Collection, transport and general processing of clinical specimens in Microbiology laboratory

Sánchez-Romero, María Isabel; García-Lechuz, J.M.; López, Juan Jorge Piernas; Mira, Nieves Orta

doi:10.1016/j.eimce.2017.12.005

Cited by 19 publications

(31 citation statements)

References 11 publications

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“…Upon arrival at the laboratory, all samples were processed immediately or (if the return from field measurements occurred in the evening or at night) placed in a refrigerator at 4 °C until the next day [18,19]. The samples were always processed not later than 24 hours from the moment of their collection.…”

Section: Methodsmentioning

confidence: 99%

Viral, bacterial, and fungal contamination of Automated Teller Machines (ATMs)

Górny¹,

Stobnicka-Kupiec²,

Gołofit-Szymczak³

et al. 2022

Ann Agric Environ Med.

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Introduction andObjective. While the qualitative information about bacterial and fungal pollution of automated teller machine (ATM) surfaces is available in the scientific literature, there are practically no studies precisely quantifying this type of contamination. Regarding viruses, such data in relation to ATM surfaces are not available at all. Materials and method. The quantitative and qualitative control of adeno-and coronaviruses, including SARS-CoV-2 (based on qPCR/RT-qPCR and v-qPCR/v-RT-qPCR), bacterial and fungal contaminants (based on morphological and biochemical characteristics followed by PCR/RAPD typing) deposited on internal and external ATM surfaces (swab sampling), as well as present in the air of premises housing the ATM machines (inertial impaction sampling) belonging to the network of one of the largest Polish banks was performed. Results. As the air of premises housing ATMs was relatively clean, the internal (i.e. safe boxes and cash dispenser tracks) and external (i.e. touch screens and keypads) ATM surfaces were heavily polluted, reaching 599 CFU/cm 2 , 522 CFU/cm 2 , 17288 gc/cm 2 and 2512 gc/cm 2 for bacterial, fungal, coronaviral and adenoviral contaminants, respectively. The application of propidium monoazide (PMA) dye pretreatment for v-qPCR/v-RT-qPCR allows detection of the potentially infectious SARS-CoV-2 and adenoviral particulates on ATM surfaces. Conclusions. The packaged banknotes and people involved in their distribution, as well as general population using ATMs, can be the sources of this type of contamination and its potential victims. Highly efficient hygienic measures should be introduced to prevent unwanted pollution of both the distributed means of payment and ATM surfaces, and to avoid subsequent dissemination of microbial contaminants.

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Section: Methodsmentioning

confidence: 99%

Viral, bacterial, and fungal contamination of Automated Teller Machines (ATMs)

Górny¹,

Stobnicka-Kupiec²,

Gołofit-Szymczak³

et al. 2022

Ann Agric Environ Med.

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“…Viral RNA extracted from cell culture supernatants are produced cleanly in a lab and are quickly stored properly to minimize viral and RNA degradation, thus giving higher quality samples. Clinical samples, on the other hand, are usually obtained on farm and the subsequent handling, shipping, and storage of clinical samples will inevitably increase viral and RNA degradation and decrease sample quality, resulting in lower sequencing yields, while RT-qPCR, which is less sensitive to these conditions, can still detect the presence of the virus [60]. The detection accuracy of the raw PRRSV reads was determined by comparing the top BLAST hit to the known ORF5 sequence and/or whole genome sequence (Table 3).…”

Section: Determination Of Minimal Viral Copy Level Needed For Sequencingmentioning

confidence: 99%

Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools

Tan

Dvorak

Murtaugh

2019

Viruses

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Prompt detection and effective control of porcine reproductive and respiratory syndrome virus (PRRSV) during outbreaks is important given its immense adverse impact on the swine industry. However, the diagnostic process can be challenging due to the high genetic diversity and high mutation rate of PRRSV. A diagnostic method that can provide more detailed genetic information about pathogens is urgently needed. In this study, we evaluated the ability of Oxford Nanopore MinION direct RNA sequencing to generate a PRRSV whole genome sequence and detect and discriminate virus at the strain-level. A nearly full length PRRSV genome was successfully generated from raw sequence reads, achieving an accuracy of 96% after consensus genome generation. Direct RNA sequencing reliably detected the PRRSV strain present with an accuracy of 99.9% using as few as 5 raw sequencing reads and successfully differentiated multiple co-infecting strains present in a sample. In addition, PRRSV strain information was obtained from clinical samples containing 10 4 to 10 6 viral copies or more within 6 hours of sequencing. Overall, direct viral RNA sequencing followed by bioinformatic analysis proves to be a promising approach for identification of the viral strain or strains involved in clinical infections, allowing for more precise prevention and control strategies during PRRSV outbreaks.2 of 18 against a new introduction from outside the farm indicates a need for enhanced biosecurity, while a re-break of a resident strain suggests better strategies for an elimination or vaccination program are needed. Another big challenge for PRRS control is that PRRSV vaccine is not completely effective at preventing and controlling infection due to the high genetic diversity of the virus, thus outbreaks still occur in vaccinated herds [13][14][15][16]. A diagnostic method which can provide genetic information about the strain causing infection would allow for identification of potential reasons for vaccination failure, such as limited cross-protection due to high genetic divergence from vaccine [17], or in the case of genetic similarity to vaccine, perhaps a reversion to virulence (escape mutation) of the vaccine itself [18]. In addition to the clinical challenges mentioned above, PRRSV has widely divergent genetic lineages and is a rapidly evolving pathogen with novel variants which seem to be more divergent and virulent than those in the past [10,[19][20][21]. The continuous emergence of new virulent strains causes unexpected devastating outbreaks, such as the severe outbreaks of HP-PRRSV in China and MN184 and NADC30 outbreaks in the United States [22][23][24][25]. The increasing incidence of co-infections of multiple strains further complicates PRRS diagnosis and control [26]. Hence, diagnostic tools that can provide more genetic information are extremely important for investigation, prevention, and control strategies for PRRSV outbreaks.Prompt detection of pathogens during an outbreak is essential for efficient disease control. Real-time quantitative...

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“…Care should be taken not to overturn the samples. These precautions will prevent bacterial growth that may result in overestimation of actual sample load [40].…”

Section: Transportation Of Samplesmentioning

confidence: 99%

The production of on-line dialysis water for extracorporeal dialysis: proposals for an increased safety upgrade: a viewpoint

Bolasco

2019

J Nephrol

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Introduction At the start of the 2000s, the progressive diffusion of high-flux extracorporeal dialysis and membranes saw an increased use of high infusion volumes injected into the patient’s blood circuit following the advent of on-line water production plants. Methodology Our 15-year experience with on-line extracorporeal methodologies using very high infusion volumes has led to the detection of errors and weaknesses, thus allowing us to correct and provide for the implementation of appropriate technology in dialysis water production plants with the aim of ensuring a higher chemical-physical, bacteriological and endotoxin quality. The initial procedures had already been outlined in the 2005 Italian Guidelines, although still today Health Technicians and Nephrologists operating in the field are unable to take on board specific integrations for on-line methods due to a lack of upgrading of documentation in both European and non-European Guidelines. Results After more than 17 years’ experience, and in view of the technological implementations developed since 2005, we wish to put forward a series of suggestions in an attempt to improve the safety of on-line water, with uses ranging from drinking water, pre-treatment, osmosis, distribution circuit, hemodialysis monitors up to the most recent update of microbiological cultures. Discussion Additional, more stringent measures are required to prevent the occurrence of acute accidents during dialysis sessions and to reduce chronic inflammation-oxidation deriving from the use of not totally ultra-pure/sterile dialysis fluids. Conclusion Our point of view based on our long-standing experience, the proposals made relate to procedures to be applied in technological maintenance, which the consultant nephrologist and other relevant personnel such as microbiologists, biologists, and technical operators should adhere to rigorously to ensure that the production of dialysis water on-line is viewed on a par with a pharmacological administration.

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Collection, transport and general processing of clinical specimens in Microbiology laboratory

Cited by 19 publications

References 11 publications

Viral, bacterial, and fungal contamination of Automated Teller Machines (ATMs)

Viral, bacterial, and fungal contamination of Automated Teller Machines (ATMs)

Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools

The production of on-line dialysis water for extracorporeal dialysis: proposals for an increased safety upgrade: a viewpoint

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