Digital PCR for Detection and Quantification of Fluoroquinolone Resistance in Legionella pneumophila

Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings

Digital polymerase chain reaction (dPCR) has emerged as a groundbreaking technology in molecular biology and diagnostics, offering exceptional precision and sensitivity in nucleic acid detection and quantification. This review highlights the core principles and transformative potential of dPCR, particularly in infectious disease diagnostics and environmental surveillance. Emphasizing its evolution from traditional PCR, dPCR provides accurate absolute quantification of target nucleic acids through advanced partitioning techniques. The review addresses the significant impact of dPCR in sepsis diagnosis and management, showcasing its superior sensitivity and specificity in early pathogen detection and identification of drug-resistant genes. Despite its advantages, challenges such as optimization of experimental conditions, standardization of data analysis workflows, and high costs are discussed. Furthermore, we compare various commercially available dPCR platforms, detailing their features and applications in clinical and research settings. Additionally, the review explores dPCR's role in water microbiology, particularly in wastewater surveillance and monitoring of waterborne pathogens, underscoring its importance in public health protection. In conclusion, future prospects of dPCR, including methodological optimization, integration with innovative technologies, and expansion into new sectors like metagenomics, are explored.

Efficacy of omadacycline in the treatment of Legionella pneumonia: a case report

Legionella, one of the main pathogens that causes community-acquired pneumonia, can lead to Legionella pneumonia, a condition characterized predominantly by severe pneumonia. This disease, caused by the bacterium Legionella pneumophila, can quickly progress to critical pneumonia and is often associated with damage to multiple organs. As a result, it requires close attention in terms of clinical diagnosis and treatment. Omadacycline, a new type of tetracycline derivative belonging to the aminomethylcycline class of antibiotics, is a semi-synthetic compound derived from minocycline. Its key structural feature, the aminomethyl modification, allows omadacycline to overcome bacterial resistance and broadens its range of effectiveness against bacteria. Clinical studies have demonstrated that omadacycline is not metabolized in the body, and patients with hepatic and renal dysfunction do not need to adjust their dosage. This paper reports a case of successful treatment of Legionella pneumonia with omadacycline in a patient who initially did not respond to empirical treatment with moxifloxacin. The patient also experienced electrolyte disturbance, as well as dysfunction in the liver and kidneys, delirium, and other related psychiatric symptoms.

Value of digital PCR in the early diagnosis of sepsis: A systematic review and meta-analysis

BACKGROUND

We systematically assessed whether a digital polymerase chain reaction (PCR) could detect pathogenic microorganisms in patients with sepsis early and accurately.

METHODS

We searched the Cochrane Library, MEDLINE, Embase, CNKI, CBM, and Wanfang Data databases for eligible studies to compare the detection of pathogenic microorganisms in blood samples by digital PCR with the gold standard. The Quality Assessment of Diagnostic Accuracy Studies 2 was used to evaluate bias risk, and a random-effects meta-analysis approach was used for sensitivity and specificity calculations.

RESULTS

Among the eight articles, there were eight identified studies with a total of 1278 subjects. The pooled sensitivity of digital PCR was 94% (95% confidence interval [CI], 85%-98%), the specificity was 87% (95% CI, 76%-94%), the positive likelihood ratio was 7.3 (95% CI, 3.8-14.2), the negative likelihood ratio was 0.07 (95% CI, 0.03-0.17), the positive predictive value was 84.7%, the negative predictive value was 89.2%, the diagnostic odds ratio was 105 (95% CI, 37-303), and the area under the receiver operating characteristic curve was 0.97 (95% CI, 0.95-1.00). Digital PCR can shorten the detection time of pathogenic microorganisms in patients with sepsis.

CONCLUSIONS

Digital PCR can detect pathogenic microorganisms in patients with sepsis earlier than blood culture. Therefore, digital PCR can be used as a potential strategy for the detection of pathogenic microorganisms in patients with sepsis.

Case report: A prosthetic valve endocarditis caused by Legionella bozemanae in an immunocompetent patient

Extrapulmonary infections with Legionella species are rare, but important to acknowledge. We report a case of infective endocarditis (IE) with Legionella bozemanae in a 66-year-old immunocompetent man with an aortic homograft. The diagnosis was made by direct 16S rRNA gene amplification from valve material, confirmed by a targeted Legionella-PCR in serum and the detection of L. bozemanae specific antibodies. To our knowledge, this is the first confirmed case of IE with L. bozemanae as causative pathogen. The infected aortic prosthesis was replaced by a homograft, and the patient was successfully treated with levofloxacin and azithromycin for 6 weeks.

Droplet Digital PCR-Based Detection and Quantification of GyrA Thr-86-Ile Mutation Based Fluoroquinolone-Resistant Campylobacter jejuni

Fluoroquinolone (FQ)-resistant Campylobacter jejuni is a serious problem worldwide that limits effective treatment of infections. The traditional detection method depends on bacterial isolation and MIC testing, or traditional PCR, which is time-consuming and hard to identify the FQ-resistant C. jejuni in a high abundance wild-type background. This study aimed to develop a rapid and accurate ddPCR assay to detect FQ-resistant C. jejuni mutants based on the crucial resistance mutation C257T (Thr-86-Ile) in gyrA. Our ddPCR gyrA assay showed high specificity and accuracy. Sanger sequencing and the qPCR assay could only recognize gyrA mutant sequences when the ratios of wild-type/mutant were 1:1 or 10:1, respectively. Our ddPCR gyrA assay was able to detect gyrA mutant sequences in the mixtures with up to at least 1000:1 wild-type/mutant ratios, which suggested a significant advantage to distinguish the low mutant signal from the wild-type background. We further monitored the occurrence of gyrA mutations under ciprofloxacin pressure using our ddPCR gyrA assay, and clearly showed that the transition of a dominant C. jejuni subpopulation from wild-type to gyrA C257T mutant, resulting in FQ-resistance. We tested 52 samples from live chickens and retail chicken meat and showed that four samples contained wild-type/mutant mixtures comprising 1.7%, 28.6%, 53.3%, and 87.0% gyrA C257T mutants, respectively. These results demonstrated that the ddPCR gyrA assay was a highly sensitive alternative method to distinguish and quantify FQ-resistant C. jejuni infections that could help guide the appropriate use of FQs in clinical practice.

IMPORTANCECampylobacter jejuni is considered to be the leading cause of human bacterial gastroenteritis worldwide, and fluoroquinolones (FQs) are the main choices for the treatment of bacterial gastroenteritis in clinical practice. In theory, antimicrobial susceptibility testing should help us to choose the most appropriate drugs for the treatment. However, to test the susceptibility of C. jejuni to FQs, the standardized method is bacteria isolation and MIC measurement, which will take more than 4 days. In addition, a low abundance of FQ-resistant C. jejuni is also hardly distinguished from a high abundance of wild-type background in the mixed infection. Therefore, the development of rapid and accurate detection technology for FQ-resistant C. jejuni is very important. This study provided a ddPCR gyrA assay, which is a highly sensitive alternative method to distinguish and quantify FQ-resistant C. jejuni infections that may help guide the appropriate use of FQs both in veterinary and human clinical practice.

Current commercial dPCR platforms: technology and market review

Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.

Overview of the Clinical and Molecular Features of Legionella Pneumophila: Focus on Novel Surveillance and Diagnostic Strategies

Legionella pneumophila (L. pneumophila) is one of the most threatening nosocomial pathogens. The implementation of novel and more effective surveillance and diagnostic strategies is mandatory to prevent the occurrence of legionellosis outbreaks in hospital environments. On these bases, the present review is aimed to describe the main clinical and molecular features of L. pneumophila focusing attention on the latest findings on drug resistance mechanisms. In addition, a detailed description of the current guidelines for the disinfection and surveillance of the water systems is also provided. Finally, the diagnostic strategies available for the detection of Legionella spp. were critically reviewed, paying the attention to the description of the culture, serological and molecular methods as well as on the novel high-sensitive nucleic acid amplification systems, such as droplet digital PCR.

Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa

Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.

Mycoplasma genitalium infections can comprise a mixture of both fluoroquinolone-susceptible and fluoroquinolone-resistant strains

BACKGROUND

Mycoplasma genitalium was recently added to the CDC's antimicrobial resistance threats 'watch list', as it has rapidly become resistant to mainstay treatments. In Australia, treatment failure with fluoroquinolones remain commonplace, even when Sanger sequencing fails to identify evidence of resistance mutations.

METHODS

Suspecting that Sanger sequencing may miss low-load mixed infections, we applied three additional PCR-based approaches (allele-specific primer-based PCR, probe-based PCR and amplicon deep sequencing) to detect mutations associated with fluoroquinolone susceptibility/resistance. We focused on resistance mutations at amino acid positions 83 and 87 of parC, as these were previously shown to be common in Australia.

RESULTS

Our results showed evidence of mixtures of fluoroquinolone-susceptible and -resistant strains in up to 27/423 samples (6.4%). These included 1 sample that was indicated to be mixed by Sanger sequencing and all three additional PCR methods, 6 samples detected by two or more of the additional PCRs but not by Sanger sequencing and finally 20 samples that were detected by only one of the additional PCR methods. A key question was whether Sanger sequencing failed to detect fluoroquinolone resistance in any samples; overall, we observed that Sanger sequencing failed to detect fluoroquinolone resistance in up to 3.8% (16/423) of samples.

CONCLUSIONS

The presence of mixed susceptibility infections may have important implications for clinical patient management and stresses the need for appropriate detection of resistance and selection of antimicrobials to ensure appropriate treatment of M. genitalium infections.

Digital PCR method for detection and quantification of specific antimicrobial drug-resistance mutations in human cytomegalovirus

Antimicrobial drug resistance is one of the biggest threats to human health worldwide. Timely detection and quantification of infectious agents and their susceptibility to antimicrobial drugs are crucial for efficient management of resistance to antiviral drugs. In clinical settings, viral drug resistance is most often associated with prolonged treatment of chronic infections, and assessed by genotyping methods; e.g., sequencing and PCR. These approaches have limitations: sequencing can be expensive and does not provide quantification; and qPCR quantification is hampered by a lack of reference materials for standard curves. In recent years, digital PCR has been introduced, which provides absolute quantification without the need for reference materials for standard curves. Using digital PCR, we have developed a rapid, sensitive and accurate method for genotyping and quantification of the most prevalent mutations that cause human cytomegalovirus resistance to ganciclovir.

Antibiotic-Resistant Community-Acquired Bacterial Pneumonia

Antimicrobial resistance is a global concern, and prudent use of antibiotics is essential to preserve the current armamentarium of effective drugs. Acute respiratory tract infection is the most common reason for antibiotic prescription in adults. In particular, community-acquired pneumonia poses a significant health challenge and economic burden globally, especially in the current landscape of a dense and aging population. By updating the knowledge on the common antimicrobial-resistant pathogens in community-acquired respiratory tract infections, their prevalence, and resistance may pave the way to enhancing appropriate antibiotic use in the ambulatory and health care setting.

Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella

Legionella species are environmental gram-negative bacteria able to cause a severe form of pneumonia in humans known as Legionnaires’ disease. Since the identification of Legionella pneumophila in 1977, four decades of research on Legionella biology and Legionnaires’ disease have brought important insights into the biology of the bacteria and the molecular mechanisms that these intracellular pathogens use to cause disease in humans. Nowadays, Legionella species constitute a remarkable model of bacterial adaptation, with a genus genome shaped by their close coevolution with amoebae and an ability to exploit many hosts and signaling pathways through the secretion of a myriad of effector proteins, many of which have a eukaryotic origin. This review aims to discuss current knowledge of Legionella infection mechanisms and future research directions to be taken that might answer the many remaining open questions. This research will without a doubt be a terrific scientific journey worth taking.

Legionella: a reemerging pathogen

PURPOSE OF REVIEW

The present review summarizes new knowledge about Legionella epidemiology, clinical characteristics, community-associated and hospital-based outbreaks, molecular typing and molecular epidemiology, prevention, and detection in environmental and clinical specimens.

RECENT FINDINGS

The incidence of Legionnaire's disease is rising and the mortality rate remains high, particularly for immunocompromised patients. Extracorporeal membrane oxygenation may help support patients with severe respiratory failure. Fluoroquinolones and macrolides appear to be equally efficacious for treating Legionnaires' disease. Whole genome sequencing is an important tool for determining the source for Legionella infections and for understanding routes of transmission and mechanisms by which new pathogenic clones emerge. Real-time quantitative polymerase chain reaction testing of respiratory specimens may improve our ability to diagnose Legionnaire's disease. The frequency of viable but nonculturable organisms is quite high in some water systems but their role in causing clinical disease has not been defined.

SUMMARY

Legionellosis remains an important public health threat. To prevent these infections, staff of municipalities and large buildings must implement effective water system management programs that reduce Legionella growth and transmission and all Medicare-certified healthcare facilities must have water management policies. In addition, we need better methods for detecting Legionella in water systems and in clinical specimens to improve prevention strategies and clinical diagnosis.