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Li M, Wang J, Yao Z, Liao H, Su S, Yang X, Xie M, Zheng Y. Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit. Front Public Health 2023; 11:1177069. [PMID: 37397737 PMCID: PMC10309210 DOI: 10.3389/fpubh.2023.1177069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Background Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection. Methods Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection. Results A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021. Conclusions Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.
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Affiliation(s)
- Meijin Li
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jing Wang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zhongwei Yao
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Hailing Liao
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Shufen Su
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xuying Yang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingzhou Xie
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Yinan Zheng
- Department of Pediatric Intensive Care Unit, Guangdong Women and Children Hospital, Guangzhou, China
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Wang S, Tang J, Tan Y, Song Z, Qin L. Prevalence of atypical pathogens in patients with severe pneumonia: a systematic review and meta-analysis. BMJ Open 2023; 13:e066721. [PMID: 37041056 PMCID: PMC10106036 DOI: 10.1136/bmjopen-2022-066721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
OBJECTIVES We aimed to summarise the prevalence of atypical pathogens in patients with severe pneumonia to understand the prevalence of severe pneumonia caused by atypical pathogens, improve clinical decision-making and guide antibiotic use. DESIGN Systematic review and meta-analysis. DATA SOURCES PubMed, Embase, Web of Science and Cochrane Library were searched through November 2022. ELIGIBILITY CRITERIA English language studies enrolled consecutive cases of patients diagnosed with severe pneumonia, with complete aetiological analysis. DATA EXTRACTION AND SYNTHESIS We conducted literature retrieval on PubMed, Embase, Web of Science and The Cochrane Library to estimate the prevalence of Chlamydia, Mycoplasma and Legionella in patients with severe pneumonia. After double arcsine transformation of the data, a random-effects model was used for meta-analyses to calculate the pooled prevalence of each pathogen. Meta-regression analysis was also used to explore whether the region, different diagnostic method, study population, pneumonia categories or sample size were potential sources of heterogeneity. RESULTS We included 75 eligible studies with 18 379 cases of severe pneumonia. The overall prevalence of atypical pneumonia is 8.1% (95% CI 6.3% to 10.1%) In patients with severe pneumonia, the pooled estimated prevalence of Chlamydia, Mycoplasma and Legionella was 1.8% (95% CI 1.0% to 2.9%), 2.8% (95% CI 1.7% to 4.3%) and 4.0% (95% CI 2.8% to 5.3%), respectively. We noted significant heterogeneity in all pooled assessments. Meta-regression showed that the pneumonia category potentially influenced the prevalence rate of Chlamydia. The mean age and the diagnostic method of pathogens were likely moderators for the prevalence of Mycoplasma and Legionella, and contribute to the heterogeneity of their prevalence. CONCLUSIONS In severe pneumonia, atypical pathogens are notable causes, especially Legionella. The diagnostic method, regional difference, sample size and other factors contribute to the heterogeneity of prevalence. The estimated prevalence and relative heterogeneity factors can help with microbiological screening, clinical treatment and future research planning. PROSPERO REGISTRATION NUMBER CRD42022373950.
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Affiliation(s)
- Sidan Wang
- The Second Department of Gastrointestinal Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiaoqi Tang
- Emergency Department, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Yurong Tan
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Zhi Song
- The Second Department of Gastrointestinal Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ling Qin
- Department of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Shi X, Sun H, Li H, Wei S, Jin J, Zhao C, Wang J, Li H. Preparation of IgY Oriented Conjugated Fe3O4 MNPs as Immunomagnetic Nanoprobe for Increasing Enrichment Efficiency of Staphylococcus aureus Based on Adjusting the pH of the Solution System. Front Public Health 2022; 10:865828. [PMID: 35669739 PMCID: PMC9163370 DOI: 10.3389/fpubh.2022.865828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Immunomagnetic separation based on Fe3O4 magnetic nanoparticles (MNPs) has been widely performed in sample pretreatment. The oriented conjugation strategy can achieve a better capture effect than the N-(3-dimethylamlnopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) /N-hydroxysuccinimide (NHS) method. However, immunoglobulin yolk (IgY) cannot be oriented through an SPA strategy like immunoglobulin G (IgG). In this article, an oriented conjugation nanoprobe was prepared for the enrichment of bacteria based on pH adjusting. The main factors affecting the enrichment efficiency were studied, such as the pH of the buffer system, the concentration of IgY, the concentration of nanoprobe, and the enrichment time. Under the optimal conditions, the enrichment efficiency toward target bacteria could reach 92.8%. Combined with PCR, the limit of detection (LOD) was found to be 103 CFU/ml, which was lower than the PCR only. In conclusion, we provided a new protocol for the oriented conjugation of IgY and high sensitivity detection with simple pretreatment.
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Affiliation(s)
- Xuening Shi
- School of Public Health, Jilin University, Changchun, China
| | - Hongbin Sun
- China-Japan Union Hospital of Jilin University, Changchun, China
| | - Hang Li
- School of Public Health, Jilin University, Changchun, China
| | - Shengnan Wei
- School of Public Health, Jilin University, Changchun, China
| | - Jin Jin
- School of Public Health, Jilin University, Changchun, China
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun, China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun, China
- *Correspondence: Juan Wang
| | - Hui Li
- School of Public Health, Jilin University, Changchun, China
- Hui Li
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Leitner E, Bozic M, Kienesberger S, Cosic A, Landt O, Högenauer C, Kessler HH. Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato. Clin Microbiol Infect 2022; 28:690-694. [PMID: 34582979 DOI: 10.1016/j.cmi.2021.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated. METHODS DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method. RESULTS With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%. CONCLUSION Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.
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Affiliation(s)
- Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria.
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria; Field of Excellence BioHealth, University of Graz, Austria
| | - Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | - Christoph Högenauer
- BioTechMed-Graz, Austria; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Harald H Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
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Lapa SA, Miftakhov RA, Klochikhina ES, Ammur YI, Blagodatskikh SA, Shershov VE, Zasedatelev AS, Chudinov AV. Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens. Mol Biol 2021; 55:828-838. [PMID: 34955557 PMCID: PMC8682033 DOI: 10.1134/s0026893321040063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]
Abstract
A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.
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Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Yu I Ammur
- Mechnikov Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - S A Blagodatskikh
- Scientific Center of Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - V E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction. PLoS One 2021; 16:e0258694. [PMID: 34648603 PMCID: PMC8516298 DOI: 10.1371/journal.pone.0258694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/02/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae. Materials Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae. Results Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml. Conclusion The Smart Gene® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene® system is suitable for point-of-care testing in both hospital and outpatient settings.
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Feng C, Xu M, Kang J, Wen F, Chen Y, Zhang J, Xiao W, Zhang Z, Yang L, Huo J, Cao J, Zhao L, Xia S, Yin Y, Wang W. Atypical Pathogen Distribution in Chinese Hospitalized AECOPD Patients: A Multicenter Cross-Sectional Study. Int J Chron Obstruct Pulmon Dis 2021; 16:1699-1708. [PMID: 34135581 PMCID: PMC8200156 DOI: 10.2147/copd.s300779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/09/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose The proportion of atypical pathogens in patient with AECOPD within mainland China is unknown. The objectives of this study were to determine the distribution of atypical pathogens among Chinese patients with AECOPD, to evaluate the clinical characteristics of different atypical pathogen infections, and to compare different detection methods for atypical pathogens. Patients and Methods Specimens were collected from patients with AECOPD from March 2016 to November 2018 at eleven medical institutions in eight cities in China. Double serum, sputum, and urine samples were obtained from 145 patients. Serological and nucleic acid tests were used to assess for Mycoplasma pneumonia and Chlamydia pneumoniae; serological, urinary antigen, and nucleic acid tests were applied to detect Legionella pneumophila. The clinical characteristics of atypical pathogen-positive and -negative groups were also compared. Results The overall positivity rate for Mycoplasma pneumoniae was 20.69% (30/145), with the highest rate being 20.00% (29/145) when determined by passive agglutination.The overall positive rates for Chlamydia pneumoniae and Legionella pneumophila were 29.66% (43/145) and 10.34% (15/145), respectively. The most common serotype of Legionella pneumophila was type 6. The maximum hospitalized body temperature, ratio of eosinophils, C-reactive protein (CRP) level, and procalcitonin (PCT) level of the Mycoplasma pneumoniae-positive group were significantly higher than those of the Mycoplasma pneumoniae-negative group. Patients in the Chlamydia pneumoniae-positive group smoked more, had higher proportions of comorbidities and frequent aggravations in the previous two years than those in the Chlamydia pneumoniae-negative group. Furthermore, the forced expiratory volume in one second to forced vital capacity (FEV1/FVC) ratio assessment of lung function was higher, and the concentration of arterial blood bicarbonate (HCO3 -) was lower in the Legionella pneumophila-positive group than in the Legionella pneumophila-negative group. Conclusion Overall, atypical pathogens play an important role in AECOPD. Regarding the testing method, serological testing is a superior method to nucleic acid testing.
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Affiliation(s)
- Chenye Feng
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Mingtao Xu
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Jian Kang
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Fuqiang Wen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University and Division of Pulmonary Disease, State Key Laboratory of Biotherapy of China, Chengdu, Sichuan, People's Republic of China
| | - Yahong Chen
- Department of Respiratory and Critical Care Medicine, Peking University, Third Hospital, Beijing, People's Republic of China
| | - Jing Zhang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Wei Xiao
- Department of Pulmonary Medicine, Qilu Hospital, Shandong University, Jinan, Shandong, People's Republic of China
| | - Zhonghe Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaonign, People's Republic of China
| | - Lan Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Jianmin Huo
- Department of Respiratory, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, People's Republic of China
| | - Jie Cao
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Li Zhao
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Shuyue Xia
- Department of Pulmonary Medicine, Central Hospital Affiliated with Shenyang Medical College, Shenyang, People's Republic of China
| | - Yan Yin
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Wei Wang
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Diseases, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
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Meng M, Zhong K, Jiang T, Liu Z, Kwan HY, Su T. The current understanding on the impact of KRAS on colorectal cancer. Biomed Pharmacother 2021; 140:111717. [PMID: 34044280 DOI: 10.1016/j.biopha.2021.111717] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023] Open
Abstract
KRAS (kirsten rat sarcoma viral oncogene) is a member of the RAS family. KRAS mutations are one of most dominant mutations in colorectal cancer (CRC). The impact of KRAS mutations on the prognosis and survival of CRC patients drives many research studies to explore potential therapeutics or target therapy for the KRAS mutant CRC. This review summarizes the current understanding of the pathological consequences of the KRAS mutations in the development of CRC; and the impact of the mutations on the response and the sensitivity to the current front-line chemotherapy. The current therapeutic strategies for treating KRAS mutant CRC, the difficulties and challenges will also be discussed.
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Affiliation(s)
- Mingjing Meng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Keying Zhong
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Ting Jiang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
| | - Hiu Yee Kwan
- Centre for Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Tao Su
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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Abstract
Community-acquired pneumonia (CAP) is the prominent cause of mortality and morbidity with important clinical impact across the globe. India accounts for 23 per cent of global pneumonia burden with case fatality rates between 14 and 30 per cent, and Streptococcus pneumoniae is considered a major bacterial aetiology. Emerging pathogens like Burkholderia pseudomallei is increasingly recognized as an important cause of CAP in Southeast Asian countries. Initial management in the primary care depends on clinical assessment while the hospitalized patients require combinations of clinical scores, chest radiography and various microbiological and biomarker assays. This comprehensive diagnostic approach together with additional sampling and molecular tests in selected high-risk patients should be practiced. Inappropriate therapy in CAP in hospitalized patients lengthens hospital stay and increases cost and mortality. In addition, emergence of multidrug-resistant organisms poses tough challenges in deciding empirical as well as definitive therapy. Developing local evidence on the cause and management should be a priority to improve health outcomes in CAP.
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Affiliation(s)
- Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Jordi Rello
- Department of Critical Care, Vall d'Hebron Research Institute; Clinical Research & Innovation in Pneumonia and Sepsis, Barcelona, Spain
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Abstract
PURPOSE OF REVIEW Pneumonia is the main global cause of sepsis, and has been associated with high morbidity and high short and long-term mortality rates. As it may be caused by a wide spectrum of microorganisms, microbial diagnosis is challenging and the choice of adequate therapy remains an important problem. This review focuses on recently published studies of microbiological diagnostic tests and clinical assessments for pneumonia, including community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia. RECENT FINDINGS Over the past decade, the microbiological diagnosis of pneumonia has improved significantly - thanks to the development and implementation of molecular diagnostic tests for identifying the most frequent pathogens causing pneumonia and for determining their patterns of resistance. Molecular methods for the diagnosis of pneumonia focus on multiple target detection systems and pathogen detection arrays, and, more recently, have been used in combination with mass spectrometry. SUMMARY The implementation of rapid diagnostic techniques in routine clinical practice able to identify and determine the resistance patterns of the causative microbes may transform the management of pneumonia, improving the selection and administration of antimicrobial therapies especially in critically ill patients. The validation of new diagnostic technology platforms is crucial in order to assess their usefulness and to guide antimicrobial treatment in this population.
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Al-Khikani FO, Kadim M. COVID-19 and non culturable bacteria: A plausible association. INDIAN JOURNAL OF MEDICAL SPECIALITIES 2021. [DOI: 10.4103/injms.injms_98_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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12
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Diagnostic tools for bacterial infections in travellers: Current and future options. Travel Med Infect Dis 2020; 37:101856. [PMID: 32841728 DOI: 10.1016/j.tmaid.2020.101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022]
Abstract
International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.
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Leung YH, Lam CK, Cheung YY, Chan CW, Chuang SK. Epidemiology of Legionnaires' Disease, Hong Kong, China, 2005-2015. Emerg Infect Dis 2020; 26:1695-1702. [PMID: 32687025 PMCID: PMC7392469 DOI: 10.3201/eid2608.191244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We reviewed findings of clinical, epidemiologic, and environmental investigations for 288 confirmed case-patients with Legionnaires’ disease reported in Hong Kong, China, during January 2005−December 2015. We found that chronic renal failure/impairment (adjusted odds ratio [aOR] 4.09), chronic pulmonary diseases (aOR 3.22), malignancy (aOR 3.04), and heart diseases (aOR 2.15) were independently associated with a higher risk for severe Legionnaires’ disease. However, patients with hyperlipidemia had a lower risk for severe outcome (aOR 0.17). Legionella positivity rate was 22% for 1,904 water samples collected. We found a higher positivity rate in summer months (28%−30%), which corroborated with months of highest rainfalls. Our novel finding that Legionnaires’ disease patients with hyperlipidemia had a lower risk for severe outcome deserves further study to confirm the observation and ascertain the underlying reason.
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Mycoplasma pneumoniae in Children With and Without Community-acquired Pneumonia. What do PCR and Serology Say? Pediatr Infect Dis J 2020; 39:e104-e108. [PMID: 32118860 DOI: 10.1097/inf.0000000000002636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND IgM titers of Mycoplasma pneumoniae can remain high for months or years, and specific DNA can be detected in asymptomatic people. METHODS We compared the performance of serology and PCR in children with and without community-acquired pneumonia (CAP) for the diagnosis of M. pneumoniae. RESULTS In children with CAP, a positive test by M. pneumoniae (PCR and/or paired serology or both) were found in 13.9%. Of these, 10.3% were positive by multiplex PCR (Seeplex-Seegen), and 6.7% exhibited quadrupled titers (22 for IgG, 6 for IgM and 5 for both). Both tests were positive in 2.8% of cases. In the group without CAP, 3.3% were positive by PCR. Thirty-two percent of children with CAP and 38.3% of healthy children had IgM titers >11 in the acute phase. CONCLUSIONS The detection of IgM is not useful for diagnosing acute M. pneumoniae infection, and a positive PCR result can be due to colonization and not infection. New and better diagnostic techniques are required.
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Bakare OO, Fadaka AO, Klein A, Keyster M, Pretorius A. Diagnostic approaches of pneumonia for commercial-scale biomedical applications: an overview. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1826363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Olalekan Olanrewaju Bakare
- Bioinformatics Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Environmental Biotechnology Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Adewale Oluwaseun Fadaka
- Bioinformatics Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
- Department of Science and Technology/Mintek Nanotechnology Innovation Centre, Bio-labels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Ashwil Klein
- Environmental Biotechnology Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Ashley Pretorius
- Bioinformatics Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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Wagner K, Imkamp F, Pires VP, Keller PM. Evaluation of Lightmix Mycoplasma macrolide assay for detection of macrolide-resistant Mycoplasma pneumoniae in pneumonia patients. Clin Microbiol Infect 2018; 25:383.e5-383.e7. [PMID: 30391582 DOI: 10.1016/j.cmi.2018.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Rapid detection of macrolide resistance-associated mutations in Mycoplasma pneumoniae is crucial for effective antimicrobial treatment. We evaluated the Lightmix Mycoplasma macrolide assay for the detection of point mutations at nucleotide positions 2063 and 2064 in the 23S ribosomal RNA (rRNA) gene of M. pneumoniae that confer macrolide resistance. METHODS Samples from 3438 patients with a respiratory tract infection were analysed by M. pneumoniae real-time PCR, and 208 (6%) of them were tested positive. In this retrospective study, 163 M. pneumoniae real-time PCR-positive samples were analysed by the Lightmix assay, and results were compared to targeted 23S rRNA sequencing. RESULTS Macrolide-resistant M. pneumoniae were found in 15 (9%) of 163 retrospectively analysed samples. The Lightmix assay showed a sensitivity of 100% (95% confidence interval, 78.2-100) and a specificity of 100% (95% confidence interval, 97.5-100) as the detected M. pneumoniae genotype (148 wild type and 15 non-wild type) was confirmed by 23S rRNA sequencing in all samples. CONCLUSIONS The Lightmix assay is an easy-to-use and accurate molecular test that allows rapid determination of macrolide resistance in M. pneumoniae.
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Affiliation(s)
- K Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - F Imkamp
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - V P Pires
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - P M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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