Antibiotic Resistance Diagnostic Methods for Pathogenic Bacteria

Marroki, Ahmed; Bousmaha-Marroki, Leila

doi:10.1016/b978-0-12-818731-9.00133-6

Cited by 8 publications

(6 citation statements)

References 153 publications

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“…The method is highly reproducible, and the MIC value is highly informative. However, users might face time limitations and a lack of flexibility regarding antibiotic choice [ 44 ].…”

Section: Current Methods For the Clinical Diagnosis Of Bacterial Infe...mentioning

confidence: 99%

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives

2023

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Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).

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“…The method is highly reproducible, and the MIC value is highly informative. However, users might face time limitations and a lack of flexibility regarding antibiotic choice [ 44 ].…”

Section: Current Methods For the Clinical Diagnosis Of Bacterial Infe...mentioning

confidence: 99%

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives

2023

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“…Following inoculation of MH–F agar as previously described, plastic strips with a gradient concentration of the antibiotic of interest to which the strain showed resistance during AST were placed onto the surface of the agar medium, allowing for the diffusion of the antimicrobial agent into the agar and thus providing, after overnight incubation at 37 °C, an inhibition ellipse where the MIC corresponds to the value at the point of intersection of the growth and inhibition zone with the extremity of the strip. The E-test MICs (in μg/mL or ppm) can be read directly from the upper of the Petri dish [ 63 ] (pp. 323–324).…”

Section: Methodsmentioning

confidence: 99%

Characterization and Antibiotic Resistance of Listeria monocytogenes Strains Isolated from Greek Myzithra Soft Whey Cheese and Related Food Processing Surfaces over Two-and-a-Half Years of Safety Monitoring in a Cheese Processing Facility

Andritsos

Mataragas²

2023

Foods

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Listeriosis is a serious infectious disease with one of the highest case fatality rates (ca. 20%) among the diseases manifested from bacterial foodborne pathogens in humans, while dairy products are often implicated as sources of human infection with Listeria monocytogenes. In this study, we characterized phenotypically and genetically by whole-genome sequencing (WGS) 54 L. monocytogenes strains isolated from Myzithra, a traditional Greek soft whey cheese (48 isolates), and swabs collected from surfaces of a cheese processing plant (six isolates) in the Epirus region of Greece. All but one strain of L. monocytogenes belonged to the polymerase chain reaction (PCR) serogroups IIa (16.7%) and IIb (81.5%), corresponding to serotypes 1/2a, 3a and 1/2b, 3b, 7, respectively. The latter was identified as a PCR-serogroup IVb strain (1.8%) of serotypes 4b, 4d, 4e. Bioinformatics analysis revealed the presence of five sequence types (STs) and clonal complexes (CCs); ST1, ST3, ST121, ST 155, ST398 and CC1, CC3, CC121, CC155, CC398 were thus detected in 1.9, 83.3, 11.0, 1.9, and 1.9% of the L. monocytogenes isolates, respectively. Antibiograms of the pathogen against a panel of seven selected antibiotics (erythromycin, tetracycline, benzylpenicillin, trimethoprim-sulfamethoxazole, ampicillin, ciprofloxacin, and meropenem) showed that 50 strains (92.6%), the six surface isolates also included, were intermediately resistant to ciprofloxacin and susceptible to the rest of the six antimicrobial agents tested, whereas strong resistance against the use of a single from three implicated antibiotics was recorded to four strains (7.4%) of the pathogen isolated from Myzithra cheese samples. Thence, the minimum inhibitory concentrations (MICs) were determined for erythromycin (MIC = 0.19 μg/mL), ciprofloxacin (MIC ≥ 0.19 μg/mL), and meropenem (MIC = 0.64 μg/mL), and finally, just one strain was deemed resistant to the latter antibiotic. The phylogenetic positions of the L. monocytogenes strains and their genetic variability were determined through WGS, whilst also stress response and virulence gene analysis for the isolates was conducted. Findings of this work should be useful as they could be utilized for epidemiological investigations of L. monocytogenes in the food processing environment, revealing possible contamination scenarios, and acquired antimicrobial resistance along the food production chain.

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“…This test determines the minimal inhibitory concentration (MICs) and involves diluting the antimicrobial agent in bacterial media. Specifically, a microdilution assay is the standard method to obtain MIC values (Marroki and Bousmaha-Marroki, 2021). However, researchers in this study rarely utilised dilution methods compared to diffusion methods.…”

Section: Dilution Methods For Antimicrobial Resistance In Fish and Po...mentioning

confidence: 99%

Antimicrobial resistance in fish and poultry: Public health implications for animal source food production in Nigeria, Egypt, and South Africa

Okon

Okocha²,

Adesina³

et al. 2022

Front. Antibiot.

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Antimicrobial resistance (AMR) is a significant threat to global public health. Specifically, excessive usage of antimicrobials in food animal production is one significant reason for AMR development in humans. Therefore, it is essential to identify the trends of AMR in fish and poultry and develop better surveillance strategies for the future. Despite this imperative need, such information is not well documented, especially in Africa. This study used a systematic review to assess AMR trend, spatial distribution, and incidence in fish and poultry research in Nigeria, Egypt, and South Africa. A literature assessment was conducted for published studies on AMR between 1989 and 2021 using the Scopus and Web of Science databases. One hundred and seventy-three relevant articles were obtained from the database search. Egypt was the leading exponent of antimicrobial resistance research (43.35%, 75 studies), followed by Nigeria (39.31%, 68 studies), then South Africa (17.34%, 30 studies). The majority of the antimicrobial resistance studies were on poultry in Egypt (81%, 61 studies), Nigeria (87%, 59 studies), and South Africa (80%, 24 studies). Studies on fish were 17% (13 studies), 9% (6 studies), and 10% (3 studies) in Egypt, Nigeria, and South Africa, respectively. Antimicrobial resistance patterns showed multiple drug resistance and variations in resistant genes. AMR research focused on sulfamethoxazole groups, chloramphenicol, trimethoprim, tetracycline, erythromycin, and ampicillin. Most studies employed the disk diffusion method for antimicrobial susceptibility tests. Among the four mechanisms of AMR, limiting drug uptake was the most reported in this study (both in fish and poultry). The findings reveal public and environmental health threats and suggest that it would be useful to promote and advance AMR research, particularly for countries on the global hotspot for antimicrobial use.

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Antibiotic Resistance Diagnostic Methods for Pathogenic Bacteria

Cited by 8 publications

References 153 publications

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives

Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics—Current State and Whole Genome Sequencing Implementation Perspectives

Characterization and Antibiotic Resistance of Listeria monocytogenes Strains Isolated from Greek Myzithra Soft Whey Cheese and Related Food Processing Surfaces over Two-and-a-Half Years of Safety Monitoring in a Cheese Processing Facility

Antimicrobial resistance in fish and poultry: Public health implications for animal source food production in Nigeria, Egypt, and South Africa

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