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The American Board of Pathology now requires an increasing sophistication in information management from candidates for certification. Thus, this book is intended for pathologists and residents in pathology, clinical laboratory scientists, and laboratory and information managers. Following the broad-based introduction on laboratory informatics, the book's topics include: computer basics; development and validation of the laboratory information system; computer networks; security and confidentiality on computer systems and networks; total cost of ownership; essential software; interfaces; process modeling; artificial intelligence and expert systems; bar coding in the laboratory; image analysis and computer-assisted quantitation; and telepathology.

Developing the Laboratory Information System. Validation of the Laboratory Information System. Security and Confidentiality on Laboratory Computer Systems. The intellectual property rights related to the sequencing of Middle East respiratory syndrome coronavirus MERS-CoV and the subsequent patenting of a diagnostic assay have reinforced the legal and ethical challenges of sharing microbial genetic material and data transfer The standardization of quality metrics, such as calibration standards, validation methods, acceptable data reliability, test robustness, result reproducibility, and data storage, are critically needed for microbial WGS.

Additionally, proficiency testing programs that cover both wet in vitro testing and dry in silico analysis portions of genomic assays are urgently required. Appropriate data storage guidelines regarding the type of data that should be stored, the means of storage, and the duration of storage are necessary, as the cost of storage will soon exceed the cost of data generation. Another question that is relevant in this era, which is placing a growing emphasis on patients' genetic rights, is the unresolved question of who owns the data and whose responsibility it is to procure it. Are there certain sequences that are reportable to public health agencies?

Should an individual's microbiomic data be protected as carefully as an individual's human genomic data , ? Although current efforts to improve microbial identification are still focused on creating better ways to culture organisms , the use of culture-free identification by means of massively parallel nucleic acid sequencing has shown potential in clinical studies 55 , 56 , The use of nucleic acid analysis directly from samples can overcome culture bias 55 , , In the future, genomic or metagenomic microbial analyses might replace or augment the current approach in clinical microbiology of culturing and identifying isolated microbes.

Also, our perspective of what constitutes a species or a taxon might fundamentally change as DNA sequencing continues to become more commonplace and as the computational tools associated with these analyses continue to improve.

Microbiology systematics might fundamentally shift to a taxonomic system based upon genotyping The identification and classification of infection might also change dramatically. Computer algorithms can analyze and classify complex infections by using more variables than can currently be considered by a clinician or microbiologist. Analyses may unravel the variables that enable a pathogenic microbial ecosystem to take hold in a susceptible host. In the future, the microbiology laboratory might be expected to understand, evaluate, and recommend therapies based upon the analysis of pathobiomes , functionally equivalent pathogroups , supragenomes , , epigenomes , , or impaired or pathogenic microbiomes , — The use of WGS and MGS may provide more complete quantitative and qualitative identification of all of the microbes and relevant resistance and virulence genes that are present in a sample, and these types of analyses have the potential to better direct patient care 55 , 56 , , , Therapies such as probiotics or fecal microbiota transplantation may be indicated depending on the results of the laboratory evaluation of a patient's microbiome , Local clinical microbiology laboratories are responsible for reporting the identification of certain infectious agents to various public health agencies city, county, and state.

These reports are used by public agencies to track incidences and attempt to identify outbreaks. The reportable findings are somewhat dynamic, often with annual modifications, so informatics support requires ongoing vigilance to keep up with expectations of public health authorities. Additionally, the local clinical microbiology laboratory is involved in recognizing local institutional outbreaks and working to prevent them Informatics tools and electronic communication are key in efficiently communicating with public health agencies and rapidly identifying outbreaks Fig.

Once identified, there are needs for data and reports throughout the incident, often with evolving parameters of interest. Having informatics experts participate in incident management from the beginning, to assist those in the microbiology laboratory as well as those managing the outbreak outside the laboratory, is optimal.

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Agents of notifiable infectious diseases and their associated data often travel through layers of agencies, including clinics, laboratories, and public health registries. This generic figure depicts the flow of information associated with a patient diagnosed with gastroenteritis who is tested for Salmonella.

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Although human input or interpretation may be required at various nodes, information is often generated, transmitted, and received digitally solid arrows. However, many clinical laboratories still use paper to transmit information. The more often information is exchanged between two nodes, the more incentive exists to create a robust electronic interface between these nodes. Therefore, transmitting information by paper via fax or post is most likely to be used between nodes that rarely communicate with each other.

Electronic reporting can expedite information communication and therefore expedite the detection of outbreak clusters. Information between the patient and clinician is often exchanged verbally dotted arrows , although electronic communication with patients is likely to become more common. Laboratory reporting of reportable infectious agents to public health agencies or departments is not currently a seamless electronic process. A first step in streamlining the reporting process is to have all the stakeholders share a nomenclature. The goal of electronic reporting to public health agencies is to capture more reportable events, with increased timeliness and completeness, than those obtained with paper reporting, and this possibility has been demonstrated 7 , Timely detection of infectious disease outbreaks is needed globally, regionally, and locally.

The responsibility of identifying widespread outbreaks is largely shouldered by state public health agencies, the CDC, and the World Health Organization Detecting, tracking, and modeling outbreaks are areas of continued interest in academia and public health , Rapid detection is of key importance, because decreasing the time to detection can significantly decrease the adverse impact of an outbreak Detection of the emergence or increasing prevalence of antimicrobial-resistant organisms is a concern for both local and global clinical microbiology.

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Software exists that can link the local laboratory with other regional and global laboratories in the bidirectional exchange of antimicrobial susceptibility data. Until recently, both WHONET and TSN were used to analyze antimicrobial susceptibility data from multiple laboratories to determine patterns of microbial susceptibility, and these networks continue to be used to share information , , However, as of , the TSN is not supported and is no longer available. A software utility, BacLink, can be used to facilitate this translation. Because the data are translated into a universal file format, the local data can be shared and compiled so that regional, national, or international groups can analyze the data The system is designed to enable individual laboratories or groups of laboratories to manage their AST results, identify the emergence of resistant microbes, identify the spread of resistant strains, and identify trends in AST quality control testing , Analyses which WHONET can facilitate include examples such as the identification of changes in Escherichia coli isolate resistance within a country over time , , prospective surveillance of Shigella outbreaks in a country , , and, potentially, a means of global strain tracking Although local laboratories are not usually considered directly responsible for identifying regional and global outbreaks, local laboratories are essential in providing information to public health agencies so that identification of these outbreaks is possible.

The role that the local laboratory plays in the detection of global outbreaks is typically confined to its responsibility to report the detection of notifiable infectious agents to the public health agencies which oversee the laboratory's region However, the detection of some local outbreaks carries global public health significance, and all identification of global outbreaks begins locally. One way to facilitate timely identification of regional outbreaks is to provide the regional public health agencies with clinical and microbiological information from the local laboratory in as timely a way as possible.

The rapidity of regional outbreak identification can be enhanced by using electronic reporting by local laboratories 7 , Local clinical microbiology laboratories actively play a role in the detection of local disease outbreaks. These local outbreaks could be community-acquired infections e. Software has been used successfully to mine the data of clinical microbiology laboratories in search of aberrancies that may be an indication of a community outbreak Software has also been used to identify nosocomial infections by autonomously reviewing laboratory data and medical records, and this software has demonstrated increased sensitivity over the manual analysis of records for the identification of nosocomial infections 17 , 51 , Outbreak detection can be accomplished by at least these three ways: prospective organism surveillance, laboratory surveillance including virtual surveillance , and syndromic surveillance.

Prospective surveillance using environmental biosensors is the most rapid means of detection , but the local microbiology laboratory does not typically play a role in this type of screening.

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The local laboratory is integral to the traditional surveillance systems that are in place, which typically identify outbreaks after they have occurred. A goal of laboratory outbreak surveillance is to transform this surveillance from a retrospective means of surveillance into a real-time means of proactive surveillance by using informatics tools to continually analyze laboratory data, with the goal of identifying outbreaks as they are occurring Syndromic surveillance is increasingly being used to attempt early identification of outbreaks or bioterrorism , One of the most highly publicized systems using syndromic surveillance is Google Flu Trends , Unlike prospective organism surveillance and laboratory surveillance, syndromic surveillance does not rely on definitive clinical diagnoses or the identification of microbes.

Instead, syndromic surveillance infers the presence of an outbreak by analyzing patient signs and symptoms or analyzing public behavior , Syndromic surveillance is performed completely in silico and has the potential to identify an outbreak before the laboratory can identify a causative agent. This surveillance does not require the implementation of new physical tests but relies on the analysis of already available information. Obtaining information from Internet users is often a part of syndromic surveillance For example, Yelp.

Syndromic surveillance has a lower specificity of detection than laboratory surveillance, so it has been suggested that syndromic surveillance can be used as a screening tool for detecting an outbreak, which can then be confirmed using laboratory surveillance. In this situation, detection of a potential outbreak by syndromic surveillance would alert the local laboratory to increase its vigilance or adjust its testing protocols so as to increase the laboratory's sensitivity and rapidity of identifying an outbreak Although this type of integrated system is feasible and would improve patient care, it has not yet been employed.

Increasingly, standardized electronic reporting, such as NEDSS, is being used by local laboratories to report to their regional health agencies, and standardized electronic reporting correlates with improved completeness and rapidity of reporting, which allow for quicker detection of regional outbreaks.


Additionally, data analysis surveillance software has demonstrated improved detection of local disease outbreaks beyond that which humans have been able to identify without these tools. With the growing clinical use of WGS and MGS, the need for globally integrated informatics tools that can identify and characterize whole genomes, such as GMI, are needed for outbreak detection Integration of prospective, laboratory, and syndromic surveillance systems in combination with rapid standardized reporting of events has the potential to improve outbreak detection beyond what any one of these systems can do independently.

The clinical microbiology laboratory is required to generate, analyze, and interpret an ever-increasing amount of information. Incorporating the use of informatics tools to improve the quality of laboratory workflow and processes is paramount for data to effectively and efficiently be evaluated and communicated. Informatics tools can help microbiologists to more capably keep track of specimen work-ups in the laboratory, automate their workloads, identify clinically relevant characteristics of microorganisms, remotely share digital images for teleconsultation, quickly distribute accurate and appropriate results, perform more thorough and rapid disease surveillance, and most importantly provide patients and the public with better health care.

The continued development and implementation of informatics tools are needed in order to continue to help the laboratory to produce, interpret, and communicate the most useful information. Guidance is required in order to best develop and implement these informatics tools, specifically in areas of telemicrobiology and microbial MGS and WGS. When used properly, informatics tools can help the clinical microbiology laboratory to do more with less while improving the quality of patient and public health care.

None of the authors have any financial interests or support from institutions or companies mentioned in the article. Daniel D. In , he received a B. While studying chronic wounds there, he acquired his interest in biofilm infections and his desire to unravel the complexity of microbial communities by using informatics tools.

In , Dan received his M. Dan has accepted a Medical Microbiology Fellowship at the Cleveland Clinic for the — academic year. His research focuses on infectious disease informatics, bacterial genomics-guided public health laboratory surveillance, and disease control.

He has authored two books and more than scientific papers. He has been actively involved in disease outbreak investigations and the design of biosurveillance systems.

Carol A. Rauch received her M. Through 20 years in clinical laboratories and clinical microbiology, her interests have included patient safety, quality in laboratory testing, and bioterrorism preparedness. Her professional experience has led to an appreciation of the critical role of pathology informatics in healthcare, as well as the special needs of microbiology in information systems as drivers of quality medical and public health information.

Pantanowitz obtained his M. He subsequently completed cytopathology and hematopathology fellowships. He has published many peer-reviewed articles and book chapters, written several textbooks, and given talks around the world. Europe PMC requires Javascript to function effectively. Recent Activity. The snippet could not be located in the article text. This may be because the snippet appears in a figure legend, contains special characters or spans different sections of the article.

Clin Microbiol Rev. PMID: Corresponding author. Address correspondence to Daniel D. Rhoads, moc. All Rights Reserved. This article has been cited by other articles in PMC. Abstract SUMMARY The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. Open in a separate window. Multiple-Derivative Tracking Samples sent to the microbiology laboratory often produce more than a single result, and the final type and number of results are typically not known until the testing is under way.

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