Gram-negative isolates had acc(6')-Ib gene and 12 (38.7%) Gram-negative isolates acc(3')-II gene. CONCLUSION: Conclusions: A high frequency of multi-drug resistance and extensive-drug resistance of isolates were recognized, and an alarming percentage of amino-glycosides resistance to acc(6')-Ib and acc(3')-II.202337010165
1430130.9996Prevalence of multidrug-resistant Gram-negative bacteria from blood cultures and rapid detection of beta-lactamase-encoding genes by multiplex PCR assay. INTRODUCTION: This study aimed to determine the prevalence of multidrug-resistant Gram-negative bacteria (GNB) from blood cultures in a tertiary-care hospital and the multiplex PCR assay's ability to detect resistance genes. METHODS: A total of 388 GNB isolates obtained from hospitalized patients between November 2019 and November 2021 were included in the study. Antimicrobial susceptibility testing was done by VITEK 2 system and broth microdilution method. Beta-lactamase-encoding genes were detected by multiplex PCR assays, BioFire-Blood Culture Identification 2 (BCID2) panel (bioMérieux, France). Extended-spectrum beta-lactamases (ESBLs) were detected phenotypically with VITEK AST-GN71 card (bioMérieux, France). The isolates of GNB were classified into multidrug-resistant, extensively-drug-resistant, and pandrug-resistant categories, and their prevalence and distribution in different wards, including coronavirus diseases 2019 (COVID-19) intensive care units (ICU), were calculated. RESULTS: Results revealed that all isolates of Acinetobacter baumannii and Pseudomonas aeruginosa were multidrug-resistant as well as 91.6% of Enterobacter cloacae, 80.6% of Proteus mirabilis, and 76.1% of Klebsiella pneumoniae, respectively. In fermentative bacteria, bla(OXA-48-like) (58.1%), bla(NDM) (16.1%), bla(KPC) (9.7%) and bla(VIM) (6.5%) genes were detected. More than half of Enterobacter cloacae (58.3%) and Klebsiella pneumoniae (53.7%) produced ESBLs. Among non-fermenters, the bla(NDM) gene was carried by 55% of Pseudomonas aeruginosa and 19.5% of Acinetobacter baumannii. In the COVID-19 ICU, Acinetobacter baumannii was the most common isolate (86.1%). CONCLUSIONS: This study revealed high proportions of multidrug-resistant blood isolates and various underlying resistance genes in Gram-negative strains. The BCID2 panel seems to be helpful for the detection of the most prevalent resistance genes of fermentative bacteria.202238021186
1470140.9996Occurrence of extended-spectrum beta-lactamase (ESBL) in Gram-negative bacterial isolates from high vaginal swabs in a teaching hospital in Nigeria. OBJECTIVE: This study aims to determine the antibiotic susceptibility pattern and incidence of extended-spectrum beta-lactamase (ESBL) genes in isolates from vaginal discharge of symptomatic female patients. STUDY DESIGN: Cross-sectional study. PARTICIPANT: Pregnant and non-pregnant women between 18 and 50 years who presented with genital tract infection and had not received antimicrobial therapy in the two weeks prior. INTERVENTIONS: The study determines the prevalence of bacteria in the vaginal discharge of female patients of reproductive age, the antibiotic susceptibility pattern of the isolates and the incidence of ESBL genes in Gram-negative isolates from the sample. RESULTS: Bacteria were found in 74 (80.4%) and 88 (81.5%) samples from pregnant and non-pregnant women, respectively. Escherichia coli (n=48; 27.6%) occurred mostly in the samples, followed by Staphylococcus aureus (n=38; 21.8%). Among the Gram-positive, all Streptococcus. pneumoniae and Staphylococcus. epidermidis were sensitive to imipenem and meropenem (100%). S. aureus was the most resistant to cephalexin (71.4%), cefoxitin (60.5%) carbenicillin (60.5%) and ceftazidime (57.9%). Escherichia coli was highly resistant to carbenicillin (85.4%), cephalexin (64.6%) and cefotaxime (56.3%). Klebsiella pneumoniae showed the highest level of imipenem resistance (31.6%), followed by E. coli (29.2%). The prevalence of ESBL genes in Gram-negative isolates from pregnant women was 25.6% (11/43), compared to 30.3% (23/76) in non-pregnant women. Both bla (TEM) and bla (SHV) had the highest occurrence of 14.3% (17/119) of the isolates. CONCLUSION: This study found Gram-negative pathogens isolated from the vaginal tract of both pregnant and non-pregnant women to be resistant to multiple antibiotics and have ESBL genes. FUNDING: None declared.202440585516
1449150.9996A prospective surveillance study to determine the prevalence of 16S rRNA methyltransferase-producing Gram-negative bacteria in the UK. OBJECTIVES: To determine the prevalence of 16S rRNA methyltransferase- (16S RMTase-) producing Gram-negative bacteria in patients in the UK and to identify potential risk factors for their acquisition. METHODS: A 6 month prospective surveillance study was conducted from 1 May to 31 October 2016, wherein 14 hospital laboratories submitted Acinetobacter baumannii, Enterobacterales and Pseudomonas aeruginosa isolates that displayed high-level amikacin resistance according to their testing methods, e.g. no zone of inhibition with amikacin discs. Isolates were linked to patient travel history, medical care abroad, and previous antibiotic exposure using a surveillance questionnaire. In the reference laboratory, isolates confirmed to grow on Mueller-Hinton agar supplemented with 256 mg/L amikacin were screened by PCR for 16S RMTase genes armA, rmtA-rmtH and npmA, and carbapenemase genes (blaKPC, blaNDM, blaOXA-48-like and blaVIM). STs and total antibiotic resistance gene complement were determined via WGS. Prevalence was determined using denominators for each bacterial species provided by participating hospital laboratories. RESULTS: Eighty-four isolates (44.7%), among 188 submitted isolates, exhibited high-level amikacin resistance (MIC >256 mg/L), and 79 (94.0%) of these harboured 16S RMTase genes. armA (54.4%, 43/79) was the most common, followed by rmtB (17.7%, 14/79), rmtF (13.9%, 11/79), rmtC (12.7%, 10/79) and armA + rmtF (1.3%, 1/79). The overall period prevalence of 16S RMTase-producing Gram-negative bacteria was 0.1% (79/71 063). Potential risk factors identified through multivariate statistical analysis included being male and polymyxin use. CONCLUSIONS: The UK prevalence of 16S RMTase-producing Gram-negative bacteria is low, but continued surveillance is needed to monitor their spread and inform intervention strategies.202134142130
1251160.9996Biofilm Formation and Plasmid-Mediated Quinolone Resistance Genes at Varying Quinolone Inhibitory Concentrations in Quinolone-Resistant Bacteria Superinfecting COVID-19 Inpatients. The likelihood of antimicrobial failure in COVID-19 patients with bacterial superinfection arises from both phenotypic (biofilms) and genotypic mechanisms. This cross-sectional study aimed to determine the inhibitory concentrations of quinolones-nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and levofloxacin-in biofilm formers (minimum biofilm inhibitory concentration [MBIC]) and nonformers (minimum inhibitory concentration [MIC]) and correlate inhibitory concentrations with plasmid-mediated quinolone resistance (PMQR) genes in quinolone-resistant bacteria isolated from COVID-19 inpatients. Quinolone-resistant bacteria (n = 193), verified through disc diffusion, were tested for quinolone inhibitory concentrations using broth microdilution and biofilm formation using microtiter plate methods. The polymerase chain reaction was used to detect PMQR genes. Study variables were analyzed using SPSS v.17.0, with a significance level set at P <0.05. MIC-to-MBIC median fold increases for ciprofloxacin, ofloxacin, and levofloxacin were 128 (2-8,192), 64 (4-1,024), and 32 (4-512) in gram-positive cocci (GPC, n = 43), respectively, whereas they were 32 (4-8,192), 32 (4-2,048), and 16 (2-1,024) in fermentative gram-negative bacilli (F-GNB, n = 126) and 16 (4-4,096), 64 (2-64), and 16 (8-512) in nonfermentative gram-negative bacilli (NF-GNB, n = 24). In biofilm-forming F-GNB and NF-GNB, qnrB (10/32 versus 3/10), aac(6')-Ib-cr (10/32 versus 4/10), and qnrS (9/32 versus 0/10) genes were detected. A 32-fold median increase in the MIC-to-MBIC of ciprofloxacin was significantly (P <0.05) associated with qnrA in F-GNB and qnrS in NF-GNB. Biofilms formed by F-GNB and NF-GNB were significantly associated with the aac(6')-Ib-cr and qnrS genes, respectively. Nearly one-third of the superinfecting bacteria in COVID-19 patients formed biofilms and had at least one PMQR gene, thus increasing the need for quinolones at higher inhibitory concentrations.202539561392
1445170.9996Rapid Detection of Beta-Lactamases Genes among Enterobacterales in Urine Samples by Using Real-Time PCR. The objective of this study was to develop and evaluate newly improved, rapid, and reliable strategies based on real-time PCR to detect the most frequent beta-lactamase genes recorded in clinical Enterobacterales strains, particularly in Tunisia (bla(SHV12) , bla(TEM) , bla(CTX-M-15) , bla(CTX-M-9) , bla(CMY-2) , bla(OXA-48) , bla(NDM-1) , and bla(IMP) ) directly from the urine. Following the design of primers for a specific gene pool and their validation, a series of real-time PCR reactions were performed to detect these genes in 78 urine samples showing high antibiotic resistance after culture and susceptibility testing. Assays were applied to DNA extracted from cultured bacteria and collected urine. qPCR results were compared for phenotypic sensitivity. qPCR results were similar regardless of whether cultures or urine were collected, with 100% sensitivity and specificity. Out of 78 multiresistant uropathogenic, strains of Enterobacterales (44 E. coli and 34 K. pneumoniae strains) show the presence of the genes of the bla group. In all, 44% E. coli and 36 of K. pneumoniae clinical strains harbored the bla group genes with 36.4%, 52.3%, 70.5%, 68.2%, 18.2%, and 4.5% of E. coli having bla(SHV-12) , bla(TEM) , bla(CTX-M 15) , bla(CTX-M-9) , bla(CMY-2) , and bla(OXA-48) group genes, respectively, whereas 52.9%, 67.6%, 76.5%, 35.5%, 61.8, 14.7, and 1.28% of K. pneumoniae had bla(SHV-12) , bla(TEM) , bla(CTX-M 15) , bla(CTX-M-9) , bla(CMY-2) , bla(OXA-48) , and bla(NDM-1) group genes, respectively. The time required to have a result was 3 hours by real-time PCR and 2 to 3 days by the conventional method. Resistance genes of Gram-negative bacteria in urine, as well as cultured bacteria, were rapidly detected using qPCR techniques. These techniques will be used as rapid and cost-effective methods in the laboratory. Therefore, this test could be a good candidate to create real-time PCR kits for the detection of resistance genes directly from urine in clinical or epidemiological settings.202235978630
1469180.9996Investigation 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
1485190.9996Evaluation of Verigene Blood Culture Test Systems for Rapid Identification of Positive Blood Cultures. The performance of molecular tests using the Verigene Gram-Positive and Gram-Negative Blood Culture nucleic acid tests (BC-GP and BC-GN, resp.; Naosphere, Northbrook, IL, USA) was evaluated for the identification of microorganisms detected from blood cultures. Ninety-nine blood cultures containing Gram-positive bacteria and 150 containing Gram-negative bacteria were analyzed using the BC-GP and BC-GN assays, respectively. Blood cultures were performed using the Bactec blood culture system (BD Diagnostic Systems, Franklin Lakes, NJ, USA) and conventional identification and antibiotic-susceptibility tests were performed using a MicroScan system (Siemens, West Sacramento, CA, USA). When a single strain of bacteria was isolated from the blood culture, Verigene assays correctly identified 97.9% (94/96) of Gram-positive bacteria and 93.8% (137/146) of Gram-negative bacteria. Resistance genes mecA and vanA were correctly detected by the BC-GP assay, while the extended-spectrum β-lactamase CTX-M and the carbapenemase OXA resistance gene were detected from 30 cases cultures by the BC-GN assay. The BC-GP and BC-GN assays showed high agreement with conventional identification and susceptibility tests. These tests are useful for rapid identification of microorganisms and the detection of clinically important resistance genes from positive Bactec blood cultures.201626904669