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The Microbiology Laboratory
Published in Keith Struthers, Clinical Microbiology, 2017
The microbiology department provides a clinical and laboratory service for users in the hospital and community and is also an integral part of the hospital's infection control team (ICT). The work centres on timely processing of specimens, to identify organisms by a range of tests and issue a report, with interpretative comments, to be used in patient management. In the case of bacteria (and yeasts), appropriate antibiotic susceptibility testing is done. Concise clinical details must be included on the request form, as this information is a key part of the overall diagnostic process. It also alerts staff to the possibility of organisms that pose a risk to them (e.g. a travel history, possible enteric fever, Salmonella Typhi/Paratyphi), so that the specimen is processed in the correct containment room. Examples of the range of organisms and tests are shown in Tables 5.1, 5.2.
Unique Aspects in the Nursing Home Setting
Published in Thomas T. Yoshikawa, Shobita Rajagopalan, Antibiotic Therapy for Geriatric Patients, 2005
Chesley L. Richards, Joseph G. Ouslander
The guideline also suggests appropriate diagnostic testing for febrile or potentially infected residents. When diagnostic evaluation is performed, only limited tests are available in many nursing homes. In the overwhelming majority of nursing homes, laboratory testing is not performed in an on-site laboratory but is performed in a hospital or in a commercial laboratory. The delay between obtaining specimens and actual laboratory processing may be substantial. When combined with delays in getting reports back to clinicians in nursing homes, suboptimal timeliness of reporting is the norm and, in some situations, may lead to poor decisions regarding empirical or continued antimicrobial use. Medical directors should work with nursing home administators, directors of nursing, and laboratory providers in both improving specimen collection and reporting results. Where possible, laboratory providers should provide a facility-specific antibiotic susceptibility testing profile (i.e., antibio-gram), either for the individual facility or for the network of nursing homes. The availability of a specific antibiogram may improve the initial selection of empirical antimicrobial therapy. Furthermore, improving the availability of accurate microbiological results may allow clinicians to re-evaluate the resident at 48-72 hr with the goal of individualizing antimicrobial therapy to the identified pathogen and antimicrobial susceptibility profile. Acutely ill residents or those residents who require diagnostic studies not available in nursing homes may be transferred to acute care hospitals for further evaluation and therapy. Residents with presumed infections account for one-quarter of all hospital transfers from nursing homes (27).
Micafungin
Published in M. Lindsay Grayson, Sara E. Cosgrove, Suzanne M. Crowe, M. Lindsay Grayson, William Hope, James S. McCarthy, John Mills, Johan W. Mouton, David L. Paterson, Kucers’ The Use of Antibiotics, 2017
Nicholas D. Beyda, Russell E. Lewis, Dimitrios P. Kontoyiannis
The in vitro activity of micafungin can be assessed using several different methods, including E-test strips, disk-diffusion, broth macrodilution, and broth microdilution. Broth microdilution is a widely used technique for antifungal susceptibility testing in the clinical microbiology laboratory, and standardized methods have been developed by the Clinical Laboratory Standards Institute (CLSI) and European Committee on Antibiotic Susceptibility Testing (EUCAST) for testing echinocandins against yeast and molds (CLSI, 2008a, 2012; EUCAST, 2008; Arendrup et al., 2012, 2014). Notable differences between CLSI and EUCAST methods of broth microdilution include the use of round-bottom versus flat-bottom wells, a glucose content of 0.2% versus 2%, and a starting inoculum size of 0.5–2.5 · 10∧3 versus 0.5–2.5 · 10∧5 CFU/ml, respectively. Both the CLSI and EUCAST have established species specific epidemiological cutoff values (ECVs) and clinical breakpoints (CBPs) for micafungin and most Candida species (Table 147.1) in order to identify strains of Candida likely to harbor acquired FKS mutations associated with echinocandin resistance and treatment failure. Despite the methodological differences, essential agreement minimum inhibitory concentration [MIC] ± 2 doubling dilutions) and categorical agreement (MIC falls within same interpretive category) between the two methods has been demonstrated to be excellent with micafungin (Table 147.1) (Montagna et al., 2015; Pfaller et al., 2014). In contrast, significant inter- and intra-lab variability has been observed with caspofungin utilizing both CLSI and EUCAST methods (Espinell-Ingroff et al., 2013). The reason for this variability in caspofungin MICs has not been completely identified but may be a result of differences in the potency between drug lots or possible binding of caspofungin to treated polystyrene microtiter plates (Fothergill et al., 2016). Nevertheless, this variability has not been observed with micafungin.
Disseminated Mycobacterium szulgai in an immunocompromised patient
Published in Baylor University Medical Center Proceedings, 2022
Akanksha Verma, Laura Shevy, Abu Baker Sheikh, David Clanon
Antibiotic susceptibility testing is one of the most helpful tools when choosing an antibiotic regimen to treat a complicated infection. Regrettably, this could not be performed as the organism was no longer viable. Based on the official 2003 American Thoracic Society/Infectious Diseases Society of America statement,5M. szulgai is susceptible to most antituberculous drugs (isoniazid, rifampin, ethambutol, or pyrazinamide), macrolides, and fluoroquinolones. Treatment is most successful with a combination regimen of more than two susceptible antibiotics. While no optimal duration of treatment has been established, in cases of pulmonary involvement, treatment is considered adequate when 12 months of negative sputum cultures are obtained while on therapy. In cases of extrapulmonary involvement, treatment is considered adequate after 4 to 6 months of therapy. In our patient, treatment is prolonged and is ongoing at 9 months due to immunosuppression and drug-induced neutropenia.
Post-Traumatic Endophthalmitis: Clinico-Microbiological Profile, Antimicrobial Susceptibility and Prognostic Factors at a Tertiary Eye Care Centre in Eastern India
Published in Seminars in Ophthalmology, 2021
Sanchita Mitra, Tushar Agarwal, Abhijit Naik, Tapas Ranjan Padhi, Soumyava Basu, Umesh Chandra Behera
The vitreous or other additional samples were processed for microbiology as follows: direct smears were stained with Gram stain and calcofluor white fluorescence stain and samples were inoculated onto solid media (blood and chocolate agars, Sabouraud’s dextrose and potato dextrose agars or SDA and PDA) and liquid media (brain heart infusion broth, thioglycolate broth and Robertson’s cooked meat media), incubated at 37°C for all media except SDA and PDA incubated at 26°C for fungal growth. The media were examined daily for any significant growth of pathogens as per previously published criteria, and identified by standard microbiological procedures and confirmed by Vitek 2 compact system.11,12 Antibiotic susceptibility testing (AST) for the bacterial isolates were done by either Kirby-Bauer disc diffusion method or by E-strip test and Vitek AST method. Multidrug resistance (MDR) was defined as resistance to more than or equal to 1 antibiotic from 3 or more different classes of antibiotics. Conventional polymerase chain reaction for the samples were sent for Propionibacterium acnes, if there was a clinical suspicion of such infection.
Optimization of the empirical antibiotic choice during the treatment of acute prosthetic joint infections: a retrospective analysis of 91 patients
Published in Acta Orthopaedica, 2019
Joost H J Van Erp, Adriaan C Heineken, Remco J A Van Wensen, Robin W T M Van Kempen, Johannes G E Hendriks, Marjolijn Wegdam-Blans, Judith M Fonville, M C (Marieke) Van Der Steen
After routine laboratory antibiotic susceptibility testing of the micro-organisms as described above, the measured susceptibility patterns were supplemented with known intrinsic and derived resistance information as described by EUCAST (Leclercq et al. 2013). The resistance pattern for cefazolin was equated to the resistance of cefuroxime. Resistance was further inferred from related antibiotics and literature studies as follows. Corynebacterium, Finegoldia, Granulicatella, Peptoniphilus, Cutibacterium acnes, and streptococcal species were set to be sensitive to cefuroxime when sensitive to penicillin. Streptococci and Granulicatella species were set to be sensitive to amoxicillin/clavulanic acid when sensitive to penicillin, whilst Enterococcus faecium was set to be resistant to amoxicillin/clavulanic acid. For some combinations of micro-organism and antibiotic, the resistance pattern could not be inferred from known patterns or literature studies. Susceptibility was then set as unknown.