The Intercontinental ‘Omics’ mining of Antibiotic Resistant Genes in Mycobacterium tuberculosis

Background: Mycobacterium is a genus of Actinobacteriaceae and the Mycobacterium family, including important pathogens, such as Mycobacterium tuberculosis (i.e., the cause of tuberculosis) and Mycobacterium leprae (i.e., the cause of leprosy). Tuberculosis is still a major cause of death in human societies. Objectives: The current study aimed to evaluate the effect of ethanolic extract of garlic on Mycobacterium tuberculosis isolated from patients in Zabol, Iran, and investigate the presence of antibiotic-resistant genes in Mycobacterium tuberculosis. Methods: Garlic (Allium sativum) was collected from Zabol, and the ethanolic extract of garlic leaf was obtained. In this study, 50 strains of Mycobacterium tuberculosis were obtained from the patients in Zabol. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. Some antibiotics, such as isoniazid, pyrazinamide, ethambutol, amikacin, streptomycin, and rifampicin, were used for positive control. Genomic deoxyribonucleic acid was extracted by the sodium dodecyl sulfate method. Furthermore, the presence of antibiotic-resistant genes, namely KatG, PncA, embC, embA1, embA2, embB1, embB2, rrs, rpsL, and ropB, in Mycobacterium tuberculosis was investigated using polymerase chain reaction. Results: The lowest MIC and MBC of garlic ethanolic extract against Mycobacterium tuberculosis were 3.25 and 7.5 ppm, respectively. The highest MIC and MBC were 60 and 120 ppm, respectively. Following the investigation of the presence of antibiotic-resistant genes in Mycobacterium tuberculosis, it was determined that it contains KatG, PncA, embC, embA1, embA2, ropB, rpsL, rrs, embB2, and embB1 genes. The highest resistance of Mycobacterium tuberculosis was against rifampin (81%) and then amikacin (76.6%) belonging to ropB and rrs genes, respectively. Conclusions: The results of the present study showed that the ethanolic extract of garlic was very effective in Mycobacterium tuberculosis and the most effective genes in mycobacteria were ropB and rrs. Although garlic is very effective in Mycobacterium tuberculosis, it is not recommended to directly use the results of this study. Therefore, it is required to perform clinical trials to confirm the results.

Download Full-text

Effect of earthworms in reduction and fate of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) during clinical laboratory wastewater treatment by vermifiltration

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.145152 ◽

2021 ◽

Vol 773 ◽

pp. 145152

Author(s):

Sudipti Arora ◽

Sakshi Saraswat ◽

Ankur Rajpal ◽

Harshita Shringi ◽

Rinki Mishra ◽

...

Keyword(s):

Wastewater Treatment ◽

Clinical Laboratory ◽

Resistant Bacteria ◽

Antibiotic Resistant Bacteria ◽

Antibiotic Resistant ◽

Resistant Genes

Download Full-text

Thermophilic rather than mesophilic sludge anaerobic digesters possess lower antibiotic resistant genes abundance

Bioresource Technology ◽

10.1016/j.biortech.2021.124924 ◽

2021 ◽

pp. 124924

Author(s):

Yan Zhang ◽

Qiuyan Mao ◽

Yu-ao Su ◽

Huimin Zhang ◽

He Liu ◽

...

Keyword(s):

Anaerobic Digesters ◽

Antibiotic Resistant ◽

Resistant Genes

Download Full-text

Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

Foot & Ankle Orthopaedics ◽

10.1177/2473011420s00027 ◽

2020 ◽

Vol 5 (4) ◽

pp. 2473011420S0002

Author(s):

Yoonjung Choi ◽

Irvin Oh

Keyword(s):

Next Generation Sequencing ◽

False Positive ◽

Bacterial Genome ◽

Rrna Gene ◽

Next Generation ◽

Antibiotic Resistant ◽

Streptococcus Species ◽

Resistant Genes ◽

Standard Culture ◽

Generation Sequencing

Category: Other Introduction/Purpose: Foot infections are often polymicrobial with diverse microbiomes. Accurate identification of the main pathogen in diabetic foot ulcer (DFU) remain challenging due to contamination or negative cultures often leading to ineffective post-surgical antibiotic treatment. Application of molecular diagnostics, such as next generation sequencing (NGS) has been explored as an alternative to standard culture in orthopaedic infections. NGS is highly sensitive and detects an entire bacterial genome along with pharmacologic resistant genes in a given sample. We sought to investigate the potential use of NGS for accurate diagnosis and quantification of various species in infected DFU. We hypothesize that NGS will provide a more accurate means of diagnosing and profiling microorganisms in infected DFU compared to the standard culture method. Methods: We investigated 30 infected DFU patients who underwent surgical treatment by a single academic orthopaedic surgeon from October 2018 to September 2019. The average age of the patient was 60.4 (range 33-82) years-old. Surgical procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Quantitative PCR was performed to determine the bacterial burden present in the sample. DNA was amplified by PCR from a highly conserved region of the rRNA gene in the bacteria (16S rRNA). Once a high level of DNA was generated and determined, it was compared against NIH GenBank database. Concordance between the standard culture and NGS was assessed. Results: In 28 of 29 patients, pathogens were identified by both NGS and culture, with complete consistency of organisms in 13 cases (concordance rate: 43.3%). NGS provided relative quantitative measures and the presence of antibiotic resistant genes for each pathogen. In NGS, Anaerococcus species (79.3%) was the most common organism, followed by Streptococcus species (44.8%), Prevotella species (44.8%), Finegoldia magna (44.8%). In culture, S. aureus (58.6%) was the most common, followed by Streptococcus species (34.5%), coagulase-negative Staphylococci (24.1%), Corynebacterium species (20.7%). On average, NGS revealed 5.1 (1-11) number of pathogens, whereas standard culture revealed 2.6 (1-6) pathogens in a given sample. NGS identified 2 cases with false positive standard culture and detected antibiotic resistant organisms in 15 specimens. Conclusion: NGS is an emerging method of microbial identification in orthopedic infection. It is particularly helpful in profiling diverse microbes in polymicrobial infected DFU. It can identify major pathogens and may correct false positive or false negative culture. NGS may allow a faster invitation of postoperative targeted antibiotic therapy. [Table: see text]

Download Full-text