The role of multiplex PCR test in identification of bacterial pathogens in lower respiratory tract infections

Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes

BACKGROUND

Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes.

METHODS

Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients.

RESULTS

The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections.

CONCLUSIONS

Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.

Simultaneous Genetically Detection of Streptococcuspyogenes, Streptococcuspneumoniae and Haemophilusinfluenzae in Patients with Treatment-Resistant Respiratory Infection

Background & Objective

Streptococcus pneumoniae, Haemophilus influenzae and Streptococcus pyogenes are among the most important causes of infection in human. Inventing rapid methods to identify these species can help in providing appropriate and effective treatment options. Therefore, the current study aimed to develop a multiplex touch-down PCR method to identify rapidly the aforementioned species patients' sputum samples, simultaneously.

Methods

A total of 50 sputum samples of patients with respiratory infections resistant to treatment were collected. After DNA extraction and primer design, the complete capsule (CAP) region II, capsular polysaccharide biosynthesis (cpsA) and the structural regulator of transcription (spy) genes were amplified for detecting H. influenzae, S. pneumoniae and S. pyogenes by multiplex touch-down PCR.

Results

Among 50 samples prepared from patients with different diseases, 27 samples were positive for amplified genes. The frequency of presence of pathogens in the collected samples included 14% H. influenzae, 20% S. pneumoniae and 20% S. pyogenes. Also, in some patients, the simultaneous presence of two or three pathogens were observed.

Conclusion

In general, it can be concluded that the PCR touchdown method developed in the present study is an effective and fast method for the simultaneous identification of H. influenzae, S. pneumoniae and S. pyogenes pathogens in clinical samples of patients.

Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran

BACKGROUND

This study aimed to evaluate the occurrence of Streptococcus pneumoniae and Haemophilus influenzae in sputum of patients with community-acquired pneumonia (CAP) using culture and multiplex polymerase chain reaction (M-PCR) methods and to survey the antibiotic resistance patterns of aforesaid isolates.

RESULT

In total, 23.9 % (n = 22/92) of sputum samples showed positive results in the culture method. S. pneumoniae and H. influenzae were isolated from 15 (16.3 %) and 7 (7.6%) samples, respectively. Using M-PCR, 44 (47.8 %) samples were positive for S. pneumoniae and H. influenzae. Of these, S. pneumoniae and H. influenzae were detected in 33 (35.8%) and 11 (11.9%) of the sputum samples, respectively. The sensitivity, specificity, and accuracy rates of PCR in detection of S. pneumoniae in comparison with culture method were 100, 76.6, and 83.6%, respectively. While, the sensitivity, specificity, and accuracy rates of PCR in detection of H. influenzae in comparison with culture method were 100, 95.3, and 95.8%, respectively. Out of 11 isolates of H. influenzae, two strains confirmed as H. influenzae type b (Hib) and 3 isolates were type f. However, 6 isolates were non-typable. The co-trimoxazole and amoxicillin/clavulanate were the less effective antibiotics against S. pneumonia and H. influenzae, respectively. Ceftriaxone with 13.3% resistance rates was the most effective antibiotic against S. pneumoniae, while, clarithromycin, ceftriaxone, and gentamicin with resistance rates of 28.6% for each one were the most effective chemicals against H. influenzae isolates.

CONCLUSION

In this study, the prevalence of S. pneumoniae was more than H. influenzae using culture and M-PCR methods. The M-PCR provided better efficiency in detecting the bacterial agents in CAP patients compared to culture method. This method can improve the early detection of pathogens contributed to CAP. The drug resistant S. pneumoniae and H. influenzae indicated the need to develop a codified monitoring program to prevent further spread of these strains.

Emergence of Highly Multidrug-Resistant Bacteria Isolated from Patients with Infections Admitted to Public Hospitals in Southwest Iran

Background

The emergence of multidrug-resistant (MDR) microorganisms causing infections is increasing worldwide and becoming more serious in developing countries. Among those, Acinetobacter species are becoming prominent.

Objectives

The aim of this study was to determine the rate of antimicrobial resistance of the bacteria causing infections, Acinetobacter species in particular, in local public hospitals in Firuzabad, Fars province, Iran.

Methods

This cross-sectional study was performed on different clinical specimens collected from patients who were suspected of infections hospitalized from March 2016 to March 2019 in local hospitals of Firuzabad, Fars province, Iran. The bacterial isolates were identified following standard microbiological methods. Clinical and Laboratory Standards Institute guidelines were used to identify the antibiotic susceptibility of these isolates.

Results

Overall, 1778 bacterial etiologies were isolated from 1533 patients diagnosed with infection. Of these, 1401 (78.8%) were Gram-negative and the remaining were Gram-positive bacteria. Escherichia coli (37.1%), Klebsiella spp. (13.9%), and Acinetobacter species (10.4%) were the most common isolated bacteria. Antibiotic sensitivity testing in this study showed a high resistance rate of Acinetobacter species to all antibiotics tested except Colistin. During the study period, the rate of infection with highly multidrug-resistant Acinetobacter species increased from 7.2% to 13.3%.

Conclusions

This study highlights the emergence of MDR bacterial agents such as Acinetobacter species as a new threat in our region. However, a decrease in the rate of infection with Pseudomonas aeruginosa was noticeable.

Performance of a Semiquantitative Multiplex Bacterial and Viral PCR Panel Compared With Standard Microbiological Laboratory Results: 396 Patients Studied With the BioFire Pneumonia Panel

Background

Microbiologic results are critical to optimal management of patients with lower respiratory tract infection, but standard methods may take several days. The multiplex polymerase chain reaction BioFire Pneumonia (PN) panel detects 15 common bacterial species semiquantitatively as copy number/mL, 8 viral species, and 7 resistance genes in about an hour within the clinical laboratory.

Methods

We tested 396 unique endotracheal or bronchoalveolar lavage specimens with the BioFire Pneumonia panel and compared the bacterial detections to conventional gram stain and culture results.

Results

Of the 396 patients, 138 grew at least 1 bacterium that had a target on the PN panel, and 136/138 (98.6%) were detected by the panel. A total of 177 isolates were recovered in culture and the PN panel detected 174/177 (98.3%). A further 20% of patients had additional targets detected that were not found on standard culture (specificity 69%, positive predictive value 63%, and negative predictive value 98.9%). Copy number was strongly related to standard semiquantitative growth on plates reported by the laboratory (eg, 1+, 2+, 3+ growths) and was significantly higher in those specimens that grew a potential pathogen. Both higher copy number and bacterial detections found by the PN panel, but not found in culture, were strongly positively related to the level of white blood cells reported in the initial gram stain.

Conclusions

Higher copy number and bacterial detections by the PN panel are related to the host respiratory tract inflammatory response. If laboratories can achieve a rapid turnaround time, the PN panel should have a significant impact both on patient management and on antibiotic stewardship.

Molecular detection of respiratory pathogens among children aged younger than 5 years hospitalized with febrile acute respiratory infections: A prospective hospital-based observational study in Niamey, Niger

BACKGROUND AND AIMS

In Niger, acute respiratory infections (ARIs) are the second most common cause of death in children aged younger than 5 years. However, the etiology of ARI is poorly understood in the country. This study aims to describe viral and bacterial infections among children aged younger than 5 years hospitalized with febrile ARI at two hospitals in Niamey, Niger's capital city, and the reported clinical procedures.

METHODS

We conducted a prospective study among children aged younger than 5 years hospitalized with febrile ARI at two national hospitals in Niamey between January and December 2015. Clinical presentation and procedures during admission were documented using a standardized case investigation form. Nasopharyngeal specimens collected from each patient were tested for a panel of respiratory viruses and bacteria using the Fast Track Diagnostic 21 Plus kit.

RESULTS

We enrolled and tested 638 children aged younger than 5 years, of whom 411 (64.4%) were aged younger than 1 year, and 15 (2.4%) died during the study period. Overall, 496/638 (77.7%) specimens tested positive for at least one respiratory virus or bacterium; of these, 195 (39.3%) tested positive for respiratory viruses, 126 (25.4%) tested positive for respiratory bacteria, and 175 (35.3%) tested positive for both respiratory viruses and bacteria. The predominant viruses detected were respiratory syncytial virus (RSV) (149/638; 23.3%), human parainfluenza virus (HPIV) types 1 to 4 (78/638; 12.2%), human rhinovirus (HRV) (62/638; 9.4%), human adenovirus (HAV) (60/638; 9.4%), and influenza virus (INF) (52/638; 8.1%). Streptococcus pneumoniae (249/638; 39.0%) was the most frequently detected bacterium, followed by Staphylococcus aureus (112/638; 12.2%) and Haemophilus influenzae type B (16/638; 2.5%). Chest X-rays were performed at the discretion of the attending physician on 301 (47.2%) case patients. Of these patients, 231 (76.7%) had abnormal radiological findings. A total of 135/638 (21.2%) and 572/638 (89.7%) children received antibiotic treatment prior to admission and during admission, respectively.

CONCLUSION

A high proportion of respiratory viruses was detected among children aged younger than 5 years with febrile ARI, raising concerns about excessive use of antibiotics in Niger.

Comparative Study of CDST & Multiplex PCR to Detect MBL Producing Gram-Negative Bacilli among VAP Patients Admitted in a Public Medical College Hospital of Bangladesh

Background: Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in intensive care units (ICU), which accounts for 25% of all ICU infection. Documenting carbapenem-resistant gram-negative bacilli is very important as these strains may often cause outbreaks in the ICU setting and are responsible for the increased mortality and morbidity or limiting therapeutic options. The classical phenotypic method cannot provide an efficient means of diagnosis of the metallo-β-lactamases (MBLs) producer. Polymerase chain reaction (PCR) assays have lessened the importance of the phenotypic approach by detecting metallo-β-lactamase resistance genes such as New Delhi metallo-β-lactamase (NDM), Imipenemase (IMP), Verona integron-encoded metallo-β-lactamase (VIM), Sao Paulo metallo-β-lactamase (SPM), Germany Imipenemase (GIM). Objective: To compare the results of the Combined Disc Synergy Test (CDST) with that of the multiplex PCR to detect MBL-producing gram-negative bacilli. Materials and Method: A total of 105 endotracheal aspirates (ETA) samples were collected from the ICU of a public school in Bangladesh. This cross-sectional study was carried out in the Department of Microbiology, Chittagong for quantitative culture, CDST test, and multiplex PCR for bla_IMP, bla_VIM, bla_NDM genes of MBL producers. Results: Among the 105 clinically suspected VAP cases, the quantitative culture was positive in 95 (90%) and among 95 g-negative bacilli isolated from VAP patients, 46 (48.42%) were imipenem resistant, 30 (65.22%) were MBL producers by CDST, 21 (45.65%) were identified as MBL producers by multiplex PCR. Conclusion: PCR was highly sensitive and specific for the detection of MBL producers.

A Thermostabilized, One-Step PCR Assay for Simultaneous Detection of Klebsiella pneumoniae and Haemophilus influenzae

Klebsiella pneumoniae and Haemophilus influenzae are two common pathogens associated with respiratory tract infections. The identification of these pathogens using conventional molecular diagnostic tests requires trained personnel, cold-chain transportation, and storage-dependance, which does not render them user-friendly. The aim of this study was to develop a thermostabilized, cold-chain-free, one-step multiplex PCR for simultaneous detection of K. pneumoniae and H. influenzae. The multiplex PCR assay was designed to amplify the php gene of K. pneumoniae (202 bp) and p6 gene of H. influenzae (582 bp). In addition, the specific primer to amplify glm gene of Helicobacter pylori (105 bp) was included as an internal amplification control. Subsequently, the designed primers and all PCR reagents were thermostabilized by lyophilization. The stability of the thermostabilized PCR was evaluated using the Q¹⁰ method. The sensitivity and specificity of performances for thermostabilized PCR were evaluated using 127 clinical isolates and were found to be 100% sensitive and specific. The thermostabilized PCR mix was found to be stable for 30 days and the Q10 accelerated stability was found to be 3.02 months. A cold-chain-free, PCR assay for easy, rapid, and simultaneous detection of K. pneumoniae and H. influenzae was successfully developed in this study.

Assessment of the quantity of microorganisms associated with bronchiectasis in saliva, sputum and nasal lavage after periodontal treatment: a study protocol of a randomised controlled trial

INTRODUCTION

The association between periodontal disease (PD) and chronic obstructive pulmonary disease (COPD) has been widely studied, with aspiration of periodontal pathogens being one of the most accepted causal mechanisms for pulmonary exacerbation. Periodontal treatment (PT) was associated with a decrease in these exacerbations. Bronchiectasis is a pulmonary disease that has many similarities to COPD; however, there are no studies correlating this condition to PD thus far. This study will evaluate if PT reduces proinflammatory cytokines in serum and saliva, as well as halitosis and the amount of microorganisms associated with exacerbation of bronchiectasis in saliva, sputum and nasal lavage 3 months after PT.

METHODS AND ANALYSIS

A total of 182 patients with PD and bronchiectasis will be randomly allocated to group 1 (positive control; scaling and root planing (SRP)+oral hygiene (OH)) or group 2 (experimental; SRP+photodynamic therapy+OH). After 3 months, samples of saliva, nasal lavage and sputum will be collected to determine the level of Pseudomonas aeruginosa, Staphylococcus aureus and Porphyromonas gingivalis by quantitative PCR. This protocol will determine the efficacy of PT in reducing the most likely niches of bronchiectasis exacerbation by comparing pre- and post-treatment microbiology samples. Furthermore, there will be assessment of oral halitosis and verification of inflammatory cytokines in serum and saliva.

ETHICS AND DISSEMINATION

This protocol has been approved by the Research Ethics Committee of Universidade Nove de Julho. Data will be published in a peer-reviewed journal.

TRIAL REGISTRATION NUMBER

NCT02514226.

Bronchoscopy, Imaging, and Concurrent Diseases in Dogs with Bronchiectasis: (2003-2014)

Background

Bronchiectasis is a permanent and debilitating sequel to chronic or severe airway injury, however, diseases associated with this condition are poorly defined.

Objective

To evaluate results of diagnostic tests used to document bronchiectasis and to characterize underlying or concurrent disease processes.

Animals

Eighty‐six dogs that had bronchoscopy performed and a diagnosis of bronchiectasis.

Methods

Retrospective case series. Radiographs, computed tomography, and bronchoscopic findings were evaluated for features of bronchiectasis. Clinical diagnoses of pneumonia (aspiration, interstitial, foreign body, other), eosinophilic bronchopneumopathy (EBP), and inflammatory airway disease (IAD) were made based on results of history, physical examination, and diagnostic testing, including bronchoalveolar lavage fluid analysis and microbiology.

Results

Bronchiectasis was diagnosed in 14% of dogs (86/621) that had bronchoscopy performed. Dogs ranged in age from 0.5 to 14 years with duration of signs from 3 days to 10 years. Bronchiectasis was documented during bronchoscopy in 79/86 dogs (92%), thoracic radiology in 50/83 dogs (60%), and CT in 34/34 dogs (100%). Concurrent airway collapse was detected during bronchoscopy in 50/86 dogs (58%), and focal or multifocal mucus plugging of segmental or subsegmental bronchi was found in 41/86 dogs (48%). Final diagnoses included pneumonia (45/86 dogs, 52%), EBP (10/86 dogs, 12%) and IAD (31/86 dogs, 36%). Bacteria were isolated in 24/86 cases (28%), with Streptococcus spp, Pasteurella spp, enteric organisms, and Stenotrophomonas isolated most frequently.

Conclusions and Clinical Importance

Bronchiectasis can be anticipated in dogs with infectious or inflammatory respiratory disease. Advanced imaging and bronchoscopy are useful in making the diagnosis and identifying concurrent respiratory disease.

Viral and bacterial etiology of severe acute respiratory illness among children < 5 years of age without influenza in Niger

Background

Globally, pneumonia is the leading cause of morbidity and mortality in children, with the highest burden experienced in sub-Saharan Africa and Asia. However, there is a dearth of information on the etiology of severe acute respiratory illness (SARI) in Africa, including Niger.

Methods

We implemented a retrospective study as part of national influenza sentinel surveillance in Niger. We randomly selected a sample of nasopharyngeal specimens collected from children <5 years of age hospitalized with SARI from January 2010 through December 2012 in Niger. The samples were selected from individuals that tested negative by real-time reverse transcription polymerase chain reaction (rRT-PCR) for influenza A and B virus. The samples were analyzed using the Fast Track Diagnostic Respiratory Pathogens 21plus Kit (BioMérieux, Luxemburg), which detects 23 respiratory pathogens including 18 viral and 5 bacterial agents.

Results

Among the 160 samples tested, 138 (86 %) tested positive for at least one viral or bacterial pathogen; in 22 (16 %) sample, only one pathogen was detected. We detected at least one respiratory virus in 126 (78 %) samples and at least one bacterium in 102 (64 %) samples. Respiratory syncytial virus (56/160; 35 %), rhinovirus (47/160; 29 %) and parainfluenza virus (39/160; 24 %) were the most common viral pathogens detected. Among bacterial pathogens, Streptococcus pneumoniae (90/160; 56 %) and Haemophilus influenzae type b (20/160; 12 %) predominated.

Conclusions

The high prevalence of certain viral and bacterial pathogens among children <5 years of age with SARI highlights the need for continued and expanded surveillance in Niger.

Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease

BACKGROUND

Bacterial infection of the lower respiratory tract is believed to play a major role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and acute exacerbations of COPD (AECOPD). This study investigates the potential relationship between AECOPD and the load of six common bacterial pathogens in the lower respiratory tract using real-time quantitative PCR (RT-qPCR) in COPD patients.

METHODS

Protected specimen brush (PSB) and bronchoalveolar lavage fluid (BALF) samples from the lower respiratory tract of 66 COPD patients and 33 healthy subjects were collected by bronchoscopy. The load of Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae, and Moraxella catarrhalis were detected by RT-qPCR.

RESULTS

High Klebsiella pneumoniae, Pseudomonos aeruginosa, Haemophilus influenzeae and Moraxella catarrhalis burden were detected by RT-qPCR in both PSB and BALF samples obtained from stable COPD and AECOPD patients compared with healthy subjects. The load of the above four pathogenic strains in PSB and BALF samples obtained from AECOPD patients were significantly higher compared with stable COPD patients. Finally, positive correlations between bacterial loads and inflammatory mediators such as neutrophil count and cytokine levels of IL-1β, IL-6 and IL-8, as well as negative correlations between bacterial loads and the forced expiratory volume in one second (FEV1) % predicted, forced vital capacity (FVC) % predicted, and FEV1/FVC ratio, were detected.

CONCLUSIONS

These findings suggest that increased bacterial loads mediated inflammatory response in the lower respiratory tract and were associated with AECOPD. In addition, these results provide guidance for antibiotic therapy of AECOPD patients.