Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review

Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.

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New update on molecular diversity of clinical Staphylococcus aureus isolates in Iran: Antimicrobial resistance, adhesion and virulence factors, biofilm formation and SCCmec typing

10.21203/rs.3.rs-473636/v1 ◽

2021 ◽

Author(s):

Mahtab Tabandeh ◽

Hami Kaboosi ◽

Mojtaba Taghizadeh Armaki ◽

Abazar Pournajaf ◽

Fatemeh Peyravii Ghadikolaii

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Virulence Factors ◽

Resistance Genes ◽

Biofilm Formation ◽

Clonal Selection ◽

Clinical Samples ◽

Inducible Resistance ◽

Antibiotic Susceptibility Test ◽

Wide Range

Abstract Staphylococcus. aureus is often considered as a potential pathogen and resistant to a wide range of antibiotics. The pathogenicity of this bacterium is due to the presence of multiple virulence factors and ability to form biofilm. SCCmec types I, II and III are mainly attributed to HA-MRSA, while SCCmec types IV and V have usually been reported in CA-MRSA infections. In this study, we performed a cross-sectional study in order to determine the antimicrobial resistance, adhesion and virulence factors, biofilm formation and SCCmec typing of clinical S. aureus isolates in Iran. S. aureus isolate was identified using microbiological standard methods and antibiotic susceptibility test was performed as described by the Clinical and Laboratory Standards Institute (CLSI) guidelines. Inducible resistance phenotype and biofilm formation were determined using D-test and tissue culture plate methods, respectively. Multiplex-PCRs were performed to detect adhesion and virulence factors, antibiotic resistance genes, biofilm formation and SCCmec typing by specific primers. Among 143 clinical samples, 67.8% were identified as MRSA. All isolates were susceptible to vancomycin. The prevalence of cMLSB, iMLSB and MS phenotypes were 61.1%, 22.2% and 14.8%, respectively. The TCP method revealed that 71.3% of isolates were able to form biofilm. The predominant virulence and inducible resistance genes in both MRSA and MSSA isolates were related to sea and ermC respectively. SCCmec type III was the predominant type. Data show the high prevalence rates of virulence elements among S. aureus isolates, especially MRSA strains. This result might be attributed to antibiotic pressure, facilitating clonal selection.

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A point-of-care diagnostic for differentiating Ebola from endemic febrile diseases

Science Translational Medicine ◽

10.1126/scitranslmed.aat0944 ◽

2018 ◽

Vol 10 (471) ◽

pp. eaat0944 ◽

Cited By ~ 19

Author(s):

David Sebba ◽

Alexander G. Lastovich ◽

Melody Kuroda ◽

Eric Fallows ◽

Joshua Johnson ◽

...

Keyword(s):

Ebola Virus ◽

Clinical Symptoms ◽

Point Of Care ◽

Hemorrhagic Fever ◽

Diagnostic Methods ◽

Outbreak Detection ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Live Virus ◽

And Control

Hemorrhagic fever outbreaks such as Ebola are difficult to detect and control because of the lack of low-cost, easily deployable diagnostics and because initial clinical symptoms mimic other endemic diseases such as malaria. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need. Although rapid tests such as lateral flow can be broadly deployed, they are typically not well-suited for differentiating among multiple diseases presenting with similar symptoms. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect and differentiate infection with Ebola virus from other more common febrile diseases. Here, we developed and tested an immunoassay technology that uses surface-enhanced Raman scattering (SERS) tags to simultaneously detect antigens from Ebola, Lassa, and malaria within a single blood sample. Results are provided in <30 min for individual or batched samples. Using 190 clinical samples collected from the 2014 West African Ebola outbreak, along with 163 malaria positives and 233 negative controls, we demonstrated Ebola detection with 90.0% sensitivity and 97.9% specificity and malaria detection with 100.0% sensitivity and 99.6% specificity. These results, along with corresponding live virus and nonhuman primate testing of an Ebola, Lassa, and malaria 3-plex assay, indicate the potential of the SERS technology as an important tool for outbreak detection and clinical triage in low-resource settings.

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Detection of LytA Genes in Streptococcus pneumoniae Isolated from sputum pneumonia patients

Biomedika ◽

10.31001/biomedika.v13i1.718 ◽

2020 ◽

Vol 13 (1) ◽

pp. 23-30

Author(s):

Mustika Sari Hutabarat ◽

Firdaus Hamid ◽

Irawaty Djaharuddin ◽

Alfian Zainuddin ◽

Rossana Agus ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

False Negative ◽

Pneumococcal Infection ◽

Diagnostic Methods ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Biochemical Tests ◽

Negative Results ◽

False Negative Results ◽

Polymerase Chain

Streptococcus pneumoniae (pneumococcus) is a Gram-positive facultative anaerobic bacterium that is a major cause of morbidity and mortality worldwide. But the lack of reporting of disease by this bacterium in Indonesia, one of the causes is because the diagnosis of pneumococcal infection is often clinically not typical and conventional methods which are still the standard gold method often give false-negative results. So the purpose of this study was to evaluate the performance of culture and molecular diagnostic methods using the Polymerase Chain Reaction (PCR) technique in detecting Streptococcus pneumoniae in sputum clinical samples using the Autolysin (LytA) gene which is a virulence factor of this bacterium. 57 isolates from 60 samples were confirmed as Streptococcus sp through microscopic identification, culture, and biochemical tests. Then the sensitivity test with an optochin test of 9 (9%) compared the results descriptively with the PCR technique using the Autolysin A (LytA) gene which was obtained more sensitive by 15 (25%).

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Trends in antibiotic resistance patterns of methicillin resistant and methicillin sensitive Staphylococcus aureus in Khwaja Yunus Ali Medical College Hospital

KYAMC Journal ◽

10.3329/kyamcj.v9i1.36596 ◽

2018 ◽

Vol 9 (1) ◽

pp. 6-10 ◽

Cited By ~ 1

Author(s):

Abdullah Akhtar Ahmed ◽

Md Abdus Salam ◽

Md Shakhaowat Hossain ◽

Md Babul Aktar ◽

Nusrat Akhtar Juyee ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Pathogenic Bacteria ◽

Current Status ◽

Clinical Samples ◽

Sensitivity Testing ◽

Methicillin Resistant ◽

Resistance Patterns ◽

Antibiotic Resistance Patterns

Background: Antimicrobial resistance in pathogens is a growing concern for health. It is a great concern around the globe about the threat of increasing antimicrobial resistance. In response to this concerns, medical experts have proposed initiatives to curtail the spread of antimicrobial resistance in pathogenic bacteria. We have taken this surveillance study in KYAMCH to contain the spread of antimicrobial resistance.Objectives: To determine the prevalence of MRSA from different clinical samples and to record its current status to commonly used anti Staphylococcus antibiotics.Methods: The clinical samples were taken to the laboratory and within four hours cultured for isolates and identification pathogens. Finally, antibiotic sensitivity testing of the isolated Staphylococcus aureus was performed. Results: More than 80% of MRSA isolates were resistant to ampicillin (98%) followed by amoxicillin, cefixime and azithromycin with 94%, 93.5% and 85% respectively and maximum sensitivity toward tobramycin with 86% followed by 85% gentamicin and 79% meropenem.Conclusion: The detected trend in antibiotic resistance patterns of methicillin-resistant and methicillin-sensitive Staphylococcus aureus in this study is alarming. This has created a huge clinical burden in the hospital settings as well as in the community.KYAMC Journal Vol. 9, No.-1, April 2018, Page 6-10

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Antibiotic Resistance in Staphylococcus aureus in Patients Hospitalized in Imam Reza Hospital of Kermanshah, Iran (2016 - 2018)

Journal of Kermanshah University of Medical Sciences ◽

10.5812/jkums.118807 ◽

2021 ◽

Vol In Press (In Press) ◽

Author(s):

Mohammad Hossein Zamanian ◽

Marya Shirvani ◽

Alireza Janbakhsh ◽

Babak Sayad ◽

Siavash Vaziri ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antibiotic Resistance ◽

Opportunistic Pathogen ◽

Cross Sectional Study ◽

Penicillin G ◽

Diffusion Method ◽

Disk Diffusion Method ◽

Cross Sectional ◽

Healthcare Settings ◽

Wide Range

Background: Staphylococcus aureus is an opportunistic pathogen, which often causes asymptomatic diseases. This bacterium could cause several disorders, ranging from skin infections to life-threatening diseases. S. aureus could also develop resistance to a wide range of antibiotics. Objectives: The present study aimed to investigate the prevalence and pattern of antibiotic resistance in isolated S. aureus in Imam Reza Hospital of Kermanshah, Iran. Methods: This descriptive cross-sectional study was conducted on 2,228 patients with a positive S. aureus culture who were admitted to Imam Reza Hospital during 2016 - 2018. In accordance with the CLSI protocol, bacterial isolates were separated using laboratory tests, and antibiotic susceptibility was assessed using the standard disk-diffusion method. Data analysis was performed in SPSS version 24. Results: Most of the S. aureus-positive cases were isolated from the emergency ward (43.7%), blood samples (40.1%), and urine samples (23.9%). The highest antibiotic resistance was observed against erythromycin, penicillin G, ofloxacin, cefoxitin, clindamycin, and piperacillin. With 93.3% and 81.8% sensitivity, vancomycin and teicoplanin were respectively the most effective antibiotics against S. aureus. Conclusions: According to the results, the prevalence of resistant S. aureus strains could be due to the long-term hospitalization of patients and the overuse of antibiotics in infection treatment. Therefore, proper monitoring and development of effective infection control methods are essential in these healthcare settings.

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Antimicrobial Resistance Patterns and Plasmid Profiles of Methicillin Resistant Staphylococcus aureus Isolated from Clinical Samples

Nepal Journal of Biotechnology ◽

10.3126/njb.v7i1.26945 ◽

2019 ◽

Vol 7 (1) ◽

pp. 8-14

Author(s):

Gaurav Agrahari ◽

Amrit Koirala ◽

Roshan Thapa ◽

Mahesh Kumar Chaudhary ◽

Reshma Tuladhar

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Antibiotic Susceptibility ◽

Methicillin Resistant Staphylococcus Aureus ◽

Plasmid Profile ◽

Diffusion Method ◽

Clinical Samples ◽

Methicillin Resistant ◽

Plasmid Profiles ◽

Resistance Patterns

Methicillin-resistant Staphylococcus aureus (MRSA), showing resistance to several antibiotics is a global health problem associated with considerable mortality and morbidity. Antibiotic susceptibility test is a commonly used method to characterize MRSA in epidemiologic studies. Additionally, plasmid profile has been reported to be useful in tracing the epidemiology of antibiotic resistance. This research was conducted to determine the antimicrobial resistance patterns and plasmid profiles of MRSA isolated from clinical samples at KIST Medical College, Imadol, Kathmandu, Nepal. All the clinical specimens sent to the laboratory were processed by standard microbiological techniques and antibiotic susceptibility testing was done by the modified Kirby Bauer disc diffusion method. Further, plasmid profiling was done by Alkaline-lysis method. A total of 27 (38.02%) MRSA were isolated from 71 S. aureus positive samples. MRSA showed the highest resistance towards penicillin (92.60%) and ampicillin (92.60%). In contrast, high levels of sensitivity were shown towards vancomycin (85.19%) and tetracycline (85.19%). Out of 27 MRSA positive samples, single plasmids were isolated from only 6 (22.22%) MRSA isolates. Antibiograms alone are inadequate to accomplish the characterization of MRSA during epidemiological studies. However, plasmid profile analysis in conjunction with the antibiotic susceptibility pattern is valuable in the epidemiological investigation of MRSA, and for reducing MRSA prevalence and treatment cost.

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OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution

Biomedicines ◽

10.3390/biomedicines9101314 ◽

2021 ◽

Vol 9 (10) ◽

pp. 1314

Author(s):

Eduarda Carvalho-Correia ◽

Carla Calçada ◽

Fernando Branca ◽

Nuria Estévez-Gómez ◽

Loretta De Chiara ◽

...

Keyword(s):

Cross Reactivity ◽

Diagnostic Methods ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Analytical Sensitivity ◽

S Gene ◽

Genomic Knowledge ◽

Gene Assay ◽

One Step

Extensive transmission of SARS-CoV-2 during the COVID-19 pandemic allowed the generation of thousands of mutations within its genome. While several of these become rare, others largely increase in prevalence, potentially jeopardizing the sensitivity of PCR-based diagnostics. Taking advantage of SARS-CoV-2 genomic knowledge, we designed a one-step probe-based multiplex RT-qPCR (OmniSARS2) to simultaneously detect short fragments of the SARS-CoV-2 genome in ORF1ab, E gene and S gene. Comparative genomics of the most common SARS-CoV-2 lineages, other human betacoronavirus and alphacoronavirus, was the basis for this design, targeting both highly conserved regions across SARS-CoV-2 lineages and variable or absent in other Coronaviridae viruses. The highest analytical sensitivity of this method for SARS-CoV-2 detection was 94.2 copies/mL at 95% detection probability (~1 copy per total reaction volume) for the S gene assay, matching the most sensitive available methods. In vitro specificity tests, performed using reference strains, showed no cross-reactivity with other human coronavirus or common pathogens. The method was compared with commercially available methods and detected the virus in clinical samples encompassing different SARS-CoV-2 lineages, including B.1, B.1.1, B.1.177 or B.1.1.7 and rarer lineages. OmniSARS2 revealed a sensitive and specific viral detection method that is less likely to be affected by lineage evolution oligonucleotide–sample mismatch, of relevance to ensure the accuracy of COVID-19 molecular diagnostic methods.

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spa typing and antimicrobial resistance of Staphylococcus aureus from healthy humans, pigs and dogs in Tanzania

The Journal of Infection in Developing Countries ◽

10.3855/jidc.6790 ◽

2016 ◽

Vol 10 (02) ◽

pp. 143-148 ◽

Cited By ~ 2

Author(s):

Abdul Sekemani Katakweba ◽

Amandus Pachificus Muhairwa ◽

Carmen Espinosa-Gongora ◽

Luca Guardabassi ◽

Madundo M A Mtambo ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Tetracycline Resistance ◽

Nasal Carriage ◽

Opportunistic Pathogen ◽

Diffusion Method ◽

Spa Typing ◽

Healthy Humans ◽

Mueller Hinton ◽

Spa Types

Introduction: Staphylococcus aureus is an opportunistic pathogen causing infections in humans and animals. Here we report for the first time the prevalence of nasal carriage, spa typing and antimicrobial resistance of S. aureus in a Tanzanian livestock community. Methodology: Nasal swabs were taken from 100 humans, 100 pigs and 100 dogs in Morogoro Municipal. Each swab was enriched in Mueller Hinton broth with 6.5% NaCl and subcultured on chromogenic agar for S. aureus detection. Presumptive S. aureus colonies were confirmed to the species level by nuc PCR and analysed by spa typing. Antimicrobial susceptibility patterns were determined by disc diffusion method. Results: S. aureus was isolated from 22 % of humans, 4 % of pigs and 11 % of dogs. A total of 21 spa types were identified: 13, 7 and 1 in human, dogs, and pigs, respectively. Three spa types (t314, t223 and t084) were shared between humans and dogs. A novel spa type (t10779) was identified in an isolate recovered from a colonized human. Antimicrobials tested revealed resistance to ampicillin in all isolates, moderate resistances to other antimicrobials with tetracycline resistance being the most frequent. Conclusion: S. aureus carrier frequencies in dogs and humans were within the expected range and low in pigs. The S. aureus spa types circulating in the community were generally not shared by different hosts and majority of types belonged to known clones. Besides ampicillin resistance, moderate levels of antimicrobial resistance were observed irrespective of the host species from which the strains were isolated.

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Rapid Detection and Differentiating of the Predominant Salmonella Serovars in Chicken Farm by TaqMan Multiplex Real-Time PCR Assay

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.759965 ◽

2021 ◽

Vol 11 ◽

Author(s):

Suhua Xin ◽

Hong Zhu ◽

Chenglin Tao ◽

Beibei Zhang ◽

Lan Yao ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Epidemiologic Study ◽

Clinical Diagnostics ◽

Diagnostic Methods ◽

Molecular Diagnostic ◽

Clinical Samples ◽

Analytical Sensitivity ◽

Pcr Assay ◽

Chicken Farm

Salmonella has been known as an important zoonotic pathogen that can cause a variety of diseases in both animals and humans. Poultry are the main reservoir for the Salmonella serovars Salmonella Pullorum (S. Pullorum), Salmonella Gallinarum (S. Gallinarum), Salmonella Enteritidis (S. Enteritidis), and Salmonella Typhimurium (S. Typhimurium). The conventional serotyping methods for differentiating Salmonella serovars are complicated, time-consuming, laborious, and expensive; therefore, rapid and accurate molecular diagnostic methods are needed for effective detection and prevention of contamination. This study developed and evaluated a TaqMan multiplex real-time PCR assay for simultaneous detection and differentiation of the S. Pullorum, S. Gallinarum, S. Enteritidis, and S. Typhimurium. In results, the optimized multiplex real-time PCR assay was highly specific and reliable for all four target genes. The analytical sensitivity corresponded to three colony-forming units (CFUs) for these four Salmonella serovars, respectively. The detection limit for the multiplex real-time PCR assay in artificially contaminated samples was 500 CFU/g without enrichment, while 10 CFU/g after pre-enrichment. Moreover, the multiplex real-time PCR was applied to the poultry clinical samples, which achieved comparable results to the traditional bacteriological examination. Taken together, these results indicated that the optimized TaqMan multiplex real-time PCR assay will be a promising tool for clinical diagnostics and epidemiologic study of Salmonella in chicken farm and poultry products.

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Molecular Characteristics of Staphylococcus aureus From Food Samples and Food Poisoning Outbreaks in Shijiazhuang, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652276 ◽

2021 ◽

Vol 12 ◽

Author(s):

Guoping Lv ◽

Ruiping Jiang ◽

Han Zhang ◽

Lei Wang ◽

Lijie Li ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Potential Risk ◽

Food Poisoning ◽

Opportunistic Pathogen ◽

Food Samples ◽

Staphylococcal Enterotoxin ◽

Molecular Characteristics ◽

Resistant Gene ◽

Human Infections ◽

The Relationship

As an opportunistic pathogen worldwide, Staphylococcus aureus can cause food poisoning and human infections. This study investigated the sequence typing, the penicillin (blaZ) and methicillin (mec) resistance profiles of S. aureus from food samples and food poisoning outbreaks in Shijiazhuang City, and the staphylococcal enterotoxin (SE) types of the S. aureus isolates from food poisoning. A total of 138 foodborne S. aureus isolates were distributed into 8 clonal complexes (CCs) and 12 singletons. CC1, CC5, CC8, CC15, CC97, CC59, CC398, CC88, and CC7 were the predominant CCs of foodborne S. aureus isolates. Moreover, CC59, CC15, and CC5 were the most prevalent CCs in food poisoning outbreaks. SEE was the most commonly detected SE in food poisoning isolates. One hundred thirty-three S. aureus isolates harbored the penicillin-resistant gene blaZ, and nine isolates carried the mec gene. The present study further explained the relationship between S. aureus and foods and food poisoning and indicated the potential risk of S. aureus infection.

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