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Zhang X, Zhang D, Zhang X, Zhang X. Artificial intelligence applications in the diagnosis and treatment of bacterial infections. Front Microbiol 2024; 15:1449844. [PMID: 39165576 PMCID: PMC11334354 DOI: 10.3389/fmicb.2024.1449844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/04/2024] [Indexed: 08/22/2024] Open
Abstract
The diagnosis and treatment of bacterial infections in the medical and public health field in the 21st century remain significantly challenging. Artificial Intelligence (AI) has emerged as a powerful new tool in diagnosing and treating bacterial infections. AI is rapidly revolutionizing epidemiological studies of infectious diseases, providing effective early warning, prevention, and control of outbreaks. Machine learning models provide a highly flexible way to simulate and predict the complex mechanisms of pathogen-host interactions, which is crucial for a comprehensive understanding of the nature of diseases. Machine learning-based pathogen identification technology and antimicrobial drug susceptibility testing break through the limitations of traditional methods, significantly shorten the time from sample collection to the determination of result, and greatly improve the speed and accuracy of laboratory testing. In addition, AI technology application in treating bacterial infections, particularly in the research and development of drugs and vaccines, and the application of innovative therapies such as bacteriophage, provides new strategies for improving therapy and curbing bacterial resistance. Although AI has a broad application prospect in diagnosing and treating bacterial infections, significant challenges remain in data quality and quantity, model interpretability, clinical integration, and patient privacy protection. To overcome these challenges and, realize widespread application in clinical practice, interdisciplinary cooperation, technology innovation, and policy support are essential components of the joint efforts required. In summary, with continuous advancements and in-depth application of AI technology, AI will enable doctors to more effectivelyaddress the challenge of bacterial infection, promoting the development of medical practice toward precision, efficiency, and personalization; optimizing the best nursing and treatment plans for patients; and providing strong support for public health safety.
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Affiliation(s)
- Xiaoyu Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Deng Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xifan Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xin Zhang
- First Department of Infectious Diseases, The First Affiliated Hospital of China Medical University, Shenyang, China
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2
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Shen H, Rösch P, Popp J. Fiber Probe-Based Raman Spectroscopic Identification of Pathogenic Infection Microorganisms on Agar Plates. Anal Chem 2022; 94:4635-4642. [PMID: 35254815 DOI: 10.1021/acs.analchem.1c04507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid identification of microorganisms is clinically meaningful, and it helps to decelerate the spread of drug resistance and improve patient treatment. In this study, we present a rapid fiber probe-based Raman technique with an excitation wavelength of 785 nm, which is applied to classify and identify nine different species of microorganisms. The cost-effective fiber probe compresses the dimension of the system and provides a more reliable and stable database. All microorganisms were simply cultivated on Luria-Bertani (LB) agar, and Raman spectra were obtained directly from the microbial colonies with the fiber probe within 30 s. The classification model consists of principal component analysis (PCA) in combination with linear discriminant analysis (LDA) and was examined by applying leave-one-batch-out cross-validation (LOBOCV). This model achieved an accuracy of 98.9%. In addition, the validation and identification processes based on independent replicates achieved accuracies of 99.8% and 100%, respectively. The results demonstrated that fiber probe Raman spectroscopy in combination with chemometric analysis allowed a rapid classification and identification of microorganisms only with a normal culture. Therefore, it is promising especially for medical applications and could moreover be helpful to investigate and identify microorganisms rapidly in further studies.
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Affiliation(s)
- Haodong Shen
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
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3
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Greimel TM, Stampfer L, Leitner E, Kienesberger S, Zechner EL, Bozic M, Wagner GE, Unterhauser K, Kitsera M, Hauer AC, Gorkiewicz G, Wurm P, Valitutti F, Högenauer C, Hoffmann KM. Toxin-Producing Klebsiella oxytoca in Healthy Infants: Commensal or Pathobiont? J Pediatr Gastroenterol Nutr 2022; 74:e1-e7. [PMID: 34520403 DOI: 10.1097/mpg.0000000000003299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Klebsiella oxytoca is a gastrointestinal pathobiont with the potential to produce the toxins tilivalline and tilimycin, which cause antibiotic-associated hemorrhagic colitis. Overgrowth of toxigenic K oxytoca has recently been implicated in necrotizing enterocolitis. K oxytoca colonizes 2-9% of healthy adults, however, there is no systematic data on colonization in healthy children. We investigated K oxytoca colonization and its toxigenic properties in healthy infants. METHODS We sampled stool of healthy infants and determined K oxytoca colonization using stool culture and PCR (pehX). Toxin in stool was measured with HPLC/high-resolution mass spectrometry. K oxytoca isolates were typed using multi-locus sequence typing (MLST) and K oxytoca toxin PCR (npsA/B). Cytotoxin production of isolates was analyzed by MTT assay. RESULTS K oxytoca was detected in 30 of 61 infants (49%) using stool culture and in 45 of 61 (73%) using PCR (pehX). Toxin marker PCR (npsA/B) was positive in 66% of stool samples positive for K oxytoca PCR. Stool toxin levels were too low for quantitation but traces of tilivalline were detected. Contrarily, 49% of K oxytoca isolates demonstrated toxicity in the MTT assay. MLST revealed 36 distinct sequence types affiliated with all known K oxytoca sequence type clusters (A, B1 and B2). CONCLUSIONS More than 70% of healthy infants were colonized with K oxytoca. Toxin quantities in stool of colonized healthy infants were below detection level, yet half of the isolates produced toxin in vitro demonstrating their pathobiont potential. The high occurrence of toxigenic K oxytoca in healthy infants has to be considered for future disease association studies.
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Affiliation(s)
- Theresa M Greimel
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Laura Stampfer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | | | | | - Almuthe C Hauer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Austria
- BioTechMed-Graz
| | - Philipp Wurm
- Institute of Pathology, Medical University of Graz, Austria
| | | | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz
- BioTechMed-Graz
| | - Karl Martin Hoffmann
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
- Kinderärzte Zentrum Graz-Raaba, Raaba-Grambach, Austria
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4
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Shimizu T, Tsuyuki Y, Shimoike K, Iyori K, Miyamoto T, Harada K. Antimicrobial resistance and multilocus sequence types of Stenotrophomonas maltophilia isolated from dogs and cats in Japan. J Med Microbiol 2021; 70. [PMID: 33826489 DOI: 10.1099/jmm.0.001344] [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: 01/17/2023] Open
Abstract
As the representative multidrug-resistant pathogen, Stenotrophomonas maltophilia has multiple intrinsic and acquired resistances, including carbapenem resistance. In companion animals, the antimicrobial susceptibility and sequence types (STs) of S. maltophilia are not well understood due to its limited isolation rate. We investigated the antimicrobial susceptibilities and multilocus sequence types (MLSTs) of 38 S. maltophilia strains isolated from dogs and cats in Japan. Prevalence of resistance was detected for imipenem (100 %), aztreonam (94.7 %), piperacillin (65.8 %), trimethoprim-sulfamethoxazole (65.8 %), and ceftazidime (60.5 %). Rates of resistances to chloramphenicol, minocycline, and levofloxacin were low (2.6-5.3 %). MLST analysis revealed that all 38 strains were assigned to 34 STs, including 11 previously reported STs and 23 newly identified STs. Phylogenetic analysis of MLSTs enabled categorization of 13 isolates (34.2 %) into genogroup 6, which is a major genogroup of human isolates. Multinational surveillance would be needed to clarify the significance of antimicrobial-resistant S. maltophilia isolates from companion animals.
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Affiliation(s)
- Takae Shimizu
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori-shi, Tottori 680-8553, Japan
| | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory Inc., 2-5-8 Kuji, Takatsu, Kawasaki-shi, Kanagawa 213-0032, Japan
| | - Kenta Shimoike
- Vet Derm Tokyo Inc., 910 Shobuzawa, Fujisawa-shi, Kanagawa 252-0823, Japan
| | - Keita Iyori
- Vet Derm Tokyo Inc., 910 Shobuzawa, Fujisawa-shi, Kanagawa 252-0823, Japan
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi-shi, Yamaguchi 753-0851, Japan
| | - Kazuki Harada
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori-shi, Tottori 680-8553, Japan
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5
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Ohtaki H, Takahashi A, Niwa A, Yonetamari J, Nakayama A, Kuchibiro T, Ohta H, Ito H, Baba H, Murakami N, Ohkusu K. Evaluation of presumptive identification of
Enterobacterales
using CHROMagar Orientation medium and rapid biochemical tests. J Clin Lab Anal 2020; 34:e23453. [PMID: 32594571 PMCID: PMC7595914 DOI: 10.1002/jcla.23453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/07/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022] Open
Abstract
Background The use of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry is gradually spreading among large‐scale laboratories; however, this method is impractical for small‐scale laboratories. In laboratories without access to these rapid identification methods, problems related to them remain unsolved. In this study, we aimed to develop a rapid and inexpensive method to presumptively identify Enterobacterales using CHROMagar Orientation medium. Methods The algorithm for presumptive identification of Enterobacteriaceae using CHROMagar Orientation medium was based on our previous studies. Modified property tests for indole, lysine decarboxylase, ornithine decarboxylase, and hydrogen sulfide were performed to evaluate the differentiation of the bacterial species. Results Using the type strains and clinical isolates, it was possible to conduct the property tests at a low cost, within 4 hours. The spot indole test was performed without any nonspecific reactions for the bacteria forming colored colonies. The presumptive identification of bacteria was thereby possible within 24 hours after specimen submission. Conclusion All these results suggest that the rapid presumptive identification of Enterobacterales is possible with this new identification method using CHROMagar Orientation medium. This is therefore a prompt and economical method that can be used in routine laboratory work.
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Affiliation(s)
- Hirofumi Ohtaki
- Department of Clinical Laboratory Science Graduate School of Kansai University of Health Sciences Osaka Japan
- Department of Informative Clinical Medicine Gifu University Graduate School of Medicine Gifu Japan
| | - Akifumi Takahashi
- Department of Clinical Laboratory Science Graduate School of Kansai University of Health Sciences Osaka Japan
| | - Ayumi Niwa
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Jun Yonetamari
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Asami Nakayama
- Department of Clinical Laboratory Yamagata University Hospital Yamagata Japan
| | - Tomokazu Kuchibiro
- Department of Clinical Laboratory Naga Municipal Hospital Kinokawa Japan
| | - Hirotoshi Ohta
- Department of Clinical Laboratory Gifu University Hospital Gifu Japan
| | - Hiroyasu Ito
- Department of Informative Clinical Medicine Gifu University Graduate School of Medicine Gifu Japan
| | - Hisashi Baba
- Center for Nutrition Support & Infection Control Gifu University Hospital Gifu Japan
| | - Nobuo Murakami
- Center for Nutrition Support & Infection Control Gifu University Hospital Gifu Japan
| | - Kiyofumi Ohkusu
- Department of Microbiology Tokyo Medical University Tokyo Japan
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6
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Kimura Y, Harada K, Shimizu T, Sato T, Kajino A, Usui M, Tamura Y, Tsuyuki Y, Miyamoto T, Ohki A, Watarai M. Species distribution, virulence factors, and antimicrobial resistance of Acinetobacter spp. isolates from dogs and cats: a preliminary study. Microbiol Immunol 2018; 62:462-466. [PMID: 29752821 DOI: 10.1111/1348-0421.12601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/30/2018] [Accepted: 05/11/2018] [Indexed: 11/29/2022]
Abstract
We investigated the prevalence of virulence factors and antimicrobial resistance among 67 Acinetobacter spp. isolates, consisting of 21 Acinetobacter baumannii and 46 non-baumannii Acinetobacter from companion animals. The PCR analysis showed that the most prevalent virulence gene was afa/draBC (29.9%), followed by papC (22.4%) and cvaC (20.9%). Antimicrobial susceptibility testing revealed that resistance to gentamicin (14.9%) and ciprofloxacin (11.9%) was relatively prevalent. Five gentamicin- and/or ciprofloxacin-resistant A. baumannii strains were assigned to ST25, ST149, ST164, ST203, and ST1198. All ciprofloxacin-resistant isolates harbored point mutations in gyrA and/or parC. This is the first preliminary monitoring of animal-origin Acinetobacter spp. in Japan.
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Affiliation(s)
- Yui Kimura
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi 753-0851, Japan
| | - Kazuki Harada
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori 680-8553, Japan
| | - Takae Shimizu
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
- Department of Veterinary Internal Medicine, Tottori University, Minami 4-101, Koyama, Tottori 680-8553, Japan
| | - Tomomi Sato
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Akari Kajino
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University, 582 Midori, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory, 2-5-8 Kuji, Takatsu, Kawasaki, Kanagawa 213-0032, Japan
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi 753-0851, Japan
| | - Asami Ohki
- Fujifilm Monoris Co., Ltd., 1-49-18 Nishikoigakubo, Kokubunji, Tokyo 185-0013, Japan
| | - Masahisa Watarai
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
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Msaad Guerfali M, Djobbi W, Charaabi K, Hamden H, Fadhl S, Marzouki W, Dhaouedi F, Chevrier C. Evaluation of Providencia rettgeri pathogenicity against laboratory Mediterranean fruit fly strain (Ceratitis capitata). PLoS One 2018; 13:e0196343. [PMID: 29734397 PMCID: PMC5937750 DOI: 10.1371/journal.pone.0196343] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 04/11/2018] [Indexed: 12/27/2022] Open
Abstract
The Mediterranean fruit fly (medfly) Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), is often referred to as the most severe agricultural pest. Its biological control is mainly through the Sterile Insect Technique (SIT). Colonization, mass-rearing conditions and the irradiation process impact the competitiveness of sterile males and disrupt symbiotic associations by favoring some bacterial species and suppressing others. Levels of Providencia species have been shown to fluctuate considerably in the gut of the medfly laboratory strain Vienna 8 under irradiation, increasing by up to 22%. This study aimed to determine the pathogenicity of Providencia rettgeri isolated from the gut of laboratory Vienna 8 medfly strains by examining the effects of 1) two different treatment doses on egg-hatching and development and 2) two infection methodologies (ingestion and injection) of male and female adults according to their mating status. Treatment of eggs with P. rettgeri (2%) significantly decreased the mean egg to pupae recovery rate. Our data showed significant high mortality in flies with both injection and ingestion after 24 hours without any effect of sex. Microbial counts demonstrated that the bacteria could proliferate and replicate in adult flies. There was a significant sex-dependent effect after infection, with mortality decreasing significantly for males more than females. Providencia rettgeri can be considered as a potential pathogen of C. capitata. Mating protected males and females against infection by P. rettgeri by triggering an immune response leading to double the levels of Cecropin being secreted compared to infected virgin adults, thus reducing the virulence of the bacteria.
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Affiliation(s)
- Meriem Msaad Guerfali
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
- * E-mail:
| | - Wafa Djobbi
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Kamel Charaabi
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Heithem Hamden
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Salma Fadhl
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Wafa Marzouki
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Ferjani Dhaouedi
- Laboratory of biotechnology and nuclear technologies, LR16CNSTN01, National centre of nuclear sciences and technologies, Technopole Sidi Thabet, Tunis, Tunisia
| | - Claude Chevrier
- UMRCNRS, 6035, Insect Research Biology Institute (IRBI), Faculty of Science and Technology, Tours, France
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Sadahira T, Wada K, Araki M, Ishii A, Watanabe T, Nasu Y, Tsugawa M, Takenaka T, Nasu Y, Kumon H. Impact of selective media for detecting fluoroquinolone-insusceptible/extended-spectrum beta-lactamase-producingEscherichia colibefore transrectal prostate biopsy. Int J Urol 2017; 24:842-847. [DOI: 10.1111/iju.13447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/09/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Takuya Sadahira
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Koichiro Wada
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Motoo Araki
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Ayano Ishii
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Toyohiko Watanabe
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Yoshitsugu Nasu
- Okayama Urological Research Group; Okayama Japan
- Department of Urology; Okayama Rosai Hospital; Okayama Japan
| | - Masaya Tsugawa
- Okayama Urological Research Group; Okayama Japan
- Department of Urology; Okayama City General Medical Center; Okayama Japan
| | - Tadasu Takenaka
- Okayama Urological Research Group; Okayama Japan
- Department of Urology; Japanese Red Cross Okayama Hospital; Okayama Japan
| | - Yasutomo Nasu
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
| | - Hiromi Kumon
- Department of Urology; Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences; Okayama Japan
- Okayama Urological Research Group; Okayama Japan
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Shimizu T, Harada K, Tsuyuki Y, Kimura Y, Miyamoto T, Hatoya S, Hikasa Y. In vitro efficacy of 16 antimicrobial drugs against a large collection of β-lactamase-producing isolates of extraintestinal pathogenic Escherichia coli from dogs and cats. J Med Microbiol 2017; 66:1085-1091. [PMID: 28749329 DOI: 10.1099/jmm.0.000535] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The aim of this study was to assess the in vitro efficacy of candidate antimicrobials against extended-spectrum β-lactamase (ESBL)-producing isolates of extraintestinal pathogenic Escherichia coli (ExPEC) from companion animals. METHODOLOGY A total of 90 ESBL-producing ExPEC isolates from dogs and cats were tested for susceptibility to 16 antimicrobials with the agar dilution method. We also identified the ESBLs and AmpC β-lactamases of these isolates with PCR and DNA sequencing.Results/Key findings. All isolates were susceptible to meropenem, tebipenem and amikacin (AMK), and various proportions were susceptible to latamoxef (LMX, 97.8 %), fosfomycin (FOM, 97.8 %), faropenem (FPM, 96.7 %), nitrofurantoin (NFT, 96.7 %), flomoxef (FMX, 93.3 %), piperacillin/tazobactam (PTZ, 92.2 %), cefmetazole (CMZ, 91.1 %), chloramphenicol (80.0 %), trimethoprim/sulfamethoxazole (64.4 %), amoxicillin/clavulanic acid (63.3 %), ceftibuten (60.0 %), tetracycline (52.2 %) and enrofloxacin (10.0 %). A genetic analysis showed that 83 of the 90 (92.2 %) isolates were positive for CTX-M-type genes: CTX-M-14 (n=26), CTX-M-27 (n=20), CTX-M-55 (n=17), CTX-M-15 (n=12), CTX-M-2 (n=5), CTX-M-24 (n=2), CTX-M-104 (n=2) and CTX-M-3 (n=1). Eight isolates also expressed AmpC β-lactamase phenotypes. CONCLUSION This study demonstrates that the susceptibility rates to PTZ, CMZ, LMX, AMK, FOM, FPM, NFT and FMX were similar to those to carbapenems (>90 %), implying that these drugs are available alternatives to carbapenems for the treatment of companion animals infected with ExPEC-producing CTX-M-type ESBLs. Further in vivo studies of the effective use of these antimicrobials are required.
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Affiliation(s)
- Takae Shimizu
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi-shi, Yamaguchi 753-8511, Japan.,Joint Department of Veterinary Medicine, Tottori University, Minami 4-101, Koyama-cho, Tottori-shi, Tottori 680-8553, Japan
| | - Kazuki Harada
- Joint Department of Veterinary Medicine, Tottori University, Minami 4-101, Koyama-cho, Tottori-shi, Tottori 680-8553, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi-shi, Yamaguchi 753-8511, Japan
| | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory, 2-5-8 Kuji, Takatsuku, Kawasaki, Kanagawa 213-0032, Japan
| | - Yui Kimura
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi-shi, Yamaguchi 753-0851, Japan
| | - Tadashi Miyamoto
- Miyamoto Animal Hospital, 2265-8 Kurokawa, Yamaguchi-shi, Yamaguchi 753-0851, Japan
| | - Shingo Hatoya
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Yoshiaki Hikasa
- The United Graduate School of Veterinary Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi-shi, Yamaguchi 753-8511, Japan.,Joint Department of Veterinary Medicine, Tottori University, Minami 4-101, Koyama-cho, Tottori-shi, Tottori 680-8553, Japan
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10
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Phenotypic and molecular characterization of antimicrobial resistance in Enterobacter spp. isolates from companion animals in Japan. PLoS One 2017; 12:e0174178. [PMID: 28328967 PMCID: PMC5362103 DOI: 10.1371/journal.pone.0174178] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/04/2017] [Indexed: 01/13/2023] Open
Abstract
The emergence of antimicrobial resistance among Enterobacter spp., including resistance to extended-spectrum cephalosporins (ESC), is of great concern in both human and veterinary medicine. In this study, we investigated the prevalence of antimicrobial resistance among 60 isolates of Enterobacter spp., including E. cloacae (n = 44), E. aerogenes (n = 10), and E. asburiae (n = 6), from clinical specimens of dogs and cats from 15 prefectures in Japan. Furthermore, we characterized the resistance mechanisms harbored by these isolates, including extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR); and assessed the genetic relatedness of ESC-resistant Enterobacter spp. strains by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Antimicrobial susceptibility testing demonstrated the resistance rates to ampicillin (93.3%), amoxicillin-clavulanic acid (93.3%), cefmetazole (93.3%), chloramphenicol (46.7%), ciprofloxacin (43.3%), tetracycline (40.0%), ceftazidime (33.3%), cefotaxime (33.3%), trimethoprim/sulfamethoxazole (28.3%), gentamicin (23.3%), and meropenem (0%). Phenotypic testing detected ESBLs in 16 of 18 ESC-resistant E. cloacae isolates but not in the other species. The most frequent ESBL was CTX-M-15 (n = 8), followed by SHV-12 (n = 7), and CTX-M-3 (n = 1). As for AmpC β-lactamases, CMY-2 (n = 2) and DHA-1 (n = 2) were identified in ESC-resistant E. cloacae strains with or without ESBLs. All of the ESC-resistant E. cloacae strains also harbored one or two PMQRs, including qnrB (n = 15), aac(6’)-Ib-cr (n = 8), and qnrS (n = 2). Based on MLST and PFGE analysis, E. cloacae clones of ST591-SHV-12, ST171-CTX-M-15, and ST121-CTX-M-15 were detected in one or several hospitals. These results suggested intra- and inter-hospital dissemination of E. cloacae clones co-harboring ESBLs and PMQRs among companion animals. This is the first report on the large-scale monitoring of antimicrobial-resistant isolates of Enterobacter spp. from companion animals in Japan.
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Culture of Urine Specimens by Use of chromID CPS Elite Medium Can Expedite Escherichia coli Identification and Reduce Hands-On Time in the Clinical Laboratory. J Clin Microbiol 2016; 54:2767-2773. [PMID: 27582518 DOI: 10.1128/jcm.01376-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
Urine is one of the most common specimen types submitted to the clinical microbiology laboratory; the use of chromogenic agar is one method by which the laboratory might expedite culture results and reduce hands-on time and materials required for urine culture analysis. The objective of our study was to compare chromID CPS Elite (bioMérieux), a chromogenic medium, to conventional primary culture medium for evaluation of urine specimens. Remnant urine specimens (n = 200) were inoculated into conventional media and into chromID CPS Elite agar (chromID). The time to identification and consumables used were documented for both methods. Clinically significant pathogen(s) were recovered from 51 cultures using conventional media, with Escherichia coli being the most frequently recovered organism (n = 22). The rate of exact uropathogen agreement between conventional and chromogenic media was 82%, while overall categorical agreement was 83.5% The time interval between plating and final organism identification was decreased with chromID agar versus conventional media for E. coli (mean of 24.4 h versus 27.1 h, P < 0.001). Using chromID, clinically significant cultures required less hands-on time per culture (mean of 1 min and 2 s [1:02 min]) compared to conventional media (mean of 1:31 min). In addition, fewer consumables (2.4 versus 3.3 sticks and swabs) and rapid biochemical tests (1.0 versus 1.9) were necessary using chromID versus conventional media. Notably, antimicrobial susceptibility testing demonstrated good overall agreement (97.4%) between the chromID and conventional media for all antibiotics tested. chromID CPS Elite is accurate for uropathogen identification, reduces consumable usage, and may expedite the identification of E. coli in clinical specimens.
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Harada K, Shimizu T, Mukai Y, Kuwajima K, Sato T, Usui M, Tamura Y, Kimura Y, Miyamoto T, Tsuyuki Y, Ohki A, Kataoka Y. Phenotypic and Molecular Characterization of Antimicrobial Resistance in Klebsiella spp. Isolates from Companion Animals in Japan: Clonal Dissemination of Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae. Front Microbiol 2016; 7:1021. [PMID: 27446056 PMCID: PMC4925667 DOI: 10.3389/fmicb.2016.01021] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/15/2016] [Indexed: 12/25/2022] Open
Abstract
The emergence of antimicrobial resistance in Klebsiella spp., including resistance to extended-spectrum cephalosporins (ESC) and fluoroquinolones, is of great concern in both human and veterinary medicine. In this study, we investigated the prevalence of antimicrobial resistance in a total of 103 Klebsiella spp. isolates, consisting of Klebsiella pneumoniae complex (KP, n = 89) and K. oxytoca (KO, n = 14) from clinical specimens of dogs and cats in Japan. Furthermore, we characterized the resistance mechanisms, including extended-spectrum β-lactamase (ESBL), plasmid-mediated AmpC β-lactamase (PABL), and plasmid-mediated quinolone resistance (PMQR); and assessed genetic relatedness of ESC-resistant Klebsiella spp. strains by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Antimicrobial susceptibility testing demonstrated that resistance rates to ampicillin, cephalothin, enrofloxacin, ciprofloxacin, trimethoprim/sulfamethoxazole, cefotaxime, gentamicin, tetracycline, chloramphenicol, amoxicillin-clavulanic acid, and cefmetazole were 98.1, 37.9, 37.9, 35.9, 35.0, 34.0, 31.1, 30.1, 28.2, 14.6, and 6.8%, respectively. Phenotypic testing detected ESBLs and/or AmpC β-lactamases in 31 of 89 (34.8%) KP isolates, but not in KO isolates. Resistances to 5 of the 12 antimicrobials tested, as well as the three PMQRs [qnrB, qnrS, and aac(6′)-Ib-cr], were detected significantly more frequently in ESBL-producing KP, than in non-ESBL-producing KP and KO. The most frequent ESBL was CTX-M-15 (n = 13), followed by CTX-M-14 (n = 7), CTX-M-55 (n = 6), SHV-2 (n = 5), CTX-M-2 (n = 2), and CTX-M-3 (n = 2). Based on the rpoB phylogeny, all ESBL-producing strains were identified as K. pneumoniae, except for one CTX-M-14-producing strain, which was identified as K. quasipneumoniae. All of AmpC β-lactamase positive isolates (n = 6) harbored DHA-1, one of the PABLs. Based on MLST and PFGE analysis, ST15 KP clones producing CTX-M-2, CTX-M-15, CTX-M-55, and/or SHV-2, as well as KP clones of ST1844-CTX-M-55, ST655-CTX-M-14, and ST307-CTX-M-15, were detected in one or several hospitals. Surprisingly, specific clones were detected in different patients at an interval of many months. These results suggest that multidrug-resistant ESBL-producing KP were clonally disseminated among companion animals via not only direct but also indirect transmission. This is the first report on large-scale monitoring of antimicrobial-resistant Klebsiella spp. isolates from companion animals in Japan.
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Affiliation(s)
- Kazuki Harada
- Department of Veterinary Internal Medicine, Tottori University Tottori, Japan
| | - Takae Shimizu
- Department of Veterinary Internal Medicine, Tottori University Tottori, Japan
| | - Yujiro Mukai
- Laboratory of Veterinary Microbiology, Nippon Veterinary and Life Science University Tokyo, Japan
| | - Ken Kuwajima
- Laboratory of Veterinary Microbiology, Nippon Veterinary and Life Science University Tokyo, Japan
| | - Tomomi Sato
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University Hokkaido, Japan
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University Hokkaido, Japan
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, Rakuno Gakuen University Hokkaido, Japan
| | - Yui Kimura
- Miyamoto Animal Hospital Yamaguchi, Japan
| | | | - Yuzo Tsuyuki
- Sanritsu Zelkova Veterinary Laboratory Kanagawa, Japan
| | | | - Yasushi Kataoka
- Laboratory of Veterinary Microbiology, Nippon Veterinary and Life Science University Tokyo, Japan
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Abstract
After many years in the family Vibrionaceae, the genus Plesiomonas, represented by a single species, P. shigelloides, currently resides in the family Enterobacteriaceae, although its most appropriate phylogenetic position may yet to be determined. Common environmental reservoirs for plesiomonads include freshwater ecosystems and estuaries and inhabitants of these aquatic environs. Long suspected as being an etiologic agent of bacterial gastroenteritis, convincing evidence supporting this conclusion has accumulated over the past 2 decades in the form of a series of foodborne outbreaks solely or partially attributable to P. shigelloides. The prevalence of P. shigelloides enteritis varies considerably, with higher rates reported from Southeast Asia and Africa and lower numbers from North America and Europe. Reasons for these differences may include hygiene conditions, dietary habits, regional occupations, or other unknown factors. Other human illnesses caused by P. shigelloides include septicemia and central nervous system disease, eye infections, and a variety of miscellaneous ailments. For years, recognizable virulence factors potentially associated with P. shigelloides pathogenicity were lacking; however, several good candidates now have been reported, including a cytotoxic hemolysin, iron acquisition systems, and lipopolysaccharide. While P. shigelloides is easy to identify biochemically, it is often overlooked in stool samples due to its smaller colony size or relatively low prevalence in gastrointestinal samples. However, one FDA-approved PCR-based culture-independent diagnostic test system to detect multiple enteropathogens (FilmArray) includes P. shigelloides on its panel. Plesiomonads produce β-lactamases but are typically susceptible to many first-line antimicrobial agents, including quinolones and carbapenems.
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Affiliation(s)
- J Michael Janda
- Kern County Public Health Laboratory, Department of Public Health Services, Bakersfield, California, USA
| | - Sharon L Abbott
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, California, USA
| | - Christopher J McIver
- Microbiology Department (SEALS), St. George Hospital, Kogarah, and School of Medical Sciences, University of New South Wales, NSW, Sydney, Australia
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Payne M, Roscoe D. Evaluation of two chromogenic media for the isolation and identification of urinary tract pathogens. Eur J Clin Microbiol Infect Dis 2014; 34:303-8. [PMID: 25172638 DOI: 10.1007/s10096-014-2235-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 08/18/2014] [Indexed: 11/24/2022]
Abstract
Chromogenic media (CM) are available for urine specimens (US) to enable rapid identification of common urinary tract pathogens (UTP). Two CM, chromID™ CPS (CPS4) agar (bioMérieux, St. Laurent, QC) and UriSelect™ 4 (URS4) agar (Bio-Rad, Montreal, QC), were compared to the standard media (SM) for the isolation and identification of UTP. Over a 10-day period, US were inoculated to CPS4, URS4, and SM (BAP and MAC). CM interpretation was done according to the product inserts by one person blinded to the results of SM. SM were read by experienced technologists according to protocol and isolates were identified using BD Phoenix™. The results were grouped into significant (SG), mixed (MG), and no significant growth (NSG). A total of 903 US were studied. SM identified 239 SG, 112 MG, and 552 NSG cultures. The most common pathogens were Escherichia coli (38 %) and Enterococcus spp. (11 %). Comparing CM to SM, the exact agreement was 89.3 and 89.5 % for URS4 and CPS4, respectively. When grouped by clinical significance, agreement with SM was 93.0 and 93.1 % for URS4 and CPS4, respectively. CM were equivalent with respect to processing time. Advantages include decreased need for automated identification of certain species, particularly E. coli. In terms of workflow, CM enables same-day identification for almost 50 % of significant UTP. Overall, both CM compared well to SM and allowed for rapid preliminary identification of many UTP.
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Affiliation(s)
- M Payne
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada,
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Serum Helicobacter pylori NapA antibody as a potential biomarker for gastric cancer. Sci Rep 2014; 4:4143. [PMID: 24553293 PMCID: PMC3929916 DOI: 10.1038/srep04143] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/04/2014] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection is strongly associated with gastric cancer. However, only a minority of infected individuals ever develop gastric cancer. This risk stratification may be in part due to differences among strains. The relationship between neutrophil-activating protein (NapA) and gastric cancer is unclear. The purpose of this study is to evaluate the significance of NapA as a biomarker in gastric cancer. We used enzyme linked immunosorbent assay (ELISA) to determine the status of H. pylori infection. Indirect ELISA method was used for detection of NapA antibody titer in the serum of H. pylori infected individuals. Unconditional logistic regressions were adopted to analyze the variables and determine the association of NapA and gastric cancer. The results of study indicated serum H. pylori NapA antibody level were associated with a reduced risk for development of gastric cancer. It may be used in conjugation with other indicators for gastric cancer detection.
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Performance of SaSelect, a chromogenic medium for detection of staphylococci in clinical specimens. J Clin Microbiol 2014; 52:1041-4. [PMID: 24430448 DOI: 10.1128/jcm.03129-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a preliminary study, known staphylococcus (n = 86) and other microbial (n = 12) isolates were plated on three chromogenic media, SaSelect (Bio-Rad, Hercules, CA, USA), CHROMagar Staph. aureus (CHROMagar Microbiology, Paris, France), and S. aureus ID (bioMérieux, Marcy l'Etoile, France). The sensitivities of all the media to detect Staphylococcus aureus after 24 h of incubation were high (100.0%). However, their specificities varied at 93.3% (95% confidence interval [CI], 86.0% to 100.0%) (CHROMagar Staph. aureus), 97.8% (95% CI, 93.5% to 100.0%) (S. aureus ID), and 100.0% (SaSelect). SaSelect also showed the highest sensitivity for recovery and differentiation of other staphylococci. As the best performing chromogenic medium, SaSelect was then prospectively compared to conventional culture and identification tests for the detection of staphylococci from 2,780 clinical specimens. A total of 1,589 staphylococcal isolates were recovered. Of these, 912 were S. aureus and 677 were other staphylococci. The sensitivity and specificity of SaSelect to detect S. aureus in clinical specimens after 24 h of incubation were 99.6% and 99.9% (95% CI, 99.2% to 100.0% and 99.8% to 100.0%), respectively, whereas the sensitivity and specificity using conventional plates combined with laboratory identification methods were 96.8% and 99.5% (95% CI, 95.7 to 97.9% and 99.2% to 99.8%). For the recovery and preliminary identification of other staphylococci, the sensitivity and specificity of SaSelect were 94.4% and 99.9%. SaSelect is a well-performing chromogenic medium that significantly improved the detection of staphylococci, especially S. aureus, compared to conventional culture (P < 0.0001).
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Abstract
Microbiology laboratories continually strive to streamline and improve their urine culture algorithms because of the high volumes of urine specimens they receive and the modest numbers of those specimens that are ultimately considered clinically significant. In the current study, we quantitatively measured the impact of the introduction of CHROMagar Orientation (CO) medium into routine use in two hospital laboratories and compared it to conventional culture on blood and MacConkey agars. Based on data extracted from our Laboratory Information System from 2006 to 2011, the use of CO medium resulted in a 28% reduction in workload for additional procedures such as Gram stains, subcultures, identification panels, agglutination tests, and biochemical tests. The average number of workload units (one workload unit equals 1 min of hands-on labor) per urine specimen was significantly reduced (P < 0.0001; 95% confidence interval [CI], 0.5326 to 1.047) from 2.67 in 2006 (preimplementation of CO medium) to 1.88 in 2011 (postimplementation of CO medium). We conclude that the use of CO medium streamlined the urine culture process and increased bench throughput by reducing both workload and turnaround time in our laboratories.
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Kootallur BN, Thangavelu CP, Mani M. Bacterial identification in the diagnostic laboratory: how much is enough? Indian J Med Microbiol 2012; 29:336-40. [PMID: 22120791 DOI: 10.4103/0255-0857.90156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The major impetus for bacterial identification came after the advent of solid culture media. Morphological appearance of bacterial colonies was often sufficient for their identification in the laboratory. Even in modern times, preliminary identification of most cultivable bacteria is based on such morphological characters. Advances have been made media for the presumptive identification of common organisms encountered in clinical samples. Phenotypic characterisation of bacteria with, physiological tests with a battery of biochemical tests differentiate related bacterial genera as well as confirm their identity. . Each laboratory can select its own method(s) of identification, provided they are based on scientific / epidemiological evidence; clinical laboratory and standards institute (CLSI) is a widely accepted organization and laboratories in many parts of the world follow its recommendations for bacterial identification. Some of the latest advances in identification include Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectroscopy (MALDI-TOF) is a state of art facility used for fast and reliable species-specific identification of bacteria including Mycobacteria and fungi including yeasts. However the single most important factor that decides the method of bacterial identification in any laboratory is the cost involved. In the final analysis, selection of tests for bacterial identification should be based on their standardization with proper scientific basis. Considering the cost and lack of easy availability of commercial kits, we have put forward a simplified and rapid method of identification for most commonly encountered bacterial pathogens causing human infection in India.
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Affiliation(s)
- B N Kootallur
- Microbiological Laboratory, 12A Cowley Brown Road (East), RS Puram, Coimbatore - 641 002, India.
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Ng LSY, Tan TY, Yeow SCS. A cost-effective method for the presumptive identification of Enterobacteriaceae for diagnostic microbiology laboratories. Pathology 2010; 42:280-3. [PMID: 20350223 DOI: 10.3109/00313021003631338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS This study evaluated the use of an abbreviated algorithm for the presumptive identification of Enterobacteriaceae isolated from clinical microbiology specimens. METHODS Identification was based on primary isolation of bacterial pathogens on blood, lactose fermentation based on colonial morphology on MacConkey agar, oxidase and indole tests, and a limited number of conventional biochemical tests. The accuracy of the study algorithm was prospectively evaluated against commercial bacterial identification kits, using clinical isolates from blood, urine and superficial wound and tissue sites. RESULTS Of 534 isolates, 518 (97%) were accurately identified to genus level. Identification of the study isolates was achieved with a 56% reduction in technologist time and 85% reduction in reagent costs, when compared to the use of a conventional biochemical identification panel. The main limitation of the protocol in the tested bacterial population was that indole-negative Escherichia coli were likely to be misidentified as Enterobacter species. CONCLUSIONS This protocol may be suitable for the presumptive identification of commonly isolated Enterobacteriaceae from non-sterile sites by diagnostic laboratories in resource-constrained settings.
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Gorkiewicz G. Nosocomial and antibiotic-associated diarrhoea caused by organisms other than Clostridium difficile. Int J Antimicrob Agents 2009; 33 Suppl 1:S37-41. [PMID: 19303568 DOI: 10.1016/s0924-8579(09)70015-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Most cases of nosocomial and antibiotic-associated diarrhoea are caused by alteration of the physiological gut microflora. This alteration leads to reduced microbial metabolism of carbohydrates and primary bile acids, resulting in osmotic or secretory forms of diarrhoea. Moreover, facultative enteropathogens may experience a growth advantage due to the antibiotic-induced microflora alteration that, in turn, can harm the gut mucosa by the toxins they produce. Clostridium difficile is the major infectious agent leading to pseudomembranous colitis. However, there is increasing evidence that certain other pathogens such as enterotoxin-producing Clostridium perfringens, Staphylococcus aureus and Klebsiella oxytoca can induce mucosal deterioration and diarrhoea after antibiotic use. But, as with C. difficile, these facultative enteropathogens can also be found in the healthy population. Their contribution to disease is, therefore, controversial and their presence in the stools of antibiotic-associated diarrhoea patients is often claimed to be mere colonisation. In this respect, the causal relationship of each suspected pathogen with the development of intestinal disease has to be proved clinically and experimentally.
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Affiliation(s)
- Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, A-8036 Graz, Austria.
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21
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Long M, Luo J, Li Y, Zeng FY, Li M. Detection and evaluation of antibodies against neutrophil-activating protein of Helicobacter pylori in patients with gastric cancer. World J Gastroenterol 2009; 15:2381-8. [PMID: 19452583 PMCID: PMC2684607 DOI: 10.3748/wjg.15.2381] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect and evaluate the antibodies against Helicobacter pylori (H pylori) neutrophil-activating protein (HP-NAP) in patients with gastric cancer and other gastroduodenal diseases.
METHODS: Recombinant HP-NAP was prepared from a prokaryotic expression system in Escherichia coli. Serum positivity and level of HP-NAP-specific antibodies in sera from 43 patients with gastric cancer, 28 with chronic gastritis, 28 with peptic ulcer, and 89 healthy controls were measured by rHP-NAP-based ELISA. rHP-NAP-stimulated production of interleukin-8 (IL-8) and growth-related oncogene (GROα) cytokines in the culture supernatant of SGC7901 gastric epithelial cells was also detected.
RESULTS: The serum positivity and mean absorbance value of HP-NAP-specific antibodies in the gastric cancer group (97.7% and 1.01 ± 0.24) were significantly higher than those in the chronic gastritis group (85.7% and 0.89 ± 0.14, P < 0.005) and healthy control group (27.7% and 0.65 ± 0.18, P < 0.001). The sensitivity and specificity of ELISA for the detection of HP-NAP-specific antibodies were 95.5% and 91.5%, respectively. HP-NAP could slightly up-regulate IL-8 production in gastric epithelial cell lines but had no effect on GROα production.
CONCLUSION: Infection with virulent H pylori strains secreting HP-NAP is associated with severe gastroduodenal diseases, and HP-NAP may play a role in the development of gastric carcinoma. rHP-NAP-based ELISA can be used as a new method to detect H pylori infection. The direct effect of HP-NAP on gastric epithelial cells may be limited, but HP-NAP may contribute to inflammatory response or carcinogenesis by activating neutrophils.
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Arias JI, Aller MA, Arias J. Surgical inflammation: a pathophysiological rainbow. J Transl Med 2009; 7:19. [PMID: 19309494 PMCID: PMC2667492 DOI: 10.1186/1479-5876-7-19] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Accepted: 03/23/2009] [Indexed: 01/19/2023] Open
Abstract
Tetrapyrrole molecules are distributed in virtually all living organisms on Earth. In mammals, tetrapyrrole end products are closely linked to oxygen metabolism. Since increasingly complex trophic functional systems for using oxygen are considered in the post-traumatic inflammatory response, it can be suggested that tetrapyrrole molecules and, particularly their derived pigments, play a key role in modulating inflammation. In this way, the diverse colorfulness that the inflammatory response triggers during its evolution would reflect the major pathophysiological importance of these pigments in each one of its phases. Therefore, the need of exploiting this color resource could be considered for both the diagnosis and treatment of the inflammation.
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Evaluation of the Biomic V3 microbiology system for identification of selected species on BBL CHROMagar orientation agar and CHROMagar MRSA medium. J Clin Microbiol 2008; 46:3488-90. [PMID: 18701661 DOI: 10.1128/jcm.02460-07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Biomic V3 microbiology system identifies bacteria by reading the color of colonies selected by the user. For CHROMagar orientation, Biomic results agreed with conventional methods for 94% of the strains assayed. For CHROMagar MRSA, Biomic correctly identified 100% of the strains tested and did not misidentify two methicillin-susceptible Staphylococcus aureus strains growing on the plates.
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Abstract
Since 1990, a wide range of chromogenic culture media has been made commercially available providing useful tools for diagnostic clinical microbiology. By the inclusion of chromogenic enzyme substrates targeting microbial enzymes, such media are able to target pathogens with high specificity. Examples of target pathogens include Staphylococcus aureus, Streptococcus agalactiae, Salmonella spp. and Candida spp. The inclusion of multiple chromogenic substrates into culture media facilitates the differentiation of polymicrobial cultures, thus allowing for the development of improved media for diagnosis of urinary tract infections and media for the enhanced discrimination of yeasts. The purpose of this review is to provide some insight into how such media work and appraise their utility in routine clinical diagnostics, in comparison with conventional media.
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Affiliation(s)
- J D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, UK.
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Moore DF, Harwood VJ, Ferguson DM, Lukasik J, Hannah P, Getrich M, Brownell M. Evaluation of antibiotic resistance analysis and ribotyping for identification of faecal pollution sources in an urban watershed. J Appl Microbiol 2005; 99:618-28. [PMID: 16108804 DOI: 10.1111/j.1365-2672.2005.02612.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The accuracy of ribotyping and antibiotic resistance analysis (ARA) for prediction of sources of faecal bacterial pollution in an urban southern California watershed was determined using blinded proficiency samples. METHODS AND RESULTS Antibiotic resistance patterns and HindIII ribotypes of Escherichia coli (n = 997), and antibiotic resistance patterns of Enterococcus spp. (n = 3657) were used to construct libraries from sewage samples and from faeces of seagulls, dogs, cats, horses and humans within the watershed. The three libraries were analysed to determine the accuracy of host source prediction. The internal accuracy of the libraries (average rate of correct classification, ARCC) with six source categories was 44% for E. coli ARA, 69% for E. coli ribotyping and 48% for Enterococcus ARA. Each library's predictive ability towards isolates that were not part of the library was determined using a blinded proficiency panel of 97 E. coli and 99 Enterococcus isolates. Twenty-eight per cent (by ARA) and 27% (by ribotyping) of the E. coli proficiency isolates were assigned to the correct source category. Sixteen per cent were assigned to the same source category by both methods, and 6% were assigned to the correct category. Addition of 2480 E. coli isolates to the ARA library did not improve the ARCC or proficiency accuracy. In contrast, 45% of Enterococcus proficiency isolates were correctly identified by ARA. CONCLUSIONS None of the methods performed well enough on the proficiency panel to be judged ready for application to environmental samples. SIGNIFICANCE AND IMPACT OF THE STUDY Most microbial source tracking (MST) studies published have demonstrated library accuracy solely by the internal ARCC measurement. Low rates of correct classification for E. coli proficiency isolates compared with the ARCCs of the libraries indicate that testing of bacteria from samples that are not represented in the library, such as blinded proficiency samples, is necessary to accurately measure predictive ability. The library-based MST methods used in this study may not be suited for determination of the source(s) of faecal pollution in large, urban watersheds.
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Affiliation(s)
- D F Moore
- Orange County Public Health Laboratory, Santa Ana, CA, USA
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D'Souza HA, Campbell M, Baron EJ. Practical bench comparison of BBL CHROMagar Orientation and standard two-plate media for urine cultures. J Clin Microbiol 2004; 42:60-4. [PMID: 14715732 PMCID: PMC321721 DOI: 10.1128/jcm.42.1.60-64.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 1023 urine samples sent for routine culture were plated onto sheep blood and MacConkey agars and a BBL CHROMagar Orientation (CO; Becton Dickinson, Cockeysville, Md.) plate, and the results were compared. Of these, 250 urine samples (24%) grew >10000 CFU of one or two putative pathogens/ml and 773 showed no growth (NG), mixed growth of <10000 CFU/ml, or three or more strains (mixed). The CO and conventional medium results agreed completely for 595 cultures with NG or <10000 CFU/ml. An additional 178 urine samples yielded clinically insignificant differences. Both medium sets essentially agreed on quantities and identification for 400 single-pathogen cultures and 9 mixed cultures. With the caveat that CO cannot differentiate Klebsiella, Enterobacter, and Serratia spp., enteric pathogens were identified only by morphology and color on CO. Direct visual differentiation of group B streptococci from lactobacilli is not possible, but lactobacillus cells always exhibited easily recognizable morphology on Gram stain. Of 108 paired organism susceptibility results encompassing 2268 drug-pathogen combinations, there were 3% errors and only 1% very major errors. Use of CO allowed a >50% reduction in inoculation time and a >20% reduction in work-up time. For our laboratory, with 50% "no growth" and ca. 25% significant results (50% Escherichia coli), CO allowed time and workup cost savings for a majority of cultures. A cost analysis (time and supplies for our laboratory) showed that if CO is used alone, the break-even level for CO pricing is US dollars 1.78; if CO and blood agar are both used, the break-even pricing for CO is US dollars 1.53.
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Affiliation(s)
- Holly A D'Souza
- Department of Pathology. Department of Medicine, Stanford University Medical School, Stanford, California 94305, USA
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Filius PMG, van Netten D, Roovers PJE, Vulto AG, Gyssens IC, Verbrugh HA, Endtz HP. Comparative evaluation of three chromogenic agars for detection and rapid identification of aerobic Gram-negative bacteria in the normal intestinal microflora. Clin Microbiol Infect 2004; 9:912-8. [PMID: 14616678 DOI: 10.1046/j.1469-0691.2003.00667.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To compare three different chromogenic agars and MacConkey agar for the detection of aerobic Gram-negative bacteria in the normal intestinal microflora and to assess the accuracy of the chromogenic agars for the direct identification of Escherichia coli. METHODS A total of 164 Gram-negative clinical isolates (E. coli, Proteus, Klebsiella, Enterobacter, Morganella and Pseudomonas species) and 30 stool specimens were inoculated in parallel on four media: Chromagar E. coli/Coliform, Chromogenic urinary tract infection UTI medium, CHROMagar Orientation and MacConkey agar. All colonies that differed by color and/or morphology were selected for further identification by VITEK 1 and/or API 20E from each medium. RESULTS On E. coli/Coliform agar five out of 32 (16%) E. coli strains failed to produce the color as described by the manufacturer. No remarkable discrepancies were found for the other clinical isolates. There was no significant difference in detection rate (DR) of aerobic Gram-negative bacteria in stool specimens between the different chromogenic agars and MacConkey agar. The overall DR was about 84%, and varied from 100% for monomicrobial specimens to 33% for polymicrobial specimens. The positive predictive values (PPV) for the direct identification of E. coli on Chromagar E. coli/Coliform, Chromogenic UTI medium and CHROMagar Orientation were 1.00, 0.93 and 0.93, respectively. The negative predictive values (NPV) were 0.53, 0.68 and 0.69, respectively. CONCLUSION Chromogenic UTI medium and CHROMagar Orientation are the preferred media because of the higher NPV. The high PPV of these agars allows accurate and rapid identification of E. coli.
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Affiliation(s)
- P M G Filius
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 40, 3015 GD Rotterdam, the Netherlands.
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Kovtunovych G, Lytvynenko T, Negrutska V, Lar O, Brisse S, Kozyrovska N. Identification of Klebsiella oxytoca using a specific PCR assay targeting the polygalacturonase pehX gene. Res Microbiol 2004; 154:587-92. [PMID: 14527660 DOI: 10.1016/s0923-2508(03)00148-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacteria of the genus Klebsiella are important opportunistic pathogens responsible for nosocomial infections that are increasingly resistant to antimicrobial agents. Distinctive identification of the species K. oxytoca, K. pneumoniae, K. planticola, K. ornithinolytica and K. terrigena is difficult based on phenotypic tests and misidentifications are frequent in routine clinical microbiology. We developed a specific method to discriminate K. oxytoca from the other species of the genus Klebsiella, based on the PCR amplification of the polygalacturonase (pehX) gene. A PCR amplicon of 344 bp was obtained in all 35 K. oxytoca strains tested, but in none of the 29 K. pneumoniae, 12 K. planticola/K. ornithinolytica and 7 K. terrigena strains tested. The test was also negative for polygalacturonate-degrading species of the genus Erwinia. Analysis of 24 strains designated as K. pneumoniae from international collections (NCTC, PZH) revealed previous misidentification of six K. oxytoca strains. Key biochemical tests fully confirmed the pehX PCR results. The new K. oxytoca identification assay should be useful for both clinical and ecological monitoring of K. oxytoca strains, as well as for controlling the previous identification of collection strains.
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Affiliation(s)
- Gennadiy Kovtunovych
- Department of Regulatory Cell Mechanisms, Institute of Molecular Biology and Genetics of the National Academy of Sciences, Zabolotnoho Str 150, Kyiv 03143, Ukraine
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Kovtunovych GL, Lytvynenko T, Negrutska VV, Lar OV, Koltukova NV, Kozyrovska NO. A PCR-mediated method for discrimination of Klebsiella oxytoca between closely related bacteria in environmental and clinical specimens. ACTA ACUST UNITED AC 2003. [DOI: 10.7124/bc.00067d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- G. L. Kovtunovych
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - T. Lytvynenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. V. Negrutska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - O. V. Lar
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - N. V. Koltukova
- Gromashevsky L. V. Institute of Epidemiology and Infection Diseases, AMS of Ukraine
| | - N. O. Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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Pearman JW, Peterson AM, Lee RC, Orrell CT, Perry P, Kosaras FP, O’Brien FG. The epidemiology of a large single-strain outbreak of vancomycin-resistant Enterococcus faecium vanB in an Australian teaching hospital. ACTA ACUST UNITED AC 2003. [DOI: 10.1071/hi03077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Perry JD, Butterworth LA, Nicholson A, Appleby MR, Orr KE. Evaluation of a new chromogenic medium, Uriselect 4, for the isolation and identification of urinary tract pathogens. J Clin Pathol 2003; 56:528-31. [PMID: 12835299 PMCID: PMC1769995 DOI: 10.1136/jcp.56.7.528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIMS To compare the performance of a new chromogenic medium, Uriselect 4, with cystine lactose electrolyte deficient (CLED) agar and an established chromogenic agar, CPS ID 2 medium, for detection of urinary tract pathogens. METHODS Using a semiquantitative culture method, 777 samples were inoculated on to the three test media in duplicate. All bacterial strains that yielded a potentially significant growth were observed for colony colour and identified using standard methods. RESULTS Of the 777 samples tested, 589 urine samples yielded potentially significant growth of at least one strain. A total of 811 strains were isolated on at least one of the three media. A total of 168 urine samples yielded a mixture of at least two strains. Uriselect 4 medium showed the best sensitivity of the three media and only failed to recover 14 strains (1.7%). CPS ID 2 medium failed to recover 22 strains (2.7%). CLED medium showed the worst recovery and failed to recover 74 strains (9.1%). Both chromogenic media allowed for identification of Escherichia coli with a high degree of specificity (98% for Uriselect 4, 99.7% for CPS ID 2). Inclusion of a spot indole test increased the specificity of both chromogenic media to 100% for E coli. CONCLUSIONS Uriselect 4 and CPS ID 2 were superior to CLED medium for the isolation of urinary tract pathogens mainly because of their ability to discriminate mixed cultures. Both chromogenic media were also useful for the preliminary identification of the most common urinary tract pathogens.
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Affiliation(s)
- J D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK.
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Abstract
This paper provides a short overview of modern, molecular-based diagnostic procedures of urogenital tract infections. Although gaining importance, molecular methods have not yet become a reliable substitution for the classic procedures in terms of costs and quality standards. As an example of a new molecular approach in microbiology, a method for the detection of the most relevant uropathogens in a single PCR is presented. Furthermore, the development of a real time PCR is described.
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Affiliation(s)
- R Geisel
- Institut für Hygiene, Medizinische Einrichtungen der Heinrich-Heine-Universität Düsseldorf.
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Kronvall G, Hagelberg A. Numerical evaluation of minimal biochemical test combinations for the identification of Enterobacteriaceae species. APMIS 2002; 110:451-7. [PMID: 12193206 DOI: 10.1034/j.1600-0463.2002.100603.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Species identification of 572 clinical isolates of Enterobacteriaceae was determined using an in-house biochemical test panel and API 20E. The overall agreement was 82.7 per cent. When a numerical identification programme for Enterobacteriaceae was used to analyze the results of 440 E.coli isolates, the agreement with API 20E increased from 81.4 to 91.1 per cent. Numerical identification was then employed to evaluate 14 routine biochemical test panels used in 12 Swedish laboratories, and an additional 18 potential new test panel variants. The theoretical identification power of the panels was measured by a scoring system, based on simulated test results for the 14 most common species of Enterobacteriaceae. The results showed wide variations in the performance of different panels, with a number of panels being of insufficient quality. Among the 32 test panels, 6 panels indicated excellent performance. These should be further evaluated for routine laboratory performance. Numerical identification methods constitute powerful tools in the hands of the clinical microbiologist to aid in species identification as well as to analyze the quality of identification charts in use.
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Affiliation(s)
- Göran Kronvall
- Clinical Microbiology - MTC, Karolinska Institute, Karolinska Hospital, Stockholm, Sweden.
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