Clinical role of the microbiology laboratory - Revision history

Bosmana fem: /* FEM PAGE CONTRIBUTORS 2007 */

2023-04-10T21:42:43Z

FEM PAGE CONTRIBUTORS 2007

← Older revision		Revision as of 21:42, 10 April 2023
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	References are in the 8.1 The role of the clinical microbiology laboratory in infection prevention and control.		References are in the 8.1 The role of the clinical microbiology laboratory in infection prevention and control.
	==FEM PAGE CONTRIBUTORS 2007==		<div style="display: inline-block; width: 25%; vertical-align: top; border: 1px solid #000; background-color: #d7effc; padding: 10px; margin: 5px;">
			'''FEM PAGE CONTRIBUTORS 2007'''
	;Contributors		;Contributors
	:Smilja Kalenic		:Smilja Kalenic
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	;Original contribution from:		;Original contribution from:
	:Smilja Kalenic, University of the Zagreb School of Medicine		:Smilja Kalenic, University of the Zagreb School of Medicine
			</div>
	[[Category:The role of the clinical microbiology laboratory in infection prevention and control]]		[[Category:The role of the clinical microbiology laboratory in infection prevention and control]]

Bosmana fem: /* Point of care (POC) tests */

2023-04-08T18:20:37Z

Point of care (POC) tests

← Older revision		Revision as of 18:20, 8 April 2023
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	References are in the 8.1 The role of the clinical microbiology laboratory in infection prevention and control.		References are in the 8.1 The role of the clinical microbiology laboratory in infection prevention and control.
			==FEM PAGE CONTRIBUTORS 2007==
	Original contribution from: Smilja Kalenic,University of Zagreb School of Medicine		;Contributors
			:Smilja Kalenic
			:Vladimir Prikazsky
			;Original contribution from:
			:Smilja Kalenic, University of the Zagreb School of Medicine

	[[Category:The role of the clinical microbiology laboratory in infection prevention and control]]		[[Category:The role of the clinical microbiology laboratory in infection prevention and control]]

Bosmana fem: /* Diagnostic Methods */

2023-04-08T18:18:58Z

Diagnostic Methods

← Older revision		Revision as of 18:18, 8 April 2023
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	# direct smear of the specimen: microbial stains e.g. Gram stain can help with the interpretation of the culture results and provide a rapid clue as to the likely pathogen;		# direct smear of the specimen: microbial stains e.g. Gram stain can help with the interpretation of the culture results and provide a rapid clue as to the likely pathogen;
	# culture for bacteria and fungi followed by		# culture for bacteria and fungi followed by
	# identification (using classic biochemical/ antigen determination methods or newer methods like MALDI-TOF, SELDI-TOF, or other molecular methods) and		# identification (using classic biochemical/ antigen determination methods or newer methods like MALDI-TOF, SELDI-TOF, or other molecular methods) and antimicrobial susceptibility testing results. This is one of the most important laboratory clinical functions. Semi-quantitative testing is performed routinely; European test results should be interpreted using EUCAST standards. The laboratory will also advise on, and perform, quantitative susceptibility testing, and, where relevant, identify resistance genes;
	antimicrobial susceptibility testing results. This is one of the most important laboratory clinical functions. Semi-quantitative testing is performed routinely; test results ~~in Europe~~ should be interpreted using EUCAST standards. The laboratory will also advise on, and perform, quantitative susceptibility testing, and, where relevant, identify resistance genes;
	# microbial antigen testing e.g. for Legionella spp;		# microbial antigen testing e.g. for Legionella spp;
	# serology; as a proof of immune response to infectious agent (this usually requires specimens to be taken 10-14 days after the infection, when antibodies first appear).		# serology; as a proof of immune response to infectious agent (this usually requires specimens to be taken 10-14 days after the infection, when antibodies first appear).

Bosmana fem: /* Diagnostic Methods */

2023-04-08T18:18:17Z

Diagnostic Methods

← Older revision		Revision as of 18:18, 8 April 2023
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	# nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:		# nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:
	# advantages of nucleic acid detection methods, these comprise:		# advantages of nucleic acid detection methods, these comprise:
	*# speed, as the process does not require microbial culture,		## speed, as the process does not require microbial culture,
	## sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)		## sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)
	## specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);		## specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);
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	## one can find only what one is searching for (known: especially important where there are new AMR genes emerging)		## one can find only what one is searching for (known: especially important where there are new AMR genes emerging)
	## the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),		## the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),
	#* biological samples can often contain inhibitors to DNA/RNA amplification methods		## biological samples can often contain inhibitors to DNA/RNA amplification methods
	## they need trained staff (easier if the same equipment is used for all such tests)		## they need trained staff (easier if the same equipment is used for all such tests)
	## they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.		## they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.

Bosmana fem: /* Diagnostic Methods */

2023-04-08T18:17:48Z

Diagnostic Methods

← Older revision		Revision as of 18:17, 8 April 2023
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	# nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:		# nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:
	# advantages of nucleic acid detection methods, these comprise:		# advantages of nucleic acid detection methods, these comprise:
	## speed, as the process does not require microbial culture,		*# speed, as the process does not require microbial culture,
	## sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)		## sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)
	## specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);		## specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);

Bosmana fem: /* Diagnostic Methods */

2023-04-08T18:17:32Z

Diagnostic Methods

← Older revision		Revision as of 18:17, 8 April 2023
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	## one can find only what one is searching for (known: especially important where there are new AMR genes emerging)		## one can find only what one is searching for (known: especially important where there are new AMR genes emerging)
	## the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),		## the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),
	biological samples can often contain inhibitors to DNA/RNA amplification methods		#* biological samples can often contain inhibitors to DNA/RNA amplification methods
	## they need trained staff (easier if the same equipment is used for all such tests)		## they need trained staff (easier if the same equipment is used for all such tests)
	## they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.		## they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.

Bosmana fem: /* Diagnostic Methods */

2023-04-08T18:16:50Z

Diagnostic Methods

Bosmana fem: /* Rules for interpretative reporting */

2023-04-08T18:15:55Z

Rules for interpretative reporting

← Older revision		Revision as of 18:15, 8 April 2023
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	There should be clear rules in the laboratory for interpretative reporting.		There should be clear rules in the laboratory for interpretative reporting.

	The laboratory must have a policy not to report every microbe isolated, but only ones relevant to infections, together with their antimicrobial susceptibility results (these should be agreed by the AS committee and stated in the hospital formulary/policy).		# The laboratory must have a policy not to report every microbe isolated, but only ones relevant to infections, together with their antimicrobial susceptibility results (these should be agreed by the AS committee and stated in the hospital formulary/policy).
			# Where there is any doubt regarding the relevance of culture results, the clinical microbiologist should communicate with the clinician in agreed ways depending on the situation's urgency. Medical microbiologists should regularly contact clinicians to communicate the laboratory results and inform them of their significance.
	Where there is any doubt regarding the relevance of culture results, the clinical microbiologist should communicate with the clinician in agreed ways depending on the situation's urgency. Medical microbiologists should regularly contact clinicians to communicate the laboratory results and inform them of their significance.		# Clinicians and medical microbiologists should be aware of any issues of sensitivity and specificity when such tests are ordered. Knowledge of the local rate of occurrence of the organisms causing the various infections is important, as this will affect the tests’ positive and negative predictive values. In this way, all can best judge the significance of any results.
			# Specimen processing for microbiological diagnosis progresses in various phases (see below: direct smear, culture, organism identifications, antimicrobial susceptibilities) each should be communicated with clinicians, especially for specimens from urgent/important e.g. severe infections. The medical microbiologist informs and advises the clinicians along this diagnostic pathway. Indeed, such communication is as important as any laboratory equipment or technique for accurately interpreting microbiological culture results.
	Clinicians and medical microbiologists should be aware of any issues of sensitivity and specificity when such tests are ordered. Knowledge of the local rate of occurrence of the organisms causing the various infections is important, as this will affect the tests’ positive and negative predictive values. In this way, all can best judge the significance of any results.

	Specimen processing for microbiological diagnosis progresses in various phases (see below: direct smear, culture, organism identifications, antimicrobial susceptibilities) each should be communicated with clinicians, especially for specimens from urgent/important e.g. severe infections. The medical microbiologist informs and advises the clinicians along this diagnostic pathway. Indeed, such communication is as important as any laboratory equipment or technique for accurately interpreting microbiological culture results.

	===Diagnostic Methods===		===Diagnostic Methods===

Bosmana fem at 18:14, 8 April 2023

2023-04-08T18:14:41Z

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Bosmana fem: Created page with " Category:The role of the clinical microbiology laboratory in infection prevention and control"

2023-03-23T12:49:47Z

Created page with " Category:The role of the clinical microbiology laboratory in infection prevention and control"

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[[Category:The role of the clinical microbiology laboratory in infection prevention and control]]

← Older revision		Revision as of 18:16, 8 April 2023
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	Several diagnostic medical microbiological methods are utilised. These include:		Several diagnostic medical microbiological methods are utilised. These include:

	* direct smear of the specimen: microbial stains e.g. Gram stain can help with the interpretation of the culture results and provide a rapid clue as to the likely pathogen;		# direct smear of the specimen: microbial stains e.g. Gram stain can help with the interpretation of the culture results and provide a rapid clue as to the likely pathogen;
	culture for bacteria and fungi followed by		# culture for bacteria and fungi followed by
	* identification (using classic biochemical/ antigen determination methods or newer methods like MALDI-TOF, SELDI-TOF, or other molecular methods) and		# identification (using classic biochemical/ antigen determination methods or newer methods like MALDI-TOF, SELDI-TOF, or other molecular methods) and
	antimicrobial susceptibility testing results. This is one of the most important laboratory clinical functions. Semi-quantitative testing is performed routinely; test results in Europe should be interpreted using EUCAST standards. The laboratory will also advise on, and perform, quantitative susceptibility testing, and, where relevant, identify resistance genes;		antimicrobial susceptibility testing results. This is one of the most important laboratory clinical functions. Semi-quantitative testing is performed routinely; test results in Europe should be interpreted using EUCAST standards. The laboratory will also advise on, and perform, quantitative susceptibility testing, and, where relevant, identify resistance genes;
	* microbial antigen testing e.g. for Legionella spp;		# microbial antigen testing e.g. for Legionella spp;
	* serology; as a proof of immune response to infectious agent (this usually requires specimens to be taken 10-14 days after the infection, when antibodies first appear).		# serology; as a proof of immune response to infectious agent (this usually requires specimens to be taken 10-14 days after the infection, when antibodies first appear).
	* nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:		# nucleic acid (DNA and RNA) detection in the specimen (i.e. molecular microbiology techniques). This is a field in which there is continuing progress:
	* advantages of nucleic acid detection methods, these comprise:		# advantages of nucleic acid detection methods, these comprise:
	** speed, as the process does not require microbial culture,		## speed, as the process does not require microbial culture,
	** sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)		## sensitivity (i.e. low false negativity as, in theory, one organisms can be detected although, in practice, at least 10-100 organisms/mL are usually required)
	** specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);		## specificity (i.e. low false positives; in theory every microbial species/diagnostic toxin has amplifiable and identifiable specific gene[s]);
	** disadvantages of nucleic acid detection methods, these comprise:		## disadvantages of nucleic acid detection methods, these comprise:
	** one can find only what one is searching for (known: especially important where there are new AMR genes emerging)		## one can find only what one is searching for (known: especially important where there are new AMR genes emerging)
	** the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),		## the presence of DNA does not mean it is functioning (also important for AMR, although more complicated RNA amplification techniques can solve such issues),
	biological samples can often contain inhibitors to DNA/RNA amplification methods		biological samples can often contain inhibitors to DNA/RNA amplification methods
	** they need trained staff (easier if the same equipment is used for all such tests)		## they need trained staff (easier if the same equipment is used for all such tests)
	** they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.		## they may not be cost effective (this will depend on the organization of the hospital services, costs of reagents, equipment rental/servicing balanced against the savings from improved testing). This is another example of how the patient diagnostic and public health/epidemiological roles of the laboratory need to be considered. Incremental cost effectiveness and other econometric methodologies are used to inform decision making and will depend crucially on the current incidence of the infection/AMR problem and prevention and control interventions being proposed.

	==The challenges of consolidated microbiology laboratory==		==The challenges of consolidated microbiology laboratory==