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Öztürk AB, Ranjan R, Rani A, Yazıcı D, Bavbek S. Microbiota - The Unseen Players in Adult Asthmatic Airways. Turk Thorac J 2021; 22:75-82. [PMID: 33646108 DOI: 10.5152/turkthoracj.2020.19085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 04/30/2020] [Indexed: 11/22/2022]
Abstract
Modulation of human lung airway physiology by commensal microbiota has become one of the key mechanisms involved in the pathogenesis of adult asthma. Recent evidence suggests that the composition of respiratory microbiota plays a significant role in the manifestation of adult asthma; however, scientific evidence about the relationship between airway microbial diversity and phenotypes of adult asthma is limited. Further research is needed to understand the interactions between the airway microbiota and host immune response to develop microbiota-based strategies in management of adult asthma. This study reviews the advances in culture-independent methods for detection of airway microbiome, the current data about airway microbiota in healthy individuals and in adult patients with asthma with a focus on bacterial communities, and the future research directions in airway microbiome.
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Affiliation(s)
- Ayşe Bilge Öztürk
- Department of Allergy and Immunology, Koç University School of Medicine, İstanbul, Turkey
| | - Ravi Ranjan
- University of Massachusetts, The Institute for Applied Life Sciences (IALS), Genomics Resource Laboratory, Amherst, MA, USA
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Duygu Yazıcı
- Koç University Research Center for Translational Medicine (KUTTAM), İstanbul, Turkey
| | - Sevim Bavbek
- Department of Chest Diseases, Division of Allergy and Clinical Immunology, Ankara University School of Medicine, Ankara, Turkey
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2
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Benga L, Benten PM, Engelhardt E, Köhrer K, Hueber B, Nicklas W, Christensen H, Sager M. Differentiation Among Rodentibacter Species Based on 16S-23S rRNA Internal Transcribed Spacer Analysis. Comp Med 2020; 70:487-491. [PMID: 33121574 DOI: 10.30802/aalas-cm-99-990085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The internal transcribed spacer (ITS) regions of Rodentibacter pneumotropicus, R. heylii, R. rarus, R. ratti, and R. heidelbergensis and of a Rodentibacter- related β-hemolytic Pasteurellaceae taxon isolated from laboratory rodents were studied for their feasibility to discriminate among these species. The 6 species analyzed showed species-specific ITS patterns that were shared by the type strains and clinical isolates and that allowed their identification. Nevertheless, differentiating between the ITS band patterns of R. pneumotropicus and R. ratti is visually challenging. In all species tested, sequence analysis of the ITS fragments revealed a larger ITSile+ala, which contained the genes for tRNAIle(GAU) and tRNA Ala(UGC), and a smaller ITSglu with the tRNAGlu(UUC) gene. The ITS sequences varied among the 6 species evaluated, displaying identity levels ranging from 62% to 86% for ITSile+ala and 68% to 90% for ITSglu. Overall, ITS amplification proved to be a reliable method to differentiate among these important Pasteurellaceae species of laboratory rodents. Moreover, the ITS sequence variations recorded here might facilitate the design of probes for specific identification of these species. The ability to diagnose these organisms to the species level could increase our understanding of their clinical significance.
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Affiliation(s)
- Laurentiu Benga
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Duesseldorf, Germany;,
| | - Peter M Benten
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Duesseldorf, Germany
| | - Eva Engelhardt
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Duesseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Center (BMFZ), Heinrich-Heine University, Duesseldorf, Germany
| | | | - Werner Nicklas
- Retired, Microbiologic Diagnostics, German Cancer Research Centre, Heidelberg, Germany
| | - Henrik Christensen
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Martin Sager
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich-Heine University, Duesseldorf, Germany
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3
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Osman EA, El-Amin N, Adrees EAE, Al-Hassan L, Mukhtar M. Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan. Access Microbiol 2020; 2:acmi000096. [PMID: 32974573 PMCID: PMC7470312 DOI: 10.1099/acmi.0.000096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/28/2019] [Indexed: 11/21/2022] Open
Abstract
Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle-income countries, including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. pneumoniae isolates were collected and identified using conventional phenotypic methods, biochemically using API 20E and genotypically by amplification of 16S−23S rDNA and sequencing of rpoB, gapA and pgi. Only 139 (55.6 %) of the isolates were confirmed as K. pneumoniae genotypically by PCR and 44.4 % were identified as non-K. pneumoniae. The results demonstrate that the identification panels used by the hospitals were inaccurately identifying K. pneumonia and led to overestimation of the prevalence of this organism. The current identification methods used in Khartoum hospitals are highly inaccurate, and therefore we recommend the use of a comprehensive biochemical panel or molecular methods, when possible, for accurate identification of K. pneumoniae.
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Affiliation(s)
- Einas A Osman
- Bioscience Research Institute, Ibn-Sina University, Aljerif West, Khartoum, Sudan
| | - Nagwa El-Amin
- Microbiology Department, College of Medicine, Al-Qassim University, Al-Mulida, Saudi Arabia
| | - Emad A E Adrees
- Microbiology Department, College of Medicine, Alribat University Hospital, Khartoum, Sudan
| | - Leena Al-Hassan
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton BN1 9PX, UK
| | - Maowia Mukhtar
- Bioscience Research Institute, Ibn-Sina University, Aljerif West, Khartoum, Sudan
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4
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Molecular strain typing of multidrug-resistant Klebsiella pneumoniae: capsular wzi gene sequencing versus multiple locus variable number tandem repeat analysis. Diagn Microbiol Infect Dis 2020; 98:115139. [PMID: 32861156 DOI: 10.1016/j.diagmicrobio.2020.115139] [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] [Received: 03/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 11/23/2022]
Abstract
This study compared genotyping of Klebsiella pneumoniae isolates by 2 molecular methods. Genotyping of 50 multidrug-resistant (MDR) and 10 non-MDR K. pneumoniae subsp. pneumoniae isolates from 2 hospitals was done using multiple locus variable number tandem repeat analysis (MLVA) and capsular typing by wzi gene sequencing. Genotyping of the isolates by the 2 methods showed 100% typeability. Agreement on clustering of the isolates by the 2 methods was 82.6%. Typing by MLVA, however, was more discriminatory (97%) than by wzi gene sequencing (92%). All the 23 K. pneumoniae subsp. pneumoniae isolates randomly selected for wzi gene sequencing showed sequence identity to previously published wzi sequences, which enabled prediction of the K-types of 16 of them. The 2 methods revealed the relatedness of (8/15) isolates from 1 of the 2 hospitals. MLVA may be considered a cheaper and more discriminatory molecular typing method suitable for genotyping of K. pneumoniae isolates in developing countries.
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5
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Comin HB, Domingues R, Gaspar EB, Santos JRGDL, Cardoso FF. Genetic differences among Moraxella bovis and Moraxella bovoculi isolates from infectious bovine keratoconjunctivitis (IBK) outbreaks in southern Brazil. Genet Mol Biol 2020; 43:e20180380. [PMID: 32478794 PMCID: PMC7271659 DOI: 10.1590/1678-4685-gmb-2018-0380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/28/2019] [Indexed: 12/05/2022] Open
Abstract
The objective of this study was to evaluate the genetic diversity of
Moraxella bovis and Moraxella bovoculi
bacteria isolated from infectious bovine keratoconjunctivitis (IBK) outbreaks in
the state of Rio Grande do Sul, Brazil. The genetic diversity among
Moraxella spp. was evaluated by RAPD-PCR, JWP1-JWOPA07-PCR,
ERIC-PCR and by sequencing the 16S-23S intergenic regions. Based on the
dendrogram, two genetically differentiated clades were observed; 14 isolates
were classified as M. bovis and 17 as M.
bovoculi. Genetic distances between the M. bovis
samples ranged from 0.0379 to 0.4285, while for M. bovoculi the
dissimilarities ranged from zero to 0.7297. Alternatively, based on sequencing
analyses of the 16S-23S intergenic region, M. bovis and
M. bovoculi isolates were grouped into the same two
different clades, but it was not possible to differentiate between isolates
within clades. PCR techniques were demonstrated to be a satisfactory tool to
unravel the genetic variability among Moraxella spp., while
sequencing of the 16S-23S intergenic region was only able to differentiate two
species of the Moraxella genus. Despite sampling geographically
close regions, we demonstrate considerable genetic diversity in M.
bovis and M. bovoculi strains and genetically
distinct M. bovis strains co-infecting the same animal.
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Affiliation(s)
- Helena Brocardo Comin
- Universidade Federal de Pelotas, Programa de Pós-Graduação em Zootecnia, Pelotas, RS, Brazil
| | | | | | | | - Fernando Flores Cardoso
- Embrapa Pecuária Sul, Bagé, RS, Brazil.,Universidade Federal de Pelotas, Departamento de Zootecnia, Pelotas, RS, Brazil
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Soltan Dallal MM, Validi M, Douraghi M, Bakhshi B. Molecular typing of cytotoxin-producing Klebsiella oxytoca isolates by 16S-23S internal transcribed spacer PCR. New Microbes New Infect 2019; 30:100545. [PMID: 31193030 PMCID: PMC6514323 DOI: 10.1016/j.nmni.2019.100545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/21/2019] [Accepted: 04/02/2019] [Indexed: 12/02/2022] Open
Abstract
Cytotoxin is one of the important pathogenic factors, which plays a role in the virulence of Klebsiella oxytoca. The aim of this study was to investigate molecular typing of clinical isolates of the cytotoxin-producing K. oxytoca using internal transcribed spacer (ITS) PCR. A total of 75 isolates of K. oxytoca were isolated from clinical samples; they were verified as K. oxytoca by standard microbiological tests and PCR. Production of toxin determines the cytotoxic effects on HEp-2 cells. The genetic diversity of isolates of the cytotoxin-producing K. oxytoca were defined by ITS-PCR. Of all the isolates investigated, five K. oxytoca strains isolated from stool cultures, two strains from blood samples, one strain from a wound and one strain isolated from urine had cytotoxic effects on HEp-2 cells. The ITS-PCR patterns showed genetic diversity among cytotoxin-producing isolates. The ITS-PCR method had good discriminatory power; performance of this method and interpretation of the results were easy and repeatable. Five genetic diversity patterns were identified by ITS-PCR.
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Affiliation(s)
- M M Soltan Dallal
- Department of Food Microbiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Centre, Tehran University of Medical Sciences, Tehran, Iran
| | - M Validi
- Clinical Biochemistry Research Centre, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.,Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - M Douraghi
- Food Microbiology Research Centre, Tehran University of Medical Sciences, Tehran, Iran.,Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - B Bakhshi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Caputo A, Fournier PE, Raoult D. Genome and pan-genome analysis to classify emerging bacteria. Biol Direct 2019; 14:5. [PMID: 30808378 PMCID: PMC6390601 DOI: 10.1186/s13062-019-0234-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy. Reviewers This article was reviewed by William Martin, Eric Bapteste and James Mcinerney. Open peer review Reviewed by William Martin, Eric Bapteste and James Mcinerney.
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Affiliation(s)
- Aurélia Caputo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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8
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Dou Y, Li L, Du J, He Y, Chen R, Li Y, Ma C, Liu H. Development of a multiplex two-gene real-time PCR assay for accurate detection of Klebsiella pneumoniae. Br J Biomed Sci 2018; 76:42-45. [PMID: 29991336 DOI: 10.1080/09674845.2018.1499167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Y Dou
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
| | - L Li
- b Dongguan Research Center, Traditional Chinese Medicine and New Drug Research Institute, Guangdong Medical University , Dongguan , China
| | - J Du
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
| | - Y He
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
| | - R Chen
- c Department of Clinical Laboratory , The Second People's Hospital of Futian District , Shenzhen , China
| | - Y Li
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
| | - C Ma
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
| | - H Liu
- a Department of Clinical Laboratory , Shenzhen Shajing Hospital affiliated to Guangzhou Medical University , Shenzhen , China
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Gomes C, Martínez-Puchol S, Palma N, Horna G, Ruiz-Roldán L, Pons MJ, Ruiz J. Macrolide resistance mechanisms in Enterobacteriaceae: Focus on azithromycin. Crit Rev Microbiol 2016; 43:1-30. [DOI: 10.3109/1040841x.2015.1136261] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cláudia Gomes
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Sandra Martínez-Puchol
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Noemí Palma
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Gertrudis Horna
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maria J Pons
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Joaquim Ruiz
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
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10
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Tokajian S, Issa N, Salloum T, Ibrahim J, Farah M. 16S-23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads. Front Microbiol 2016; 7:149. [PMID: 26904019 PMCID: PMC4749711 DOI: 10.3389/fmicb.2016.00149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 11/13/2022] Open
Abstract
Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S–23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S–23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2–57.9 mol%. Five distinct ITS types were identified: ITSnone (without tRNA genes), ITSAla(TGC), ITSAla(TGC)+Ile(GAT), ITSIle(GAT)+Ala(TGC), and ITS Ile(GAT)+Pseudo. All of the identified tRNAAla(TGC) molecules consisted of 73 bases, and all of the tRNAIle(GAT) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S–23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence.
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Affiliation(s)
- Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Nahla Issa
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Joe Ibrahim
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
| | - Maya Farah
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University Byblos, Lebanon
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Zeitoun H, Kassem M, Raafat D, AbouShlieb H, Fanaki N. Microbiological testing of pharmaceuticals and cosmetics in Egypt. BMC Microbiol 2015; 15:275. [PMID: 26653032 PMCID: PMC4674922 DOI: 10.1186/s12866-015-0609-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 11/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial contamination of pharmaceuticals poses a great problem to the pharmaceutical manufacturing process, especially from a medical as well as an economic point of view. Depending upon the product and its intended use, the identification of isolates should not merely be limited to the United States Pharmacopeia (USP) indicator organisms. RESULTS Eighty-five pre-used non-sterile pharmaceuticals collected from random consumers in Egypt were examined for the eventual presence of bacterial contaminants. Forty-one bacterial contaminants were isolated from 31 of the tested preparations. These isolates were subjected to biochemical identification by both conventional tests as well as API kits, which were sufficient for the accurate identification of only 11 out of the 41 bacterial contaminants (26.8%) to the species level. The remaining isolates were inconclusively identified or showed contradictory results after using both biochemical methods. Using molecular methods, 24 isolates (58.5%) were successfully identified to the species level. Moreover, polymerase chain reaction (PCR) assays were compared to standard biochemical methods in the detection of pharmacopoeial bacterial indicators in artificially-contaminated pharmaceutical samples. CONCLUSION PCR-based methods proved to be superior regarding speed, cost-effectiveness and sensitivity. Therefore, pharmaceutical manufacturers would be advised to adopt PCR-based methods in the microbiological quality testing of pharmaceuticals in the future.
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Affiliation(s)
- Hend Zeitoun
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 1 Khartoum Square, Azarita, Alexandria 21521, Egypt.
| | - Mervat Kassem
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 1 Khartoum Square, Azarita, Alexandria 21521, Egypt.
| | - Dina Raafat
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 1 Khartoum Square, Azarita, Alexandria 21521, Egypt.
| | - Hamida AbouShlieb
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 1 Khartoum Square, Azarita, Alexandria 21521, Egypt.
| | - Nourhan Fanaki
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 1 Khartoum Square, Azarita, Alexandria 21521, Egypt.
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Zhang H, Feng S, Zhao Y, Wang S, Lu X. Detection of Yersinia enterocolitica in milk powders by cross-priming amplification combined with immunoblotting analysis. Int J Food Microbiol 2015; 214:77-82. [PMID: 26253307 DOI: 10.1016/j.ijfoodmicro.2015.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/07/2015] [Accepted: 07/25/2015] [Indexed: 11/25/2022]
Abstract
Yersinia enterocolitica (Y. enterocolitica) is frequently isolated from a wide variety of foods and can cause human yersiniosis. Biochemical and culture-based assays are common detection methods, but require a long incubation time and easily misidentify Y. enterocolitica as other non-pathogenic Yersinia species. Alternatively, cross-priming amplification (CPA) under isothermal conditions combined with immunoblotting analysis enables a more sensitive detection in a relatively short time period. A set of specific displacement primers, cross primers and testing primers was designed on the basis of six specific sequences in Y. enterocolitica 16S-23S rDNA internal transcribed spacer. Under isothermal condition, amplification and hybridization were conducted simultaneously at 63°C for 60 min. The specificity of CPA was tested for 96 different bacterial strains and 165 commercial milk powder samples. Two red lines were developed on BioHelix Express strip for all of the Y. enterocolitica strains, and one red line was shown for non-Y. enterocolitica strains. The limit of detection of CPA was 10(0)fg for genomic DNA (1000 times more sensitive than PCR assay), 10(1) CFU/ml for pure bacterial culture, and 10(0) CFU per 100 g milk powder with pre-enrichment at 37°C for 24 h. CPA combined with immunoblotting analysis can achieve highly specific and sensitive detection of Y. enterocolitica in milk powder in 90 min after pre-enrichment.
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Affiliation(s)
- Hongwei Zhang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China; Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Shaolong Feng
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yulong Zhao
- School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xiaonan Lu
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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Cao B, Liu X, Yu X, Chen M, Feng L, Wang L. A new oligonucleotide microarray for detection of pathogenic and non-pathogenic Legionella spp. PLoS One 2014; 9:e113863. [PMID: 25469776 PMCID: PMC4254607 DOI: 10.1371/journal.pone.0113863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/31/2014] [Indexed: 11/18/2022] Open
Abstract
Legionella pneumophila has been recognized as the major cause of legionellosis since the discovery of the deadly disease. Legionella spp. other than L. pneumophila were later found to be responsible to many non-pneumophila infections. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this report, we have sequenced the 16S-23S rRNA gene internal transcribed spacer (ITS) of 10 Legionella species and subspecies, including L. anisa, L. bozemanii, L. dumoffii, L. fairfieldensis, L. gormanii, L. jordanis, L. maceachernii, L. micdadei, L. pneumophila subspp. fraseri and L. pneumophila subspp. pasculleii, and developed a rapid oligonucleotide microarray detection technique accordingly to identify 12 most common Legionella spp., which consist of 11 pathogenic species of L. anisa, L. bozemanii, L. dumoffii, L. gormanii, L. jordanis, L. longbeachae, L. maceachernii, L. micdadei, and L. pneumophila (including subspp. pneumophila, subspp. fraseri, and subspp. pasculleii) and one non-pathogenic species, L. fairfieldensis. Twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria, were used to verify the oligonucleotide microarray assay. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven samples of air conditioner-condensed water with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp.
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Affiliation(s)
- Boyang Cao
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Xiangqian Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Xiang Yu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Min Chen
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Lu Feng
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
| | - Lei Wang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, TEDA College, Nankai University, Tianjin, P. R. China
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, P. R. China
- Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, P. R. China
- * E-mail:
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14
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Maatallah M, Vading M, Kabir MH, Bakhrouf A, Kalin M, Nauclér P, Brisse S, Giske CG. Klebsiella variicola is a frequent cause of bloodstream infection in the stockholm area, and associated with higher mortality compared to K. pneumoniae. PLoS One 2014; 9:e113539. [PMID: 25426853 PMCID: PMC4245126 DOI: 10.1371/journal.pone.0113539] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/27/2014] [Indexed: 01/26/2023] Open
Abstract
Clinical isolates of Klebsiella pneumoniae are divided into three phylogroups and differ in their virulence factor contents. The aim of this study was to determine an association between phylogroup, virulence factors and mortality following bloodstream infection (BSI) caused by Klebsiella pneumoniae. Isolates from all adult patients with BSI caused by K. pneumoniae admitted to Karolinska University Hospital, Solna between 2007 and 2009 (n = 139) were included in the study. Phylogenetic analysis was performed based on multilocus sequence typing (MLST) data. Testing for mucoid phenotype, multiplex PCR determining serotypes K1, K2, K5, K20, K54 and K57, and testing for virulence factors connected to more severe disease in previous studies, was also performed. Data was retrieved from medical records including age, sex, comorbidity, central and urinary catheters, time to adequate treatment, hospital-acquired infection, and mortality, to identify risk factors. The primary end-point was 30- day mortality. The three K. pneumoniae phylogroups were represented: KpI (n = 96), KpII (corresponding to K. quasipneumoniae, n = 9) and KpIII (corresponding to K. variicola, n = 34). Phylogroups were not significantly different in baseline characteristics. Overall, the 30-day mortality was 24/139 (17.3%). Isolates belonging to KpIII were associated with the highest 30-day mortality (10/34 cases, 29.4%), whereas KpI isolates were associated with mortality in 13/96 cases (13.5%). This difference was significant both in univariate statistical analysis (P = 0.037) and in multivariate analysis adjusting for age and comorbidity (OR 3.03 (95% CI: 1.10–8.36). Only three of the isolates causing mortality within 30 days belonged to any of the virulent serotypes (K54, n = 1), had a mucoid phenotype (n = 1) and/or contained virulence genes (wcaG n = 1 and wcaG/allS n = 1). In conclusion, the results indicate higher mortality among patients infected with isolates belonging to K. variicola. The increased mortality could not be related to any known virulence factors, including virulent capsular types or mucoid phenotype.
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Affiliation(s)
- Makaoui Maatallah
- Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits, Faculté de Pharmacie, University of Monastir, Montasir, Tunisia
| | - Malin Vading
- Clinical Microbiology, MTC – Karolinska Institutet, Karolinska University, Hospital Solna, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Muhammad Humaun Kabir
- Clinical Microbiology, MTC – Karolinska Institutet, Karolinska University, Hospital Solna, Stockholm, Sweden
| | - Amina Bakhrouf
- Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits, Faculté de Pharmacie, University of Monastir, Montasir, Tunisia
| | - Mats Kalin
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Pontus Nauclér
- Department of Infectious Diseases, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France
- CNRS, Paris, France
| | - Christian G. Giske
- Clinical Microbiology, MTC – Karolinska Institutet, Karolinska University, Hospital Solna, Stockholm, Sweden
- * E-mail:
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15
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Perilli M, Bottoni C, Grimaldi A, Segatore B, Celenza G, Mariani M, Bellio P, Frascaria P, Amicosante G. Carbapenem-resistant Klebsiella pneumoniae harbouring blaKPC-3 and blaVIM-2 from central Italy. Diagn Microbiol Infect Dis 2013; 75:218-21. [DOI: 10.1016/j.diagmicrobio.2012.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 09/13/2012] [Accepted: 10/05/2012] [Indexed: 11/27/2022]
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16
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Analysis of 16S–23S rRNA internal transcribed spacer regions in Pasteurellaceae isolated from laboratory rodents. J Microbiol Methods 2012; 90:342-9. [DOI: 10.1016/j.mimet.2012.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/21/2012] [Accepted: 06/24/2012] [Indexed: 11/19/2022]
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17
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Yu VCH, Yu PHF, Ho KC, Lee FWF. Isolation and identification of a new tetrodotoxin-producing bacterial species, Raoultella terrigena, from Hong Kong marine puffer fish Takifugu niphobles. Mar Drugs 2011; 9:2384-2396. [PMID: 22163191 PMCID: PMC3229240 DOI: 10.3390/md9112384] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 11/03/2011] [Accepted: 11/04/2011] [Indexed: 11/16/2022] Open
Abstract
Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF). Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.
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Affiliation(s)
- Vincent Chung-Him Yu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China; E-Mails: (V.C.-H.Y.); (P.H.-F.Y.)
| | - Peter Hoi-Fu Yu
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China; E-Mails: (V.C.-H.Y.); (P.H.-F.Y.)
| | - Kin-Chung Ho
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China; E-Mail:
| | - Fred Wang-Fat Lee
- School of Science and Technology, The Open University of Hong Kong, Hong Kong, China; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +852-2768-6868; Fax: +852-2789-1170
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18
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Use of a DNA microarray for detection and identification of bacterial pathogens associated with fishery products. Appl Environ Microbiol 2011; 77:8219-25. [PMID: 21965411 DOI: 10.1128/aem.05914-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We established a microarray for the simultaneous detection and identification of diverse putative pathogens often associated with fishery products by targeting specific genes of Listeria monocytogenes, Salmonella, Shigella, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of Proteus mirabilis and Proteus vulgaris. The microarray contained 26 specific probes and was tested against a total of 123 target bacterial strains that included 55 representative strains, 68 clinical isolates, and 45 strains of other bacterial species that belonged to 8 genera and 34 species, and it was shown to be specific and reproducible. A detection sensitivity of 10 ng DNA or 10 CFU/ml for pure cultures of each target organism demonstrated that the assay was highly sensitive and reproducible. Mock and real fishery product samples were tested by the microarray, and the accuracy was 100%. The DNA microarray method described in this communication is specific, sensitive, and reliable and has several advantages over traditional methods of bacterial culture and antiserum agglutination assays.
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19
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Ryberg A, Olsson C, Ahrné S, Monstein HJ. Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates. J Microbiol Methods 2010; 84:183-8. [PMID: 21129413 DOI: 10.1016/j.mimet.2010.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/16/2010] [Accepted: 11/19/2010] [Indexed: 12/20/2022]
Abstract
Molecular typing of Klebsiella species has become important for monitoring dissemination of β-lactamase-producers in hospital environments. The present study was designed to evaluate poly-trinucleotide (GTG)(5)- and rDNA intergenic transcribed spacer (ITS)-PCR fingerprint analysis for typing of Klebsiella pneumoniae and Klebsiella oxytoca isolates. Multiple displacement amplified DNA derived from 19 K. pneumoniae (some with an ESBL-phenotype), 35 K. oxytoca isolates, five K. pneumoniae, two K. oxytoca, three Raoultella, and one Enterobacter aerogenes type and reference strains underwent (GTG)(5) and ITS-PCR analysis. Dendrograms were constructed using cosine coefficient and the Neighbour joining method. (GTG)(5) and ITS-PCR analysis revealed that K. pneumoniae and K. oxytoca isolates, reference and type strains formed distinct cluster groups, and tentative subclusters could be established. We conclude that (GTG)(5) and ITS-PCR analysis combined with automated capillary electrophoresis provides promising tools for molecular typing of Klebsiella isolates.
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Affiliation(s)
- Anna Ryberg
- Division of Clinical Microbiology, University Hospital Linköping, Linköping University, Linköping, Sweden
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20
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Chakravorty S, Aladegbami B, Burday M, Levi M, Marras SAE, Shah D, El-Hajj HH, Kramer FR, Alland D. Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique. J Clin Microbiol 2010; 48:258-67. [PMID: 19923485 PMCID: PMC2812257 DOI: 10.1128/jcm.01725-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 10/25/2009] [Accepted: 11/07/2009] [Indexed: 11/20/2022] Open
Abstract
A real-time PCR assay with the ability to rapidly identify all pathogenic bacteria would have widespread medical utility. Current real-time PCR technologies cannot accomplish this task due to severe limitations in multiplexing ability. To this end, we developed a new assay system which supports very high degrees of multiplexing. We developed a new class of mismatch-tolerant "sloppy" molecular beacons, modified them to provide an extended hybridization range, and developed a multiprobe, multimelting temperature (T(m)) signature approach to bacterial species identification. Sloppy molecular beacons were exceptionally versatile, and they were able to generate specific T(m) values for DNA sequences that differed by as little as one nucleotide to as many as 23 polymorphisms. Combining the T(m) values generated by several probe-target hybrids resulted in T(m) signatures that served as highly accurate sequence identifiers. Using this method, PCR assays with as few as six sloppy molecular beacons targeting bacterial 16S rRNA gene segments could reproducibly classify 119 different sequence types of pathogenic and commensal bacteria, representing 64 genera, into 111 T(m) signature types. Blinded studies using the assay to identify the bacteria present in 270 patient-derived clinical cultures including 106 patient blood cultures showed a 95 to 97% concordance with conventional methods. Importantly, no bacteria were misidentified; rather, the few species that could not be identified were classified as "indeterminate," resulting in an assay specificity of 100%. This approach enables highly multiplexed target detection using a simple PCR format that can transform infectious disease diagnostics and improve patient outcomes.
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Affiliation(s)
- Soumitesh Chakravorty
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Bola Aladegbami
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Michele Burday
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Michael Levi
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Salvatore A. E. Marras
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Darshini Shah
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Hiyam H. El-Hajj
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - Fred Russell Kramer
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
| | - David Alland
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenço Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, Department of Pathology, Montefiore Medical Center, Bronx, New York, Public Health Research Institute, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey
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21
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Detection of Enterobacter sakazakii and other pathogens associated with infant formula powder by use of a DNA microarray. J Clin Microbiol 2009; 47:3178-84. [PMID: 19641057 PMCID: PMC2756907 DOI: 10.1128/jcm.00366-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogen detection is critical to the process of generating and testing powdered infant formula (PIF). An obstacle associated with PIF microbial surveillance is that most current procedures are time-consuming and labor-intensive. We have developed a rapid, DNA microarray-based detection technique to identify 10 different pathogenic bacteria associated with PIF contamination based on the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences and wzy (O antigen polymerase) gene. Using this procedure, Enterobacter sakazakii, Salmonella enterica, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli O157 were identified. One hundred eighty-five strains were used to validate the microarray assay (including 134 target pathogen strains and 51 closely related bacteria). Twenty-seven probes reproducibly detected multiple pathogens with high specificity and sensitivity (0.100 ng genomic DNA or 10(4) CFU/ml). Twenty-one real PIF samples were tested by the microarray with 100% accuracy. The data presented reveal that the designed oligonucleotide microarray is a promising method for basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance.
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