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Enhanced clinical microbiology methods in outbreak management.

ABSTRACT: Conventional microbiological investigations, including pathogen detection, antibiotic susceptibility testing and molecular epidemiological testing, are valuable tools in helping to manage nosocomial outbreaks. However, the microbiology laboratory, by using other techniques, can investigate additional microbiological aspects of outbreaks, which are often overlooked. Bacterial isolates (n=6) from an outbreak of Pseudomonas aeruginosa bacteraemia in a neonatal intensive care unit (NICU) in Belfast were examined. Enhanced microbiology testing included: (1) susceptibility of outbreak strains to biocides in common use in the unit; (2) effect of organic soils relevant to the area of the outbreak and their effect on the efficacy of biocide; and (3) the persistence of outbreak strains in organic soils. By emulating bespoke conditions of the outbreak, these methods were able to demonstrate that: (1) biocides were effective against the outbreak strains; (2) the critical concentration of soil which rendered biocide ineffective; and (3) how long the outbreak strains could persist. Enhanced microbiological analysis outside the conventional repertoire of testing may therefore offer valuable data that may help guide outbreak management teams.

SUBMITTER: Moore JE

PROVIDER: S-EPMC7841714 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Enhanced clinical microbiology methods in outbreak management.

Moore John E JE Millar Beverley C BC

Journal of infection prevention 20200829 1

Conventional microbiological investigations, including pathogen detection, antibiotic susceptibility testing and molecular epidemiological testing, are valuable tools in helping to manage nosocomial outbreaks. However, the microbiology laboratory, by using other techniques, can investigate additional microbiological aspects of outbreaks, which are often overlooked. Bacterial isolates (n=6) from an outbreak of <i>Pseudomonas aeruginosa</i> bacteraemia in a neonatal intensive care unit (NICU) in B ...[more]

PMID: 33841560

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Project description:Next-generation sequencing (NGS) of bacterial genomes has recently become more accessible and is now available to the routine diagnostic microbiology laboratory. However, questions remain regarding its feasibility, particularly with respect to data analysis in nonspecialist centers. To test the applicability of NGS to outbreak investigations, Ion Torrent sequencing was used to investigate a putative multidrug-resistant Escherichia coli outbreak in the neonatal unit of the Mercy Hospital for Women, Melbourne, Australia. Four suspected outbreak strains and a comparator strain were sequenced. Genome-wide single nucleotide polymorphism (SNP) analysis demonstrated that the four neonatal intensive care unit (NICU) strains were identical and easily differentiated from the comparator strain. Genome sequence data also determined that the NICU strains belonged to multilocus sequence type 131 and carried the bla(CTX-M-15) extended-spectrum beta-lactamase. Comparison of the outbreak strains to all publicly available complete E. coli genome sequences showed that they clustered with neonatal meningitis and uropathogenic isolates. The turnaround time from a positive culture to the completion of sequencing (prior to data analysis) was 5 days, and the cost was approximately $300 per strain (for the reagents only). The main obstacles to a mainstream adoption of NGS technologies in diagnostic microbiology laboratories are currently cost (although this is decreasing), a paucity of user-friendly and clinically focused bioinformatics platforms, and a lack of genomics expertise outside the research environment. Despite these hurdles, NGS technologies provide unparalleled high-resolution genotyping in a short time frame and are likely to be widely implemented in the field of diagnostic microbiology in the next few years, particularly for epidemiological investigations (replacing current typing methods) and the characterization of resistance determinants. Clinical microbiologists need to familiarize themselves with these technologies and their applications.

Project description:IntroductionClinical microbiology laboratories are essential for diagnosing and monitoring antimicrobial resistance (AMR). Here, we assessed the systems involved in generating, managing and analyzing blood culture data in these laboratories in an upper-middle-income country.MethodsFrom October 2023 to February 2024, we conducted a survey on the utilization of automated systems and laboratory information management systems (LIMS) for blood culture specimens in 2022 across 127 clinical microbiology laboratories (one each from 127 public referral hospitals) in Thailand. We categorized automated systems for blood culture processing into three steps: incubation, bacterial identification, and antimicrobial susceptibility testing (AST).ResultsOf the 81 laboratories that completed the questionnaires, the median hospital bed count was 450 (range, 150-1,387), and the median number of blood culture bottles processed was 17,351 (range, 2,900-80,330). All laboratories (100%) had an automated blood culture incubation system. Three-quarters of the laboratories (75%, n = 61) had at least one automated system for both bacterial identification and AST, about a quarter (22%, n = 18) had no automated systems for either step, and two laboratories (3%) outsourced both steps. The systems varied and were associated with the hospital level. Many laboratories utilized both automated systems and conventional methods for bacterial identification (n = 54) and AST (n = 61). For daily data management, 71 laboratories (88%) used commercial microbiology LIMS, three (4%) WHONET, three (4%) an in-house database software and four (5%) did not use any software. Many laboratories manually entered data of incubation (73%, n = 59), bacterial identification (27%, n = 22) and AST results (25%, n = 20) from their automated systems into their commercial microbiology LIMS. The most common barrier to data analysis was 'lack of time', followed by 'lack of staff with statistical skills' and 'difficulty in using analytical software'.ConclusionIn Thailand, various automated systems for blood culture and LIMS are utilized. However, barriers to data management and analysis are common. These challenges are likely present in other upper-middle-income countries. We propose that guidance and technical support for automated systems, LIMS and data analysis are needed.

Dataset Information

Enhanced clinical microbiology methods in outbreak management.

Publications

Enhanced clinical microbiology methods in outbreak management.

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