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Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
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Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
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2
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Capobianco CM, Bosch SN, Stacy NI, Wellehan JFX. Lactococcus garvieae-associated septicemia in a central bearded dragon. J Vet Diagn Invest 2024; 36:477-480. [PMID: 38516722 PMCID: PMC11110774 DOI: 10.1177/10406387241239912] [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] [Indexed: 03/23/2024] Open
Abstract
Lactococcus garvieae is the causative agent of lactococcosis in fish and an emerging zoonotic pathogen with high levels of antimicrobial resistance. We report a case of L. garvieae-associated septicemia in a central bearded dragon (Pogona vitticeps) confirmed via whole-blood PCR and direct sequencing. Following a 30-d course of ceftazidime (20 mg/kg IM q72h), the animal's clinical condition had not resolved; leukopenia persisted, with heterophil toxic change. Coelomic ultrasound findings were consistent with preovulatory follicular stasis, folliculitis, and coelomitis. Following surgical ovariectomy and an additional 30-d course of ceftazidime, the animal's behavior and appetite returned to normal, the animal tested negative via whole-blood PCR assay, and the CBC was unremarkable. To our knowledge, L. garvieae with L. garvieae-associated clinical disease has not been reported previously in a bearded dragon. We conclude that L. garvieae should be considered as a possible etiologic agent in cases of septicemia in bearded dragons, with the potential for zoonotic transmission warranting further investigation.
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Affiliation(s)
- Christian M. Capobianco
- Departments of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Sarah N. Bosch
- Departments of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Nicole I. Stacy
- Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - James F. X. Wellehan
- Departments of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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3
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Ivaska L, Herberg J, Sadarangani M. Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers. J Infect 2024; 88:106111. [PMID: 38307149 DOI: 10.1016/j.jinf.2024.01.010] [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: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.
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Affiliation(s)
- Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Savitehtaankatu 5, 20521 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Kiinanmyllynkatu 10, 20520 Turku, Finland.
| | - Jethro Herberg
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, Norfolk Place, London, United Kingdom.
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
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4
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Kubiak J, Morgan A, Kirmaier A, Arnaout R, Riedel S. Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes. J Clin Microbiol 2023; 61:e0095223. [PMID: 38014970 PMCID: PMC10729690 DOI: 10.1128/jcm.00952-23] [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: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Our work provides a retrospective analysis of universal PCR orders for bacteria, mycobacteria, and fungi across our institution across a 10-year period. We assessed the positivity rates for this diagnostic tool by test type and specimen type and, critically, studied whether and how the results influenced the outcomes from treatment change, to readmission, to death.
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Affiliation(s)
- Jeffrey Kubiak
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Alexandra Morgan
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Andrea Kirmaier
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ramy Arnaout
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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5
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Dumm RE, Glaser LJ, Rodino KG. Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center. Am J Clin Pathol 2023; 160:477-482. [PMID: 37458096 DOI: 10.1093/ajcp/aqad074] [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: 04/06/2023] [Accepted: 05/25/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data. METHODS Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management. RESULTS Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy. CONCLUSIONS This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.
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Affiliation(s)
- Rebekah E Dumm
- Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, Washington University, St Louis, MO, US
| | - Laurel J Glaser
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
| | - Kyle G Rodino
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
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6
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Mulder AT, Partyka M, Divers SJ, Childress A, Wellehan JFX, Stilwell JM. Chronic mandibular osteomyelitis associated with a novel probable Kocuria sp in a sugar glider (Petaurus breviceps). J Comp Pathol 2023; 206:17-21. [PMID: 37742449 DOI: 10.1016/j.jcpa.2023.08.006] [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: 05/31/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
Dental disease in sugar gliders (Petaurus breviceps) is understudied, with only limited clinical and pathological data available. An approximately 7-year-old female sugar glider presented to its primary care veterinarian for a decline in food intake, rapid weight loss and a mass involving the rostral mandible. At necropsy, the mandibular mass effaced most of the rostral mandible and adjacent musculature. Histologically, the mandible was disrupted by nodular infiltrates of variably degenerate neutrophils and macrophages encased in granulomatous inflammation and fibrous connective tissue. Within the neutrophilic cell population were segments of fragmented, necrotic bone and cloud-like colonies of gram-positive cocci. Aerobic culture yielded a heavy, pure growth of a gram-positive coccus morphologically consistent with those identified in the lesions, which was identified as a presumptively novel Kocuria sp by polymerase chain reaction and sequencing of the 16S rRNA gene. This is the first description of Kocuria infection in association with clinically significant pathology in an animal. Although isolated as a pure growth, Kocuria sp cannot be confirmed as the sole cause of lesion formation due to the case chronicity and potential for unculturable, polymicrobial infections. This report adds to our understanding of the clinical and pathological aspects of dental disease in sugar gliders.
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Affiliation(s)
- Alan T Mulder
- Department of Pathology, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Megan Partyka
- Zoological Medicine Service, Department of Small Animal Medicine & Surgery, University of Georgia, 2200 College Station Road, Athens, Georgia 30602, USA
| | - Stephen J Divers
- Zoological Medicine Service, Department of Small Animal Medicine & Surgery, University of Georgia, 2200 College Station Road, Athens, Georgia 30602, USA
| | - April Childress
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, 2015 SW 16(th) Ave, Gainesville, Florida 32608, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, University of Florida, 2015 SW 16(th) Ave, Gainesville, Florida 32608, USA
| | - Justin M Stilwell
- Department of Pathology, University of Georgia, 501 D. W. Brooks Drive, Athens, Georgia 30602, USA.
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7
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Muzahid NH, Md Zoqratt MZH, Ten KE, Hussain MH, Su TT, Ayub Q, Tan HS, Rahman S. Genomic and phenotypic characterization of Acinetobacter colistiniresistens isolated from the feces of a healthy member of the community. Sci Rep 2023; 13:12596. [PMID: 37537198 PMCID: PMC10400646 DOI: 10.1038/s41598-023-39642-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Acinetobacter species are widely known opportunistic pathogens causing severe community and healthcare-associated infections. One such emerging pathogen, Acinetobacter colistiniresistens, is known to exhibit intrinsic resistance to colistin. We investigated the molecular characteristics of A. colistiniresistens strain C-214, isolated from the fecal sample of a healthy community member, as part of a cohort study being conducted in Segamat, Malaysia. Comparison of the whole genome sequence of C-214 with other A. colistiniresistens sequences retrieved from the NCBI database showed 95% sequence identity or more with many of the genome sequences representing that species. Use of the Galleria mellonella killing assay showed that C-214 was pathogenic in this model infection system. The strain C-214 had a colistin and polymyxin B MIC of 32 and 16 mg/L, respectively. Besides, it was resistant to cefotaxime, amikacin, and tetracycline and showed moderate biofilm-producing ability. Different genes associated with virulence or resistance to major classes of antibiotics were detected. We observed mutations in lpxA/C/D in C-214 and other A. colistiniresistens strains as probable causes of colistin resistance, but the biological effects of these mutations require further investigation. This study provides genomic insights into A. colistiniresistens, a potentially pathogenic bacterium isolated from a community member and notes the public health threat it may pose.
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Affiliation(s)
- Nazmul Hasan Muzahid
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
| | | | - Kah Ern Ten
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Md Hamed Hussain
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Tin Tin Su
- South East Asia Community Observatory (SEACO), Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
- Monash University Malaysia Genomics Facility, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
- Monash University Malaysia Genomics Facility, Bandar Sunway, 47500, Subang Jaya, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine & Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
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8
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Moorlag SJCFM, Coolen JPM, van den Bosch B, Jin EHM, Buil JB, Wertheim HFL, Melchers WJG. Targeting the 16S rRNA Gene by Reverse Complement PCR Next-Generation Sequencing: Specific and Sensitive Detection and Identification of Microbes Directly in Clinical Samples. Microbiol Spectr 2023; 11:e0448322. [PMID: 37227289 PMCID: PMC10269728 DOI: 10.1128/spectrum.04483-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
The detection and accurate identification of bacterial species in clinical samples are crucial for diagnosis and appropriate antibiotic treatment. To date, sequencing of the 16S rRNA gene has been widely used as a complementary molecular approach when identification by culture fails. The accuracy and sensitivity of this method are highly affected by the selection of the 16S rRNA gene region targeted. In this study, we assessed the clinical utility of 16S rRNA reverse complement PCR (16S RC-PCR), a novel method based on next-generation sequencing (NGS), for the identification of bacterial species. We investigated the performance of 16S RC-PCR on 11 bacterial isolates, 2 polymicrobial community samples, and 59 clinical samples from patients suspected of having a bacterial infection. The results were compared to culture results, if available, and to the results of Sanger sequencing of the 16S rRNA gene (16S Sanger sequencing). By 16S RC-PCR, all bacterial isolates were accurately identified to the species level. Furthermore, in culture-negative clinical samples, the rate of identification increased from 17.1% (7/41) to 46.3% (19/41) when comparing 16S Sanger sequencing to 16S RC-PCR. We conclude that the use of 16S RC-PCR in the clinical setting leads to an increased sensitivity of detection of bacterial pathogens, resulting in a higher number of diagnosed bacterial infections, and thereby can improve patient care. IMPORTANCE The identification of the causative infectious pathogen in patients suspected of having a bacterial infection is essential for diagnosis and the start of appropriate treatment. Over the past 2 decades, molecular diagnostics have improved the ability to detect and identify bacteria. However, novel techniques that can accurately detect and identify bacteria in clinical samples and that can be implemented in clinical diagnostics are needed. Here, we demonstrate the clinical utility of bacterial identification in clinical samples by a novel method called 16S RC-PCR. Using 16S RC-PCR, we reveal a significant increase in the number of clinical samples in which a potentially clinically relevant pathogen is identified compared to the commonly used 16S Sanger method. Moreover, RC-PCR allows automation and is well suited for implementation in a diagnostic laboratory. In conclusion, the implementation of this method as a diagnostic tool is expected to result in an increased number of diagnosed bacterial infections, and in combination with adequate treatment, this could improve clinical outcomes for patients.
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Affiliation(s)
- Simone J. C. F. M. Moorlag
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Bart van den Bosch
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Elisabeth Hui-Mei Jin
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jochem B. Buil
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
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9
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Muzahid NH, Hussain MH, Huët MAL, Dwiyanto J, Su TT, Reidpath D, Mustapha F, Ayub Q, Tan HS, Rahman S. Molecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia. Microb Genom 2023; 9. [PMID: 37018035 PMCID: PMC10210948 DOI: 10.1099/mgen.0.000977] [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] [Indexed: 04/06/2023] Open
Abstract
Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections around the world. However, little is known about the persistence and dynamics of A. baumannii in a healthy community. This study investigated the role of the community as a prospective reservoir for A. baumannii and explored possible links between hospital and community isolates. A total of 12 independent A. baumannii strains were isolated from human faecal samples from the community in Segamat, Malaysia, in 2018 and 2019. Another 15 were obtained in 2020 from patients at the co-located tertiary public hospital. The antimicrobial resistance profile and biofilm formation ability were analysed, and the relatedness of community and hospital isolates was determined using whole-genome sequencing (WGS). Antibiotic profile analysis revealed that 12 out of 15 hospital isolates were MDR, but none of the community isolates were MDR. However, phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) and a pangenome analysis of core genes showed clustering between four community and two hospital strains. Such clustering of strains from two different settings based on their genomes suggests that these strains could persist in both. WGS revealed 41 potential resistance genes on average in the hospital strains, but fewer (n=32) were detected in the community strains. In contrast, 68 virulence genes were commonly seen in strains from both sources. This study highlights the possible transmission threat to public health posed by virulent A. baumannii present in the gut of asymptomatic individuals in the community.
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Affiliation(s)
- Nazmul Hasan Muzahid
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Md Hamed Hussain
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | - Jacky Dwiyanto
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Tin Tin Su
- South East Asia Community Observatory (SEACO) and Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Daniel Reidpath
- South East Asia Community Observatory (SEACO) and Global Public Health, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Faizah Mustapha
- Department of Pathology, Hospital Segamat, Jalan Genuang, Bandar Putra, 85000, Segamat, Johor, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
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10
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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11
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Etiology and Outcomes of Healthcare-Associated Meningitis and Ventriculitis—A Single Center Cohort Study. Infect Dis Rep 2022; 14:420-427. [PMID: 35735755 PMCID: PMC9222399 DOI: 10.3390/idr14030045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/04/2023] Open
Abstract
Healthcare associated meningitis and ventriculitis (HCAMV) are serious complications of neurosurgical procedures. We conducted a retrospective cohort study of patients with HCAMV treated at the University Hospital for Infectious Diseases Zagreb during the 2013–2019 period. A total of 144 patients with 151 episodes of HCAMV were included. The most common indications for neurosurgical procedures were brain tumor, hemorrhage and hydrocephalus. Etiology was identified in 90 (59.6%) episodes (either positive CSF culture or positive PCR), and in other 61 (40.39%) the diagnosis of HCAMV was made based on clinical and CSF parameters, without microbiologic confirmation. Carbapenem-resistant Acinetobacter baumannii was the most common pathogen (15.89%), followed by Staphylococcus aureus (13.91%), Pseudomonas aeruginosa (13.25%) and Coagulase negative staphylococci (7.95%). Overall, 24 (16.3%) patients died, and the majority had adverse outcomes, persistent vegetative state (8, 5.56%) and severe disability (31, 21.53%). The worst clinical outcomes were observed in A. baumannii infections. High rate of complications, the need for external ventricular drainage (re)placement often complicated with nosocomial infections and prolonged stay in intensive care units were observed. Clinicians should be aware of local microbial epidemiology on guiding proper empirical antimicrobial treatment in patients with HCAMV.
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12
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Liguori BL, Ossiboff RJ, Stacy NI, Graham EA, Oliveira LJ, Childress AL, Giglio RF, Hamel PS, Turner RC, Alexander AB, Christman JE, Heard DJ, Wellehan JFX. AUSTWICKIA CHELONAE IN A WILD GOPHER TORTOISE (GOPHERUS POLYPHEMUS) AND EVIDENCE OF POSITIVE SELECTION ON THE DIPHTHERIA-LIKE TOXIN GENE. J Wildl Dis 2022; 58:1-7. [PMID: 34780647 DOI: 10.7589/jwd-d-20-00223] [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: 12/07/2020] [Accepted: 07/29/2021] [Indexed: 11/20/2022]
Abstract
Austwickia (Dermatophilus) chelonae is a filamentous, Gram-positive Actinobacteria in the Dermatophilaceae family. It has caused fatal granulomatous disease in diverse captive reptile species on three continents, but its presence in wild or free-ranging populations was unknown. An adult female gopher tortoise (Gopherus polyphemus) was presented euhydrated, but cachectic and infested with ticks, with two firm, encapsulated masses over the cranioventral neck and right stifle. The tortoise had moderate nonregenerative anemia and evidence of inflammation; plasma biochemistry data was within normal limits. Fine needle aspirate of the neck lesion revealed abundant necrosis and aggregates of cocci. Computed tomography delineated the masses and revealed an additional mass adjacent to the left zygomatic bone. After surgical excision, histology identified chronic granulomas with intralesional filamentous bacteria. Pan-bacterial 16S rRNA PCR and sequencing of the masses identified A. chelonae. Despite treatment with oxytetracycline and ceftazidime, the tortoise deteriorated and was euthanatized. An esophageal lesion consistent with A. chelonae was seen on postmortem examination, although it was determined that the tortoise ultimately succumbed to fungal pneumonia caused by Metarhizium robertsii, an entomopathogenic biotoxin sprayed as insect control. This case reveals A. chelonae is present in free-ranging chelonians in North America. This organism produces a toxin gene similar to diphtheria toxin, one of the most potent known biotoxins, which has not been previously identified outside the genus Corynebacterium. Novel PCR primers were designed for the toxin and rpoB genes, which were amplified and sequenced from two cases and compared with two available genomes. Selection analysis revealed that the toxin gene is under positive selection, which implies it interacts significantly with the immune system, making it a good candidate for immunodiagnostic test development.
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Affiliation(s)
- Brittany L Liguori
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Robert J Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Erin A Graham
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Lilian J Oliveira
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - April L Childress
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Robson F Giglio
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Philip S Hamel
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Rachel C Turner
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Amy B Alexander
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Jane E Christman
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - Darryl J Heard
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, Florida 32608, USA
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Escalas A, Troussellier M, Melayah D, Bruto M, Nicolas S, Bernard C, Ader M, Leboulanger C, Agogué H, Hugoni M. Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiol Ecol 2021; 97:6464137. [PMID: 34918080 DOI: 10.1093/femsec/fiab163] [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: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Marc Troussellier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Delphine Melayah
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Sébastien Nicolas
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, CP 39, 75005 Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, 75005 Paris, France
| | - Christophe Leboulanger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Hélène Agogué
- Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS -La Rochelle Université, 17000 La Rochelle, France
| | - Mylène Hugoni
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.,Institut Universitaire de France (IUF)
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Noviyani NMR, Kardana IM, Mahalini DS, Suparyatha IBG, Ariawati K, Nilawati GAP, Sukmawati M. The Risk Factors of Bacterial Meningitis in Late-Onset Neonatal Sepsis. Open Access Maced J Med Sci 2021. [DOI: 10.3889/oamjms.2021.6706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Neonatal bacterial meningitis has a significant contribution on neonatal morbidity and mortality. It is the most common complication of late-onset neonatal sepsis. An understanding of the risk factors for bacterial meningitis in late-onset neonatal sepsis is required to provide comprehensive management.
AIM: To identify the risk factors of bacterial meningitis in late-onset neonatal sepsis.
METHODS: This is an analytical study with a case–control design, conducted in May 2019-February 2021, involving neonates aged 4–28 days who suffered from late-onset neonatal sepsis in Level II and III Neonatal Care Unit, Sanglah General Hospital Denpasar. Statistical analysis was performed using Chi-square and logistic regression.
RESULTS: A total of 54 patients were analyzed in this study. The mean age of subjects with neonatal bacterial meningitis was 13 days and the majority of them were male (51.9%). The risk factor of bacterial meningitis in late-onset neonatal sepsis was gestational age <37 weeks with odds ratio 4.22 (95% confidence interval 1.28–13.86, p = 0.01). There was no significant association of birth weight <2500 g, neonatal asphyxia, and invasive procedure on neonatal bacterial meningitis.
CONCLUSION: Gestational age <37 weeks is a risk factor for bacterial meningitis in late-onset neonatal sepsis.
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15
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Fournier C, Riehle E, Dietrich DR, Schleheck D. Is Toxin-Producing Planktothrix sp. an Emerging Species in Lake Constance? Toxins (Basel) 2021; 13:toxins13090666. [PMID: 34564670 PMCID: PMC8472890 DOI: 10.3390/toxins13090666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Recurring blooms of filamentous, red-pigmented and toxin-producing cyanobacteria Planktothrix rubescens have been reported in numerous deep and stratified prealpine lakes, with the exception of Lake Constance. In a 2019 and 2020 Lake Constance field campaign, we collected samples from a distinct red-pigmented biomass maximum below the chlorophyll-a maximum, which was determined using fluorescence probe measurements at depths between 18 and 20 m. Here, we report the characterization of these deep water red pigment maxima (DRM) as cyanobacterial blooms. Using 16S rRNA gene-amplicon sequencing, we found evidence that the blooms were, indeed, contributed by Planktothrix spp., although phycoerythrin-rich Synechococcus taxa constituted most of the biomass (>96% relative read abundance) of the cyanobacterial DRM community. Through UPLC-MS/MS, we also detected toxic microcystins (MCs) in the DRM in the individual sampling days at concentrations of ≤1.5 ng/L. Subsequently, we reevaluated the fluorescence probe measurements collected over the past decade and found that, in the summer, DRM have been present in Lake Constance, at least since 2009. Our study highlights the need for a continuous monitoring program also targeting the cyanobacterial DRM in Lake Constance, and for future studies on the competition of the different cyanobacterial taxa. Future studies will address the potential community composition changes in response to the climate change driven physiochemical and biological parameters of the lake.
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Affiliation(s)
- Corentin Fournier
- Microbial Ecology and Limnic Microbiology, University of Konstanz, 78457 Konstanz, Germany;
| | - Eva Riehle
- Human and Environmental Toxicology, University of Konstanz, 78457 Konstanz, Germany;
| | - Daniel R. Dietrich
- Human and Environmental Toxicology, University of Konstanz, 78457 Konstanz, Germany;
- Correspondence: (D.R.D.); (D.S.)
| | - David Schleheck
- Microbial Ecology and Limnic Microbiology, University of Konstanz, 78457 Konstanz, Germany;
- Limnological Institute, University of Konstanz, 78457 Konstanz, Germany
- Correspondence: (D.R.D.); (D.S.)
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16
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Enaigbe AA, Imade OS. Validation of the shelf life of NAFDAC-certified sachet-packed drinking water brands vended in Nigeria. Lett Appl Microbiol 2021; 73:634-645. [PMID: 34378208 DOI: 10.1111/lam.13551] [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: 11/26/2020] [Revised: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
This study was performed to validate the shelf life of commercial sachet-packed drinking water produced in the Benin City metropolis, Edo State, Nigeria. Seven brands of sachet-packed water that were freshly produced by manufacturers were collected from respective factories and subjected to standard physicochemical and microbial tests. The colour of all water brands (0·0-5·6 HU) was within the limits recommended by the World Health Organization (WHO) (≤15 HU) while the temperature (26·9-28·4°C) was above the limits recommended by WHO (≤25·0°C). The pH reported in brands 1 and 6 at week 8 of storage was below WHO recommended limits (6·5-9·5). At week 8 of storage, brands 1 and 6 had HPC (3·97-4·70 log10 CFU per ml) that were above WHO/National Agency for Food and Drug Administration and Control (NAFDAC) recommended limits (≤2 log10 CFU per ml) while TCC (<1 MPN 100 ml-1 ) in all brands were within recommended limits (≤10 MPN 100 ml-1 ). No thermo-tolerant Coliforms and Cryptosporidium were present in all brands; though, Streptococcus faecalis was detected in brand 6. Based on WHO/NAFDAC specifications for the examined parameters, brands 1 and 6 were inferred to not comply with the recommended shelf life of 2 months (approximately 8 weeks). Hence, there is a need for strict compliance to NAFDAC-specified Good Manufacturing Practice by these processing factories to prevent probable adverse health effects.
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Affiliation(s)
- A A Enaigbe
- Department of Biological Sciences, College of Natural and Applied Sciences, Igbinedion University, Okada, Nigeria
| | - O S Imade
- Department of Biological Sciences, College of Natural and Applied Sciences, Igbinedion University, Okada, Nigeria
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17
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De Vitis E, Ricci S, Nieddu F, Moriondo M, Cortimiglia M, Casini A, Lodi L, Indolfi G, Azzari C. Real-time polymerase chain reaction on filter paper spotted samples: a gateway to molecular diagnosis of invasive bacterial diseases for rural areas in low-income countries. Trans R Soc Trop Med Hyg 2021; 116:233-241. [PMID: 34328186 DOI: 10.1093/trstmh/trab107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/25/2020] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacterial culture is the gold standard for the diagnosis of invasive bacterial diseases (IBDs) but molecular methods are more specific and sensitive. Fresh liquid samples (FLSs) show patent limitations for shipping and storage. We aimed to evaluate the sensitivity and specificity of real-time polymerase chain reaction (PCR) performed on dried sample spots (DSSs) obtained from different biological fluids compared with real-time PCR or culture performed on FLSs. METHODS FLSs positive for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Escherichia coli, Streptococcus pyogenes, Staphylococcus aureus, Bordetella pertussis and/or Pseudomonas aeruginosa were spotted on filter paper. Real-time PCR was performed on both FLSs and DSSs and results were compared. The stability of the DSS results over time was evaluated. RESULTS Real-time PCR performed on 114 DSSs showed a specificity of 99.1% and a sensitivity of 91.2% for IBD diagnosis. A positive correlation was found between FLS cycle threshold (Ct) and DSS Ct (r=0.84; r2=0.71) with the Pearson statistical test and Bland-Altman analysis showing that 95% of the specimens were within agreeable limits. Although we observed a trend towards signal reduction over time in the DSSs, there was no statistical evidence of an increase in Ct values. Real-time PCR on DSSs was 2.2 times more sensitive than culture. CONCLUSIONS Real-time PCR applied to DSSs may be a useful approach in different situations, such as IBD diagnosis, both for rural areas of low-income countries and family practitioners in various settings.
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Affiliation(s)
- Elisa De Vitis
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Silvia Ricci
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Francesco Nieddu
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Maria Moriondo
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Martina Cortimiglia
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Arianna Casini
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Lorenzo Lodi
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Giuseppe Indolfi
- Department of Paediatrics, Meyer Children's University Hospital, Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
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18
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Desiderio TM, Stacy NI, Ossiboff RJ, Iredale M, Archer LL, Alexander AB, Heard DJ, Crevasse SE, Craft WF, Fredholm DVE, Donnelly KA, Rosenberg JF, Childress AL, Russell K, Wellehan JFX. Identification of a novel mortality-associated Helicobacter species in gopher tortoises (Gopherus polyphemus), qPCR test development and validation, and correlation with mortality in a wildlife rehabilitation population. Vet Microbiol 2021; 259:109136. [PMID: 34214906 DOI: 10.1016/j.vetmic.2021.109136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/25/2021] [Indexed: 11/27/2022]
Abstract
The genus Helicobacter includes spiral-shaped bacteria in the phylum Proteobacteria, class Epsilonproteobacteria, order Campylobacteriales, that have been associated with disease in animals, including reptiles. Three wild gopher tortoise (Gopherus polyphemus) index cases presented between 2012 and 2019 with nasal discharge, lethargy, and weight loss. Cytological examination of nasal discharge from all 3 tortoises identified marked heterophilic and mild histiocytic rhinitis with abundant extracellular and phagocytized spiral shaped bacteria that stained positive with Warthin-Starry stain. Polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene revealed this to be a novel Helicobacter species. Two tortoises died despite treatment attempts, and the third was moribund and was euthanized. Histological examination of the nasal mucosa (n = 3) showed granulocytic to lymphocytic rhinitis with variable mucosal hyperplasia, erosion, and ulceration; Warthin-Starry staining highlighted the presence of spiral bacteria in the untreated tortoise. Genus-specific primers were designed, and the gyrA and groEL genes were amplified by PCR and sequenced. Phylogenetic analysis shows that this organism and other previously characterized Helicobacter from tortoises form a clade. Development and cross-validation of two qPCR diagnostic assays for the gyrA and groEL genes showed significant correlation of the results of two assays (P < 0.0001). These assays were used to survey nasal wash samples from 31 rehabilitating gopher tortoises. Mortality of tortoises significantly correlated with higher Helicobacter loads detected by qPCR (P = 0.028). Appropriate quarantine protocols for tortoises during rehabilitation should consider this organism. Upper respiratory disease in tortoises may involve complex microbial ecology; factors beyond Mycoplasmopsis (Mycoplasma) agassizii should be taken into account.
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Affiliation(s)
- Tasha M Desiderio
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Nicole I Stacy
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Robert J Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Marley Iredale
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Linda L Archer
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Amy B Alexander
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Darryl J Heard
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah E Crevasse
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - William F Craft
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Daniel V E Fredholm
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Kyle A Donnelly
- Brevard Zoo and Sea Turtle Healing Center, Melbourne, FL, 32940, USA
| | - Justin F Rosenberg
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - April L Childress
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Kathy Russell
- Santa Fe College Teaching Zoo, Gainesville, FL, 32606, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610, USA.
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19
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Conley KJ, Seimon TA, Popescu IS, Wellehan JFX, Fox JG, Shen Z, Haakonsson J, Seimon A, Brown AT, King V, Burton F, Calle PP. Systemic Helicobacter infection and associated mortalities in endangered Grand Cayman blue iguanas (Cyclura lewisi) and introduced green iguanas (Iguana iguana). PLoS One 2021; 16:e0247010. [PMID: 33606766 PMCID: PMC7894872 DOI: 10.1371/journal.pone.0247010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/30/2021] [Indexed: 12/20/2022] Open
Abstract
The Blue Iguana Recovery Programme maintains a captive breeding and head-starting program for endangered Grand Cayman blue iguanas (Cyclura lewisi) on Grand Cayman, Cayman Islands. In May 2015, program staff encountered two lethargic wild Grand Cayman blue iguanas within the Queen Elizabeth II Botanic Park (QEIIBP). Spiral-shaped bacteria were identified on peripheral blood smears from both animals, which molecular diagnostics identified as a novel Helicobacter species (provisionary name Helicobacter sp. GCBI1). Between March 2015 and February 2017, 11 Grand Cayman blue iguanas were identified with the infection. Two of these were found dead and nine were treated; five of the nine treated animals survived the initial infection. Phylogenetic analysis of the 16S rRNA gene suggests Helicobacter sp. GCBI1 is most closely related to Helicobacter spp. in chelonians. We developed a Taqman qPCR assay specific for Helicobacter sp. GCBI1 to screen tissue and/or blood samples from clinical cases, fecal and cloacal samples from clinically healthy Grand Cayman blue iguanas, including previously infected and recovered iguanas, and iguanas housed adjacent to clinical cases. Fecal and/or cloacal swab samples were all negative, suggesting that Grand Cayman blue iguanas do not asymptomatically carry this organism nor shed this pathogen per cloaca post infection. Retrospective analysis of a 2014 mortality event affecting green iguanas (Iguana iguana) from a separate Grand Cayman location identified Helicobacter sp. GCBI1 in two of three cases. The source of infection and mode of transmission are yet to be confirmed. Analysis of rainfall data reveal that all infections occurred during a multi-year dry period, and most occurred shortly after the first rains at the end of seasonal drought. Additionally, further screening has identified Helicobacter sp. GCBI1 from choanal swabs of clinically normal green iguanas in the QEIIBP, suggesting they could be asymptomatic carriers and a potential source of the pathogen.
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Affiliation(s)
- Kenneth J. Conley
- Wildlife Conservation Society, Zoological Health Program, Bronx, New York, United States of America
| | - Tracie A. Seimon
- Wildlife Conservation Society, Zoological Health Program, Bronx, New York, United States of America
| | | | - James F. X. Wellehan
- Department of Comparative, Diagnostic & Population Medicine, University of Florida, Gainesville, Florida, United States of America
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jane Haakonsson
- Department of Environment, Cayman Islands Government, Grand Cayman, Cayman Islands
| | - Anton Seimon
- Center for Environmental Policy, Bard College, Annandale-on-Hudson, New York, United States of America
| | - Ania Tomaszewicz Brown
- Wildlife Conservation Society, Zoological Health Program, Bronx, New York, United States of America
| | - Veronica King
- St. Matthew’s University, School of Veterinary Medicine, Grand Cayman, Cayman Islands
| | - Fred Burton
- Department of Environment, Cayman Islands Government, Grand Cayman, Cayman Islands
| | - Paul P. Calle
- Wildlife Conservation Society, Zoological Health Program, Bronx, New York, United States of America
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20
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Ursenbach A, Schramm F, Séverac F, Hansmann Y, Lefebvre N, Ruch Y, Argemi X. Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study. BMC Infect Dis 2021; 21:190. [PMID: 33602178 PMCID: PMC7890971 DOI: 10.1186/s12879-021-05892-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05892-4.
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Affiliation(s)
- Axel Ursenbach
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France.
| | - Frédéric Schramm
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France
| | - François Séverac
- Service de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yves Hansmann
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nicolas Lefebvre
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvon Ruch
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xavier Argemi
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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21
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Tillis SB, Iredale ME, Childress AL, Graham EA, Wellehan JFX, Isaza R, Ossiboff RJ. Oral, Cloacal, and Hemipenal Actinomycosis in Captive Ball Pythons (Python regius). Front Vet Sci 2021; 7:594600. [PMID: 33490131 PMCID: PMC7820239 DOI: 10.3389/fvets.2020.594600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022] Open
Abstract
Ball pythons (Python regius) are one of the most commonly kept and bred reptiles in captivity. In a large ball python breeding colony, a unique syndrome characterized by granulomatous inflammation of the cloaca and hemipenes (phalli) was observed in 140 of 481 (29.1%) breeding males, but only one of 1,446 breeding females. Lesions were absent in virgin males (n = 201) and virgin females (n = 293). On postmortem examination (n = 13, 12 males, 1 female), numerous well-defined mucosal and submucosal granulomas were present in the hemipenes (males) and cloaca (males and female). Extension into the coelomic cavity and liver was noted in a subset of these animals. An additional small subset of breeder animals (6/2027; 0.3%) presented with oral and mandibular swellings. Postmortem examination (n = 4, all female) showed oral lesions histologically indistinguishable from the cloacal/hemipenal lesions. Aerobic bacterial culture of a hepatic granuloma of one snake resulted in the isolation of filamentous, Gram-positive bacilli; amplification, and sequencing of the 16S rRNA gene and subsequent phylogenetic analysis of the isolate identified the bacterium as a novel species of Actinomyces. Screening of cloacal and oral granulomas using a specific, heminested 16S rRNA PCR assay confirmed the presence of the agent in all 17 snakes, as well as in cloacal swabs taken at the time of necropsy in 11/13 snakes. The Actinomyces sp. was also identified by PCR of cloacal swabs of unaffected snakes (n = 94) from the affected colony and two unrelated, grossly unaffected breeding colonies. In the affected colony, 65.5% of breeding animals (n = 23) but only 11.9% of virgin animals (n = 42) tested PCR positive, with breeding status being a significant predictor of bacterium presence (P < 0.00001). This study characterizes a granulomatous mucosal disease syndrome of breeding male ball pythons associated with a novel Actinomyces. In stark contrast to male snakes, the presence of the bacterium in both breeding and virgin females was very rarely associated with clinical disease. Though additional studies are necessary, these data suggest a role for the novel bacterium in the disease process, a predilection for clinical disease in male snakes, and the potential for sexual transmission of the disease.
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Affiliation(s)
- Steven B Tillis
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Marley E Iredale
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - April L Childress
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Erin A Graham
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Ramiro Isaza
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Robert J Ossiboff
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
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22
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Raza MS, Das BK, Goyal V, Lodha R, Chaudhry R, Sood S, Sreenivas V, Nair D, Mohapatra S, Gautam H, Kapil A. IMPACT OF MOLECULAR METHOD FOR THE DIAGNOSIS OF ACUTE BACTERIAL MENINGITIS IN A TERTIARY HEALTH CARE CENTRE IN NORTH INDIA. INTERNATIONAL JOURNAL OF MEDICINE AND MEDICAL RESEARCH 2020. [DOI: 10.11603/ijmmr.2413-6077.2020.1.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background. Acute bacterial meningitis is one of the significant infectious diseases that add an immense burden to the health system. Proper management of meningitis is an invincible need to overcome the severe consequences. Objectives. The aim of the study is detection of the etiological agents of acute bacterial meningitis by PCR. Methods. Total 267 CSF samples collected from suspected bacterial meningitis cases were processed for the detection of S. pneumoniae, H. influenzae, N. meningitidis, E. coli and Group B streptococci by conventional and molecular diagnosis method. CSF was inoculated on Blood, chocolate and MacConkey agar plates and incubated at 37 °C for 24-48 hrs. Bacteria grown were identified by Matrix assisted laser desorption/ionization time of flight (MALDI-TOF). Multiplex PCR of the enlisted bacteria was performed using DNA extracted from CSF by DNA extraction kit (Qiagen, USA). Results. 5 (1.87%) out of the total 267 CSF samples were culture positive (3 S. pneumoniae and 2 E. coli) and 28 (10.49%) had detectable DNA by conventional PCR. Out of these 28 samples, 20 (71.43%) were S. pneumoniae and 8 (28.57%) were E. coli. 15 (53.57%) out of total S. pneumoniae were present in children below 5 years of age. Similarly, E. coli was predominant in neonates. Sensitivity and specificity of the PCR was 100% and 95-98% respectively. Conclusions. Streptococcus pneumoniae is the commonest cause of community acquired bacterial meningitis in children below five years of age. Hence, for the promising outcome, PCR should be implemented for the diagnosis of acute bacterial meningitis.
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23
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Kerkhoff AD, Rutishauser RL, Miller S, Babik JM. Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study. Clin Infect Dis 2020; 71:1554-1557. [PMID: 31907545 PMCID: PMC7486847 DOI: 10.1093/cid/ciz1245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/02/2020] [Indexed: 12/20/2022] Open
Abstract
We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.
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Affiliation(s)
- Andrew D Kerkhoff
- Division of HIV, Infectious Diseases, and Global Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, Department of Medicine, University of California, San Francisco, California, USA
| | - Rachel L Rutishauser
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California, USA
| | - Jennifer M Babik
- Division of Infectious Diseases, Department of Medicine, University of California, San Francisco, California, USA
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24
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Men X, Zhao G, Zhao W, Zhang J, Yang Y, Chen C. Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2427-2438. [PMID: 33042356 PMCID: PMC7539889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Antimicrobial therapy necessitates fast and accurate detection of pathogens in purulent meningitis (PM) diagnosis. Although considered a gold standard, the traditional bacterial detection and identification methods based on routine bacterial culture are time-consuming and show low sensitivity and specificity. In order to reduce PM-related deaths and improve the treatment efficiency, we employed trace DNA extraction technology and combined it with Next-Generation Sequencing technology for bacteria identification. We extracted DNA from 31 cerebrospinal fluid (CSF) samples from people with PM. The samples were collected by lumbar puncture at Xi'an Children Hospital under a stringent protocol. Ion PGMTM System Next-Generation Sequencing was used to screen for pathogens in the CSF samples based on their 16S ribosomal RNA (rRNA) genes. Of the 31 CSF samples, 29 were culture negative. Streptococcus was detected in 2 samples by culture-based methods. The species identified by Next-Generation Sequencing showed a diverse bacterial population that included Streptococcus (22.6%), Escherichia (15.9%), Peptostreptococcus (10.7%), Pseudomonas (10.5%), Rothia (8.8%), Acinetobacter (4.9%), Prevotella (4.1%), Bacillus (3.3%), Neisseria (2.5%), Catonella (2.4%), Acitinomyces (2.0%), and Citrobacter (2.0%). Clustering analysis revealed three major bacterial groups, namely Streptococcus, Escherichia and Acinetobacter, each group with a different proportion of bacterial species. The results indicated that PM may result from infections by multiple bacterial species as opposed to a single species, with infectivity determined by abundance of the dominant species. Furthermore, Next-Generation Sequencing allowed a sensitive and specific etiological basis for identification of pathogens not only in the cerebrospinal fluid specimens, but also in other clinical samples.
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Affiliation(s)
- Xin Men
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
- Microbiology Institute of ShaanxiXi’an, Shaanxi, P. R. China
| | - Guige Zhao
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
| | - Wei Zhao
- Lifegen Co. Ltd.Xi’an, Shaanxi, P. R. China
| | | | - Yuan Yang
- Lifegen Co. Ltd.Xi’an, Shaanxi, P. R. China
| | - Chao Chen
- College of Life Science, Northwest University229 North Taibai Road, Xi’an 710069, Shaanxi, P. R. China
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25
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Molecular Detection and Identification of Bacteria in Urine Samples of Asymptomatic and Symptomatic Pregnant Women by 16S rRNA Gene Sequencing. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.101136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives: The purpose of this study was to identify bacteria in urine samples of pregnant women of asymptomatic and symptomatic women by 16S rRNA gene sequencing. This study aims to identify different strains of microbes causing urinary tract infection (UTI). Methods: In the semi-quantitative culture technique, bacterial isolates such as Escherichia coli, Klebsiella, Pseudomonas, Staphylococcus, Coagulase-negative Staphylococcus, and Proteus were subjected to 16S rRNA gene sequencing followed by BLAST analysis and phylogenetic tree formation. The 16S rRNA gene sequencing was carried out to identify the specific strains of bacteria causing UTI. Results: According to the BLAST analysis, sample 1 revealed a 100% similarity to E. coli strain U5/41. Likewise, samples 2, 3, 4, 5 and 6 exhibited a 100% similarity to Klebsiella aerogenes strain F26, Pseudomonas entomophila strain 2014, Staphylococcus aureus strain NCTC13616, Staphylococcus saprophyticus strain FDAARGOS_355, Proteus mirabilis strain NCTC 11938, respectively. Conclusions: Six bacterial isolates were analyzed by 16S RNA gene sequencing followed by the construction of a phylogenetic tree construction up to the species level. This method was a valuable tool for cost-effective and accurate diagnosis of an array of uropathogens in both asymptomatic and symptomatic pregnant women.
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26
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Yaw TJ, O'Neil P, Gary JM, Ali IK, Cowart JR, Wallace RS, Estep JS. Primary amebic meningoencephalomyelitis caused by Naegleria fowleri in a south-central black rhinoceros ( Diceros bicornis minor). J Am Vet Med Assoc 2020; 255:219-223. [PMID: 31260399 DOI: 10.2460/javma.255.2.219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
CASE DESCRIPTION A 20-year-old female south-central black rhinoceros (Diceros bicornis minor) was evaluated because of an acute onset of CNS deficits. CLINICAL FINDINGS The rhinoceros had no history of illness. Clinical signs included acute lethargy, ataxia, and decreased appetite. Hematologic abnormalities included leukocytosis with neutrophilia and a profound left shift. Results of serum biochemical analysis revealed hypophosphatemia but no other abnormalities. Results of a quantitative PCR assay for West Nile virus and an assay for anti-Neosporum caninum antibodies in serum were negative; the patient was seropositive for multiple Leptospira serovars. TREATMENT AND OUTCOME Antimicrobials and anti-inflammatory agents were administered, but the condition of the rhinoceros worsened overnight; despite treatment with additional anti-inflammatory and antimicrobial agents, IV fluids, and thiamine, it became obtunded and died of respiratory arrest ≤ 24 hours later. Necropsy revealed severe, diffuse, suppurative, and histiocytic meningo-encephalomyelitis involving the cerebrum, cerebellum, and spinal cord. Amebic trophozoites were observed on histologic examination of affected tissue. Infection with Naegleria fowleri was confirmed by results of immuno-histochemical analysis and a multiplex real-time PCR assay. CLINICAL RELEVANCE Findings suggested that south-central black rhinoceros are susceptible to the free-living ameba N fowleri. Ameba-induced meningoencephalomyelitis should be considered as a differential diagnosis for rhinoceros that have an acute onset of neurologic signs. Diagnosis of N fowleri infection in an animal has a profound public health impact because of potential human exposure from the environment and the high fatality rate in people with N fowleri infection.
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27
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Al-Joufi FA, Aljarallah KM, Hagras SA, Al Hosiny IM, Salem-Bekhit MM, Youssof AME, Shakeel F. Microbial spectrum, antibiotic susceptibility profile, and biofilm formation of diabetic foot infections (2014-18): a retrospective multicenter analysis. 3 Biotech 2020; 10:325. [PMID: 32656058 DOI: 10.1007/s13205-020-02318-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
This study identifies the risk factors, microbiological properties, antimicrobial susceptibility patterns, mortality, and clinical complications associated with organisms causing diabetic foot infections (DFIs) with or without antibiotic treatment using data from a retrospective multicenter surveillance. Specimens collected from different hospitals were cultured and the extended-spectrum β-lactamase (ESBL) excretion was estimated. The antibacterial susceptibility pattern and biofilm formation were completed along with the recommended standard methods. Overall, 792 diabetic foot patients (DFPs) were enrolled and a total of 1803 causative organisms were isolated. Polymicrobial infection was identified in 48.5% of the patients. The isolated Gram-positive pathogens (46.7%) were higher than Gram-negative (38.6%) or anaerobes (7.9%). The predominant pathogens were S. aureus (22.2%), methicillin-resistant S. aureus (7.7%), Enterococcus spp. (12.8%), Pseudomonas aeruginosa (9.4%), E. coli (7.9%), Klebsiella spp. (7.5%), Proteus mirabilis (8.9%), coagulase negative staphylococci (CoNS) (6.6%), anaerobic organisms (5.9%), and fungi (2.3%). Vancomycin and clindamycin exhibited no activity against Gram-positive bacteria. However, meropenem and imipenem displayed high activity against the Gram-negative isolates. Out of the 765 tested strains, 251 showed moderate (15.8%) to high (34%) level biofilm-producing phenotype. DFIs were widespread among the diabetic patients with different microbial etiology and the major organisms were aerobic organisms. Our findings may provide an insight into the development of appropriate therapeutic strategies for the management of DFIs.
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Affiliation(s)
| | - Khalid M Aljarallah
- College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia
- College of Applied Sciences, Almaarefa University, Riyadh, Saudi Arabia
| | - Soheir A Hagras
- Inaya Medical Colleges, Riyadh, Saudi Arabia
- NCRRT, EAEA, Cairo, Egypt
| | - Ibrahim M Al Hosiny
- Microbiology and Immunology Department, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Mounir M Salem-Bekhit
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451 Saudi Arabia
| | - Abdullah M E Youssof
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451 Saudi Arabia
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451 Saudi Arabia
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28
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Leskinen S, Flowers X, Thoene K, Uhlemann AC, Goldman JE, Hickman RA. Meningomyeloencephalitis secondary to Mycobacterium haemophilum infection in AIDS. Acta Neuropathol Commun 2020; 8:73. [PMID: 32430060 PMCID: PMC7236527 DOI: 10.1186/s40478-020-00937-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/22/2020] [Indexed: 11/29/2022] Open
Abstract
Infections by opportunistic non-tuberculous mycobacteria (NTM) are rising in global incidence. One emerging, slowly growing NTM is Mycobacterium haemophilum, which can cause skin, lung, bone, and soft tissue infections in immunocompromised patients as well as lymphadenitis in immunocompetent individuals. Detection of this microorganism is difficult using conventional culture-based methods and few reports have documented involvement of this pathogen within the central nervous system (CNS). We describe the neuropathologic autopsy findings of a 39-year-old man with AIDS who died secondary to M. haemophilum CNS infection. He initially presented with repeated bouts of pyrexia, nausea and vomiting, and altered mental status that required numerous hospitalizations. CSF infectious workups were consistently negative. His most recent admission identified hyperintensities within the brainstem by MRI and despite antibiotic therapies for suspected CNS infection, he died. Autopsy revealed a swollen brain with marked widening of the brainstem. Microscopic examination of the brain and spinal cord showed focal lymphohistiocytic infiltrates, gliosis and neuronal loss that were associated with acid-fast bacilli (AFB). The brainstem was the most severely damaged and AFB were found to congregate along arterial territories lending support to the notion of hematogenous spread as a mechanism for the organisms’ dissemination. 16S rRNA sequencing on formalin-fixed paraffin-embedded tissue enabled post-mortem identification of M. haemophilum. This sequencing methodology may permit diagnosis on CSF intra-vitam.
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29
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Okafor-Elenwo EJ, Imade OS. Ready-to-eat vegetable salads served in Nigerian restaurants: a potential source of multidrug-resistant bacteria. J Appl Microbiol 2020; 129:1402-1409. [PMID: 32374900 DOI: 10.1111/jam.14693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 11/28/2022]
Abstract
AIM Public health promotion of fruit and vegetables as healthier sources of nutrition in Nigeria has led to an increase in consumption of fruit and vegetables, particularly in the form of ready-to-eat (RTE) salads. However, the continual association of drug-resistant bacteria with fruit and vegetables creates an additional challenge for consumer safety. Hence this study was carried out to determine the prevalence of multidrug-resistant bacteria (MRB) in, and characterization of MRB isolated from, RTE salads. METHODS AND RESULTS RTE vegetable salad samples were randomly selected for bacterial analysis with Wei's Urn iterative randomization technique and a One Way Analysis of Variance performed with Kruskal-Wallis test. Total viable bacteria count (TVC) was performed with pour-plate technique. Bacterial colonies from Petri plates were tested for multidrug resistance with Kirby Bauer disc diffusion test and prevalence/counts of MRB, as well as multiple antibiotic resistance indices (MAR), was/were subsequently deduced. Mean prevalence of MRB in all RTE salad samples was estimated at 54·38% while mean counts of MRB were estimated at 6·83 ± 6·42 log10 CFU per g. Prevalence of bacterial resistance to all antibiotics tested ranged from 5·92 to 100·00%. Mean MAR obtained for all RTE salad samples was estimated at 0·51 (recommended limit = 0·20) indicating that RTE salads were a potential source of MRB, with significant health risk. MRB isolated from RTE salads included Proteus vulgaris strain ATU 243, Bacillus thuringiensis strain AND 236, Citrobacter freundii strain ABC 2 and Serratia marcescens strain ADJ 212. CONCLUSION This study showed that MRB constitute a significant proportion of the bacterial community present in RTE salads served in Nigerian restaurants. SIGNIFICANCE AND IMPACT OF THE STUDY Our study provided empirical evidence which showed that RTE salads served in Nigerian restaurants were a potential source of MRB, with significant health risk.
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Affiliation(s)
- E J Okafor-Elenwo
- Department of Biological Sciences, College of Natural and Applied Sciences, Igbinedion University Okada, Edo State, Nigeria
| | - O S Imade
- Department of Biological Sciences, College of Natural and Applied Sciences, Igbinedion University Okada, Edo State, Nigeria
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30
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From 1990 to 2020. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2020. [DOI: 10.1097/ipc.0000000000000850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Purwanto DS, Loho T, Tafroji W, Mangunatmadja I, Immanuel S, Timan IS, Yusra Y, Safari D. Isolation and identification of Streptococcus pneumoniae serotype 6B from a patient with bacterial meningitis infection in Jakarta, Indonesia. Access Microbiol 2020; 2:acmi000123. [PMID: 32974581 PMCID: PMC7494185 DOI: 10.1099/acmi.0.000123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/03/2020] [Indexed: 11/20/2022] Open
Abstract
CNS infection is a life-threatening condition in developing countries and Streptococcus pneumoniae has been reported as the most common cause of bacterial meningitis; however, there is limited data on pneumococcal meningitis in Indonesia. This cross-sectional study aimed to isolate and identity S. pneumoniae strains from cerebrospinal fluid (CSF) specimens collected as part of routine testing from patients with clinically diagnosed central nervous system infection at a national referral hospital in Jakarta, Indonesia in 2017. S. pneumoniae isolation and identification were performed using conventional culture and molecular tools. Antibiotic susceptibility patterns were monitored through minimum inhibitory concentration testing. From 147 CSF specimens, one S. pneumoniae strain was identified from a patient with bacterial meningitis symptoms. The isolate was serotype 6B (ST5661) and susceptible to 18 antimicrobial agents tested, including penicillin, tetracycline, and the macrolide group. Our data provide insights into the epidemiology of invasive pneumococcal disease in Indonesia.
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Affiliation(s)
- Diana Shintawati Purwanto
- Department of Clinical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia.,Department of Biochemistry, Faculty of Medicine Sam Ratulangi University, Manado, Indonesia
| | - Tonny Loho
- Department of Clinical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Wisnu Tafroji
- Molecular Bacteriology Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Irawan Mangunatmadja
- Department of Child Health, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Suzanna Immanuel
- Department of Clinical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Ina Susianti Timan
- Department of Clinical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Yusra Yusra
- Department of Clinical Pathology, Faculty of Medicine Universitas Indonesia/Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Dodi Safari
- Molecular Bacteriology Unit, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
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32
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Flanders AJ, Speer B, Reavill DR, Roberts JF, Childress AL, Atlas A, Wellehan JFX. Development and validation of 2 probe-hybridization quantitative PCR assays for rapid detection of a pathogenic Coxiella species in captive psittacines. J Vet Diagn Invest 2020; 32:423-428. [PMID: 32188352 DOI: 10.1177/1040638720912221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Avian coxiellosis is an emerging cause of morbidity and mortality among captive psittacines, and the utility of a rapid detection test using easily obtained samples is paramount in a clinical setting. New sequences were obtained from 3 genes: groEL, dnaK, and rpoB. We developed probe-hybridization quantitative PCR (qPCR) assays using groEL and dnaK genes. Samples, including splenic aspirates, liver aspirates, whole blood, and choanal, conjunctival, and cloacal swabs, were collected from 4 psittacine species including 3 blue-and-gold macaws (Ara ararauna), 2 scarlet-chested parrots (Neophema splendida), 1 Timneh African grey parrot (Psittacus timneh), and 1 yellow-naped Amazon parrot (Amazona auropalliata). Retrospective review of postmortem findings from 3 of these psittacines included splenomegaly, hepatitis, and/or transmission electron microscopy confirmation consistent with previous reports of avian coxiellosis. There was 100% agreement between these assays and consensus PCR with sequencing. A Wilcoxon rank-sum test found a strong correlation between groEL and dnaK cycle threshold values (p < 0.001), validating these assays for detection of this avian Coxiella sp.
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Affiliation(s)
- Alison J Flanders
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - Brian Speer
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - Drury R Reavill
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - John F Roberts
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - April L Childress
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - Alvin Atlas
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
| | - James F X Wellehan
- University of Florida College of Veterinary Medicine, Gainesville, FL (Flanders, Roberts, Childress, Wellehan).,The Medical Center for Birds, Oakley, CA (Speer).,Zoo/Exotic Pathology Service, Carmichael, CA (Reavill).,College of Veterinary Medicine, Auburn University, Auburn, AL (Roberts).,Riverview Animal Clinic, Birmingham, AL (Atlas)
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33
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Development and validation of a multiplex-PCR based assay for the detection of 18 pathogens in the cerebrospinal fluid of hospitalized children with viral encephalitis. J Virol Methods 2019; 277:113804. [PMID: 31863863 DOI: 10.1016/j.jviromet.2019.113804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND The Applied Biosystems 3500 Genetic Analyzer (ABI3500) allows for automated capillary electrophoresis on multiple targets. So far, the application of this method for detecting cerebrospinal fluid pathogens has hardly been reported. METHODS To assess the performance of multiplex-PCR assay for 18 pathogens detection, 127 CSF samples from hospitalized children with suspected viral encephalitis were prospectively collected from April to November 2018. The Sanger sequencing was applied to verify this assay. RESULTS All of the 18 target pathogens can be identified by multiplex-PCR assay at 104 copies (or CFU/mL) of each virus, bacterium and fungus. In contrast, 10 control microorganisms failed to be amplified. Approximately 68.5 % of the cases tested had positive results, the enterovirus accounted for the majority of the positive cases (63.8 %). Agreement between multiplex-PCR and sequencing was 91.49 %. CONCLUSIONS Our findings suggest that the ABI3500-based multiplex-PCR detection kit could be a valuable diagnostic tool for pathogen detection in CSF of children with suspected viral encephalitis.
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Bernard C, Escalas A, Villeriot N, Agogué H, Hugoni M, Duval C, Carré C, Got P, Sarazin G, Jézéquel D, Leboulanger C, Grossi V, Ader M, Troussellier M. Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). MICROBIAL ECOLOGY 2019; 78:603-617. [PMID: 30729265 PMCID: PMC6744573 DOI: 10.1007/s00248-019-01332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/16/2019] [Indexed: 05/03/2023]
Abstract
Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L-1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.
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Affiliation(s)
- C Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France.
| | - A Escalas
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - N Villeriot
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - H Agogué
- UMR 7266 LIENSs, Université de La Rochelle - CNRS, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - M Hugoni
- UMR 5557 Ecologie Microbienne, Université Lyon 1 - CNRS - INRA, 69220, Villeurbanne Cedex, France
| | - C Duval
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - C Carré
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - P Got
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - G Sarazin
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - D Jézéquel
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - C Leboulanger
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - V Grossi
- Laboratoire de Géologie de Lyon, Université de Lyon - CNRS - UCBL - ENSL, 69220 Villeurbanne, France
| | - M Ader
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - M Troussellier
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Cobiella D, Gram D, Santoro D. Isolation of
Neisseria dumasiana
from a deep bite wound infection in a dog. Vet Dermatol 2019; 30:556-e168. [DOI: 10.1111/vde.12791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Danielle Cobiella
- Department of Small Animal Clinical Sciences College of Veterinary Medicine University of Florida 2015 SW16th Avenue Gainesville FL 32608 USA
| | - Dunbar Gram
- Department of Small Animal Clinical Sciences College of Veterinary Medicine University of Florida 2015 SW16th Avenue Gainesville FL 32608 USA
| | - Domenico Santoro
- Department of Small Animal Clinical Sciences College of Veterinary Medicine University of Florida 2015 SW16th Avenue Gainesville FL 32608 USA
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Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study. Int J Med Microbiol 2019; 309:151338. [PMID: 31444101 DOI: 10.1016/j.ijmm.2019.151338] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/20/2019] [Accepted: 08/10/2019] [Indexed: 12/13/2022] Open
Abstract
Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailored antibiotic treatment. We investigated if the 16S amplicon sequencing performed by MinION, a nanopore sequencer, was capable of rapid pathogen identification in bacterial meningitis. Six retrospective cases of confirmed bacterial meningitis and two prospective cases were included. The initial cerebrospinal fluid (CSF) samples of these patients were used for the experiments. DNA was extracted from the CSF, and PCR was performed on the 16S ribosomal DNA (16S rDNA). Sequencing libraries were prepared using the PCR products, and MinION sequencing was performed for up to 3 h. The reads were aligned to the bacterial database, and the results were compared to the conventional culture studies. Pathogenic bacteria were successfully detected from the CSF by 16S sequencing in all retrospective cases. 16S amplicon sequencing was more sensitive than conventional diagnostic tests and worked properly even in antibiotics-treated samples. MinION sequencing significantly reduced the turnaround time, and even 10 min of sequencing was sufficient for pathogen detection in certain cases. Protocol adjustment could further increase the sensitivity and reduce the turnaround time for MinION sequencing. Finally, the prospective application of MinION 16S sequencing was successful. Nanopore 16S amplicon sequencing is capable of rapid bacterial identification from the CSF of the bacterial meningitis patients. It may have many advantages over conventional diagnostic tests and should therefore be applied in a larger number of patients in the future.
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Kosecka-Strojek M, Sabat AJ, Akkerboom V, Becker K, van Zanten E, Wisselink G, Miedzobrodzki J, Kooistra-Smid AMDM, Friedrich AW. Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region. Front Cell Infect Microbiol 2019; 9:278. [PMID: 31456949 PMCID: PMC6698797 DOI: 10.3389/fcimb.2019.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Evert van Zanten
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Guido Wisselink
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna M D Mirjam Kooistra-Smid
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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38
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Flanders AJ, Rosenberg JF, Bercier M, Leissinger MK, Black LJ, Giglio RF, Craft SLM, Zoll WM, Childress AL, Wellehan JFX. Antemortem Diagnosis of Coxiellosis in a Blue and Gold Macaw ( Ara ararauna). J Avian Med Surg 2019; 31:364-372. [PMID: 29327963 DOI: 10.1647/2016-224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A 15-year-old female blue and gold macaw ( Ara ararauna) was presented for evaluation after being found laterally recumbent, reluctant to move, and lethargic. Results of a complete blood count showed an increased number of immature heterophils with increased cytoplasmic basophilia and degranulation and the presence of a left shift. Radiographs and a computed tomography scan were performed and revealed a markedly enlarged spleen. An ultrasound-guided fine-needle aspirate of the spleen was submitted for cytologic examination and aerobic bacterial culture. While the culture revealed no growth, cytologic examination identified mononuclear phagocytes with cytoplasmic vacuoles containing structures consistent with bacteria. Pan-bacterial 16S rRNA polymerase chain reaction of the splenic sample followed by direct sequencing identified a Coxiella-like agent identical to one previously isolated in the liver of a golden-mantled rosella ( Platycercus eximius). Phylogenetic analysis shows that avian coxiellosis agents and Coxiella burnetii, the agent of Q fever, represent 2 independent events of development of vertebrate pathogenicity in this group of tick endosymbionts. This report suggests diagnostic and treatment directions for coxiellosis in avian patients and indicates where further study is needed.
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39
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Niu H, Zhang W, Wei L, Liu M, Liu H, Zhao C, Zhang P, Liao Q, Liu Y, Yuan Q, Wu S, Kang M, Geng J. Rapid Nanopore Assay for Carbapenem-Resistant Klebsiella pneumoniae. Front Microbiol 2019; 10:1672. [PMID: 31417504 PMCID: PMC6682601 DOI: 10.3389/fmicb.2019.01672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023] Open
Abstract
The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly increasing worldwide in recent decades and poses a challenge for today's clinical practice. Rapid detection of CRKP can avoid inappropriate antimicrobial therapy and save lives. Traditional detection methods for CRKP are extremely time-consuming; PCR and other sequencing methods are too expensive and technologically demanding, making it hard to meet the clinical demands. Nanopore assay has been used for screening biomarkers of diseases recently because of its high sensitivity, real-time detection, and low cost. In this study, we distinguished CRKP from carbapenem-sensitive K. pneumoniae (CSKP) by the detection of increasing amount of extracted 16S ribosomal RNA (16S rRNA) from bacterial culture with antibiotics imipenem, indicating the uninhibited growth of CRKP by the imipenem. Specific signals from single channel recording of 16S rRNA bound with probes by MspA nanopore allowed the ultra-sensitive and fast quantitative detection of 16S rRNA. We proved that only 4 h of CRKP culture time was needed for nanopore assay to distinguish the CRKP and CSKP. The time-cost of the assay is only about 5% of disk diffusion method while reaching the similar accuracy. This new method has the potential application in the fast screening of drug resistance in clinical microorganism samples.
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Affiliation(s)
- Haofu Niu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Weili Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Liangwan Wei
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Meng Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hao Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Peng Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Quanfeng Liao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ya Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qingyue Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Siying Wu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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40
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Yi A, Kim CK, Kimura K, Arakawa Y, Hur M, Yun YM, Moon HW. First Case in Korea of Group B Streptococcus With Reduced Penicillin Susceptibility Harboring Amino Acid Substitutions in Penicillin-Binding Protein 2X. Ann Lab Med 2019; 39:414-416. [PMID: 30809991 PMCID: PMC6400725 DOI: 10.3343/alm.2019.39.4.414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 11/05/2018] [Accepted: 01/04/2019] [Indexed: 01/07/2023] Open
Affiliation(s)
- Ahram Yi
- Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Korea
| | | | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mina Hur
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Yeo Min Yun
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Hee Won Moon
- Department of Laboratory Medicine, Konkuk University School of Medicine, Seoul, Korea.
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41
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Hugoni M, Escalas A, Bernard C, Nicolas S, Jézéquel D, Vazzoler F, Sarazin G, Leboulanger C, Bouvy M, Got P, Ader M, Troussellier M, Agogué H. Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Mol Ecol 2018; 27:4775-4786. [DOI: 10.1111/mec.14901] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Mylène Hugoni
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Arthur Escalas
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Cécile Bernard
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Sébastien Nicolas
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Fanny Vazzoler
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | | | - Marc Bouvy
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Patrice Got
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Magali Ader
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Marc Troussellier
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Hélène Agogué
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
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Guschin VA, Manuilov VA, Makarov VV, Tkachuk AP. The proper structure of a biosafety system as a way of reducing the vulnerability of a society, economy or state in the face of a biogenic threat. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To understand how vulnerable are a society, an economy and a state in the face of a biohazard, one should attempt to identify any potential holes in the national biosafety system, such as the lack of important components or technologies for biological monitoring and the inadequacy of existing analytical methods used to prevent or counteract biogenic threats. In Russia, biological monitoring is quite advanced. However, the agencies that ensure proper functioning of its components lack collaboration and do not form a well-coordinated network. Each of such agencies alone cannot provide comprehensive information on the subject. In the Russian Federation, there are at least 4 state-funded programs that collect epidemiological data and are quite efficient in performing the narrow task of monitoring infections. But because there is no central database where epidemiological data can be channeled and subsequently shared, these agencies do not complete each other. This leaves the Russian society, economy and state vulnerable to biogenic threats. We need an adequately organized, modern, fully functional and effective system for monitoring biohazards that will serve as a basis for the national biosafety system and also a tool for the identification and elimination of its weaknesses.
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Affiliation(s)
- V. A. Guschin
- Laboratory of Population Variability Mechanisms in Pathogenic Microorganisms, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow; Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow
| | - V. A. Manuilov
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
| | - V. V. Makarov
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, Moscow
| | - A. P. Tkachuk
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
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43
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Imade OS, Akinnibosun FI. The Nigerian catfish (Clarias gariepinus) pisciculture systems: reservoirs of multidrug-resistant bacteria. J Appl Microbiol 2018; 125:1552-1568. [PMID: 30066443 DOI: 10.1111/jam.14056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022]
Abstract
AIM Control of operations of catfish farmers still lacks in Nigeria due to the absence of catfish inspection programmes by relevant regulatory agencies. Thus, this study aimed at performing comprehensive surveillance of Nigerian catfish pisciculture systems so as to provide empirical evidence on the extent of contamination with multidrug-resistant bacteria due to potential abuse of standard operational procedures by catfish farmers. METHODS AND RESULTS One-way analysis of variance was performed on pond water and catfish samples which were randomized with the Wei's-Urn randomization modelling technique. Ceftriaxone-selected bacterial colonies isolated from catfish and pond water samples collected from nursery and grow-out pond systems were tested for multidrug resistance. Haemocytotoxigenic and Shiga toxigenic virulence traits in multidrug-resistant colonies, as well as detection of hyper-Ambler class C-(AmpC) beta-lactamase and carbapenemase production, were also performed using phenotypic/molecular methods. Of the 648 ceftriaxone-selected bacterial isolates examined in this study, 515 isolates were found to be multidrug-resistant bacteria, of which 366 isolates were characterized as pathogenic multidrug-resistant bacteria. Both nursery and grow-out ponds had high frequencies of bacterial resistance to ampicillin (86-93%), cotrimoxazole (47-87%) and chloramphenicol (95-100%). However, high frequencies of bacterial resistance to amoxicillin/clavulanic acid (75-83%) were only observed in the grow-out ponds. Also, hyper-AmpC beta-lactamase-producing multidrug-resistant bacteria were only seen in the grow-out ponds. Isolated multidrug-resistant bacteria were confirmed as Enterobacter cloacae, Citrobacter freundii, Bacillus cereus, Pseudomonas aeruginosa, Escherichia coli and Enterococcus faecalis. CONCLUSION The findings in this study corroborate the urgent need for some form of international mediation to urge the Nigerian government and her regulatory agencies to commence monitoring of catfish pisciculture operations since multidrug-resistant bacteria could be transmitted to humans. SIGNIFICANCE AND IMPACT OF THE STUDY Our study provided empirical evidence that revealed the misuse/abuse of antibiotics during pisciculture operations in Nigeria; thus, constituting these pisciculture systems into reservoirs of multidrug-resistant bacteria.
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Affiliation(s)
- O S Imade
- Department of Biological Sciences, College of Natural and Applied Sciences, Igbinedion University, Okada, Edo State, Nigeria.,Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin City, Edo State, Nigeria
| | - F I Akinnibosun
- Department of Microbiology, Faculty of Life Sciences, University of Benin, Benin City, Edo State, Nigeria
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44
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Puyo CA, Peruzzi D, Earhart A, Roller E, Karanikolas M, Kollef MH, Krupnick AS, Kreisel D, Ibrahim M, Gelman AE. Endotracheal tube-induced sore throat pain and inflammation is coupled to the release of mitochondrial DNA. Mol Pain 2018; 13:1744806917731696. [PMID: 28929859 PMCID: PMC5598795 DOI: 10.1177/1744806917731696] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the absence of infection, the pathophysiology of endotracheal tube-induced sore throat pain is unclear. Activated neutrophils release elastase, reactive oxygen species, and inflammatory cytokines known to contribute to neuropathic pain. Sterile tissue injury can cause the release of damage-associated molecular patterns such as mitochondrial DNA that promote neutrophil activation. We hypothesized that endotracheal tube-induced sore throat pain is linked to mitochondrial DNA-mediated neutrophil inflammation. A nonrandomized prospective survey for sore throat pain was conducted in 31 patients who required short-term intubation and had no evidence of upper airway infection. Patterns of neutrophil abundance, activation, and mitochondrial DNA levels were analyzed in tracheal lavage fluid following intubation and prior to extubation. Thirteen of 31 patients reported sore throat pain. Sore throat patients had high neutrophilia with elevated adhesion molecule and TLR9 expression and constitutive reactive oxygen species generation. Tracheal lavage fluid from sore throat patients accumulated mitochondrial DNA and stimulated neutrophils to release mediators associated with pain in a TLR9- and DNAse-dependent fashion. Endotracheal tube-induced sore throat is linked to the release of mitochondrial DNA and can drive TLR9-mediated inflammatory responses by neutrophils reported to cause pain. Mitigating the effects of cell-free mitochondrial DNA may prove beneficial for the prevention of endotracheal tube-mediated sore throat pain.
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Affiliation(s)
- Carlos A Puyo
- 1 Department of Anesthesiology and Critical Care, 12275 Washington University School of Medicine in St. Louis , MO, USA
| | - Daniela Peruzzi
- 2 Department of Surgery, 12275 Washington University School of Medicine in St. Louis , MO, USA.,3 Department of Medical-Surgical Science and Translational Medicine, Sapienza University, Rome, Italy
| | - Alexander Earhart
- 1 Department of Anesthesiology and Critical Care, 12275 Washington University School of Medicine in St. Louis , MO, USA
| | - Evan Roller
- 1 Department of Anesthesiology and Critical Care, 12275 Washington University School of Medicine in St. Louis , MO, USA
| | - Menelaos Karanikolas
- 1 Department of Anesthesiology and Critical Care, 12275 Washington University School of Medicine in St. Louis , MO, USA
| | - Marin H Kollef
- 5 Department of Internal Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Alexander S Krupnick
- 2 Department of Surgery, 12275 Washington University School of Medicine in St. Louis , MO, USA.,4 Department of Surgery, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Daniel Kreisel
- 2 Department of Surgery, 12275 Washington University School of Medicine in St. Louis , MO, USA
| | - Mohsen Ibrahim
- 2 Department of Surgery, 12275 Washington University School of Medicine in St. Louis , MO, USA.,3 Department of Medical-Surgical Science and Translational Medicine, Sapienza University, Rome, Italy
| | - Andrew E Gelman
- 2 Department of Surgery, 12275 Washington University School of Medicine in St. Louis , MO, USA.,3 Department of Medical-Surgical Science and Translational Medicine, Sapienza University, Rome, Italy
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45
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Crossland NA, DiGeronimo PM, Sokolova Y, Childress AL, Wellehan JFX, Nevarez J, Paulsen D. Pneumonia in a Captive Central Bearded Dragon With Concurrent Detection of Helodermatid Adenovirus 2 and a Novel Mycoplasma Species. Vet Pathol 2018; 55:900-904. [DOI: 10.1177/0300985818780451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A 4-year-old captive male central bearded dragon ( Pogona vitticeps) was presented for recurrent episodic dyspnea and anorexia with occasional expulsion of oral mucoid discharge. Despite empirical antimicrobial therapy and supportive care, the animal died and was submitted for autopsy. Defining histologic features included heterophilic and lymphocytic interstitial pneumonia, with occasional amphophilic intranuclear inclusions and prominent type II pneumocyte hyperplasia. Transmission electron microscopy revealed intranuclear 80-nm, nonenveloped, hexagonal viral particles within pneumocytes. Helodermatid adenovirus 2 (HeAdV2) was determined as the etiologic agent through pan-adenoviral consensus polymerase (PCR) chain reaction and sequencing. Nucleic acid from a novel Mycoplasma sp. (provisionally called Mycoplasma pogonae) was identified by pan-generic PCR targeting the mycoplasma 16S ribosomal RNA gene with sequencing and phylogenetic analysis. As bacteria morphologically consistent with Mycoplasma sp. were not observed by special stains and transmission electron microscopy, the detection of M. pogonae nucleic acid is of indeterminate significance; however, M. pogonae and HeAdV2 coinfection may have exacerbated disease.
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Affiliation(s)
- Nicholas A. Crossland
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Peter M. DiGeronimo
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Yulia Sokolova
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - April L. Childress
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | | | - Javier Nevarez
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Daniel Paulsen
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
- Louisiana Animal Disease Diagnostic Laboratory, Louisiana State University, Baton Rouge, LA, USA
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46
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Tetz G, Tetz V. Bacteriophages as New Human Viral Pathogens. Microorganisms 2018; 6:E54. [PMID: 29914145 PMCID: PMC6027513 DOI: 10.3390/microorganisms6020054] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022] Open
Abstract
The pathogenesis of numerous human multifaceted devastating diseases, including a variety of neurodegenerative and autoimmune diseases, is associated with alterations in the gut microbiota; however, the underlying mechanisms are not completely understood. Our recent human metagenome and phagobiota proteome analyses and studies in relevant animal models suggested that bacterial viruses might be implicated in the progression and maintenance of at least some pathologies, including those associated with protein misfolding. Here, for the first time, we propose the concept of bacteriophages as human pathogens. We suggest that bacterial viruses have different ways to directly and indirectly interact with eukaryotic cells and proteins, leading to human diseases. Furthermore, we suggest different causes of bacteriophages infection on the basis of the unique ways of interplay of phages, microbiota, and the human host. This concept opens a discussion of the role of bacteriophages as previously overlooked pathogenic factors and suggests that bacterial viruses have to be further explored as a diagnostic and treatment target for therapeutic intervention.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA.
| | - Victor Tetz
- Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA.
- Tetz Laboratories, 423W 127th Street, New York, NY 10027, USA.
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47
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Gérard E, De Goeyse S, Hugoni M, Agogué H, Richard L, Milesi V, Guyot F, Lecourt L, Borensztajn S, Joseph MB, Leclerc T, Sarazin G, Jézéquel D, Leboulanger C, Ader M. Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean). Front Microbiol 2018; 9:796. [PMID: 29872424 PMCID: PMC5972316 DOI: 10.3389/fmicb.2018.00796] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 04/09/2018] [Indexed: 01/09/2023] Open
Abstract
Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the "Petite Terre" Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are actively growing in the shallow waters of the lake shores. These stromatolites are mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, dolomite, and phyllosilicates. They are morphologically and texturally diverse ranging from tabular covered by a cauliflower-like crust to columnar ones with a smooth surface. High-throughput sequencing of bacterial and archaeal 16S rRNA genes combined with confocal laser scanning microscopy (CLSM) analysis revealed that the microbial composition of the mats associated with the stromatolites was clearly distinct from that of the Arthrospira-dominated lake water. Unicellular-colonial Cyanobacteria belonging to the Xenococcus genus of the Pleurocapsales order were detected in the cauliflower crust mats, whereas filamentous Cyanobacteria belonging to the Leptolyngbya genus were found in the smooth surface mats. Observations using CLSM, scanning electron microscopy (SEM) and Raman spectroscopy indicated that the cauliflower texture consists of laminations of aragonite, magnesium-silicate phase and hydromagnesite. The associated microbial mat, as confirmed by laser microdissection and whole-genome amplification (WGA), is composed of Pleurocapsales coated by abundant filamentous and coccoid Alphaproteobacteria. These phototrophic Alphaproteobacteria promote the precipitation of aragonite in which they become incrusted. In contrast, the Pleurocapsales are not calcifying but instead accumulate silicon and magnesium in their sheaths, which may be responsible for the formation of the Mg-silicate phase found in the cauliflower crust. We therefore propose that Pleurocapsales and Alphaproteobacteria are involved in the formation of two distinct mineral phases present in the cauliflower texture: Mg-silicate and aragonite, respectively. These results point out the role of phototrophic Alphaproteobacteria in the formation of stromatolites, which may open new perspective for the analysis of the fossil record.
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Affiliation(s)
- Emmanuelle Gérard
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Siham De Goeyse
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Mylène Hugoni
- Université Lyon 1, UMR CNRS 5557 / INRA 1418, Ecologie Microbienne, Villeurbanne, France
| | - Hélène Agogué
- UMR 7266 CNRS-Université de la Rochelle, LIttoral ENvironnement Et Sociétés, La Rochelle, France
| | - Laurent Richard
- School of Mining and Geosciences, Nazarbayev University, Astana, Kazakhstan
| | - Vincent Milesi
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - François Guyot
- Museum National d’Histoire Naturelle, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS Sorbonne Universités, Université Pierre et Marie Curie, Institut de Recherche pour le Développement UMR 206, Paris, France
| | - Léna Lecourt
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Stephan Borensztajn
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Béatrice Joseph
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Thomas Leclerc
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Gérard Sarazin
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | - Didier Jézéquel
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
| | | | - Magali Ader
- UMR CNRS 7154 Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, Paris, France
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48
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Michel V, Ulber C, Pöhle D, Köpke B, Engel K, Kaim U, Fawzy A, Funk S, Fornefett J, Baums CG, Eisenberg T. Clinical infection in house rats (Rattus rattus) caused by Streptobacillus notomytis. Antonie van Leeuwenhoek 2018; 111:1955-1966. [PMID: 29671179 DOI: 10.1007/s10482-018-1085-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Rat bite fever is an under-reported, under-diagnosed emerging zoonosis with worldwide distribution. Besides Spirillum minus, Streptobacillus moniliformis is the major causative microorganism although it usually colonises rats without any clinical signs. A group of house rats (Rattus rattus) kept in a zoo exhibition for educational purposes suffered from neurological signs including disorientation, torticollis, stall walking, ataxia and death. Gross pathological and histo-pathological examinations of the investigated rats revealed high-grade otitis interna et media, from which Streptobacillus notomytis was isolated in pure culture or as the predominant microorganism. This case series underlines a previously expressed hypothesis that R. rattus might be naturally colonised with S. notomytis, whereas the traditional rat bite fever organism, S. moniliformis, might be restricted to the Norway rat (Rattus norvegicus). However, the general paucity of Streptobacillus isolates, especially from their respective animal hosts, precludes definitive proof of these host tropisms. This is the first report of S. notomytis detection outside Asia and Australia and the first evidence for its role as a facultative pathogen in house rats.
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Affiliation(s)
- Viktoria Michel
- Naturschutz-Tierpark Görlitz e. V., Zittauer Str. 43, 02826, Görlitz, Germany
| | - Claudia Ulber
- Landesuntersuchungsanstalt für das Gesundheits- und Veterinärwesen Sachsen (LUA), Jägerstr. 8/10, 01099, Dresden, Germany
| | - Dietrich Pöhle
- Landesuntersuchungsanstalt für das Gesundheits- und Veterinärwesen Sachsen (LUA), Jägerstr. 8/10, 01099, Dresden, Germany
| | - Beate Köpke
- Landesuntersuchungsanstalt für das Gesundheits- und Veterinärwesen Sachsen (LUA), Jägerstr. 8/10, 01099, Dresden, Germany
| | - Katharina Engel
- Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60, 35392, Giessen, Germany
| | - Ute Kaim
- Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60, 35392, Giessen, Germany
| | - Ahmad Fawzy
- Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60, 35392, Giessen, Germany.,Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Giza Square, 12211, Egypt.,Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität, Frankfurter Str. 89, 35392, Giessen, Germany
| | - Sophie Funk
- Veterinärmedizinische Fakultät, Zentrum für Infektionsmedizin, Institut für Bakteriologie und Mykologie, Universität Leipzig (IBML), An den Tierkliniken 29, 04103, Leipzig, Germany
| | - Juliane Fornefett
- Veterinärmedizinische Fakultät, Zentrum für Infektionsmedizin, Institut für Bakteriologie und Mykologie, Universität Leipzig (IBML), An den Tierkliniken 29, 04103, Leipzig, Germany
| | - Christoph Georg Baums
- Veterinärmedizinische Fakultät, Zentrum für Infektionsmedizin, Institut für Bakteriologie und Mykologie, Universität Leipzig (IBML), An den Tierkliniken 29, 04103, Leipzig, Germany
| | - Tobias Eisenberg
- Landesbetrieb Hessisches Landeslabor (LHL), Schubertstr. 60, 35392, Giessen, Germany. .,Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität, Frankfurter Str. 89, 35392, Giessen, Germany.
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49
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Boiten KE, Jean-Pierre H, Veloo ACM. Assessing the clinical relevance of Fenollaria massiliensis in human infections, using MALDI-TOF MS. Anaerobe 2018; 54:240-245. [PMID: 29559332 DOI: 10.1016/j.anaerobe.2018.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/09/2022]
Abstract
Within the European Network for the Rapid Identification of Anaerobes (ENRIA) project eight clinical isolates of Fenollaria massiliensis were encountered. In this study a more extensive description of this species is given and the MALDI-TOF MS database is optimized for its identification. F. massiliensis is an anaerobic Gram positive rod with the tendency to decolorize quickly. It is mostly encountered in clinical samples from the groin region. Less common and non-valid species are not represented in the MALDI-TOF MS database. Therefore, F. massiliensis can only be identified by laboratories performing 16S rDNA gene sequencing. The addition of less common and non-valid species to the database will give insight in their clinical relevance.
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Affiliation(s)
- K E Boiten
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôspital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - A C M Veloo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
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50
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Phoon HYP, Hussin H, Hussain BM, Lim SY, Woon JJ, Er YX, Thong KL. Distribution, genetic diversity and antimicrobial resistance of clinically important bacteria from the environment of a tertiary hospital in Malaysia. J Glob Antimicrob Resist 2018. [PMID: 29540306 DOI: 10.1016/j.jgar.2018.02.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES Hospital environments are potential reservoirs of bacteria associated with nosocomial infections. In this study, the distribution of cultivable environmental bacteria of clinical importance from a Malaysian tertiary hospital was determined and their resistotypes and genotypes were investigated. METHODS Swab and fluid samples (n=358) from healthcare workers' hands, frequently touched surfaces, medical equipment, patients' immediate surroundings, ward sinks and toilets, and solutions or fluids of 12 selected wards were collected. Biochemical tests, PCR and 16S rRNA sequencing were used for identification following isolation from CHROMagar™ Orientation medium. Clinically important bacteria such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter spp., Pseudomonas aeruginosa and Enterobacter spp. were further characterised by disc diffusion method and rep-PCR. RESULTS The 24 Gram-negative and 19 Gram-positive bacteria species identified were widely distributed in the hospital environment. Staphylococci were predominant, followed by Bacillus spp. and P. aeruginosa. Frequently touched surfaces, medical equipment, and ward sinks and toilets were the top three sources of bacterial species. Nine S. aureus, four Acinetobacter spp., one K. pneumoniae and one Enterobacter spp. were multidrug-resistant (MDR). The ESKAPE organisms were genetically diverse and widely dispersed across the hospital wards. A MDR MRSA clone was detected in a surgical ward isolation room. CONCLUSION The large variety of cultivable, clinically important bacteria, especially the genetically related MDR S. aureus, K. pneumoniae, Acinetobacter spp. and Enterobacter spp., from various sampling sites indicated that the surfaces and fomites in the hospital were potential exogenous sources of nosocomial infection in the hospital.
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Affiliation(s)
- Hannah Y P Phoon
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Pathology Department, Ampang Hospital, 68000 Ampang, Selangor, Malaysia
| | - Hazilawati Hussin
- Pathology Department, Ampang Hospital, 68000 Ampang, Selangor, Malaysia
| | | | - Shu Yong Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jia Jie Woon
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yi Xian Er
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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