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Xing F, Deng C, Luo Z, Zou S, Liu M, Ye H, Sun L, Tsang CC, Lo SKF, Lau SKP, Woo PCY. Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing. Mycopathologia 2024; 189:38. [PMID: 38704795 PMCID: PMC11070382 DOI: 10.1007/s11046-024-00849-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVES To describe the epidemiology of Pneumocystis jirovecii pneumonia and colonization diagnosed by next-generation sequencing (NGS) and explore the usefulness of the number of P. jirovecii sequence reads for the diagnosis of P. jirovecii pneumonia. METHODS We examined the NGS results for P. jirovecii in respiratory samples collected from patients and analysed their clinical, radiological and microbiological characteristics. RESULTS Among 285 respiratory samples collected over a 12-month period (January to December 2022), P. jirovecii sequences were detected in 56 samples from 53 patients. Fifty (94.3%) of the 53 patients were HIV-negative. Following our case definitions, 37 (69.8%) and 16 (30.2%) of the 53 patients had P. jirovecii infection and colonization respectively. P. jirovecii infection was associated with presence of underlying disease with immunosuppression (94.6% vs 18.8%, P < 0.05), positive serum 1,3-β-D-glucan (41.2% vs 0%, P < 0.01) and higher number of P. jirovecii sequence reads (P < 0.005). In contrast, P. jirovecii colonization was associated with the male sex (93.8% vs 54.1%, P < 0.01), another definitive infectious disease diagnosis of the respiratory tract (43.8% vs 2.7%, P < 0.001) and higher survival (100% vs 67.6%, P < 0.01). Although P. jirovecii pneumonia was associated with higher number of P. jirovecii reads in respiratory samples, only a sensitivity of 82.14% and a specificity of 68.75% could be achieved. CONCLUSION Detection of P. jirovecii sequences in respiratory samples has to be interpreted discreetly. A combination of clinical, radiological and laboratory findings is still the most crucial in determining whether a particular case is genuine P. jirovecii pneumonia.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chaowen Deng
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Zhendong Luo
- Department of Radiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shan Zou
- Department of Adult Intensive Care, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Min Liu
- Department of Respiratory Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Haiyan Ye
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Linlin Sun
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Chi-Ching Tsang
- School of Medical and Health Sciences, Tung Wah College, Homantin, Hong Kong, China
| | - Simon K F Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Susanna K P Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Patrick C Y Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan.
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Church DL, Griener T, Gregson D. Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing? Anaerobe 2022; 78:102640. [PMID: 36126828 DOI: 10.1016/j.anaerobe.2022.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/13/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum). METHODS VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates. RESULTS 489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups. CONCLUSIONS MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.
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Affiliation(s)
- D L Church
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada.
| | - T Griener
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
| | - D Gregson
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
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Teng JLL, Ma Y, Chen JHK, Luo R, Foo CH, Li TT, Fong JYH, Yao W, Wong SSY, Fung KSC, Lau SKP, Woo PCY. Streptococcus oriscaviae sp. nov. Infection Associated with Guinea Pigs. Microbiol Spectr 2022; 10:e0001422. [PMID: 35510851 PMCID: PMC9241640 DOI: 10.1128/spectrum.00014-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/17/2022] [Indexed: 11/20/2022] Open
Abstract
Pet bite-related infections are commonly caused by the pet's oral flora transmitted to the animal handlers through the bite wounds. In this study, we isolated a streptococcus, HKU75T, in pure culture from the purulent discharge collected from a guinea pig bite wound in a previously healthy young patient. HKU75T was alpha-hemolytic on sheep blood agar and agglutinated with Lancefield group D and group G antisera. API 20 STREP showed that the most likely identity for HKU75T was S. suis I with 85.4% confidence while Vitek 2 showed that HKU75T was unidentifiable. MALDI-TOF MS identified HKU75T as Streptococcus suis (score of 1.86 only). 16S rRNA gene sequencing showed that HKU75T was most closely related to S. parasuis (98.3% nucleotide identity), whereas partial groEL and rpoB gene sequencing showed that it was most closely related to S. suis (81.8% and 89.8% nucleotide identity respectively). Whole genome sequencing and intergenomic distance determined by ANI revealed that there was <85% identity between the genome of HKU75T and those of all other known Streptococcus species. Genome classification using concatenated sequences of 92 bacterial core genes showed that HKU75T belonged to the Suis group. groEL gene sequences identical to that of HKU75T could be directly amplified from the oral cavities of the two guinea pigs owned by the patient. HKU75T is a novel Streptococcus species, which we propose to be named S. oriscaviae. The oral cavity of guinea pigs is presumably a reservoir of S. oriscaviae. Some of the reported S. suis strains isolated from clinical specimens may be S. oriscaviae. IMPORTANCE We reported the discovery of a novel Streptococcus species, propose to be named Streptococcus oriscaviae, from the pus collected from a guinea pig bite wound in a healthy young patient. The bacterium was initially misidentified as S. suis/S. parasuis by biochemical tests, mass spectrometry. and housekeeping genes sequencing. Its novelty was confirmed by whole genome sequencing. Comparative genomic studies showed that S. oriscaviae belongs to the Suis group. S. oriscaviae sequences were detected in the oral cavities of the two guinea pigs owned by the patient, suggesting that the oral cavity of guinea pigs could be a reservoir of S. oriscaviae. Some of the reported S. suis strains may be S. oriscaviae. Further studies are warranted to refine our knowledge on this novel Streptococcus species.
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Affiliation(s)
- Jade L. L. Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuanchao Ma
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jonathan H. K. Chen
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, China
| | - Chuen-Hing Foo
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Tsz Tuen Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jordan Y. H. Fong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Weiming Yao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Samson S. Y. Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Hong Kong, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Xing F, Lo SKF, Lau SKP, Woo PCY. Listeriosis in a Metropolitan Hospital: Is Targeted Therapy a Risk Factor for Infection? Front Med (Lausanne) 2022; 9:888038. [PMID: 35572995 PMCID: PMC9100811 DOI: 10.3389/fmed.2022.888038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/13/2022] [Indexed: 01/26/2023] Open
Abstract
Targeted therapies are widely used for treatment of autoimmune diseases as well as solid organ and hematological malignancies. Various opportunistic infections have been described in patients on targeted therapies. Although case reports or a few case series of listeriosis have been reported to be associated with targeted therapy, most of the cases were related to anti-tumor necrosis factor-α monoclonal antibody. In this study, we describe the epidemiological and clinical profiles of listeriosis in a tertiary hospital in Shenzhen, a Southern Chinese metropolitan city in China. During the 9-year-and-6-month study period, a total of five cases of listeriosis were recorded and all of them had Listeria monocytogenes bacteremia. All five patients had predisposing factors, including corticosteroid (n = 3), targeted therapy (n = 2), pregnancy (n = 2) and anti-interferon gamma autoantibody (n = 1). The two patients who had targeted therapy during their course of cancer treatment received inhibitors of the epidermal growth factor receptor (EGFR)/human epidermal growth factor receptor 2 (HER2) pathway. The first one was a 52-year-old woman with metastatic adenocarcinoma of the lung. She was given gefitinib (EGFR tyrosine kinase inhibitor), osimertinib (third-generation EGFR tyrosine kinase inhibitor) and afatinib (tyrosine kinase inhibitor that can bind to EGFR, HER2 and HER4). The second one was a 40-year-old woman with carcinoma of the breast with brain metastasis. She was given trastuzumab (anti-HER2 monoclonal antibody) and lapatinib (dual tyrosine kinase inhibitor of the EGFR/HER2 pathway). These two patients represent the second and third reports of listeria infections associated with EGFR/HER2 pathway inhibitors in the literature. Targeted therapy is an important predisposing factor for listeriosis. Listeria infection is an important differential diagnosis in patients on targeted therapy who present with sepsis and/or central nervous system infection, and the use of antibiotic regimens that cover listeria is crucial for empirical treatment. Avoidance of high-risk food items in these patients is important for the prevention of listeriosis.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Xing F, Lo SKF, Ma Y, Ip JD, Chan WM, Zhou M, Gong M, Lau SKP, Woo PCY. Rapid Diagnosis of Mycobacterium marinum Infection by Next-Generation Sequencing: A Case Report. Front Med (Lausanne) 2022; 9:824122. [PMID: 35187006 PMCID: PMC8854760 DOI: 10.3389/fmed.2022.824122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
We present the first report of histology- and culture-proven Mycobacterium marinum infection diagnosed by next-generation sequencing (NGS). It took <2 days to make a microbiological diagnosis using the Oxford Nanopore Technologies' MinION device, compared to 20 days for the mycobacterium to be isolated from the tissue biopsy. NGS is particularly useful for culture-negative and slow-growing microorganism infections, such as mycobacterial, fungal and partially treated pyogenic bacterial infections. Due to its low equipment cost, short turn-around-time and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.
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Affiliation(s)
- Fanfan Xing
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Simon K. F. Lo
- Department of Clinical Microbiology and Infection Control, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Yuanchao Ma
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jonathan Daniel Ip
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Wan-Mui Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Meixun Zhou
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Miaozi Gong
- Department of Pathology, The University of Hong Kong - Shenzhen Hospital, Shenzhen, China
| | - Susanna K. P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Patrick C. Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Patrick C. Y. Woo
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Sze DTT, Lau CCY, Chan TM, Ma ESK, Tang BSF. Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels. BMC Microbiol 2021; 21:350. [PMID: 34922463 PMCID: PMC8684256 DOI: 10.1186/s12866-021-02403-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 11/25/2021] [Indexed: 12/25/2022] Open
Abstract
Background
Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST. Results
A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time. Conclusion In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02403-y.
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The clinical utility of two high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS. J Clin Microbiol 2021; 60:e0176921. [PMID: 34788113 PMCID: PMC8769742 DOI: 10.1128/jcm.01769-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens that cannot be identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming and low-throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests, which are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by respective built-in programs (MiSeq Reporter Software of Illumina and Epi2me of Nanopore) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of Nanopore 16S was 96.36%, which was identical to Sanger 16S and was better than Illumina 16S (69.07%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78h and 8.25h respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.
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Puerperal Sepsis Caused by Clostridium Innocuum in a Patient with Placenta Accreta and Literature Review. MATERNAL-FETAL MEDICINE 2020. [DOI: 10.1097/fm9.0000000000000027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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Wright WF, Utz JL, Bruckhart C, Baghli S, Janda JM. Yokenella regensburgei necrotizing fasciitis in an immunocompromised host. J Infect Chemother 2019; 25:816-819. [PMID: 31003955 DOI: 10.1016/j.jiac.2019.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/17/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
We report a case of necrotizing skin infection caused by Yokenella regensburgei in an immunosuppressed patient with orthotopic liver transplantation. Initial bacterial culture identification was suggestive of Hafnia alvei. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) confirmed identification of Y. regensburgei. Necrotizing fasciitis is potentially fatal and requires aggressive management, including early diagnosis, appropriate antibiotic selection, and operative debridement.
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Affiliation(s)
- William F Wright
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh Medical Center, Pinnacle, USA.
| | - Jena L Utz
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Memorial, USA.
| | - Christina Bruckhart
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Memorial, USA.
| | - Salim Baghli
- Division of Hospital Medicine, Department of Medicine, University of Pittsburgh Medical Center, Memorial, USA.
| | - J Michael Janda
- Department of Public Health Services, 1800 Mt Vernon Ave, Kern County, Bakersfield CA, 93306, USA.
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Elbehiry A, Marzouk E, Abdeen E, Al-Dubaib M, Alsayeqh A, Ibrahem M, Hamada M, Alenzi A, Moussa I, Hemeg HA. Proteomic characterization and discrimination of Aeromonas species recovered from meat and water samples with a spotlight on the antimicrobial resistance of Aeromonas hydrophila. Microbiologyopen 2019; 8:e782. [PMID: 30614207 PMCID: PMC6854848 DOI: 10.1002/mbo3.782] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Aeromonas is recognized as a human pathogen following ingestion of contaminated food and water. One major problem in Aeromonas identification is that certain species are phenotypically very similar. The antimicrobial resistance is another significant challenge worldwide. We therefore aimed to use mass spectrometry technology for identification and discrimination of Aeromonas species and to screen the antimicrobial resistance of Aeromonas hydrophila (A. hydrophila). A total of 150 chicken meat and water samples were cultured, and then, the isolates were identified biochemically by the Vitek® 2 Compact system. Proteomic identification was performed by MALDI‐TOF MS and confirmed by a microchannel fluidics electrophoresis assay. Principal component analysis (PCA) and single‐peak analysis created by MALDI were also used to discriminate the Aeromonas species. The antimicrobial resistance of the A. hydrophila isolates was determined by Vitek® 2 AST cards. In total, 43 samples were positive for Aeromonas and comprised 22 A. hydrophila, 12 Aeromonas caviae (A. caviae), and 9 Aeromonas sobria (A. sobria) isolates. Thirty‐nine out of 43 (90.69%) Aeromonas isolates were identified by the Vitek® 2 Compact system, whereas 100% of the Aeromonas isolates were correctly identified by MALDI‐TOF MS with a score value ≥2.00. PCA successfully separated A. hydrophila, A. caviae and A. sobria isolates into two groups. Single‐peak analysis revealed four discriminating peaks that separated A. hydrophila from A. caviae and A. sobria isolates. The resistance of A. hydrophila to antibiotics was 95.46% for ampicillin, 50% for cefotaxime, 45.45% for norfloxacin and pefloxacin, 36.36% for ceftazidime and ciprofloxacin, 31.81% for ofloxacin and 27.27% for nalidixic acid and tobramycin. In conclusion, chicken meat and water were tainted with Aeromonas spp., with a high occurrence of A. hydrophila. MALDI‐TOF MS is a powerful technique for characterizing aeromonads at the genus and species levels. Future studies should investigate the resistance of A. hydrophila to various antimicrobial agents.
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Affiliation(s)
- Ayman Elbehiry
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.,Department of Public Health, College of Public Health and Health Informatics, Qassim University, Buraidah, Saudi Arabia
| | - Eman Marzouk
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Eman Abdeen
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Musaad Al-Dubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Abdullah Alsayeqh
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia.,Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - Mohamed Hamada
- Department of Food Hygiene & Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Afrah Alenzi
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - Hassan A Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
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12
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A case of severe empyema with acute respiratory distress syndrome caused by Slackia exigua requiring veno-venous extracorporeal membrane oxygenation. Anaerobe 2017; 48:7-11. [DOI: 10.1016/j.anaerobe.2017.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 11/19/2022]
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13
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Porte L, García P, Braun S, Ulloa MT, Lafourcade M, Montaña A, Miranda C, Acosta-Jamett G, Weitzel T. Head-to-head comparison of Microflex LT and Vitek MS systems for routine identification of microorganisms by MALDI-TOF mass spectrometry in Chile. PLoS One 2017; 12:e0177929. [PMID: 28542393 PMCID: PMC5436840 DOI: 10.1371/journal.pone.0177929] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 05/05/2017] [Indexed: 12/28/2022] Open
Abstract
Background Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a new and revolutionary identification method for microorganisms and has recently been introduced into clinical microbiology in many industrialized countries in Europe and North America. Objectives Our study aimed to compare the performance and practicality of two commercial MALDI-TOF MS platforms in a head-to head manner at a routine laboratory in Chile. Methods During a five-month period in 2012–13, the diagnostic efficiency (correct identification rate) and agreement between Microflex LT (Bruker Daltonics) and Vitek MS (bioMérieux) was compared in a parallel manner to conventional identification including genotypic analysis for difficult-to-identify strains. The study included 804 microbial isolates: 252 Enterobacteriaceae, 126 non-fermenters, 36 other gram-negative rods, 279 gram-positive cocci, 32 gram-positive rods, 32 anaerobes, and 47 yeasts. Other relevant factors of the two devices such as user friendliness and connectivity were also evaluated and compared. Results Both systems correctly identified the vast majority (98%) of the isolates to the genus level. Vitek MS reached higher rates of identification to species and species complex level than Microflex LT (81% vs. 85% and 87% vs. 93%, respectively), which was mainly based on the higher performance among coagulase negative staphylococci and Candida isolates. The evaluation of user friendliness and other technical aspects showed only marginal differences, which slightly favored Vitek MS, mainly due to its ready-to-use supplies, easier connectivity and workflow integration, and availability of local technical support. Conclusions Both MALDI-TOF MS systems permitted fast and accurate identification of most microbial strains and showed a high level of user-friendliness. The observed differences were marginal and slightly favored Vitek MS, mainly due to practicality and connectivity issues within our setting.
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Affiliation(s)
- Lorena Porte
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Unidad de Microbiología, Laboratorio Clínico, Hospital Militar, Santiago, Chile
- * E-mail:
| | - Patricia García
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Stephanie Braun
- Unidad de Microbiología, Laboratorio Clínico, Hospital Militar, Santiago, Chile
| | - María Teresa Ulloa
- Programa de Microbiología, ICBM Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Alisson Montaña
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Laboratorio de Microbiología, Clínica Santa María, Santiago, Chile
| | - Carolina Miranda
- Laboratorio de Microbiología, Servicio de Laboratorios Clínicos, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Gerardo Acosta-Jamett
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral, Valdivia, Chile
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
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Savage E, Chothe S, Lintner V, Pierre T, Matthews T, Kariyawasam S, Miller D, Tewari D, Jayarao B. Evaluation of Three Bacterial Identification Systems for Species Identification of Bacteria Isolated from Bovine Mastitis and Bulk Tank Milk Samples. Foodborne Pathog Dis 2017; 14:177-187. [DOI: 10.1089/fpd.2016.2222] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Emily Savage
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Shubhada Chothe
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Valerie Lintner
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Traci Pierre
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Tammy Matthews
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Subhashinie Kariyawasam
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
| | - Dawn Miller
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Bhushan Jayarao
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania
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15
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Huang Y, Wang J, Zhang M, Zhu M, Wang M, Sun Y, Gu H, Cao J, Li X, Zhang S, Lu X. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens. J Med Microbiol 2017; 66:328-333. [PMID: 28100314 DOI: 10.1099/jmm.0.000435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yanfei Huang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, PR China
| | - Mingxin Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Min Zhu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Mei Wang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Yufeng Sun
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Haitong Gu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Jingjing Cao
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xue Li
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Shaoya Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
| | - Xinxin Lu
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, PR China
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Utilization Management in a Large Community Hospital. UTILIZATION MANAGEMENT IN THE CLINICAL LABORATORY AND OTHER ANCILLARY SERVICES 2017. [PMCID: PMC7123185 DOI: 10.1007/978-3-319-34199-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. There are numerous factors that influence laboratory utilization. Outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. CLIA’88 outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. Incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. Economies of scale define reduced unit cost per test as test volume increases. Outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. Disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, MALDI-TOF, multiplex infectious disease panels, cell-free DNA, and others. Obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms.
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17
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Karger A. Current developments to use linear MALDI-TOF spectra for the identification and typing of bacteria and the characterization of other cells/organisms related to infectious diseases. Proteomics Clin Appl 2016; 10:982-993. [PMID: 27400768 DOI: 10.1002/prca.201600038] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/30/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022]
Abstract
Within the past few years identification of bacteria by MALDI-TOF MS has become a standard technique in bacteriological laboratories for good reasons. MALDI-TOF MS identification is rapid, robust, automatable, and the per-sample costs are low. Yet, the spectra are very informative and the reliable identification of bacterial species is usually possible. Recently, new MS-based approaches for the identification of bacteria are emerging that are based on the detailed analysis of the bacterial proteome by high-resolution MS. These "proteotyping" approaches are highly discriminative and outperform MALDI-TOF MS-based identification in terms of specificity, but require a laborious proteomic workflow and far more expertise and sophisticated instrumentation than identification on basis of MALDI-TOF MS spectra, which can be obtained with relative simple and uncostly linear MALDI-TOF mass spectrometers. Thus MALDI-TOF MS identification of bacteria remains an attractive option for routine diagnostics. Additionally, MALDI-TOF MS identification protocols have been extended and improved in many respects making linear MALDI-TOF MS a versatile tool that can be useful beyond the identification of a bacterial species, e.g. for the characterization of leucocytes and arthropod vectors of infectious diseases. This review focuses on such improvements and extensions of the typical MALDI-TOF MS workflow in the field of infectious diseases.
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Affiliation(s)
- Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, , Federal Research Institute for Animal Health Südufer, Greifswald-Insel Riems, Germany.
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Teng JLL, Tang Y, Huang Y, Guo FB, Wei W, Chen JHK, Wong SSY, Lau SKP, Woo PCY. Phylogenomic Analyses and Reclassification of Species within the Genus Tsukamurella: Insights to Species Definition in the Post-genomic Era. Front Microbiol 2016; 7:1137. [PMID: 27493643 PMCID: PMC4955295 DOI: 10.3389/fmicb.2016.01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 07/07/2016] [Indexed: 12/13/2022] Open
Abstract
Owing to the highly similar phenotypic profiles, protein spectra and 16S rRNA gene sequences observed between three pairs of Tsukamurella species (Tsukamurella pulmonis/Tsukamurella spongiae, Tsukamurella tyrosinosolvens/Tsukamurella carboxy-divorans, and Tsukamurella pseudospumae/Tsukamurella sunchonensis), we hypothesize that and the six Tsukamurella species may have been misclassified and that there may only be three Tsukamurella species. In this study, we characterized the type strains of these six Tsukamurella species by tradition DNA-DNA hybridization (DDH) and "digital DDH" after genome sequencing to determine their exact taxonomic positions. Traditional DDH showed 81.2 ± 0.6% to 99.7 ± 1.0% DNA-DNA relatedness between the two Tsukamurella species in each of the three pairs, which was above the threshold for same species designation. "Digital DDH" based on Genome-To-Genome Distance Calculator and Average Nucleotide Identity for the three pairs also showed similarity results in the range of 82.3-92.9 and 98.1-99.1%, respectively, in line with results of traditional DDH. Based on these evidence and according to Rules 23a and 42 of the Bacteriological Code, we propose that T. spongiae Olson et al. 2007, should be reclassified as a later heterotypic synonym of T. pulmonis Yassin et al. 1996, T. carboxydivorans Park et al. 2009, as a later heterotypic synonym of T. tyrosinosolvens Yassin et al. 1997, and T. sunchonensis Seong et al. 2008 as a later heterotypic synonym of T. pseudospumae Nam et al. 2004. With the advancement of genome sequencing technologies, classification of bacterial species can be readily achieved by "digital DDH" than traditional DDH.
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Affiliation(s)
- Jade L. L. Teng
- Department of Microbiology, The University of Hong KongHong Kong, China
- Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China
- Carol Yu Centre for Infection, The University of Hong KongHong Kong, China
| | - Ying Tang
- Department of Microbiology, The University of Hong KongHong Kong, China
| | - Yi Huang
- Department of Microbiology, The University of Hong KongHong Kong, China
| | - Feng-Biao Guo
- Centre of Bioinformatics, Key Laboratory for NeuroInformation of the Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of ChinaChengdu, China
| | - Wen Wei
- School of Life Sciences, Chongqing UniversityChongqing, China
| | | | - Samson S. Y. Wong
- Department of Microbiology, The University of Hong KongHong Kong, China
- Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China
- Carol Yu Centre for Infection, The University of Hong KongHong Kong, China
| | - Susanna K. P. Lau
- Department of Microbiology, The University of Hong KongHong Kong, China
- Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China
- Carol Yu Centre for Infection, The University of Hong KongHong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, China
| | - Patrick C. Y. Woo
- Department of Microbiology, The University of Hong KongHong Kong, China
- Research Centre of Infection and Immunology, The University of Hong KongHong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong KongHong Kong, China
- Carol Yu Centre for Infection, The University of Hong KongHong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, China
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Elizabethkingia anophelis bacteremia is associated with clinically significant infections and high mortality. Sci Rep 2016; 6:26045. [PMID: 27185741 PMCID: PMC4868968 DOI: 10.1038/srep26045] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/26/2016] [Indexed: 11/16/2022] Open
Abstract
Unlike Elizabethkingia meningoseptica, the clinical importance of E. anophelis is poorly understood. We determined the clinical and molecular epidemiology of bacteremia caused by Elizabethkingia-like species from five regional hospitals in Hong Kong. Among 45 episodes of Elizabethkingia-like bacteremia, 21 were caused by Elizabethkingia, including 17 E. anophelis, three E. meningoseptica and one E. miricola; while 24 were caused by other diverse genera/species, as determined by 16S rRNA gene sequencing. Of the 17 cases of E. anophelis bacteremia, 15 (88%) were clinically significant. The most common diagnosis was pneumonia (n = 5), followed by catheter-related bacteremia (n = 4), neonatal meningitis (n = 3), nosocomial bacteremia (n = 2) and neutropenic fever (n = 1). E. anophelis bacteremia was commonly associated with complications and carried 23.5% mortality. In contrast, of the 24 episodes of bacteremia due to non-Elizabethkingia species, 16 (67%) were clinically insignificant. Compared to non-Elizabethkingia bacteremia, Elizabethkingia bacteremia was associated with more clinically significant infections (P < 0.01) and positive cultures from other sites (P < 0.01), less polymicrobial bacteremia (P < 0.01), and higher complication (P < 0.05) and mortality (P < 0.05) rates. Elizabethkingia bacteremia is predominantly caused by E. anophelis instead of E. meningoseptica. Elizabethkingia bacteremia, especially due to E. anophelis, carries significant morbidity and mortality, and should be considered clinically significant unless proven otherwise.
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20
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Lau SKP, Lam CSK, Ngan AHY, Chow WN, Wu AKL, Tsang DNC, Tse CWS, Que TL, Tang BSF, Woo PCY. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid identification of mold and yeast cultures of Penicillium marneffei. BMC Microbiol 2016; 16:36. [PMID: 26965891 PMCID: PMC4787007 DOI: 10.1186/s12866-016-0656-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 03/02/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in HIV-infected and other immunocompromised patients in Southeast Asia. However, laboratory diagnosis of penicilliosis, which relies on microscopic morphology and mycelial-to-yeast conversion, is time-consuming and expertise-dependent, thus delaying diagnosis and treatment. Although matrix -assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is useful for identification of various medically important fungi, its performance for identification of P. marneffei is less clear. RESULTS We evaluated the performance of the Bruker MALDI-TOF MS system for identification of mold and yeast cultures of 59 clinical strains and the type strain of P. marneffei using the direct transfer method, with results compared to four phylogenetically closely related species, P. brevi-compactum, P. chrysogenum, Talaromyces aurantiacus and T. stipitatus. Using the Bruker original database combined with BDAL v4.0.0.1 and Filamentous Fungi Library 1.0, MALDI-TOF MS failed to identify the 60 P. marneffei strains grown in mold and yeast phase (identified as P. funiculosum and P. purpurogenum with scores <1.7 respectively). However, when the combined database was expanded with inclusion of spectra from 21 P. marneffei strains in mold and/or yeast phase, all the remaining 39 P. marneffei strains grown in mold or phase were correctly identified to the species level with score >2.0. The MS spectra of P. marneffei exhibited significant difference to those of P. brevi-compactum, P. chrysogenum, T. aurantiacus and T. stipitatus. However, MALDI-TOF MS failed to identify these four fungi to the species level using the combined database with or without spectra from P. marneffei. CONCLUSIONS MALDI-TOF MS is useful for rapid identification of both yeast and mold cultures of P. marneffei and differentiation from related species. However, accurate identification to the species level requires database expansion using P. marneffei strains.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, The University of Hong Kong, Hong Kong, China.
| | | | - Antonio H Y Ngan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Alan K L Wu
- Department of Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong, China
| | | | - Cindy W S Tse
- Department of Pathology, Kwong Wah Hospital, Hong Kong, China
| | - Tak-Lun Que
- Department of Pathology, Tuen Mun Hospital, Hong Kong, China
| | | | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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Chingin K, Liang J, Liu Y, Chen L, Wu X, Hu L, Ouyang Y. Rapid detection of Mycobacterium tuberculosis cultures by direct ambient corona discharge ionization mass spectrometry of volatile metabolites. RSC Adv 2016. [DOI: 10.1039/c6ra12107a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-throughput TB screening with high chemical specificity is achieved using direct ambient corona discharge ionization MS analysis of volatile metabolites.
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Affiliation(s)
- Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation
- East China University of Technology
- Nanchang City
- P. R. China
| | - Juchao Liang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation
- East China University of Technology
- Nanchang City
- P. R. China
| | - Yanling Liu
- The Second Affiliated Hospital of Nanchang University
- Nanchang City
- P. R. China
| | - Linfei Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation
- East China University of Technology
- Nanchang City
- P. R. China
| | - Xiaoping Wu
- Department of Infections, the First Affiliated Hospital of Nanchang University
- Nanchang City
- P. R. China
| | - Longhua Hu
- The Second Affiliated Hospital of Nanchang University
- Nanchang City
- P. R. China
| | - Yongzhong Ouyang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation
- East China University of Technology
- Nanchang City
- P. R. China
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22
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Tsang CC, Hui TWS, Lee KC, Chen JHK, Ngan AHY, Tam EWT, Chan JFW, Wu AL, Cheung M, Tse BPH, Wu AKL, Lai CKC, Tsang DNC, Que TL, Lam CW, Yuen KY, Lau SKP, Woo PCY. Genetic diversity of Aspergillus species isolated from onychomycosis and Aspergillus hongkongensis sp. nov., with implications to antifungal susceptibility testing. Diagn Microbiol Infect Dis 2015; 84:125-34. [PMID: 26658315 DOI: 10.1016/j.diagmicrobio.2015.10.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 11/30/2022]
Abstract
Thirteen Aspergillus isolates recovered from nails of 13 patients (fingernails, n=2; toenails, n=11) with onychomycosis were characterized. Twelve strains were identified by multilocus sequencing as Aspergillus spp. (Aspergillus sydowii [n=4], Aspergillus welwitschiae [n=3], Aspergillus terreus [n=2], Aspergillus flavus [n=1], Aspergillus tubingensis [n=1], and Aspergillus unguis [n=1]). Isolates of A. terreus, A. flavus, and A. unguis were also identifiable by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The 13th isolate (HKU49(T)) possessed unique morphological characteristics different from other Aspergillus spp. Molecular characterization also unambiguously showed that HKU49(T) was distinct from other Aspergillus spp. We propose the novel species Aspergillus hongkongensis to describe this previously unknown fungus. Antifungal susceptibility testing showed most Aspergillus isolates had low MICs against itraconazole and voriconazole, but all Aspergillus isolates had high MICs against fluconazole. A diverse spectrum of Aspergillus species is associated with onychomycosis. Itraconazole and voriconazole are probably better drug options for Aspergillus onychomycosis.
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Affiliation(s)
- Chi-Ching Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Teresa W S Hui
- Department of Microbiology, The University of Hong Kong, Hong Kong; Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | | | - Antonio H Y Ngan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Emily W T Tam
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Jasper F W Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Andrea L Wu
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Mei Cheung
- Department of Microbiology, The University of Hong Kong, Hong Kong; Department of Pathology, Queen Elizabeth Hospital, Hong Kong
| | - Brian P H Tse
- Department of Microbiology, The University of Hong Kong, Hong Kong; Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong
| | - Alan K L Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong
| | | | | | - Tak-Lun Que
- Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong.
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First Report of Human Infection by Agromyces mediolanus, a Gram-Positive Organism Found in Soil. J Clin Microbiol 2015. [PMID: 26202108 DOI: 10.1128/jcm.01508-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report the first human infection by a member of the Agromyces genus, a group of Gram-positive bacteria found in soil. A patient with a long-term venous catheter developed bacteremia due to a non-vancomycin-susceptible isolate of Agromyces mediolanus. Rapid identification was possible by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
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To KKW, Lee KC, Wong SSY, Lo KC, Lui YM, Jahan AS, Wu AL, Ke YH, Law CY, Sze KH, Lau SKP, Woo PCY, Lam CW, Yuen KY. Lipid mediators of inflammation as novel plasma biomarkers to identify patients with bacteremia. J Infect 2015; 70:433-44. [PMID: 25727996 DOI: 10.1016/j.jinf.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 02/16/2015] [Accepted: 02/20/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Rapid diagnostic tests for bacteremia are important for early treatment to improve clinical outcome. We sought to identify plasma biomarkers that can identify patients with bacteremia using an untargeted global metabolomic analysis. METHODS Plasma metabolomic profiles were analyzed for 145 adult patients with (cases) and without (controls) bacteremia using ultra-high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). All metabolites were compared between cases and controls using a 2-tier filtering approach, and each metabolite underwent receiver operating characteristic (ROC) curve analysis. Individual metabolites that distinguish between cases and controls were characterized. Subgroup analysis was performed to identify metabolites with prognostic significance. RESULTS After 2-tier filtering, 128 molecular features were identified to be potential biomarkers that could distinguish cases from controls. Five metabolites had an area under the ROC curve (AUC) of >0.8 in ROC curve analysis, including a sphingolipid, an acylcarnitine, a fatty acid ester, and 2 glycerophosphocholines. These metabolites could distinguish cases from controls in the unsupervised hierarchical clustering analysis. Subgroup analysis of bacteremic patients showed that the level of trans-2,3,4-trimethoxycinnamate was lower in fatal than non-fatal cases. CONCLUSIONS Plasma lipid mediators of inflammation can distinguish bacteremia cases from non-bacteremia controls. These biomarkers may be used as targets for rapid test in clinical practice.
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Affiliation(s)
- Kelvin K W To
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Samson S Y Wong
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ka-Ching Lo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yin-Ming Lui
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Akhee S Jahan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Andrea L Wu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Yi-Hong Ke
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Chun-Yiu Law
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Kong-Hung Sze
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Susanna K P Lau
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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26
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Abstract
Abstract
BACKGROUND
First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identification of grown bacteria and fungi based on automated analysis of the mass distribution of bacterial proteins.
CONTENT
This review provides a historical perspective on this new technology. Modern applications in the clinical microbiology laboratory are reviewed with a focus on the most recent publications in the field. Identification of aerobic and anaerobic bacteria, mycobacteria, and fungi are discussed, as are applications for testing urine and positive blood culture bottles. The strengths and limitations of MALDI-TOF MS applications in clinical microbiology are also addressed.
SUMMARY
MALDI-TOF MS is a tool for rapid, accurate, and cost-effective identification of cultured bacteria and fungi in clinical microbiology. The technology is automated, high throughput, and applicable to a broad range of common as well as esoteric bacteria and fungi. MALDI-TOF MS is an incontrovertibly beneficial technology for the clinical microbiology laboratory.
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Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
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27
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Gordonia species as emerging causes of continuous-ambulatory-peritoneal-dialysis-related peritonitis identified by 16S rRNA and secA1 gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). J Clin Microbiol 2014; 53:671-6. [PMID: 25428146 DOI: 10.1128/jcm.02971-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report here four cases of continuous ambulatory peritoneal dialysis-related peritonitis caused by three different species of Gordonia. The portal of entry was likely through Tenckhoff catheters. 16S rRNA and secA1 gene sequencing are so far the most reliable methods for the accurate identification of Gordonia species.
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Teng JLL, Huang Y, Tse H, Chen JHK, Tang Y, Lau SKP, Woo PCY. Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus. Genome Biol Evol 2014; 6:2930-43. [PMID: 25331233 PMCID: PMC4224358 DOI: 10.1093/gbe/evu232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Yi Huang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Herman Tse
- Department of Microbiology, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Jonathan H K Chen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ying Tang
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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Subcutaneous phaeohyphomycotic nodule due to Phialemoniopsis hongkongensis sp. nov. J Clin Microbiol 2014; 52:3280-9. [PMID: 24966363 DOI: 10.1128/jcm.01592-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phialemoniopsis species are ubiquitous dematiaceous molds associated with a wide variety of superficial and systemic infections in human. In this study, we isolated a mold from the forearm nodule biopsy specimen from a patient with underlying liver cirrhosis, ankylosing spondylosis, and tuberculosis. He was treated with itraconazole, but unfortunately, he succumbed as a result of disseminated tuberculosis with multiorgan failure. The histology results of the skin biopsy showed necrotizing granulomas in which numerous fungal elements were found. On Sabouraud dextrose agar, the fungal isolate grew as white-to-cream and smooth-to-velvety colonies. Microscopically, oval-to-cylindrical conidia were observed from abundant adelophialides, which possessed barely visible parallel collarettes but no basal septa. The azole drugs voriconazole, itraconazole, and posaconazole, as well as amphotericin B, showed high activities against this fungus. Internal transcribed spacer, 28S nuclear ribosomal DNA (nrDNA), and β-actin and β-tubulin gene sequencing showed that this fungus is most closely related to but distinct from Phialemonium curvata. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and hierarchical cluster analysis showed that the MALDI-TOF MS spectrum of this fungus is most closely related to that of Phialemonium pluriloculosa. We propose a new species, Phialemoniopsis hongkongensis sp. nov., to describe this fungus.
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Li Y, Gu B, Liu G, Xia W, Fan K, Mei Y, Huang P, Pan S. MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria. J Thorac Dis 2014; 6:517-23. [PMID: 24822113 DOI: 10.3978/j.issn.2072-1439.2014.02.15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 02/26/2014] [Indexed: 12/29/2022]
Abstract
BACKGROUND Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. METHODS Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. RESULTS Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. CONCLUSIONS Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.
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Affiliation(s)
- Yang Li
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Bing Gu
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Genyan Liu
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Wenying Xia
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Kun Fan
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Yaning Mei
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Peijun Huang
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Shiyang Pan
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
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Suwantarat N, Romagnoli M, Wakefield T, Carroll KC. Ventriculoperitoneal shunt infection caused by Bifidobacterium breve. Anaerobe 2014; 28:1-3. [PMID: 24755114 DOI: 10.1016/j.anaerobe.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/02/2014] [Accepted: 04/05/2014] [Indexed: 12/20/2022]
Abstract
Bifidobacterium breve is a rare cause of human infections. Previously, bacteremia and meningitis caused by this organism linked to probiotic use have been reported in a neonate. We report the first case of a ventriculoperitoneal shunt infection caused by B. breve in an adult without a history of probiotic use.
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Affiliation(s)
- Nuntra Suwantarat
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Mark Romagnoli
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Teresa Wakefield
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
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Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory. J Clin Microbiol 2014; 52:1089-97. [PMID: 24452159 DOI: 10.1128/jcm.02399-13] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reported matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification rates of Gram-positive rods (GPR) are low compared to identification rates of Gram-positive cocci. In this study, three sample preparation methods were compared for MALDI-TOF MS identification of 190 well-characterized GPR strains: direct transfer, direct transfer-formic acid preparation, and ethanol-formic acid extraction. Using the interpretation criteria recommended by the manufacturer, identification rates were significantly higher for direct transfer-formic acid preparation and ethanol-formic acid extraction than for direct transfer. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification rates. In a subsequent prospective study, 215 clinical GPR isolates were analyzed by MALDI-TOF MS, and the results were compared to those for identification using conventional methods, with discrepancies being resolved by 16S rRNA and rpoB gene analysis. Using the direct transfer-formic acid preparation and a species cutoff of 1.7, congruencies on the genus and species levels of 87.4% and 79.1%, respectively, were achieved. In addition, the rate of nonidentified isolates dropped from 12.1% to 5.6% when using an extended database, i.e., the Bruker database amended by reference spectra of the 190 GPR of the retrospective study. Our data demonstrate three ways to improve GPR identification by the Bruker MALDI Biotyper, (i) optimize sample preparation using formic acid, (ii) reduce cutoff scores for species identification, and (iii) expand the database. Based on our results, we suggest an identification algorithm for the clinical laboratory combining MALDI-TOF MS with nucleic acid sequencing.
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