Review
. 2014 Oct; 27(4):1025-47.
doi: 10.1128/CMR.00049-14.

Clinical microbiology informatics

Daniel D Rhoads 1 Vitali Sintchenko 2 Carol A Rauch 3 Liron Pantanowitz 4 
Affiliations
  • PMID: 25278581
  •     168 References
  •     18 citations

Abstract

The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.

Improving empiric antibiotic selection using computer decision support.
R S Evans, D C Classen, +2 authors, J P Burke.
Arch Intern Med, 1994 Apr 25; 154(8). PMID: 8154950
The clinical microbiology laboratory director in the United States hospital setting.
Richard B Thomson, Michael L Wilson, Melvin P Weinstein.
J Clin Microbiol, 2010 Aug 27; 48(10). PMID: 20739497    Free PMC article.
Incidence and predictors of microbiology results returning postdischarge and requiring follow-up.
Robert El-Kareh, Christopher Roy, +2 authors, Eric G Poon.
J Hosp Med, 2011 Jun 11; 6(5). PMID: 21661103    Free PMC article.
Building phylogenetic trees from molecular data with MEGA.
Barry G Hall.
Mol Biol Evol, 2013 Mar 15; 30(5). PMID: 23486614
Highly Cited.
The world's microbiology laboratories can be a global microbial sensor network.
Thomas F O'Brien, John Stelling.
Biomedica, 2014 Jun 27; 34 Suppl 1. PMID: 24968031    Free PMC article.
Reporting practices of microbiology laboratories.
V P Ackerman, R C Pritchard, +2 authors, A Lee.
J Clin Pathol, 1980 Sep 01; 33(9). PMID: 7430395    Free PMC article.
Computer-assisted decision support for the diagnosis and treatment of infectious diseases in intensive care units.
C A M Schurink, P J F Lucas, I M Hoepelman, M J M Bonten.
Lancet Infect Dis, 2005 Apr 28; 5(5). PMID: 15854886
Review.
Standard operating procedure for optimal identification of mycobacteria using 16S rRNA gene sequences.
Enrico Tortoli.
Stand Genomic Sci, 2011 Feb 10; 3(2). PMID: 21304744    Free PMC article.
Monitoring influenza activity in the United States: a comparison of traditional surveillance systems with Google Flu Trends.
Justin R Ortiz, Hong Zhou, +3 authors, Christopher H Goss.
PLoS One, 2011 May 11; 6(4). PMID: 21556151    Free PMC article.
Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.
Sandra Reuter, Matthew J Ellington, +11 authors, Sharon J Peacock.
JAMA Intern Med, 2013 Jul 17; 173(15). PMID: 23857503    Free PMC article.
Highly Cited.
Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.
Amber L Hartman, Sean Riddle, +2 authors, Jonathan A Eisen.
BMC Bioinformatics, 2010 Jun 15; 11. PMID: 20540779    Free PMC article.
The Danish Microbiology Database (MiBa) 2010 to 2013.
M Voldstedlund, M Haarh, K Mølbak, MiBa Board of Representatives.
Euro Surveill, 2014 Jan 18; 19(1). PMID: 24434175
Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
Jennifer L Gardy, James C Johnston, +16 authors, Patrick Tang.
N Engl J Med, 2011 Feb 25; 364(8). PMID: 21345102
Highly Cited.
Syndromic surveillance and bioterrorism-related epidemics.
James W Buehler, Ruth L Berkelman, David M Hartley, Clarence J Peters.
Emerg Infect Dis, 2003 Nov 12; 9(10). PMID: 14609452    Free PMC article.
Review.
Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP).
Scot E Dowd, Randall D Wolcott, +3 authors, Daniel Rhoads.
PLoS One, 2008 Oct 04; 3(10). PMID: 18833331    Free PMC article.
Highly Cited.
Real-time PCR in clinical microbiology: applications for routine laboratory testing.
M J Espy, J R Uhl, +8 authors, T F Smith.
Clin Microbiol Rev, 2006 Jan 19; 19(1). PMID: 16418529    Free PMC article.
Highly Cited. Review.
Telemicrobiology: feasibility study.
W J McLaughlin, R B Schifman, +4 authors, R S Weinstein.
Telemed J, 1998 May 23; 4(1). PMID: 9599069
CLIA program and HIPAA privacy rule; patients' access to test reports. Final rule.
Centers for Medicare & Medicaid Services (CMS), HHS, Centers for Disease Control and Prevention (CDC), HHS, Office for Civil Rights (OCR), HHS.
Fed Regist, 2014 Mar 13; 79(25). PMID: 24605389
Using online reviews by restaurant patrons to identify unreported cases of foodborne illness - New York City, 2012-2013.
Cassandra Harrison, Mohip Jorder, +8 authors, Centers for Disease Control and Prevention (CDC).
MMWR Morb Mortal Wkly Rep, 2014 May 23; 63(20). PMID: 24848215    Free PMC article.
Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB.
Patrick C Y Woo, Jade L L Teng, +3 authors, Kwok-Yung Yuen.
J Clin Microbiol, 2011 Mar 11; 49(5). PMID: 21389154    Free PMC article.
Laboratory-guided detection of disease outbreaks: three generations of surveillance systems.
Vitali Sintchenko, Blanca Gallego.
Arch Pathol Lab Med, 2009 Jun 06; 133(6). PMID: 19492884
Review.
Modern clinical microbiology: new challenges and solutions.
Pierre-Edouard Fournier, Michel Drancourt, +3 authors, Didier Raoult.
Nat Rev Microbiol, 2013 Sep 11; 11(8). PMID: 24020074    Free PMC article.
Highly Cited. Review.
User interface reengineering. Innovative applications of bar coding in a clinical microbiology laboratory.
K E Willard, C J Shanholtzer.
Arch Pathol Lab Med, 1995 Aug 01; 119(8). PMID: 7646327
OpenCFU, a new free and open-source software to count cell colonies and other circular objects.
Quentin Geissmann.
PLoS One, 2013 Mar 05; 8(2). PMID: 23457446    Free PMC article.
Highly Cited.
Automatic electronic laboratory-based reporting of notifiable infectious diseases at a large health system.
Anil A Panackal, Nkuchia M M'ikanatha, +12 authors, Lee H Harrison.
Emerg Infect Dis, 2002 Jul 04; 8(7). PMID: 12095435    Free PMC article.
Image analysis approach for development of a decision support system for detection of malaria parasites in thin blood smear images.
Keerthana Prasad, Jan Winter, +2 authors, Gopalakrishna K Prabhu.
J Digit Imaging, 2011 Dec 08; 25(4). PMID: 22146834    Free PMC article.
Matrix-assisted laser desorption ionization-time of flight mass spectrometry in clinical microbiology.
Robin Patel.
Clin Infect Dis, 2013 Apr 19; 57(4). PMID: 23595835
Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria.
Jenna Rychert, Carey-Ann D Burnham, +12 authors, John A Branda.
J Clin Microbiol, 2013 May 10; 51(7). PMID: 23658261    Free PMC article.
The complex methylome of the human gastric pathogen Helicobacter pylori.
Juliane Krebes, Richard D Morgan, +10 authors, Sebastian Suerbaum.
Nucleic Acids Res, 2013 Dec 05; 42(4). PMID: 24302578    Free PMC article.
An intranet-based automated system for the surveillance of nosocomial infections: prospective validation compared with physicians' self-reports.
Samir Bouam, Emmanuelle Girou, +2 authors, Eric Lepage.
Infect Control Hosp Epidemiol, 2003 Feb 01; 24(1). PMID: 12558236
Concordance between whole-slide imaging and light microscopy for routine surgical pathology.
W Scott Campbell, Subodh M Lele, +3 authors, Steven H Hinrichs.
Hum Pathol, 2012 May 18; 43(10). PMID: 22591912
Automated bacterial identification by angle resolved dark-field imaging.
Benjamin K Wilson, Genevieve D Vigil.
Biomed Opt Express, 2013 Sep 21; 4(9). PMID: 24049690    Free PMC article.
A genomic day in the life of a clinical microbiology laboratory.
S Wesley Long, Dawn Williams, +4 authors, Randall J Olsen.
J Clin Microbiol, 2013 Jan 25; 51(4). PMID: 23345298    Free PMC article.
Electronic laboratory reporting for the infectious diseases physician and clinical microbiologist.
Rebecca Wurtz, Bruce J Cameron.
Clin Infect Dis, 2005 May 13; 40(11). PMID: 15889362
Automation in clinical microbiology.
Paul P Bourbeau, Nathan A Ledeboer.
J Clin Microbiol, 2013 Mar 22; 51(6). PMID: 23515547    Free PMC article.
Review.
Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review.
Giovanni Cammarota, Gianluca Ianiro, Antonio Gasbarrini.
J Clin Gastroenterol, 2014 Jan 21; 48(8). PMID: 24440934
Highly Cited. Systematic Review.
DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences.
Erik S Wright, L Safak Yilmaz, Daniel R Noguera.
Appl Environ Microbiol, 2011 Nov 22; 78(3). PMID: 22101057    Free PMC article.
Highly Cited.
Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs.
Katherine K Perez, Randall J Olsen, +5 authors, James M Musser.
Arch Pathol Lab Med, 2012 Dec 12; 137(9). PMID: 23216247
Highly Cited.
Performance of Kiestra total laboratory automation combined with MS in clinical microbiology practice.
Nico T Mutters, Caspar J Hodiamont, +3 authors, Caroline E Visser.
Ann Lab Med, 2014 Mar 14; 34(2). PMID: 24624346    Free PMC article.
Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing.
Daniel D Rhoads, Stephen B Cox, +2 authors, Randall D Wolcott.
BMC Infect Dis, 2012 Nov 28; 12. PMID: 23176603    Free PMC article.
Automated detection of infectious disease outbreaks in hospitals: a retrospective cohort study.
Susan S Huang, Deborah S Yokoe, +8 authors, Richard Platt.
PLoS Med, 2010 Feb 27; 7(2). PMID: 20186274    Free PMC article.
The successful implementation of a licensed data management interface between a Sunquest(®) laboratory information system and an AB SCIEX™ mass spectrometer.
Deborah French, Enrique Terrazas.
J Pathol Inform, 2013 Apr 20; 4. PMID: 23599901    Free PMC article.
Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases.
Jill E Clarridge.
Clin Microbiol Rev, 2004 Oct 19; 17(4). PMID: 15489351    Free PMC article.
Highly Cited. Review.
16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls.
J Michael Janda, Sharon L Abbott.
J Clin Microbiol, 2007 Jul 13; 45(9). PMID: 17626177    Free PMC article.
Highly Cited. Review.
Development of an automated MODS plate reader to detect early growth of Mycobacterium tuberculosis.
G Comina, D Mendoza, +5 authors, M Zimic.
J Microsc, 2011 Jan 22; 242(3). PMID: 21250995
Experience with multimodality telepathology at the University of Pittsburgh Medical Center.
Liron Pantanowitz, Clayton A Wiley, +5 authors, Anil V Parwani.
J Pathol Inform, 2013 Feb 02; 3. PMID: 23372986    Free PMC article.
Extended-spectrum beta-lactamases: a clinical update.
David L Paterson, Robert A Bonomo.
Clin Microbiol Rev, 2005 Oct 15; 18(4). PMID: 16223952    Free PMC article.
Highly Cited. Review.
SpectraBank: an open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting.
Karola Böhme, Inmaculada C Fernández-No, +3 authors, Pilar Calo-Mata.
Electrophoresis, 2012 Jul 24; 33(14). PMID: 22821489
16S rRNA gene sequencing and the routine clinical microbiology laboratory: a perfect marriage?
Michael Boudewijns, Judith M Bakkers, Patrick D J Sturm, Willem J G Melchers.
J Clin Microbiol, 2006 Sep 07; 44(9). PMID: 16954306    Free PMC article.
Comparison of culture and molecular identification of bacteria in chronic wounds.
Daniel D Rhoads, Randall D Wolcott, Yan Sun, Scot E Dowd.
Int J Mol Sci, 2012 Apr 11; 13(3). PMID: 22489109    Free PMC article.
Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics.
Muriel Vayssier-Taussat, Emmanuel Albina, +8 authors, Thierry Candresse.
Front Cell Infect Microbiol, 2014 Mar 19; 4. PMID: 24634890    Free PMC article.
Highly Cited. Review.
Classification of Mycobacterium tuberculosis in images of ZN-stained sputum smears.
Rethabile Khutlang, Sriram Krishnan, +4 authors, Tania S Douglas.
IEEE Trans Inf Technol Biomed, 2009 Sep 04; 14(4). PMID: 19726269    Free PMC article.
Publication of OIG compliance program guidance for clinical laboratories--HHS. Notice.
Fed Regist, 1998 Jul 29; 63(163). PMID: 10182693
Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions.
W Florian Fricke, David A Rasko.
Nat Rev Genet, 2013 Nov 28; 15(1). PMID: 24281148
Review.
Antibiotic resistance monitoring: a laboratory perspective.
S Trevino.
Mil Med, 2000 Aug 02; 165(7 Suppl 2). PMID: 10920637
Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes.
J Stelling, W K Yih, +9 authors, Collaborative Group WHONET-Argentina.
Epidemiol Infect, 2009 Oct 03; 138(6). PMID: 19796449    Free PMC article.
Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome.
Bruno P Chumpitazi, Emily B Hollister, +6 authors, Robert J Shulman.
Gut Microbes, 2014 Mar 19; 5(2). PMID: 24637601    Free PMC article.
Antimicrobial resistance of Escherichia coli isolated from urine in Thailand from 2000 to 2005.
Pitimon Polwichai, Surang Dejsirilert, +3 authors, Piroon Mootsikapun.
J Med Assoc Thai, 2009 Aug 01; 92 Suppl 4. PMID: 21298846
Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.
Kai Shen, Sameera Sayeed, +20 authors, Fen Z Hu.
Infect Immun, 2006 Aug 24; 74(9). PMID: 16926421    Free PMC article.
Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.
Henrik Hasman, Dhany Saputra, +4 authors, Frank M Aarestrup.
J Clin Microbiol, 2013 Nov 01; 52(1). PMID: 24172157    Free PMC article.
Highly Cited.
Effectiveness of barcoding for reducing patient specimen and laboratory testing identification errors: a Laboratory Medicine Best Practices systematic review and meta-analysis.
Susan R Snyder, Alessandra M Favoretto, +9 authors, Edward B Liebow.
Clin Biochem, 2012 Jul 04; 45(13-14). PMID: 22750145    Free PMC article.
Systematic Review.
Automation in clinical bacteriology: what system to choose?
G Greub, G Prod'hom.
Clin Microbiol Infect, 2011 Apr 28; 17(5). PMID: 21521409
Review.
The methylomes of six bacteria.
Iain A Murray, Tyson A Clark, +7 authors, Richard J Roberts.
Nucleic Acids Res, 2012 Oct 05; 40(22). PMID: 23034806    Free PMC article.
Highly Cited.
Impact of automated alerts on follow-up of post-discharge microbiology results: a cluster randomized controlled trial.
Robert El-Kareh, Christopher Roy, Deborah H Williams, Eric G Poon.
J Gen Intern Med, 2012 Jan 27; 27(10). PMID: 22278302    Free PMC article.
Three clinically distinct chronic pediatric airway infections share a common core microbiota.
Christopher J van der Gast, Leah Cuthbertson, +6 authors, Lucas R Hoffman.
Ann Am Thorac Soc, 2014 Mar 07; 11(7). PMID: 24597615    Free PMC article.
Statewide system of electronic notifiable disease reporting from clinical laboratories: comparing automated reporting with conventional methods.
P Effler, M Ching-Lee, +3 authors, D Jernigan.
JAMA, 1999 Nov 26; 282(19). PMID: 10573276
TBC: a clustering algorithm based on prokaryotic taxonomy.
Jae-Hak Lee, Hana Yi, +2 authors, Jongsik Chun.
J Microbiol, 2012 Apr 28; 50(2). PMID: 22538644
National Electronic Disease Surveillance System (NEDSS): a standards-based approach to connect public health and clinical medicine.
National Electronic Disease Surveillance System Working Group.
J Public Health Manag Pract, 2001 Nov 21; 7(6). PMID: 11713753
Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.
Stephen J Salipante, Dhruba J Sengupta, +13 authors, Noah G Hoffman.
PLoS One, 2013 Jun 05; 8(5). PMID: 23734239    Free PMC article.
Highly Cited.
The Use of High Performance Liquid Chromatography to Speciate and Characterize the Epidemiology of Mycobacteria.
Joseph Jeong, Sung-Ryul Kim, +7 authors, Davey M Smith.
Lab Med, 2011 Oct 01; 42(10). PMID: 24443588    Free PMC article.
Public health genomics and the new molecular epidemiology of bacterial pathogens.
M W Gilmour, M Graham, A Reimer, G Van Domselaar.
Public Health Genomics, 2013 Apr 04; 16(1-2). PMID: 23548714
Review.
Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks.
Simon R Harris, M E Török, +3 authors, Julian Parkhill.
Nat Biotechnol, 2013 Jul 11; 31(7). PMID: 23839141    Free PMC article.
An informatics model for guiding assembly of telemicrobiology workstations for malaria collaborative diagnostics using commodity products and open-source software.
West Suhanic, Ian Crandall, Peter Pennefather.
Malar J, 2009 Jul 21; 8. PMID: 19615074    Free PMC article.
A novel semi-automatic image processing approach to determine Plasmodium falciparum parasitemia in Giemsa-stained thin blood smears.
Minh-Tam Le, Timo R Bretschneider, Claudia Kuss, Peter R Preiser.
BMC Cell Biol, 2008 Apr 01; 9. PMID: 18373862    Free PMC article.
Automated image processing method for the diagnosis and classification of malaria on thin blood smears.
Nicholas E Ross, Charles J Pritchard, David M Rubin, Adriano G Dusé.
Med Biol Eng Comput, 2006 Aug 29; 44(5). PMID: 16937184
Development of an automated antibiotic consultant.
R S Evans, S L Pestotnik, D C Classen, J P Burke.
MD Comput, 1993 Jan 01; 10(1). PMID: 8418386
Expert systems in clinical microbiology.
Trevor Winstanley, Patrice Courvalin.
Clin Microbiol Rev, 2011 Jul 08; 24(3). PMID: 21734247    Free PMC article.
Review.
Implementation of FocalPoint GS location-guided imaging system: experience in a clinical setting.
Angelique W Levi, David C Chhieng, +2 authors, Malini Harigopal.
Cancer Cytopathol, 2012 Apr 17; 120(2). PMID: 22505211
Laboratory-based prospective surveillance for community outbreaks of Shigella spp. in Argentina.
María R Viñas, Ezequiel Tuduri, +12 authors, Group MIDAS - Argentina.
PLoS Negl Trop Dis, 2013 Dec 19; 7(12). PMID: 24349586    Free PMC article.
Does electronic clinical microbiology results reporting influence medical decision making: a pre- and post-interview study of medical specialists.
Marjan J Bruins, Gijs J H M Ruijs, +2 authors, Jos E C M Aarts.
BMC Med Inform Decis Mak, 2011 Mar 31; 11. PMID: 21447199    Free PMC article.
Disease surveillance and the academic, clinical, and public health communities.
Robert W Pinner, Catherine A Rebmann, Anne Schuchat, James M Hughes.
Emerg Infect Dis, 2003 Aug 02; 9(7). PMID: 12890317    Free PMC article.
A regional informatics platform for coordinated antibiotic-resistant infection tracking, alerting, and prevention.
Abel N Kho, Bradley N Doebbeling, +7 authors, J Marc Overhage.
Clin Infect Dis, 2013 Apr 12; 57(2). PMID: 23575195    Free PMC article.
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.
Patrick D Schloss, Dirk Gevers, Sarah L Westcott.
PLoS One, 2011 Dec 24; 6(12). PMID: 22194782    Free PMC article.
Highly Cited.
Integrated Multilevel Surveillance of the World's Infecting Microbes and Their Resistance to Antimicrobial Agents.
Thomas F O'Brien, John Stelling.
Clin Microbiol Rev, 2011 Apr 13; 24(2). PMID: 21482726    Free PMC article.
Review.
Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory.
W M Dunne, L F Westblade, B Ford.
Eur J Clin Microbiol Infect Dis, 2012 Jun 09; 31(8). PMID: 22678348
Review.
Detecting delayed microbiology results after hospital discharge: improving patient safety through an automated medical informatics tool.
John W Wilson, William F Marshall, Lynn L Estes.
Mayo Clin Proc, 2011 Dec 03; 86(12). PMID: 22134937    Free PMC article.
Effective object recognition for automated counting of colonies in Petri dishes (automated colony counting).
J Marotz, C Lübbert, W Eisenbeiss.
Comput Methods Programs Biomed, 2001 Sep 12; 66(2-3). PMID: 11551392
Radical improvements in the display of clinical microbiology results: a Web-based clinical information system.
K E Willard, D P Connelly, J R Johnson.
Am J Med, 1996 Nov 01; 101(5). PMID: 8948279
Gram-staining characterisation of activated sludge filamentous bacteria by automated colour analysis.
Denis Pandolfi, Marie-Noëlle Pons.
Biotechnol Lett, 2005 Jan 27; 26(24). PMID: 15672225
Automation in the clinical microbiology laboratory.
Susan M Novak, Elizabeth M Marlowe.
Clin Lab Med, 2013 Aug 13; 33(3). PMID: 23931839
Review.
Experimental and analytical tools for studying the human microbiome.
Justin Kuczynski, Christian L Lauber, +4 authors, Rob Knight.
Nat Rev Genet, 2011 Dec 20; 13(1). PMID: 22179717    Free PMC article.
Highly Cited. Review.
Technical description of RODS: a real-time public health surveillance system.
Fu-Chiang Tsui, Jeremy U Espino, +3 authors, Michael M Wagner.
J Am Med Inform Assoc, 2003 Jun 17; 10(5). PMID: 12807803    Free PMC article.
Antimicrobial stewardship programs.
Kimberly D Leuthner, Gary V Doern.
J Clin Microbiol, 2013 Aug 09; 51(12). PMID: 23926165    Free PMC article.
Review.
Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.
Claudio U Köser, Matthew J Ellington, +8 authors, Sharon J Peacock.
PLoS Pathog, 2012 Aug 10; 8(8). PMID: 22876174    Free PMC article.
Highly Cited. Review.
Rapid accurate entry of microbiology results.
R D Aller, W Friedman.
Arch Pathol Lab Med, 1996 Jan 01; 120(1). PMID: 8554446
Opinion: Re-evaluating prokaryotic species.
Dirk Gevers, Frederick M Cohan, +8 authors, Jean Swings.
Nat Rev Microbiol, 2005 Sep 03; 3(9). PMID: 16138101
Highly Cited. Review.
Application of a new informatics tool for contamination screening in the HIV sequencing laboratory.
Mark T W Ebbert, Melanie A Mallory, +2 authors, David R Hillyard.
J Clin Virol, 2013 Apr 16; 57(3). PMID: 23583427
Image processing techniques for identifying Mycobacterium tuberculosis in Ziehl-Neelsen stains.
P Sadaphal, J Rao, G W Comstock, M F Beg.
Int J Tuberc Lung Dis, 2008 Apr 19; 12(5). PMID: 18419897    Free PMC article.
Evaluation of the integrated database network system (IDNS) SmartGene software for analysis of 16S rRNA gene sequences for identification of Nocardia species.
Patricia S Conville, Patrick R Murray, Adrian M Zelazny.
J Clin Microbiol, 2010 Jun 25; 48(8). PMID: 20573863    Free PMC article.
Google trends: a web-based tool for real-time surveillance of disease outbreaks.
Herman Anthony Carneiro, Eleftherios Mylonakis.
Clin Infect Dis, 2009 Oct 23; 49(10). PMID: 19845471
Highly Cited. Review.
Automated counting of bacterial colony forming units on agar plates.
Silvio D Brugger, Christian Baumberger, +3 authors, Kathrin Mühlemann.
PLoS One, 2012 Mar 27; 7(3). PMID: 22448267    Free PMC article.
The changing pattern of antimicrobial resistance within 42,033 Escherichia coli isolates from nosocomial, community and urology patient-specific urinary tract infections, Dublin, 1999-2009.
Ivor M Cullen, Rustom P Manecksha, +8 authors, John A Thornhill.
BJU Int, 2011 Sep 03; 109(8). PMID: 21883861
Automation in diagnostic bacteriology.
R E Williams, R E Trotman.
J Clin Pathol Suppl Coll Pathol, 1969 Jan 01; 3. PMID: 4918154    Free PMC article.
Antimicrobial resistance in key bloodstream bacterial isolates: electronic surveillance with the Surveillance Network Database--USA.
D F Sahm, M K Marsilio, G Piazza.
Clin Infect Dis, 1999 Sep 07; 29(2). PMID: 10476722
Internet-based surveillance systems for monitoring emerging infectious diseases.
Gabriel J Milinovich, Gail M Williams, Archie C A Clements, Wenbiao Hu.
Lancet Infect Dis, 2013 Dec 03; 14(2). PMID: 24290841    Free PMC article.
Highly Cited. Review.
Serratia ureilytica sp. nov., a novel urea-utilizing species.
Bhaskar Bhadra, Pradosh Roy, Ranadhir Chakraborty.
Int J Syst Evol Microbiol, 2005 Sep 17; 55(Pt 5). PMID: 16166724
Development and implementation of an electronic interface for complex clinical laboratory instruments without a vendor-provided data transfer interface.
Gary E Blank, Mohamed A Virji.
J Pathol Inform, 2011 Mar 09; 2. PMID: 21383937    Free PMC article.
Use of bar code readers and programmable keypads to improve the speed and accuracy of manual data entry in the clinical microbiology laboratory: experience of two laboratories.
R Shaw, J E Coia, J Michie.
J Clin Pathol, 1999 May 27; 52(1). PMID: 10343613    Free PMC article.
Transforming clinical microbiology with bacterial genome sequencing.
Xavier Didelot, Rory Bowden, +2 authors, Derrick W Crook.
Nat Rev Genet, 2012 Aug 08; 13(9). PMID: 22868263    Free PMC article.
Highly Cited. Review.
Assessing the consequences of denoising marker-based metagenomic data.
John M Gaspar, W Kelley Thomas.
PLoS One, 2013 Mar 29; 8(3). PMID: 23536909    Free PMC article.
The BACTLAB system - a data system for bacteriological routine.
F Bergqvist, S Bengtsson.
Comput Programs Biomed, 1975 Mar 01; 4(3). PMID: 1139914
Automated and unsupervised detection of malarial parasites in microscopic images.
Yashasvi Purwar, Sirish L Shah, +2 authors, Atis Muehlenbachs.
Malar J, 2011 Dec 15; 10. PMID: 22165867    Free PMC article.
WHONET: an information system for monitoring antimicrobial resistance.
T F O'Brien, J M Stelling.
Emerg Infect Dis, 1995 Apr 01; 1(2). PMID: 8903165    Free PMC article.
Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species.
Amr M Mohamed, Dan J Kuyper, +3 authors, Steven H Hinrichs.
J Clin Microbiol, 2005 Aug 06; 43(8). PMID: 16081916    Free PMC article.
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.
P C Y Woo, S K P Lau, +2 authors, K-Y Yuen.
Clin Microbiol Infect, 2008 Oct 03; 14(10). PMID: 18828852
Highly Cited. Review.
Development of a clinically comprehensive database and a simple procedure for identification of molds from solid media by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
Anna F Lau, Steven K Drake, +2 authors, Adrian M Zelazny.
J Clin Microbiol, 2012 Dec 28; 51(3). PMID: 23269728    Free PMC article.
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.
Dazhi Jiao, Yuzhen Ye, Haixu Tang.
PLoS Comput Biol, 2013 Apr 05; 9(3). PMID: 23555216    Free PMC article.
Computer-based consultations in clinical therapeutics: explanation and rule acquisition capabilities of the MYCIN system.
E H Shortliffe, R Davis, +3 authors, S N Cohen.
Comput Biomed Res, 1975 Aug 01; 8(4). PMID: 1157471
Classifying laboratory incident reports to identify problems that jeopardize patient safety.
Michael L Astion, Kaveh G Shojania, +2 authors, Valerie L Ng.
Am J Clin Pathol, 2003 Jul 18; 120(1). PMID: 12866368
Performance of CellaVision DM96 in leukocyte classification.
Lik Hang Lee, Adnan Mansoor, +3 authors, Christopher Naugler.
J Pathol Inform, 2013 Jul 17; 4. PMID: 23858389    Free PMC article.
Bacterial plurality as a general mechanism driving persistence in chronic infections.
Garth D Ehrlich, Fen Ze Hu, +2 authors, J Christopher Post.
Clin Orthop Relat Res, 2005 Aug 02; (437). PMID: 16056021    Free PMC article.
Review.
Validating whole slide imaging for diagnostic purposes in pathology: guideline from the College of American Pathologists Pathology and Laboratory Quality Center.
Liron Pantanowitz, John H Sinard, +8 authors, College of American Pathologists Pathology and Laboratory Quality Center.
Arch Pathol Lab Med, 2013 May 03; 137(12). PMID: 23634907    Free PMC article.
Highly Cited. Review.
"Proof-of-concept" evaluation of an automated sputum smear microscopy system for tuberculosis diagnosis.
James J Lewis, Violet N Chihota, +5 authors, Gavin J Churchyard.
PLoS One, 2012 Dec 05; 7(11). PMID: 23209666    Free PMC article.
Analysis and presentation of cumulative antibiograms: a new consensus guideline from the Clinical and Laboratory Standards Institute.
Janet F Hindler, John Stelling.
Clin Infect Dis, 2007 Feb 17; 44(6). PMID: 17304462
Review.
The remote diagnosis of malaria using telemedicine or e-mailed images.
Clinton K Murray, Rupal M Mody, +4 authors, Ronald W Muntz.
Mil Med, 2007 Jan 30; 171(12). PMID: 17256675
Automated versus manual sample inoculations in routine clinical microbiology: a performance evaluation of the fully automated InoqulA instrument.
P Froment, H Marchandin, P Vande Perre, B Lamy.
J Clin Microbiol, 2013 Dec 20; 52(3). PMID: 24353001    Free PMC article.
DySC: software for greedy clustering of 16S rRNA reads.
Zejun Zheng, Stefan Kramer, Bertil Schmidt.
Bioinformatics, 2012 Jun 26; 28(16). PMID: 22730435
Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
Claudio U Köser, Matthew T G Holden, +17 authors, Sharon J Peacock.
N Engl J Med, 2012 Jun 15; 366(24). PMID: 22693998    Free PMC article.
Highly Cited.
Gene patenting--the Supreme Court finally speaks.
Aaron S Kesselheim, Robert M Cook-Deegan, David E Winickoff, Michelle M Mello.
N Engl J Med, 2013 Jul 12; 369(9). PMID: 23841703    Free PMC article.
The future of diagnostic bacteriology.
S Matthews, J Deutekom.
Clin Microbiol Infect, 2011 Apr 28; 17(5). PMID: 21521408
Review.
Can laboratory reference strains mirror "real-world" pathogenesis?
C A Fux, M Shirtliff, P Stoodley, J W Costerton.
Trends Microbiol, 2005 Feb 01; 13(2). PMID: 15680764
Review.
Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology.
Andrew E Clark, Erin J Kaleta, Amit Arora, Donna M Wolk.
Clin Microbiol Rev, 2013 Jul 05; 26(3). PMID: 23824373    Free PMC article.
Highly Cited. Review.
High prevalence of human Parechovirus (HPeV) genotypes in the Amsterdam region and identification of specific HPeV variants by direct genotyping of stool samples.
K Benschop, X Thomas, +2 authors, K Wolthers.
J Clin Microbiol, 2008 Oct 24; 46(12). PMID: 18945833    Free PMC article.
The application of ecological theory toward an understanding of the human microbiome.
Elizabeth K Costello, Keaton Stagaman, +2 authors, David A Relman.
Science, 2012 Jun 08; 336(6086). PMID: 22674335    Free PMC article.
Highly Cited. Review.
An automatic device for detection and classification of malaria parasite species in thick blood film.
Saowaluck Kaewkamnerd, Chairat Uthaipibull, +3 authors, Sissades Tongsima.
BMC Bioinformatics, 2013 Jan 11; 13 Suppl 17. PMID: 23281600    Free PMC article.
WHONET: removing obstacles to the full use of information about antimicrobial resistance.
T F O'Brien, J M Stelling.
Diagn Microbiol Infect Dis, 1996 Aug 01; 25(4). PMID: 8937840
Review.
Creating a virtual slide map from sputum smear images for region-of-interest localisation in automated microscopy.
Bhavin Patel, Tania S Douglas.
Comput Methods Programs Biomed, 2012 Jan 20; 108(1). PMID: 22257649    Free PMC article.
Antimicrobial selection by a computer. A blinded evaluation by infectious diseases experts.
V L Yu, L M Fagan, +6 authors, S N Cohen.
JAMA, 1979 Sep 21; 242(12). PMID: 480542
Mycolic acid analysis by high-performance liquid chromatography for identification of Mycobacterium species.
W R Butler, L S Guthertz.
Clin Microbiol Rev, 2001 Oct 05; 14(4). PMID: 11585782    Free PMC article.
Review.
CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.
Kyuin Hwang, Jeongsu Oh, +6 authors, Kyung Mo Kim.
PLoS One, 2013 May 08; 8(5). PMID: 23650520    Free PMC article.
Clinical microbiology informatics--developments in Sweden. 1939.
Urban Forsum, Göran Kronvall.
APMIS, 2007 May 17; 115(5). PMID: 17504399
Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia.
Eric J Duncavage, Haley J Abel, +2 authors, John D Pfeifer.
Mod Pathol, 2012 Mar 20; 25(6). PMID: 22425908
Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory.
J A Kellogg, D A Bankert, +3 authors, G E Pfyffer.
J Clin Microbiol, 2001 Mar 07; 39(3). PMID: 11230412    Free PMC article.
Outbreak detection through automated surveillance: a review of the determinants of detection.
David L Buckeridge.
J Biomed Inform, 2006 Nov 11; 40(4). PMID: 17095301
Review.
Rapid bacterial genome sequencing: methods and applications in clinical microbiology.
C Bertelli, G Greub.
Clin Microbiol Infect, 2013 Apr 23; 19(9). PMID: 23601179
Review.
Hunting health care-associated infections from the clinical microbiology laboratory: passive, active, and virtual surveillance.
Lance R Peterson, Stephen E Brossette.
J Clin Microbiol, 2002 Jan 05; 40(1). PMID: 11773083    Free PMC article.
Review.
A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.
Nicholas J Loman, Chrystala Constantinidou, +9 authors, Mark J Pallen.
JAMA, 2013 Apr 11; 309(14). PMID: 23571589
Highly Cited.
Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.
Brian O'Farrell, Jana K Haase, +2 authors, Mark Achtman.
PLoS One, 2012 Nov 13; 7(10). PMID: 23144721    Free PMC article.
Reducing antimicrobial therapy for asymptomatic bacteriuria among noncatheterized inpatients: a proof-of-concept study.
Jerome A Leis, Gabriel W Rebick, +6 authors, Allison McGeer.
Clin Infect Dis, 2014 Mar 01; 58(7). PMID: 24577290
Real-time validation and presentation of the cumulative antibiogram and implications of presenting a standard format using a novel in-house software: ABSOFT.
Godwin Wilson, Shaherudeen Badarudeen, Angela Godwin.
Am J Infect Control, 2010 Jul 16; 38(9). PMID: 20627367
Data mining and infection control.
Stephen E Brossette, Patrick A Hymel.
Clin Lab Med, 2008 Jan 16; 28(1). PMID: 18194722
Genomic variation landscape of the human gut microbiome.
Siegfried Schloissnig, Manimozhiyan Arumugam, +11 authors, Peer Bork.
Nature, 2012 Dec 12; 493(7430). PMID: 23222524    Free PMC article.
Highly Cited.
Detection of a community infection outbreak with virtual surveillance.
Lance R Peterson, Donna M Hacek, Diana Rolland, Stephen E Brossette.
Lancet, 2003 Nov 15; 362(9395). PMID: 14615133
Telemicrobiology: a novel telemedicine capability for mission support in the field of infectious medicine.
Patrick Scheid, David M Lam, Alois Thömmes, Lothar Zöller.
Telemed J E Health, 2007 May 11; 13(2). PMID: 17489697
Automated alerts coupled with antimicrobial stewardship intervention lead to decreases in length of stay in patients with gram-negative bacteremia.
Jason M Pogue, Ryan P Mynatt, +7 authors, Keith S Kaye.
Infect Control Hosp Epidemiol, 2014 Jan 21; 35(2). PMID: 24442074
Automation in the clinical microbiology laboratory.
Carey-Ann D Burnham, W Michael Dunne, +2 authors, Robin Patel.
Clin Chem, 2013 May 22; 59(12). PMID: 23690497
ACP Journal Club: a clinical decision-support system with interactive alerts improved CD4 cell count in HIV.
Michael A Polis.
Ann Intern Med, 2013 Apr 17; 158(8). PMID: 23588764
Computer algorithms to detect bloodstream infections.
William E Trick, Brandon M Zagorski, +5 authors, Robert A Weinstein.
Emerg Infect Dis, 2004 Oct 23; 10(9). PMID: 15498164    Free PMC article.
The outcome and long-term follow-up of 94 patients with recurrent and refractory Clostridium difficile infection using single to multiple fecal microbiota transplantation via retention enema.
C H Lee, J E Belanger, +4 authors, P T Kim.
Eur J Clin Microbiol Infect Dis, 2014 Mar 15; 33(8). PMID: 24627239
The frequency and potential clinical impact of non-analytical errors in the RCPA Microbiology QAP 1987-2008.
Arthur J Morris, Elizabeth Haremza, Debra A Walker.
Pathology, 2011 Apr 27; 43(4). PMID: 21519289
The application of information technology to regional, national, and global surveillance of antimicrobial resistance.
Daniel F Sahm, Clyde Thornsberry, James A Karlowsky.
Curr Pharm Des, 2003 Apr 08; 9(12). PMID: 12678862
Review.
Surveillance of antimicrobial resistance: the WHONET program.
J M Stelling, T F O'Brien.
Clin Infect Dis, 1997 Jan 01; 24 Suppl 1. PMID: 8994799
A computer-assisted management program for antibiotics and other antiinfective agents.
R S Evans, S L Pestotnik, +5 authors, J P Burke.
N Engl J Med, 1998 Jan 22; 338(4). PMID: 9435330
Highly Cited.
Ability of the VITEK 2 advanced expert system To identify beta-lactam phenotypes in isolates of Enterobacteriaceae and Pseudomonas aeruginosa.
C C Sanders, M Peyret, +4 authors, W E Sanders.
J Clin Microbiol, 2000 Feb 03; 38(2). PMID: 10655347    Free PMC article.
Etiology of diarrhea in Bangladeshi infants in the first year of life analyzed using molecular methods.
Mami Taniuchi, Shihab U Sobuz, +7 authors, Eric R Houpt.
J Infect Dis, 2013 Sep 18; 208(11). PMID: 24041797    Free PMC article.
Highly Cited.
Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.
Anthony P Underwood, Tim Dallman, +10 authors, John Wain.
J Clin Microbiol, 2012 Nov 09; 51(1). PMID: 23135946    Free PMC article.
Actionable diagnosis of neuroleptospirosis by next-generation sequencing.
Michael R Wilson, Samia N Naccache, +19 authors, Charles Y Chiu.
N Engl J Med, 2014 Jun 05; 370(25). PMID: 24896819    Free PMC article.
Highly Cited.
Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.
Frank M Aarestrup, Eric W Brown, +17 authors, Jørgen Schlundt.
Emerg Infect Dis, 2012 Oct 25; 18(11). PMID: 23092707    Free PMC article.
MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation.
Yu-Chieh Liao, Hsin-Hung Lin, +2 authors, Frank A Scannapieco.
J Microbiol Methods, 2015 Apr 26; 113. PMID: 25911337    Free PMC article.
Review of Telemicrobiology.
Daniel D Rhoads, Blaine A Mathison, +2 authors, Liron Pantanowitz.
Arch Pathol Lab Med, 2015 Sep 01; 140(4). PMID: 26317376    Free PMC article.
Review.
Identification of Low-Level Vancomycin Resistance in Staphylococcus aureus in the Era of Informatics.
Bradley A Ford.
J Clin Microbiol, 2016 Feb 13; 54(4). PMID: 26865694    Free PMC article.
Design of a Tablet Computer App for Facilitation of a Molecular Blood Culture Test in Clinical Microbiology and Preliminary Usability Evaluation.
Lasse L Samson, Louise Pape-Haugaard, +3 authors, Ole Hejlesen.
JMIR Mhealth Uhealth, 2016 Mar 20; 4(1). PMID: 26993432    Free PMC article.
Comparison of the diagnostic utility of digital pathology systems for telemicrobiology.
Daniel D Rhoads, Nadia F Habib-Bein, +6 authors, Liron Pantanowitz.
J Pathol Inform, 2016 Apr 15; 7. PMID: 27076988    Free PMC article.
Clinical and laboratory considerations for the rapid detection of carbapenem-resistant Enterobacteriaceae.
Ritu Banerjee, Romney Humphries.
Virulence, 2016 May 12; 8(4). PMID: 27168451    Free PMC article.
Review.
Antimicrobial Stewardship: How the Microbiology Laboratory Can Right the Ship.
Philippe Morency-Potvin, David N Schwartz, Robert A Weinstein.
Clin Microbiol Rev, 2016 Dec 16; 30(1). PMID: 27974411    Free PMC article.
Review.
Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.
Varvara K Kozyreva, Chau-Linda Truong, +3 authors, Vishnu Chaturvedi.
J Clin Microbiol, 2017 Jun 09; 55(8). PMID: 28592550    Free PMC article.
Addressing the key communication barriers between microbiology laboratories and clinical units: a qualitative study.
Brita Skodvin, Karina Aase, +3 authors, Ingrid Smith.
J Antimicrob Chemother, 2017 Jun 22; 72(9). PMID: 28633405    Free PMC article.
Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory.
Daniel D Rhoads.
J Clin Microbiol, 2018 Jun 29; 56(9). PMID: 29950328    Free PMC article.
In-Vitro Biofilm Formation and Antimicrobial Resistance of Escherichia coli in Diabetic and Nondiabetic Patients.
Sunayana Raya, Ankit Belbase, +3 authors, Nabin Kishor Bimali.
Biomed Res Int, 2019 Oct 24; 2019. PMID: 31641666    Free PMC article.
Optimization of Turnaround Time for Group A Streptococcus PCR.
Thomas J S Durant, Jacob Merwede, Jesse Reynolds, David R Peaper.
J Clin Microbiol, 2019 Jun 21; 57(9). PMID: 31217271    Free PMC article.
Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies.
Olivier Vandenberg, Géraldine Durand, +5 authors, Alex van Belkum.
Clin Microbiol Rev, 2020 Feb 28; 33(2). PMID: 32102900    Free PMC article.
Review.
Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond.
Marina Oviaño, Germán Bou.
Clin Microbiol Rev, 2018 Nov 30; 32(1). PMID: 30487165    Free PMC article.
Review.
Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist.
Daniel D Rhoads.
J Clin Microbiol, 2020 Apr 17; 58(6). PMID: 32295889    Free PMC article.
Digital microbiology.
A Egli, J Schrenzel, G Greub.
Clin Microbiol Infect, 2020 Jul 01; 26(10). PMID: 32603804    Free PMC article.
Review.
Development and evaluation of a novel user interface for reviewing clinical microbiology results.
Adam Wright, Pamela M Neri, +7 authors, Gianna Zuccotti.
J Am Med Inform Assoc, 2018 Mar 22; 25(8). PMID: 29562338    Free PMC article.
Leapfrogging laboratories: the promise and pitfalls of high-tech solutions for antimicrobial resistance surveillance in low-income settings.
Iruka N Okeke, Nicholas Feasey, +5 authors, Sharon J Peacock.
BMJ Glob Health, 2020 Dec 04; 5(12). PMID: 33268385    Free PMC article.
Review.