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Lee AWT, Ng ICF, Wong EYK, Wong ITF, Sze RPP, Chan KY, So TY, Zhang Z, Ka-Yee Fung S, Choi-Ying Wong S, Tam WY, Lao HY, Lee LK, Leung JSL, Chan CTM, Ng TTL, Zhang J, Chow FWN, Leung PHM, Siu GKH. Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics. Food Microbiol 2024; 121:104493. [PMID: 38637066 DOI: 10.1016/j.fm.2024.104493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/20/2024]
Abstract
Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.
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Affiliation(s)
- Annie Wing-Tung Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Iain Chi-Fung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Evelyn Yin-Kwan Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ivan Tak-Fai Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Rebecca Po-Po Sze
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kit-Yu Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Tsz-Yan So
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Zhipeng Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sharon Ka-Yee Fung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Sally Choi-Ying Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Wing-Yin Tam
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Jiaying Zhang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China.
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Li J, Li Y, Zhou L, Li C, Liu J, Liu D, Fu Y, Wang Y, Tang J, Zhou L, Tan S, Wang L. The human microbiome and benign prostatic hyperplasia: Current understandings and clinical implications. Microbiol Res 2024; 281:127596. [PMID: 38215640 DOI: 10.1016/j.micres.2023.127596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/14/2024]
Abstract
The research of the human microbiome in the preceding decade has yielded novel perspectives on human health and diseases. Benign prostatic hyperplasia (BPH) is a common disease in middle-aged and elderly males, which negatively affects the life quality. Existing evidence has indicated that the human microbiome, including urinary, intra-prostate, gut, oral and blood microbiome may exert a significant impact on the natural progression of BPH. The dysbiosis of the microbiome may induce inflammation at either a local or systemic level, thereby affecting the BPH. Moreover, metabolic syndrome (MetS) caused by the microbiome can also be involved in the development of BPH. Additionally, alterations in the microbiome composition during the senility process may serve as another cause of the BPH. Here, we summarize the influence of human microbiome on BPH and explore how the microbiome is linked to BPH through inflammation, MetS, and senility. In addition, we propose promising areas of investigation and discuss the implications for advancing therapeutic approaches.
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Affiliation(s)
- Jiaren Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Youyou Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Liang Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Cheng Li
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jiahao Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Dingwen Liu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yunlong Fu
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Yichuan Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin Tang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Lei Zhou
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Shuo Tan
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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Man MA, Ungur RA, Motoc NS, Pop LA, Berindan-Neagoe I, Ruta VM. Lung Microbiota in Idiopathic Pulmonary Fibrosis, Hypersensitivity Pneumonitis, and Unclassified Interstitial Lung Diseases: A Preliminary Pilot Study. Diagnostics (Basel) 2023; 13:3157. [PMID: 37835899 PMCID: PMC10572521 DOI: 10.3390/diagnostics13193157] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
(1) Introduction: Although historically, the lung has been considered a sterile organ, recent studies through 16S rRNA gene sequencing have identified a substantial number of microorganisms. The human microbiome has been considered an "essential organ," carrying about 150 times more information (genes) than are found in the entire human genome. The purpose of the present study is to characterize and compare the microbiome in three different interstitial lung diseases: idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis, and nondifferential interstitial lung disease. (2) Material and methods: This was a prospective cohort study where the DNA of 28 patients with ILD was extracted from the lavage and then processed using the standard technique of 16S RNA gene sequencing. In a tertiary teaching hospital in the northern, western part of Romania, samples were collected through bronchoscopy and then processed. (3) Results: The same four species were found in all the patients but in different quantities and compositions: Firmicutes, Actinobacteria, Proteobacteria and Bacteroides. Streptococcus was the most prevalent genus, followed by Staphylococcus and Prevotella. Statistically significant differences in the OUT count for the ten most abundant taxa were found for the genus: Gemella, Actinobacteria, Prevotella, Neisseria, Haemophilus, and Bifidobacterium. The comparative analysis showed a richer microbiota in patients with IPF, as shown by the alpha diversity index. (4) Conclusions: In interstitial lung diseases, the microorganisms normally found in the lung are reduced to a restricted flora dominated by the Firmicutes family. These changes significantly disrupt the continuity of the observed bacterial pattern from the oropharynx to the bronchial tree and lung, possibly impacting the evolution and severity of interstitial lung diseases.
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Affiliation(s)
- Milena Adina Man
- Department of Medical Sciences-Pulmonology, Faculty of Medicine, University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
| | - Rodica Ana Ungur
- Department of Medical Specialties-Rehabilitation Medicine, Faculty of Medicine, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Nicoleta Stefania Motoc
- Department of Medical Sciences-Pulmonology, Faculty of Medicine, University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
| | - Laura Ancuta Pop
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (L.A.P.); (I.B.-N.)
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine, and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania; (L.A.P.); (I.B.-N.)
| | - Victoria Maria Ruta
- “Leon Daniello” Clinical Hospital of Pneumophtysiology, 400371 Cluj-Napoca, Romania;
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Shaikh N, Lee S, Krumbeck JA, Kurs-Lasky M. Support for the Use of a New Cutoff to Define a Positive Urine Culture in Young Children. Pediatrics 2023; 152:e2023061931. [PMID: 37691613 PMCID: PMC10914346 DOI: 10.1542/peds.2023-061931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/20/2023] [Indexed: 09/12/2023] Open
Abstract
BACKGROUND Conventional urine culture selects for a narrow range of organisms that grow well in aerobic conditions. In contrast, examination of bacterial gene sequences in the urine provides a relatively unbiased evaluation of the organisms present. Thus, by using 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing as the reference standard, we now have the ability to assess the accuracy of urine culture in diagnosing urinary tract infection (UTI). METHODS We enrolled febrile children 1 month to 3 years of age that underwent bladder catheterization for suspected UTI. Using 16S rRNA gene amplicon sequencing as the reference standard, we calculated the accuracy of urine culture at various cutoffs (10 000, 50 000, and 100 000 colony forming units per milliliter). Children with ≥80% relative abundance of any organism on 16S rRNA gene amplicon sequencing with elevated urinary markers of inflammation were defined as having a UTI. RESULTS When using a cutoff of 10 000 CFU/mL, the sensitivity and specificity of urine culture were 98% (95% confidence interval [CI]: 93%-100%) and 99% (95% CI: 97%-100%), respectively. Using a cutoff of 50 000 colony forming units per mL decreased sensitivity to 80% (95% CI: 68%-93%) without changing the specificity. Using a cutoff of 100 000 further decreased sensitivity to 70% (95% CI: 55%-84%). CONCLUSIONS Conventional culture remains an accurate method of diagnosing UTIs in young children; however, these data suggest that a cutoff of 10 000 colony forming units per mL provides the optimal balance between sensitivity and specificity for children undergoing bladder catheterization.
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Affiliation(s)
- Nader Shaikh
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, Pennsylvania
| | - Sojin Lee
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, Pennsylvania
| | | | - Marcia Kurs-Lasky
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, Pennsylvania
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Wald ER, Eickhoff JC. Determining the Best Definition for a Positive Urine Culture in Young Children. Pediatrics 2023; 152:e2023062883. [PMID: 37691605 DOI: 10.1542/peds.2023-062883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/12/2023] Open
Affiliation(s)
- Ellen R Wald
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Jens C Eickhoff
- Department of Biostatistics and Medical Informatics, American Family Children's Hospital, Madison, Wisconsin
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Cole EB, Khemmani M, Liu H, Halverson TM, Noronha MF, Forster CS, Wolfe AJ, Shaikh N. Urogenital urobiome of healthy children does not differ from that of children with bladder and bowel dysfunction. J Pediatr Urol 2023; 19:368.e1-368.e8. [PMID: 37117081 PMCID: PMC10524508 DOI: 10.1016/j.jpurol.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/30/2023]
Abstract
INTRODUCTION The pediatric urinary microbiome (urobiome) has been studied in the context of healthy children and children with genitourinary pathologies including neuropathic bladder, urinary tract infection (UTI) and nephrolithiasis. Little is known about the urobiome of children with bladder and bowel dysfunction (BBD), a condition that is an established risk factor of UTI. We hypothesized that the symptoms of a child with BBD may be related to urobiome composition. OBJECTIVE To evaluate the urogenital urobiome's role in BBD, we compared the urogenital urobiomes of children with and without BBD. STUDY DESIGN We performed a prospective case-control pilot study at a single large, academic children's hospital. Cases included toilet trained prepubertal females over 2 years of age with BBD established through a validated scoring system and controls included asymptomatic, presumably healthy, children. Children were excluded if they had symptoms or lab work consistent with a concurrent UTI or antibiotic course for any reason within the prior 14 days. We performed 16 S ribosomal RNA gene sequencing and expanded quantitative urine culture on clean catch urine samples. To compare within sample (alpha) diversity, we used the Kruskal-Wallis test. To compare between sample (beta) diversity, we calculated the Bray-Curtis distance and performed the PERMANOVA test. RESULTS Data from 25 children with BBD and 8 asymptomatic controls were analyzed. The demographic and clinical characteristics of the two comparison groups were similar, though a higher proportion of Black children were included in the asymptomatic control group. Neither alpha diversity nor beta diversity was significantly different between the two groups. The core microbiome of the BBD group included all the genera in the core urogenital urobiome of the controls, plus additional genera associated with opportunistic infection and/or UTI, including Escherichia, Campylobacter and Streptococcus. DISCUSSION The results of both the 16 S sequencing and expanded quantitative urine culture in this small study suggest that the urogenital urobiomes of children with BBD do not differ significantly from those of asymptomatic children. However, the core urogenital urobiome of children with BBD included genera associated with opportunistic infection and/or UTI. This study was limited by the sample collection method ("clean catch" midstream voided urine samples, which introduce the possibility of vulvovaginal contamination), small sample size, and unequal balance of patient characteristics between the two study groups. CONCLUSION The urogenital urobiomes of children with and without BBD do not appear to significantly differ. Larger studies are needed to confirm these findings.
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Affiliation(s)
- Elisabeth B Cole
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Mark Khemmani
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Hui Liu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Thomas M Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Melline Fontes Noronha
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Catherine S Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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Goel N, Wattal C. 16S Ribosomal RNA Analysis for the Diagnosis of Urinary Tract Infection of Infants: Has the Time Arrived? Indian J Pediatr 2023:10.1007/s12098-023-04627-4. [PMID: 37247183 DOI: 10.1007/s12098-023-04627-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/30/2023]
Affiliation(s)
- Neeraj Goel
- Institute of Clinical Microbiology and Immunology, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Chand Wattal
- Institute of Clinical Microbiology and Immunology, Sir Ganga Ram Hospital, New Delhi, 110060, India.
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Jiang S, Wei Y, Ke H, Song C, Liao W, Meng L, Sun C, Zhou J, Wang C, Su X, Dong C, Xiong Y, Yang S. Building a nomogram plot based on the nanopore targeted sequencing for predicting urinary tract pathogens and differentiating from colonizing bacteria. Front Cell Infect Microbiol 2023; 13:1142426. [PMID: 37265501 PMCID: PMC10229875 DOI: 10.3389/fcimb.2023.1142426] [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: 01/11/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Background The identification of uropathogens (UPBs) and urinary tract colonizing bacteria (UCB) conduces to guide the antimicrobial therapy to reduce resistant bacterial strains and study urinary microbiota. This study established a nomogram based on the nanopore-targeted sequencing (NTS) and other infectious risk factors to distinguish UPB from UCB. Methods Basic information, medical history, and multiple urine test results were continuously collected and analyzed by least absolute shrinkage and selection operator (LASSO) regression, and multivariate logistic regression was used to determine the independent predictors and construct nomogram. Receiver operating characteristics, area under the curve, decision curve analysis, and calibration curves were used to evaluate the performance of the nomogram. Results In this study, the UPB detected by NTS accounted for 74.1% (401/541) of all urinary tract microorganisms. The distribution of ln(reads) between UPB and UCB groups showed significant difference (OR = 1.39; 95% CI, 1.246-1.551, p < 0.001); the reads number in NTS reports could be used for the preliminary determination of UPB (AUC=0.668) with corresponding cutoff values being 7.042. Regression analysis was performed to determine independent predictors and construct a nomogram, with variables ranked by importance as ln(reads) and the number of microbial species in the urinary tract of NTS, urine culture, age, urological neoplasms, nitrite, and glycosuria. The calibration curve showed an agreement between the predicted and observed probabilities of the nomogram. The decision curve analysis represented that the nomogram would benefit clinical interventions. The performance of nomogram with ln(reads) (AUC = 0.767; 95% CI, 0.726-0.807) was significantly better (Z = 2.304, p-value = 0.021) than that without ln(reads) (AUC = 0.727; 95% CI, 0.681-0.772). The rate of UPB identification of nomogram was significantly higher than that of ln(reads) only (χ2 = 7.36, p-value = 0.009). Conclusions NTS is conducive to distinguish uropathogens from colonizing bacteria, and the nomogram based on NTS and multiple independent predictors has better prediction performance of uropathogens.
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Affiliation(s)
- Shengming Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yangyan Wei
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hu Ke
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chao Song
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenbiao Liao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lingchao Meng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chang Sun
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiawei Zhou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuan Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaozhe Su
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Caitao Dong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yunhe Xiong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sixing Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, China
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Lee AWT, Chan CTM, Wong LLY, Yip CY, Lui WT, Cheng KC, Leung JSL, Lee LK, Wong ITF, Ng TTL, Lao HY, Siu GKH. Identification of microbial community in the urban environment: The concordance between conventional culture and nanopore 16S rRNA sequencing. Front Microbiol 2023; 14:1164632. [PMID: 37125165 PMCID: PMC10133568 DOI: 10.3389/fmicb.2023.1164632] [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: 02/13/2023] [Accepted: 03/14/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Microbes in the built environment have been implicated as a source of infectious diseases. Bacterial culture is the standard method for assessing the risk of exposure to pathogens in urban environments, but this method only accounts for <1% of the diversity of bacteria. Recently, full-length 16S rRNA gene analysis using nanopore sequencing has been applied for microbial evaluations, resulting in a rise in the development of long-read taxonomic tools for species-level classification. Regarding their comparative performance, there is, however, a lack of information. Methods Here, we aim to analyze the concordance of the microbial community in the urban environment inferred by multiple taxonomic classifiers, including ARGpore2, Emu, Kraken2/Bracken and NanoCLUST, using our 16S-nanopore dataset generated by MegaBLAST, as well as assess their abilities to identify culturable species based on the conventional culture results. Results According to our results, NanoCLUST was preferred for 16S microbial profiling because it had a high concordance of dominant species and a similar microbial profile to MegaBLAST, whereas Kraken2/Bracken, which had similar clustering results as NanoCLUST, was also desirable. Second, for culturable species identification, Emu with the highest accuracy (81.2%) and F1 score (29%) for the detection of culturable species was suggested. Discussion In addition to generating datasets in complex communities for future benchmarking studies, our comprehensive evaluation of the taxonomic classifiers offers recommendations for ongoing microbial community research, particularly for complex communities using nanopore 16S rRNA sequencing.
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