scholarly journals Electronic Processing of Antimicrobial Susceptibilities to Enhance Communicable Disease Surveillance

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Emily Roberts
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Agent ◽  
Antimicrobial Susceptibility ◽  
Disease Surveillance ◽  
Antimicrobial Agents ◽  
Communicable Disease ◽  
Test Method ◽  
Health Concern ◽  
Acinetobacter Species ◽  
Department Of Health

ObjectiveIllustrate how the Utah Department of Health automatically processes antimicrobial susceptibility results that are received electronically.IntroductionThe emerging threat of antimicrobial resistant organisms is a pressing public health concern. Surveillance for antimicrobial resistance can prevent infections, protect patients in the healthcare setting and improve antimicrobial use. In 2018, the Utah Department of Health mandated the reporting of antimicrobial susceptibility panels performed on selected organisms. Utah utilizes the Electronic Message Staging Area (EMSA), a home-grown application to translate, process, and enter electronic laboratory results into UT-NEDSS, Utah’s integrated disease surveillance system. Processing these results electronically is challenging due to the need to interpret results based on the antimicrobial agent combined with the organism it was performed on. The receipt of antimicrobial susceptibility panels has required enhancements to EMSA for these results to be automatically processed.MethodsStand-alone antimicrobial susceptibility LOINCs are configured within EMSA to concatenate during the preprocessing stage. This tells EMSA that when this LOINC is sent within an HL7 message to find the organism name in the corresponding OBR 26.3 (the parent result field). EMSA then creates a new fabricated code that combines the antimicrobial agent with the organism identified from the culture (example: ‘18906-8 Pseudomonas aeruginosa’ is the fabricated code for Ciprofloxacin susceptibility to Pseudomonas aeruginosa).Once these new fabricated antimicrobial susceptibility codes are created, interpretation rules are programmed using current Clinical and Laboratory Standards Institute (CLSI) breakpoints for each unique organism/antimicrobial combination to determine if the result is Susceptible/Intermediate/Resistant. The interpreted test is then run through a set of condition-specific rules to determine how it should be included into UT-NEDSS.ResultsAntimicrobial susceptibility panels performed on Acinetobacter species, Escherichia coli, Klebsiella species, Pseudomonas aeruginosa, Enterobacter species, Candida auris/haemulonii, Mycobacterium tuberculosis, Neisseria gonorrhoeae, Salmonella species, Shigella species, Streptococcus pneumoniae and invasive Staphylococcus aureus are now included in Utah’s Communicable Disease Reporting Rule. Currently, there are 36 antimicrobial agents programmed into EMSA and there are a total of 217 antimicrobial susceptibility codes programmed into the system.ConclusionsProcessing electronic antimicrobial susceptibility results presents unique challenges for processing. Interpretation of results can vary based on test method, performing laboratory, and organism. Enhancing functionality within EMSA was necessary for combining the antimicrobial agent and organism it was performed on. Implementing systems capable of automatically processing complicated antimicrobial susceptibility results should be a priority for any health department interested in expanding their communicable disease rule to include antimicrobial susceptibility testing.

scholarly journals HL7 Terminology Management for Disease Surveillance

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Emily Roberts ◽  
Theron Jeppson ◽  
Rachelle Boulton ◽  
Josh Ridderhoff
Keyword(s):  
Disease Surveillance ◽  
Communicable Disease ◽  
Laboratory Data ◽  
Data Entry ◽  
High Volume ◽  
Electronic Data ◽  
Disease Surveillance System ◽  
Department Of Health ◽  
Message Structure ◽  
Set Up

Objective: The objective of this abstract is to illustrate how the Utah Department of Health processes a high volume of electronic data. We do this by translating what reporters send within an HL7 message into "epidemiologist" language for consumption into our disease surveillance system.Introduction: In 2013, the Utah Department of Health (UDOH) began working with hospital and reference laboratories to implement electronic laboratory reporting (ELR) of reportable communicable disease data. Laboratories utilize HL7 message structure and standard terminologies such as LOINC and SNOMED to send data to UDOH. These messages must be evaluated for validity, translated, and entered into Utah’s communicable disease surveillance system (UT-NEDSS), where they can be accessed by local and state investigators and epidemiologists. Despite the development and use of standardized terminologies, reporters may use different, outdated versions of these terminologies, may not use the appropriate codes, or may send local, home-grown terminologies. These variations cause problems when trying to interpret test results and automate data processing. UDOH has developed a two-step translation process that allows us to first standardize and clean incoming messages, and then translate them for consumption by UT-NEDSS. These processes allow us to efficiently manage several different terminologies and helps to standardize incoming data, maintain data quality, and streamline the data entry process.Methods: UDOH uses the Electronic Message Staging Area (EMSA) to receive ELR messages, manage terminologies such as LOINC and SNOMED, translate messages, and automatically enter laboratory data into UT-NEDSS. LOINCs and other terms, such as facility name, sent by reporting facilities in an HL7 message are considered child terms. All child terms are mapped to a master LOINC or term and each master LOINC or term is mapped to a specific value within UT-NEDSS. In EMSA, the rules engine used for automated processing of electronic data is set to run at the master level and these rules will determine how the message is processed. No rules are set up or run on child terms.Results: As of 09/20/2017, EMSA contains 2,613 unique child LOINCs that are mapped to 906 master LOINCs. Those 906 master LOINCs are mapped to 179 UT-NEDSS test types and 2003 child facility names are mapped to 1043 master facility namesConclusions: Mapping child terminologies from an HL7 message to a master vocabulary helps us to standardize incoming data, allows us to accept non-standard terminologies and correct reporting errors. Translating this data into a format that is understandable to epidemiologists and investigators enables UT-NEDSS to work effectively in identifying outbreaks and improving health outcomes. This framework is working for ELR and will continue to grow and accept more data and the different terminologies that come with that.

scholarly journals Heterogeneous Antimicrobial Susceptibility Characteristics inPseudomonas aeruginosaIsolates from Cystic Fibrosis Patients

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Xuan Qin ◽  
Chuan Zhou ◽  
Danielle M. Zerr ◽  
Amanda Adler ◽  
Amin Addetia ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Susceptibility ◽  
Antimicrobial Agents ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Parental Origin ◽  
Adaptive Mutations ◽  
Wide Range ◽  
Susceptibility Patterns

ABSTRACTClinical isolates ofPseudomonas aeruginosafrom patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability.Pseudomonas aeruginosaisolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n= 224 from 56 CF patients,n= 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CFP. aeruginosaisolates in comparison to non-CFP. aeruginosaisolates. On the basis of whole-genome sequencing of 19 CFP. aeruginosaisolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CFP. aeruginosaclonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs betweenP. aeruginosacoisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CFP. aeruginosaanalyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations inmutL,mutS, anduvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being “locked” inside a host focal airway environment for prolonged periods.IMPORTANCEPatients with cystic fibrosis endure “chronic focal infections” with a variety of microorganisms. One microorganism,Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains ofP. aeruginosaemerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains ofP. aeruginosadevelop vastly different susceptibility patterns to actively used antimicrobial agents—a phenomenon we define as “heterogeneous MICs.” By sequencing pairs ofP. aeruginosaisolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilitiesin vitrowith treatment implications.

Plaquelike Clearings Induced by Antimicrobial Agents on Lawns of Pseudomonas aeruginosa

1970 ◽  
Vol 1 (2) ◽  
pp. 190-194
Author(s):  
Marian W. Wolfe ◽  
Daniel Amsterdam
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Susceptibility ◽  
Antimicrobial Agents ◽  
Biochemical Properties ◽  
Plaque Formation ◽  
Previous Exposure ◽  
Susceptibility Pattern ◽  
Antimicrobial Susceptibility Pattern ◽  
The Relationship

Plaques similar in appearance to those induced by phage were observed adjacent to chloramphenicol and tetracycline discs on Pseudomonas aeruginosa lawns used for the determination of antibiotic susceptibility. Thirteen strains were selected for study, 10 of which exhibited the plaquing phenomenon. The ability to form plaques induced by tetracycline was not related to any of the biochemical properties of the strains studied, their overall antimicrobial susceptibility pattern, or their pathological source. Some pseudomonad strains were capable of pyocin production; however, the relationship between plaque formation and pyocin production was not apparent. Supernatant fluids of resuspended plaque contents of eight strains originally demonstrating clearings could induce plaques on sensitive indicator lawns only when collected from tetracycline-induced plaque areas; supernatant fluids of the same strains could not produce clearings without previous exposure to the drug. Of the eight supernatant fluids capable of plaque induction, three were active on their homologous indicator lawns. In a subsequent survey of 95 P. aeruginosa strains, it was found that 28 isolates exhibited plaques. Of these, 17 were associated with tetracycline, 7 were associated with chloramphenicol, 3 were associated with triple sulfa; and 1 was associated with nalidixic acid.

scholarly journals Identification of veterinary pathogens by use of commercial identification systems and new trends in antimicrobial susceptibility testing of veterinary pathogens.

1994 ◽  
Vol 7 (3) ◽  
pp. 346-356 ◽  
Author(s):  
J L Watts ◽  
R J Yancey
Keyword(s):  
Antimicrobial Agent ◽  
Antimicrobial Susceptibility ◽  
Antimicrobial Agents ◽  
Susceptibility Testing ◽  
Bacterial Species ◽  
Antimicrobial Susceptibility Testing ◽  
Human Pathogens ◽  
Host Animal ◽  
Isolation And Identification ◽  
Accurate Identification

Veterinary diagnostic microbiology is a unique specialty within microbiology. Although isolation and identification techniques are similar to those used for human pathogens, many veterinary pathogens require unique cultivation or identification procedures. Commercial identification systems provide rapid, accurate identification of human pathogens. However, the accuracy of these systems with veterinary pathogens varies widely depending on the bacterial species and the host animal from which it was isolated. Increased numbers of veterinary strains or species in the data bases of the various systems would improve their accuracy. Current procedures and interpretive criteria used for antimicrobial susceptibility testing of veterinary pathogens are based on guidelines used for human pathogens. The validity of these guidelines for use with veterinary pathogens has not been established. As with fastidious human pathogens, standardized methodologies and quality control isolates are needed for tests of organisms such as Actinobacillus pleuropneumoniae and Haemophilus somnus. Furthermore, interpretive criteria for veterinary antimicrobial agents based on the MIC for veterinary pathogens, the pharmacokinetics of the antimicrobial agent in the host animal, and in vivo efficacy of the antimicrobial agent are needed. This article reviews both the commercial identification systems evaluated with veterinary pathogens and current methods for performing and interpreting antimicrobial susceptibility tests with veterinary pathogens. Recommendations for future improvements in both areas are discussed.

scholarly journals Antimicrobials as Single and Combination Therapy for Colistin-Resistant Pseudomonas aeruginosa at a University Hospital in Thailand

Antibiotics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 475
Author(s):  
Supanun Pungcharoenkijkul ◽  
Jantima Traipattanakul ◽  
Sudaluck Thunyaharn ◽  
Wichai Santimaleeworagun
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Susceptibility ◽  
Test Method ◽  
University Hospital ◽  
Minimal Inhibitory Concentrations ◽  
High Prevalence ◽  
Group A ◽  
Lactamase Gene ◽  
The Impact

Global infections with colistin-resistant Pseudomonas aeruginosa (CoR-PA) are increasing; there are currently very few studies focused on the antimicrobial susceptibility of CoR-PA isolates, and none from Thailand. Here, we investigated the impact of various antimicrobials, alone and in combination, via the in vitro testing of CoR-PA clinical isolates. Eighteen CoR-PA isolates were obtained from patients treated at Phramongkutklao Hospital from January 2010 through June 2019; these were classified into six different clonal types by using the enterobacterial repetitive intergenic consensus (ERIC)-PCR method, with a high prevalence of Group A (27.8%). The antimicrobial susceptibility was determined as the minimal inhibitory concentrations (MICs) using the epsilometer-test (E-test) method. The synergistic activities of six antimicrobial combinations were reported via the fractional-inhibitory-concentration index. All CoR-PA isolates were susceptible to amikacin, meropenem, and ceftolozane/tazobactam, but only 5.56% were susceptible to imipenem. In vitro synergistic activities were detected for amikacin with aztreonam, piperacillin/tazobactam, meropenem, and ceftazidime for 16.67%, 11.11%, 11.11%, and 5.55%, respectively. One CoR-PA isolate carried the blaVIM metallo-β-lactamase gene; none carried mcr-1 genes or detected plasmid-mediated AmpC β-lactamase or an overproduction of chromosomal AmpC β-lactamase. Seven CoR-PA isolates (38.89%) were capable of biofilm formation. In conclusion, CoR-PA isolates are highly susceptible to antimicrobials; the synergy observed in response to the various agents should be examined in a clinical setting.

scholarly journals Substrate Specificities of MexAB-OprM, MexCD-OprJ, and MexXY-OprM Efflux Pumps in Pseudomonas aeruginosa

2000 ◽  
Vol 44 (12) ◽  
pp. 3322-3327 ◽  
Author(s):  
Nobuhisa Masuda ◽  
Eiko Sakagawa ◽  
Satoshi Ohya ◽  
Naomasa Gotoh ◽  
Hideto Tsujimoto ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Agent ◽  
Antimicrobial Agents ◽  
Efflux Pumps ◽  
Polymyxin B ◽  
The Other ◽  
Substrate Specificities ◽  
Isogenic Mutants

ABSTRACT To find the exact substrate specificities of three species of tripartite efflux systems of Pseudomonas aeruginosa, MexAB-OprM, MexCD-OprJ, and MexXY-OprM, we constructed a series of isogenic mutants, each of which constitutively overproduced one of the three efflux systems and lacked the other two, and their isogenic mutants, which lacked all these systems. Comparison of the susceptibilities of the constructed mutants to 52 antimicrobial agents belonging to various groups suggested the following substrate specificities. All of the efflux systems extrude a wide variety of antimicrobial agent groups, i.e., quinolones, macrolides, tetracyclines, lincomycin, chloramphenicol, most penicillins (all but carbenicillin and sulbenicillin), most cephems (all but cefsulodin and ceftazidime), meropenem, and S-4661, but none of them extrude polymyxin B or imipenem. Extrusion of aminoglycosides is specific to MexXY-OprM, and extrusion of a group of the β-lactams, i.e., carbenicillin, sulbenicillin, ceftazidime, moxalactam, and aztreonam, is specific to MexAB-OprM. Moreover, MexAB-OprM and MexCD-OprJ extrude novobiocin, cefsulodin, and flomoxef, while MexXY-OprM does not. These substrate specificities are distinct from those reported previously.

scholarly journals Susceptibility of enterococci and epidemiology of enterococcal infections in the 1980s

1989 ◽  
Vol 103 (3) ◽  
pp. 403-413 ◽  
Author(s):  
R. C. George ◽  
A. H. C. Uttley
Keyword(s):  
Disease Surveillance ◽  
Antimicrobial Agents ◽  
Communicable Disease ◽  
Sensu Stricto ◽  
Laboratory Service ◽  
Minimal Inhibitory Concentrations ◽  
Enterococcal Infection ◽  
The Usa ◽  
The Uk ◽  
High Level

Enterococcisensu strictoform part of the normal gut flora (1) and may be found in the mouth, vagina and anterior urethra (2). They are opportunist pathogens which can cause serious infection including endocarditis. Nosocomial enterococcal infection appears to be increasing both in the UK (Public Health Laboratory Service [PHLS] Communicable Disease Surveillance Centre [CDSC], unpublished) and the USA (3) and to correspond to usage of broad spectrum β-lactam antimicrobial agents (4−7) and invasive surgical devices (8, 9). At the same time, the incidence of enterococci resistant or tolerant to previously commonly employed antimicrobial agents or their synergistic combinations is increasing and is compromising therapy of serious enterococcal infection. Strains of enterococci with high-level resistance to streptomycin and kanamycin (minimal inhibitory concentrations [MICs] > 2000 mg/L) were first reported in 1970 (10, 11) and rapidly became widespread (8, 12−14).

scholarly journals Evaluation of the PASCO Strep Plus Broth Microdilution Antimicrobial Susceptibility Panels for Testing Streptococcus pneumoniae and Other Streptococcal Species

2000 ◽  
Vol 38 (5) ◽  
pp. 1713-1716 ◽  
Author(s):  
M. Jasmine Mohammed ◽  
Fred C. Tenover
Keyword(s):  
Streptococcus Pneumoniae ◽  
Antimicrobial Agent ◽  
Antimicrobial Susceptibility ◽  
Antimicrobial Agents ◽  
Clinical Laboratory ◽  
Reference Method ◽  
National Committee ◽  
Broth Microdilution ◽  
Streptococcal Species ◽  
Commercial Method

Antimicrobial resistance continues to increase worldwide among isolates of Streptococcus pneumoniae and other species of streptococci. Increasing rates of penicillin resistance, particularly in viridans group streptococci, and resistance to multiple classes of antimicrobial agents, including β-lactams, macrolides, and fluoroquinolones, in pneumococci have increased the importance of having accurate antimicrobial susceptibility testing results for guiding therapy. One commercial method of assessing resistance in streptococci is the PASCO Strep Plus panel. This broth microdilution-based method has recently been expanded to include a variety of newer antimicrobial agents. Therefore, we compared the results of the new PASCO Strep Plus panels for 26 antimicrobial agents against the results generated using the National Committee for Clinical Laboratory Standards (NCCLS) broth microdilution reference method for 75 pneumococci and 68 other streptococcal isolates. Only 4 (0.2%) very major errors (all with pneumococci and each with a different antimicrobial agent) were observed. There were 5 (0.3%) major errors observed with pneumococci (each with a different antimicrobial agent), but only 1 major error with nonpneumococcal streptococci. All of the very major and major errors resolved on retesting. Of the 65 (3.9%) and 17 (1.6%) minor errors observed with pneumococci and other streptococci, respectively, all were within 1 dilution of the broth microdilution reference MIC result. Thus, the PASCO Strep Plus panel has comparable accuracy to the NCCLS broth microdilution reference method.

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