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Bamford C, Blumberg LH, Bosman M, Frean J, Hoek KG, Miles J, Sriruttan C, Vorster I, Oosthuizen MC. Neoehrlichiosis in Symptomatic Immunocompetent Child, South Africa. Emerg Infect Dis 2023; 29:407-410. [PMID: 36692458 PMCID: PMC9881780 DOI: 10.3201/eid2902.221451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We describe a case of neoehrlichiosis in an immunocompetent child with acute febrile illness in South Africa. Neoehrlichiosis was diagnosed by PCR on 16S rDNA from bone marrow aspirate. Phylogenetic analysis indicated an organism closely related to Candidatus Neoehrlichia. Clinicians should be aware of possible ehrlichiosis even in immunocompetent patients.
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Targeted metagenomics using next generation sequencing in laboratory diagnosis of culture negative endophthalmitis. Heliyon 2021; 7:e06780. [PMID: 33997374 PMCID: PMC8099753 DOI: 10.1016/j.heliyon.2021.e06780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022] Open
Abstract
To study the feasibility of 16S rRNA metagenomics using next generation sequencing (NGS) along with broad range PCR assay for 762 bp region of 16S rRNA gene with Sanger's sequencing, in microbial diagnosis of culture negative endophthalmitis. Vitreous fluid from 16 culture negative and one culture positive endophthalmitis patients, admitted to a tertiary care hospital were processed for targeted metagenomics. NGS of 7 variable regions of 16S rRNA gene was done using Ion Torrent Personal Genome Machine (PGM). Sequence data were analyzed using Ion Reporter software using QIIME and BLSATN tools and Greengenes and NCBI–Genbank databases. Bacterial genome sequences were detected in 15 culture negative and culture positive vitreous specimens. The sequence reads varied between 25,245–540,916 with read length between 142bp–228bp and coverage depth was 41.0X and 81.2X. Operational taxonomic unit (OTUs) of multiple bacterial genera and species were detected in 13 culture negative vitreous specimens and OTUs of a single bacterial species were detected in 2 culture negative and 1 culture positive specimens; one negative specimen had no bacterial DNA. Maximum numbers of OTUs detected by NGS for a bacterial species from any vitreous specimen was the one which was detected and identified by Sanger's sequencing in broad range PCR. All the bacteria were belonging to clinically relevant species. Broad range PCR with sequencing failed to identify bacteria from 5 of the 16 (31.25%) culture negative vitreous specimens. Metagenomics could detect and identify bacterial pathogens in 15 of the 16 culture negative vitreous specimen's up to species level. With rapidly decreasing cost, metagenomics has a potential to be used widely in endophthalmitis diagnosis, in which culture negativity is usually high.
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Stephenson T, Lee K, Griffith JE, McLelland DJ, Wilkes A, Bird PS, Trott DJ, Speight KN, Hemmatzadeh F, Woolford L. Pulmonary Actinomycosis in South Australian Koalas ( Phascolarctos cinereus). Vet Pathol 2021; 58:416-422. [PMID: 33461422 DOI: 10.1177/0300985820973459] [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: 11/17/2022]
Abstract
Pneumonia has been reported in both free-ranging and captive koalas and a number of causative agents have been described. Between 2016 and 2019, 16 free-ranging and 1 captive koala (Phascolarctos cinereus) from the Mount Lofty Ranges of South Australia were identified with pyogranulomatous lobar pneumonia, which involved the left caudal lobe in 14/17 (82%) cases. Within lesions, numerous gram-positive or gram-variable, non-acid-fast filamentous bacteria were observed in association with Splendore-Hoeppli phenomenon. Culture yielded growth of anaerobic bacteria, which were unidentifiable by MALDI-TOF-MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) analysis in 5/5 cases. Sequencing of the bacterial 16S rRNA gene identified a novel Actinomyces species in 4 samples, confirming a diagnosis of pulmonary actinomycosis. Concurrent examination of resin lung casts from healthy koalas suggested greater laminar flow of air to the left caudal lung lobe in koalas. Actinomyces spp. have been reported as commensals of the oral microbiome in other species, and an association with similar pulmonary lesions in other species. Considering the predilection for involvement of the left caudal lung lobe, aspiration is suggested as the likely cause in some cases of pulmonary actinomycosis in koalas. Pulmonary actinomycosis has not been previously described in koalas and further work needs to be undertaken in order to classify this organism within the Actinomyces genus.
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Affiliation(s)
| | - Ken Lee
- University of Adelaide, Adelaide, South Australia, Australia
| | | | - David J McLelland
- University of Adelaide, Adelaide, South Australia, Australia.,Adelaide Zoo, ZoosSA, Adelaide, South Australia, Australia
| | - Anthony Wilkes
- University of Adelaide, Adelaide, South Australia, Australia
| | - Philip S Bird
- The University of Queensland, Gatton, Queensland, Australia
| | - Darren J Trott
- University of Adelaide, Adelaide, South Australia, Australia
| | | | | | - Lucy Woolford
- University of Adelaide, Adelaide, South Australia, Australia
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Lee GE, Kim JJ, Kim HS, Sul WJ. Metagenomic analysis of the dust particles collected from the suction tube and the suction funnel of a dermatological laser smoke evacuator system. Lasers Med Sci 2020; 36:1249-1260. [PMID: 33079312 DOI: 10.1007/s10103-020-03165-1] [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: 06/24/2020] [Accepted: 10/15/2020] [Indexed: 10/23/2022]
Abstract
In the last few decades, there has essentially been an explosion in the use of lasers in medicine, especially in the area of cosmetic dermatology. Potentially harmful substances are liberated when tissues are vaporized with laser. This creates numerous risks, including the spread of infectious disease. Smoke evacuators are devices that capture and filter laser plume, thereby maintaining a safe environment for the surgical team and patient. Our aim was to characterize the microbial community structure within the suction tube and funnel of the smoke evacuator system, identify their origin, and evaluate pathogenicity. Dust particles were collected from the instruments with a cotton swab. DNA was extracted from the swabs and the transport media, and sequencing was performed using the Illumina HiSeq Xplatform. Metagenomic analysis was conducted using the Empowering the Development of Genomics Expertise (EDGE) Bioinformatics pipeline and custom Python scripts. The most abundant bacterial species were Micrococcus luteus and Brevibacterium casei in the suction tube, and Dermacoccus sp. Ellin 185 and Janibacter hoylei in the suction funnel. A total of 15 medium- to high-quality metagenome-assembled genomes (MAGs) were constructed where we found 104 antibiotic-resistant genes (ARGs) and 741 virulence factors. Findings indicate that the suction tube and funnel are likely a reservoir of virulence factor genes and ARGs, which can possibly be passed on to other bacteria via horizontal gene transfer. We would like to emphasize the health risk these microorganisms pose and the need to reevaluate the current hygiene standards with regard to the smoke evacuator system.
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Affiliation(s)
- Ga-Eun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea.,Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Hei Sung Kim
- Dr Philip Frost Department of Dermatology and Cutaneous Surgery, Miami Itch Center, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Department of Dermatology, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, 06591, South Korea. .,Department of Biomedicine & Health Sciences, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, South Korea.
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea.
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Mishra D, Satpathy G, Wig N, Fazal F, Ahmed NH, Panda SK. Evaluation of 16S rRNA broad range PCR assay for microbial detection in serum specimens in sepsis patients. J Infect Public Health 2020; 13:998-1002. [PMID: 32061569 DOI: 10.1016/j.jiph.2020.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 12/23/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Early and accurate laboratory diagnosis and appropriate management of infection improves the survival rate in sepsis. In this study we evaluated broad range 16S rRNA and 16 S-23 S intergenic spacer region (ISR) PCR assays followed by nucleotide sequencing directly from patients' serum and automated blood culture for laboratory diagnosis in admitted sepsis patients. METHODS A broad range 16S rRNA PCR and 16 S-23 S ISR PCR assay followed by nucleotide sequencing was used directly from patients' serum in hospital admitted patients in 62 sepsis and 16 suspected blood stream infection (sBSI) patients. Automated blood culture was also used in the same patients. Nucleotide sequences were analyzed against NCBI Genbank database and organisms were identified using CLSI MM18A guidelines. RESULTS Bacterial culture were positive in 10/62 (16.12%) sepsis and 3/16 (18.75%) suspected BSI patients along with 3 detected fungi (2 in sepsis and 1 in suspected BSI group). PCR assay was positive in 36/62 (58.06%) sepsis and 6/16 (37.5%) suspected BSI patients respectively. All but 2 bacteria (both from culture negative patients) detected by PCR assay could be identified from nucleotide sequencing. Survival in sepsis patients was 77%. PCR assay could detect bacteria in 9/14 (64.28%) of sepsis patients with death. CONCLUSION Broad range PCR assay was far superior for early diagnosis of infection. The bacteria which could not be detected by culture and were not commonly reported from this centre, were detected by the broad range PCR assays. Detection of these rare bacteria/fungi had significant clinical correlation with patient's underlying clinical conditions, immune status and prognosis. The tests could provide definitive diagnosis of infection in >58% of sepsis patients, which helped in patient management and better survival.
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Affiliation(s)
- Deepanshi Mishra
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Gita Satpathy
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India; Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Farhan Fazal
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Nishat Hussain Ahmed
- Ocular Microbiology, Dr. R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Subrat Kumar Panda
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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Mishra D, Satpathy G, Chawla R, Venkatesh P, Ahmed NH, Panda SK. Utility of broad-range 16S rRNA PCR assay versus conventional methods for laboratory diagnosis of bacterial endophthalmitis in a tertiary care hospital. Br J Ophthalmol 2018; 103:152-156. [DOI: 10.1136/bjophthalmol-2018-312877] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 11/04/2022]
Abstract
BackgroundEndophthalmitis, a sight-threatening intraocular infection, can be of postsurgical, post-traumatic or endogenous origin. Laboratory diagnosis-based appropriate therapy can be vision-saving. Conventional culture-based laboratory diagnosis takes time and lacks sensitivity. In this study a broad-range PCR assay was assessed against conventional and automated culture methods in vitreous specimens for accurate microbiological diagnosis.AimsTo use broad-range PCR assay targeting 16S ribosomal RNA (rRNA) region of bacteria and to assess its performance vis-à-vis conventional and automated culture methods in the laboratory diagnosis of endophthalmitis.MethodsVitreous specimens from 195 patients with clinically diagnosed endophthalmitis were processed for classical and automated culture methods, antimicrobial sensitivity and broad-range PCR assay targeting 762 bp region of 16S rRNA followed by nucleotide sequencing by Sanger’s method. Causative agents were identified from the nucleotide sequences analysed against the GenBank database, and organisms were identified using the Clinical and Laboratory Standards Institute (CLSI) MM18A guidelines.ResultsBacteria could be detected from 127 (65.13%) of the 195 vitreous specimens by broad-range PCR assay; bacterial isolation was possible from 17 (8.7%) and 60 (30.76%) of these specimens by conventional and automated culture methods, respectively (p<0.0001). PCR assay could detect two uncultured bacterium, and in five cases the bacterial identity could not be determined from NCBI database matching.ConclusionBroad-range PCR assay could provide definitive microbial diagnosis within 24 hours in significantly more patients (p<0.0001). Some rare organisms could be detected, useful in treatment modalities. Automated culture was significantly more sensitive than conventional culture.
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Comparative evaluation of 16S rRNA gene in world-wide strains of Streptococcus iniae and Streptococcus parauberis for early diagnostic marker. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0542-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Moore JE, Huang J, Yu P, Ma C, Moore PJ, Millar BC, Goldsmith CE, Xu J. High diversity of bacterial pathogens and antibiotic resistance in salmonid fish farm pond water as determined by molecular identification employing 16S rDNA PCR, gene sequencing and total antibiotic susceptibility techniques. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 108:281-286. [PMID: 25105488 DOI: 10.1016/j.ecoenv.2014.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 06/03/2023]
Abstract
The aim of this study was to examine the microbiological and related parameters (antibiotic resistance and pathogen identification) of water at two salmonid fish farms in Northern Ireland. Total Bacterial Counts at the Movanagher Fish Farm was 1730 colony forming units (cfu)/ml water (log10 3.24cfu/ml) and 3260cfu/ml (log10 3.51cfu/ml) at the Bushmills Salmon Station. Examination of resulting organisms revealed 10 morphological phenotypes, which were subsequently sequenced to determine their identification. All these organisms were Gram-negative and no Gram-positive organisms were isolated from any water sample. From these phenotypes, eight different genera were identified including Acinetobacter, Aeromonas, Chryseobacterium, Erwinia, Flavobacterium, Pseudomonas and Rheinheimera. One unnamed novel taxon was identified from water at the Movanagher Fish Farm, belonging to the genus Acinetobacter and has been tentatively named Acinetobacter movanagherensis. No other novel taxa were observed. All but one of these environmental organisms (Erwinia) are potential pathogens of fish disease. Total antibiotic resistance was observed to varying degrees in water specimens. The most resistant populations were observed in water taken from the Bushmills Salmon Station inlet, followed by water from the Movanagher Fish Farm. No resistance was observed against tetracycline and there was only one occurrence of resistance against ciprofloxacin. Overall, this study indicates that potential fish pathogens made up the majority of environmental organisms identified, even in the absence of recorded fish disease. There was also relatively high levels of total antibiotic resistance in the bacterial water populations examined, where tetracycline was the only antibiotic with zero resistance. These data indicate that the threat of bacterial disease is relatively close due to the indigenous colonization of farm water and that husbandry standards should be maintained at a high standard to avert bacterial disease outbreaks, rather than relying on the absence of specific pathogens in the immediate farm environment.
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Affiliation(s)
- John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK; School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK; Centre for Infection & Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Health Sciences, Building, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7BL, UK.
| | - Junhua Huang
- Department of Medical Technology, Xi'an Medical College, Xi'an, Shaanxi 710021, China
| | - Pengbo Yu
- Shaanxi Center for Disease Control and Prevention, 3 Jian Dong Street, Xi'an, Shaanxi 710054, China
| | - Chaofeng Ma
- Xi'an Center for Disease Control and Prevention, Xi'an, Shaanxi 710054, China
| | - Peter Ja Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK; Ballymena Academy, Galgorm Road, Ballymena, Co. Antrim, Northern Ireland, BT42 1AJ, UK
| | - Beverley C Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK
| | - Colin E Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK
| | - Jiru Xu
- Department of Pathogenic Biology, Xian Jiatong University, Xi'an, Shaanxi, China
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Septicemia caused by Leifsonia aquatica in a healthy patient after retinal reattachment surgery. J Clin Microbiol 2013; 51:3886-8. [PMID: 23946520 DOI: 10.1128/jcm.01339-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leifsonia aquatica is an aquatic bacterium that is typically found in environmental water habitats. Infections due to L. aquatica are rare and commonly catheter associated in immunocompromised patients. We report the first case of an acute septicemia caused by L. aquatica in a healthy immunocompetent host after cryopexy in the absence of a catheter.
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Jenkins C, Ling CL, Ciesielczuk HL, Lockwood J, Hopkins S, McHugh TD, Gillespie SH, Kibbler CC. Detection and identification of bacteria in clinical samples by 16S rRNA gene sequencing: comparison of two different approaches in clinical practice. J Med Microbiol 2012; 61:483-488. [DOI: 10.1099/jmm.0.030387-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Claire Jenkins
- Colindale Microbiological Services, Health Protection Agency, Colindale, London NW9 5AT, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Clare L. Ling
- Colindale Microbiological Services, Health Protection Agency, Colindale, London NW9 5AT, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Holly L. Ciesielczuk
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Julianne Lockwood
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Susan Hopkins
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
| | - Stephen H. Gillespie
- School of Medicine, University of St Andrews, North Haugh, St Andrews, Fife KY16 9TF, UK
- Centre for Clinical Microbiology, Department of Infection, Royal Free Campus, UCL, London NW3 2QG, UK
| | - Christopher C. Kibbler
- Department of Medical Microbiology, Royal Free Hospital NHS Trust, Pond Street, London NW3 2PF, UK
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Characterization and transfer of antibiotic resistance in lactic acid bacteria from fermented food products. Curr Microbiol 2011; 62:1081-9. [PMID: 21212956 DOI: 10.1007/s00284-010-9856-2] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 12/16/2010] [Indexed: 01/16/2023]
Abstract
The study provides phenotypic and molecular analyses of the antibiotic resistance in lactic acid bacteria (LAB) from fermented foods in Xi'an, China. LAB strains (n = 84) belonging to 16 species of Lactobacillus (n = 73), and Streptococcus thermophilus (n = 11) were isolated and identified by sequencing their 16S rRNA gene. All strains were susceptible to ampicillin, bacitracin, and cefsulodin, and intrinsically resistant to nalidixic acid, kanamycin, and vancomycin (except L. bulgaricus, L. acidophilus, and S. thermophilus, which were susceptible to vancomycin). Some strains had acquired resistance for penicillin (n = 2), erythromycin (n = 9), clindamycin (n = 5), and tetracycline (n = 14), while resistance to gentamycin, ciprofloxacin, streptomycin, and chloramphenicol was species dependent. Minimum inhibitory concentrations presented in this study will help to review microbiological breakpoints for some of the species of Lactobacillus. The erm(B) gene was detected from two strains of each of L. fermentum and L. vaginalis, and one strain of each of L. plantarum, L. salivarius, L. acidophilus, L. animalis, and S. thermophilus. The tet genes were identified from 12 strains of lactobacilli from traditional foods. This is the first time, the authors identified tet(S) gene from L. brevis and L. kefiri. The erm(B) gene from L. fermentum NWL24 and L. salivarius NWL33, and tet(M) gene from L. plantarum NWL22 and L. brevis NWL59 were successfully transferred to Enterococcus faecalis 181 by filter mating. It was concluded that acquired antibiotic resistance is well dispersed in fermented food products in Xi'an, China and its transferability to other genera should be monitored closely.
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Tsukamurella: An Unrecognized Mimic of Atypical Mycobacterial Keratitis? The First Case Report. Cornea 2010; 29:362-4. [DOI: 10.1097/ico.0b013e3181ae2594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Maeda Y, Stanley T, Stirling J, Griffiths M, Calvert A, Stuart Elborn J, Cherie Millar B, Goldsmith CE, Rendall J, Loughrey A, Rooney PJ, Moore JE. No Evidence of Transmission of Bacteria Between Reptiles and a CF Patient - A Case Report of a Young Adult CF Patient and Reptiles. Zoonoses Public Health 2009; 57:e47-53. [DOI: 10.1111/j.1863-2378.2009.01293.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Elshibly S, Xu J, McClurg RB, Rooney PJ, Millar BC, Alexander HD, Kettle P, Moore JE. Central line-related bacteremia due toRoseomonas mucosain a patient with diffuse large B-cell non-Hodgkin's lymphoma. Leuk Lymphoma 2009; 46:611-4. [PMID: 16019492 DOI: 10.1080/10428190400029908] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A 42-year-old male patient with a history of diffuse large B-cell non-Hodgkin's lymphoma (DLBCL) developed a central line-related bacteremia due to the presence of a Gram-negative bacillus, which was difficult to identify conventionally. Sequencing of a partial region of the 16S rRNA gene identified the organism as Roseomonas mucosa with a homology score of 100% with 1003 bases called. Due to difficulties with the phenotypic identification of this genus, coupled with its emergence in line-related bacteremia in hematology patients with malignancy, Roseomonas spp. should be considered in cases of line-related infection in such patients with atypical Gram-negative organisms. Although several cases have been reported in the literature of line-related sepsis due to Roseomonas gilardii, only a few cases have been reported of Roseomonas mucosa infection in patients with hematological malignancy. This report highlights the benefits of the integration of a sequence-based typing approach in the identification of difficult-to-identify bacterial isolates employing partial regions of the 16S rRNA gene. Continued routine adoption of such techniques by clinical diagnostic laboratories may prove beneficial for the correct identification of blood-borne infections, as well as for the correct epidemiological characterization of unusual causal agents of bacteremia in immunocompromised individuals.
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Affiliation(s)
- Salah Elshibly
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, Northern Ireland, UK
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Stirling J, Maeda Y, Millar BC, McClurg RB, Rooney PJ, Loughrey A, Goldsmith CE, Moore JE. Mucoid Staphylococcus aureus isolated from a patient with a suspected urinary tract infection. J Med Microbiol 2008; 57:1436-1437. [PMID: 18927427 DOI: 10.1099/jmm.0.2008/001644-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jonathan Stirling
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - Yasunori Maeda
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - B Cherie Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - Robert B McClurg
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - Paul J Rooney
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - Anne Loughrey
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - Colin E Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
| | - John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AD, Northern Ireland, UK
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Abstract
The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air microbiota will be valuable for improving designs of surveillance for natural or man-made release of virulent pathogens.
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Stanley T, Crothers L, McCalmont M, Xu J, Millar BC, Goldsmith CE, Moore JE. The potential misidentification of Tsukamurella pulmonis as an atypical Mycobacterium species: a cautionary tale. J Med Microbiol 2006; 55:475-478. [PMID: 16533999 DOI: 10.1099/jmm.0.46355-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Timothy Stanley
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - Lester Crothers
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - Mark McCalmont
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - Jiru Xu
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - B Cherie Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - Colin E Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
| | - John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast BT9 7AD, UK
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Moore JE, Xu J, Millar BC. A simple and economic preservation method for genomic bacterial DNA from clinically significant pathogens. J Microbiol Methods 2004; 60:131-3. [PMID: 15567233 DOI: 10.1016/j.mimet.2004.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
Bacterial culture was allowed to dry to completeness on Columbia agar base with defibrinated horse blood. Following 6 months storage at room temperature, microbial DNA was extracted and successfully amplified by PCR. This storage technique has the advantage over other methods of not requiring (i) a DNA extraction protocol prior to storage and (ii) refrigeration and/or freezing. This technique maybe useful in the transportation of bacterial genomic DNA in nonviable cells as well as reliable method for the storage of DNA in underdeveloped countries.
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Affiliation(s)
- John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast BT9 7AD, Northern Ireland, United Kingdom.
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