Antibiotic Susceptibility Testing
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Tafese Beyene Tufa ◽  
Colin R. Mackenzie ◽  
Hans Martin Orth ◽  
Tobias Wienemann ◽  
Tamara Nordmann ◽  

Abstract Background Infectious diseases are among the leading causes of death in many low-income countries, such as Ethiopia. Without reliable local data concerning causative pathogens and antimicrobial resistance, empiric treatment is suboptimal. The objective of this study was to characterize gram-negative bacteria (GNB) as pathogens and their resistance pattern in hospitalized patients with infections in central Ethiopia. Methods Patients ≥ 1 year of age with fever admitted to the Asella Referral and Teaching Hospital from April 2016 to June 2018 were included. Blood and other appropriate clinical specimens were collected and cultured on appropriate media. Antibiotic susceptibility testing (AST) was performed using the Kirby–Bauer method and VITEK® 2. Species identification and detection of resistance genes were conducted using MALDI-ToF MS (VITEK® MS) and PCR, respectively. Results Among the 684 study participants, 54.2% were male, and the median age was 22.0 (IQR: 14–35) years. Blood cultures were positive in 5.4% (n = 37) of cases. Among other clinical samples, 60.6% (20/33), 20.8% (5/24), and 37.5% (3/8) of swabs/pus, urine and other body fluid cultures, respectively, were positive. Among 66 pathogenic isolates, 57.6% (n = 38) were GNB, 39.4% (n = 26) were gram-positive, and 3.0% (n = 2) were Candida species. Among the isolated GNB, 42.1% (16/38) were Escherichia coli, 23.7% (9/38) Klebsiella pneumoniae and 10.5% (4/38) Pseudomonas aeruginosa. In total, 27/38 gram-negative isolates were available for further analysis. Resistance rates were as follows: ampicillin/sulbactam, 92.6% (n = 25); cefotaxime, 88.9% (n = 24); ceftazidime, 74.1% (n = 20); cefepime, 74.1% (n = 20); gentamicin, 55.6% (n = 15); piperacillin/tazobactam, 48.1% (n = 13); meropenem, 7.4% (n = 2); and amikacin, 3.7% (n = 1). The blaNDM-1 gene was detected in one K. pneumoniae and one Acinetobacter baumannii isolate, which carried an additional blaOXA-51 gene. The ESBL enzymes were detected in 81.5% (n = 22) of isolates as follows: TEM, 77.2% (n = 17); CTX-M-1 group, 68.2% (n = 15); SHV group, 27.3% (n = 6); and CTX-M-9 group, 9.1% (n = 2). Based on the in vitro antimicrobial susceptibility results, empiric treatment initiated in 13 of 18 (72.2%) patients was likely ineffective. Conclusion We report a high prevalence of ESBL-producing bacteria (81.5%) and carbapenem resistance (7.4%), with more than half of GNB carrying two or more ESBL enzymes resulting in suboptimal empiric antibiotic therapy. These findings indicate a need for local and national antimicrobial resistance surveillance and the strengthening of antimicrobial stewardship programs.

2022 ◽  
Emily F Wissel ◽  
Brooke M Talbot ◽  
Bjorn A Johnson ◽  
Robert A Petit ◽  
Vicki Hertzberg ◽  

The use of shotgun metagenomics for AMR detection is appealing because data can be generated from clinical samples with minimal processing. Detecting antimicrobial resistance (AMR) in clinical genomic data is an important epidemiological task, yet a complex bioinformatic process. Many software tools exist to detect AMR genes, but they have mostly been tested in their detection of genotypic resistance in individual bacterial strains. It is important to understand how well these bioinformatic tools detect AMR genes in shotgun metagenomic data. We developed a software pipeline, hAMRoaster (, for assessing accuracy of prediction of antibiotic resistance phenotypes. For evaluation purposes, we simulated a short read (Illumina) shotgun metagenomics community of eight bacterial pathogens with extensive antibiotic susceptibility testing profiles. We benchmarked nine open source bioinformatics tools for detecting AMR genes that 1) were conda or Docker installable, 2) had been actively maintained, 3) had an open source license, and 4) took FASTA or FASTQ files as input. Several metrics were calculated for each tool including sensitivity, specificity, and F1 at three coverage levels. This study revealed that tools were highly variable in sensitivity (0.25 - 0.99) and specificity (0.2 - 1) in detection of resistance in our synthetic FASTQ files despite similar databases and methods implemented. Tools performed similarly at all coverage levels (5x, 50x, 100x). Cohen’s kappa revealed low agreement across tools.

2021 ◽  
Vol 23 (4) ◽  
pp. 290-296
Rojina Darnal ◽  
Mehraj Ansari ◽  
Ganesh Rai ◽  
Kul Raj Rai ◽  
Shiba Kumar Rai

Carbapenemases are the enzymes that catalyze β–lactam groups of antibiotics. The carbapenemase producers are resistant to β–lactam antibiotics and are usually multidrug-resistant bacteria challenging widely used therapeutics and treatment options. Therefore, the detection of carbapenemase activity among clinical isolates is of great therapeutic importance. We aimed to study the MDR and carbapenemase-producing Klebsiella pneumoniae and Pseudomonas aeruginosa isolated from various clinical samples at a tertiary care hospital in Nepal. A total of 3,579 clinical samples were collected from the patients visiting the Department of Microbiology, B&B Hospital, Gwarko, Lalitpur. The samples were processed to isolate K. pneumoniae and P. aeruginosa and then subjected to antibiotic susceptibility testing (AST) by the Kirby-Bauer disk diffusion method. Phenotypic detection of carbapenemase activity was performed in the imipenem-resistant isolates by the modified Hodge test (MHT). Of the total samples, 1,067 (29.8%) samples showed significant growth positivity, out of which 190 (17.3%) isolates were K. pneumoniae and 121 (11.3%) were P. aeruginosa. Multidrug resistance was seen in 70.5% of the K. pneumoniae isolates and 65.3% of the P. aeruginosa isolates. Carbapenemase production was confirmed in 11.9%, and 12.2% of the imipenem-resistant K. pneumoniae and P. aeruginosa isolates, respectively, by the MHT. This study determined the higher prevalence of MDR among K. pneumoniae and P. aeruginosa; however, carbapenemase production was relatively low.

2021 ◽  
Vol 9 (12) ◽  
pp. 553-558
Ankana Chakraborty B.A. Dalal ◽  
S.M. Bhatawadekar ◽  
C.S. Deshmukh ◽  
K.K. Lahiri ◽  

Introduction: Infertility has been known to cause serious social and emotional problems worldwide. Besides other causes of female infertility, the role of female reproductive tract infection is well recognized. Lower genital tract infection, be it symptomatic or asymptomatic, need to be diagnosed and treated properly. In view of this our study was done. Aim & Objectives: To evaluate the bacteriological profile of lower genital tract in infertile females. Methodology: It was a cross sectional type of study. After taking consent, three swabs (high vaginal swab, endocervical swab and swab from lateral vaginal wall) were taken from 100 infertile women. A questionnaire covering demographic data, menstrual history, medical history, history of infertility, etc. was completed for each of the participants. Isolation and identification of the isolates were done as per conventional techniques. Antibiotic Susceptibility Testing was done for the aerobic isolates as per CLSI guidelines. Results: In our study, 47% of females were asymptomatic and majority them showed positive microbiological growth. E.coli and S.aureus were the most common aerobic isolates and Prevotella spp. was the most common anaerobic isolate. Majority of the anaerobes were associated with bacterial vaginosis. Majority of our isolates were susceptible to Gentamicin. Conclusion: The absence of clinical symptoms does not rule out the possibility of an ongoing acute inflammatory state due infective agents. Hence, both asymptomatic and symptomatic females should be screened for lower genital tract infections as the consequences may lead to infertility.

Antibiotics ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 35
Basit Zeshan ◽  
Mohmed Isaqali Karobari ◽  
Nadia Afzal ◽  
Amer Siddiq ◽  
Sakeenabi Basha ◽  

Antimicrobial resistance (AMR) is a global health issue that plays a significant role in morbidity and mortality, especially in immunocompromised patients. It also becomes a serious threat to the successful treatment of many bacterial infections. The widespread and irrelevant use of antibiotics in hospitals and local clinics is the leading cause of AMR. Under this scenario, the study was conducted in a tertiary care hospital in Lahore, Pakistan, from 2 August 2021 to 31 October 2021 to discover the prevalence of bacterial infections and AMR rates in COVID-19 patients admitted in surgical intensive care units (SICUs). Clinical samples were collected from the patients and we proceeded to identify bacterial isolates, followed by antibiotic susceptibility testing (AST) using the Kirby Bauer disk diffusion method and minimum inhibitory concentration (MIC). The data of other comorbidities were also collected from the patient’s medical record. The current study showed that the most common pathogens were E. coli (32%) and Klebsiella pneumoniae (17%). Most E. coli were resistant to ciprofloxacin (16.8%) and ampicillin (19.8%). Klebsiella pneumoniae were more resistant to ampicillin (13.3%) and amoxycillin (12.0%). The most common comorbidity was chronic kidney disease (CKD) and urinary tract infections (UTIs). Around 17 different types of antibiotic, the carbapenem, fluoroquinolones, aminoglycoside, and quinolones, were highly prevalent in ICU patients. The current study provides valuable data on the clinical implication of antibiotics consumed by COVID-19 patients in SICUs and the AMR rates, especially with different comorbidities.

2021 ◽  
Ronal Turner ◽  
Rachel Kirkby ◽  
Emma Meader ◽  
John R Wain

Background Urinary tract infections (UTIs) are one of the most common bacterial infections seen in primary care. The current standard for the definitive diagnosis of a UTI is culture and sensitivity testing of a mid-stream urine sample at a clinical laboratory; however, this technique is costly, labour intensive and is not directly relevant clinically - typically taking 2-3 days to yield a result. Study design and Objective This is a nonexperimental cross-sectional study. The aim of this study was to evaluate the efficacy of U-treat, a bioluminescent approach for rapid detection of bacteriuria and quantitative determination of the antimicrobial susceptibility profiles of uropathogens in clinical urine specimens - in under an hour. Method The evaluation was carried out in two UK-based Medical Centres using urine samples from patients presenting with symptoms of a UTI (n=249). The U-treat technology is a two test, two reagent process. Test 1 detects the presence of a bacterial UTI > 104 bacteria/mL (5-10 minutes). Test 2 produces quantitative antibiotic susceptibility (<50 minutes). Only urine samples testing positive for bacteria in Test 1 underwent Test 2 (n=82). U-treat results were compared retrospectively against reference laboratory culture and sensitivity findings. The influence of the technology on patient treatment outcomes was also analysed. Results Relative to reference laboratory analysis, Test 1 showed a sensitivity of 97.1% and specificity of 92.0%. (PPV: 89.3%; NPV: 97.8%). Test 2 produced an overall sensitivity (measurement of true susceptibility) of 94.1% (Predictive value: 96%) and an overall specificity (measurement of true resistance) of 90.5% (Predictive value 86.4%). Analysis of treatment data demonstrated that had the physicians had access to U-treat results at the point of care, the percentage of patients treated successfully would have risen from 68.3% to 92.7%. Conclusion U-treat represents the first technology, world-wide, capable of providing UTI treatment data to physicians at the point of care, in less than 60 minutes.

2021 ◽  
Özden Baltekin ◽  
Alexander T. A. Johnsson ◽  
Alicia Y. W. Wong ◽  
Kajsa Nilsson ◽  
Bêrivan Mert ◽  

Blood stream infection (BSI) is related to high mortality and morbidity. Early antimicrobial therapy is crucial in treating patients with BSI. The most common Gram-negative bacteria causing BSI is Escherichia coli. Targeted effective treatment of patients with BSI is only possible if it is based on antibiotic susceptibility testing (AST) data after blood culture positivity. However, there are very few methods available for rapid phenotypic AST and the fastest method takes 4 h. Here we analyzed the performance of a 30 min ultra-rapid method for AST of E. coli directly from positive blood cultures (BC). In total, 51 positive BC with E. coli were studied, and we evaluated the ultra-rapid method directly on positive BC as well as on E. coli colonies cultured on agar plates. The results obtained by the new method were compared with disk diffusion. The method provided accurate AST result in 30 min to Ciprofloxacin and Gentamicin for 92% and 84% of the positive BC samples, respectively. For E. coli isolates retrieved from agar plates, 86% and 96% of the AST results were accurate for Ciprofloxacin and Gentamicin, respectively, after 30 min of assay time. When time to result was modulated in-silico from 30 to 60 minutes for the agar plate samples, accuracy of AST results went up to 92% for Ciprofloxacin and to 100% for Gentamicin. The present study shows that the method is reliable and delivers ultra-rapid AST data in 30 minutes directly from positive BC and as well as from agar plates.

András Kállai ◽  
Márta Kelemen ◽  
Noémi Molnár ◽  
Adrienn Tropotei ◽  
Balázs Hauser ◽  

MICy is a new, simple and rapid flow cytometry based antibiotic susceptibility testing (AST) method that produces susceptibility profile a workday earlier than the microdilution method or other classical phenotypic AST methods. Shortening the length of AST can accelerate clinical decision-making as targeted antibiotic treatment improves clinical outcomes and reduces mortality, duration of artificial ventilation, and length of stay in intensive care unit.

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