The role of microbiologyInternational in healthcare-associated Journal prevention of Infection Control Kalenić et al. www.ijic.info ISSN 1996-9783

extended abstract

The role of the laboratory in healthcare-associated infection prevention

Smilja Kalenić, Ana Budimir Croatian Society for and , Section for Healthcare-associated Infection Prevention and Control, Zagreb, Croatia

doi: 10.3396/ijic.V5i2.014.09

Introduction the laboratory. Dramatic changes in microbiological Healthcare associated (HAI) are a big diagnostic techniques in the last decades – rapid problem worldwide, increasing morbidity and mortality diagnostic methods and precise typing methods – of hospitalized patients, as well as increasing cost have emphasised even more the role of microbiology of healthcare. Many hospitals throughout the world laboratory. have good systems for HAI prevention and control, but others have not and are forced to develop such Diagnosis of infections systems nowadays. Having microbiology laboratory For the accurate etiological diagnosis of infection as a part of the hospital diagnostic , is several conditions should be fulfilled: first, clinician a huge advantage for HAI prevention and control. should put right for this diagnostics; Ideally, a microbiology laboratory should be set up furthermore, the right sample should be taken; then, inside the hospital, working every day on a 24 hour all data needed for the laboratory should be put on the basis. If it is not possible, then hospital should contract request (name of the patient and the , location microbiology services with the geographically nearest of the patient, date and of specimen collection, laboratory. working diagnosis or differential diagnosis, underlying patient conditions, if Microbiology laboratory has two main functions in already instituted). the hospital: one is diagnosis of infection in individual patient, directly related to the patient care and the Specimens sent to the microbiology laboratory have other is support to the HAI prevention and control. to be taken on the right time (depending on the But the first role – diagnosis of infection – has also a of the infection), from appropriate sites function in HAI prevention: if the etiological diagnosis using proper techniques, in a quantity that will ensure of infection is rapid and accurate, the patient will be good workout in the laboratory. conditions treated properly at the beginning of infection, so time from the patient to the laboratory are to be carefully of dispersing will be shorter. maintained. Microbiology laboratory staff can assist in ensuring good specimens by educating clinical staff. Every microbiology laboratory should have quality assurance procedures in place, and if possible, external Rapid and accurate diagnosis and sensitivity test are quality control of main procedures performed by of outmost importance for the direct patient care. In

Int J Infect Control 2009, v5:i2 doi: 10.3396/ijic.V5i2.014.09 Page 1 of 6 not for citation purposes The role of microbiology laboratory in healthcare-associated infection prevention Kalenić et al. the laboratory methodology it is necessary to provide Methods used in the diagnosis of infections are: rapid tests (like pneumococcal urine in the 1. Classical methods, like case of community acquired , or • Direct smear latex agglutination for detection of rotavirus in faeces • Culture etc). For diagnosis to be accurate, laboratory has to • Antigen detection develop procedures for quality assurance and has • Serological tests external quality control system in function. 2. Molecular methods (not very often used in Microbiology laboratory should be able to examine routine work) blood, cerebrospinal fluid, urine, stool, • Hybridization exudate or swab, respiratory secretions, and perform • Amplification basic serological tests (HIV, HBV, HCV, ). • Real-time amplification

Microbiological laboratory should be able to identify at As identification of the infectious agent is gradual, least the following and fungi: the laboratory has to communicate with the attendant aureus, , Group A streptococci, Group B clinician preliminary and definite diagnosis, as well as streptococci, enterococci, pneumoniae, sensitivity test results (Figure 1). Haemophilus influenzae, Neiserria meningitidis and Neiserria gonorrhoeae, , Shigella, For sensitivity testing the most used method is disc- Campylobacter jejuni/coli, difficile, diffusion, although nowadays many laboratories are , , using automated methods. Some laboratories use other enterobacteria, Candida albicans, aspergilli MIC determination, either by classical MIC dilution (and other, depending on local epidemiological techniques or by E-tests. Sensitivity test results are situation); also, it should be able to diagnose specific used immediately for the patient care. Adequate viral infections (eg some of causing diarrhoeal antimicrobial leads to better outcomes and is ), but mostly using serological methods (HIV, vital for individual patient care, as well as the decrease HBV, HCV, influenza, or other viruses, depending on of to other patients. But local epidemiological situation). also, laboratory should perform periodical reports of

Attendant Microbiologist Physician

Specimen Transport

Taking Primary Specimen Workout Constant Information Patient: Flow Culture Indication Identification Treatment Sensitivity

Written Report

Figure 1. Communication between attendant physician and microbiologist for ethiological diagnosis of infection

Int J Infect Control 2009, v5:i2 doi: 10.3396/ijic.V5i2.014.09 Page 2 of 6 not for citation purposes The role of microbiology laboratory in healthcare-associated infection prevention Kalenić et al. sensitivity of bacteria (broken down by bacteria and • The method has to be simple, unambiguous to specimen) isolated in patient on the specific ward interpret, and inexpensive (unit) – and this would mostly be – for the design of of infections in that There are two groups of typing methods: specific ward (unit). a) phenotyping b) genotyping The role in HAI prevention 1. Rapid communication a) Phenotyping means that we are determining Infection control practitioner’s (ICP) day should ideally characteristics that are expressed in the bacterial start in the microbiology laboratory, personally or culture, like: virtually. This would be the best and the most rapid • Antigenic structure (serotyping) communication of everyday infectious problems ICP • Physiologic properties/metabolic reactions can encounter in the hospital. If this is not possible, (biotyping) then laboratory workers should communicate • Susceptibility to antimicrobial agents by phone or personally with the ICP every new (resistotyping) important isolated in patients. This rapid • Susceptibility to colicines (colicinotyping), or communication is crucial and is the base of any good • Susceptibility to bacteriophages (phage typing) collaboration between microbiology laboratory and infection control. Very important limiting factor of phenotypic methods is the fact that bacterial are not always expressed 2. Accurate speciation and typing of isolated pathogen and so two phenotypically different strains can To be useful for epidemiological studies of HAI, actually have the same genetic background or two isolated bacterial strains should be identified to the phenotypically identical strains can actually differ level. Many this is enough for definite genetically. The other limiting factor is that sometimes epidemiological analysis of small clusters or even one unique phenotype is widespread and frequent, and outbreaks of HAI if are involved in that cases genotyping will be required for outbreak (e.g. Salmonella Enteritidis food poisoning outbreak management. originated from hospital kitchen). But, if the isolated bacteria are only opportunistic (e.g. S. b) Genotyping can demonstrate the relatedness aureus, E. coli, cloacae, enterococci etc) or difference between two isolates of the same it is necessary to type those isolates to be sure that species very precisely. Diagnosis can be rapid the cluster or outbreak patients are connected. To – because it is not dependent on waiting for type means to determine characteristics which differ bacterial growth in cultures. Genotyping requires between different strains of the same bacterial species. sophisticated and expensive equipment and Namely, the individual bacteria inside the same species materials and also well trained staff. Genotyping could differ in their as much as 30%, and in methods are either imaging (based on restriction of the individual bacterial clone (clone= offsprings of the part or whole genome with the endonucleases and common ancestor) these differences are very small or electrophoresis of fragments), or sequence-based even non-existent. (which means definite biological information and is more and more used). Typing of bacteria is possible by several methods. Main characteristics of typing methods are: Some imaging methods have a low reproducibility, • Typability, i.e., the method types most or all especially in interlaboratory comparisons, and strains of the same species interpretation of results is neither always simple nor • Discriminatory power, i.e., the method unambiguous. differentiates between different types • Inter/intra laboratory reproducibility, i.e., the Genotyping methods are not very often used in routine method provides the same typing results in microbiology laboratory. Therefore it is important for repeated testing on same or different sites a hospital laboratory to be connected with

Int J Infect Control 2009, v5:i2 doi: 10.3396/ijic.V5i2.014.09 Page 3 of 6 not for citation purposes The role of microbiology laboratory in healthcare-associated infection prevention Kalenić et al. laboratories in the country, or other types of central Sometimes during the outbreak analysis, epidemiologist laboratories that are able to perform such genotyping would ask laboratory some additional types of tests, in the time of the outbreak. to clarify the situation. These can be for example microbiological tests of blood products, environmental 3. Participation in outbreak management surfaces, and , air, water, hands The early of a new or unusual microorganism of personnel, nostrils of personnel. enables the ICP to take appropriate measures to stop it from spreading at the very beginning. Any new 4. Participation in HAI surveillance isolates should be reported immediately to the wards Surveillance of HAI is an important task of a well and the ICP. Laboratory staff may also report clustering organized infection control. If outcome surveillance of infections (two related isolates in different patients is performed, inherent to some infection definitions in the same time frame), which then enables ICP to go (BSI, UTI) is an isolation of the causative , and check these cases. but also important in all other infection definitions. Furthermore, in alert or multi- resistant (MDR) In an outbreak suspected to be caused by one and surveillance the role of microbiology the same causative agent it is very helpful (sometimes laboratory is crucial. The most important ‘alert’ even necessary) for the agent to be isolated, identified microorganisms are: to the species level and also typed. • -resistant (MRSA) • -intermediate S. aureus (VISA) Bacterial typing determines if two or more strains are • Vancomycin-resistant enterococci (VRE) really related and if they differ from strains that are • MDR Pseudomonas aeruginosa not epidemiologically connected. If two (or more) • MDR Acinetobacter baumannii strains are unrelated, the patients do not belong to the • MDR same outbreak, and it is very simple to interpret that • ESBL enterobacteria pattern. But, if two (or more) strains are related after • Clostridium difficile we performed typing it is very difficult to say that the patients are involved in an outbreak without sound epidemiological analysis.

MRSA infections in surgical intensive care unit

Figure 2. MRSA infections in Surgical Intensive Care Unit, time series

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The microbiology laboratory should produce routine 7. Microbiologist as a member of Infection Control reports to allow the ICP to make graphs for specific Committee (ICC)/Infection Control Team (ICT) and pathogens, wards, and groups of patients. A ‘baseline Committee (AC) ’ can be then established and any new isolate As microbiologist has specialist knowledge necessary incidence can be compared with this incidence. If such for infection control and antibiotic use he/she is an graphs are in the form of time series, they will enable indispensable member of ICC/ICT and AC in hospitals. the ICP to discover the beginning of an outbreak earlier Other members of ICC and AC in hospital do not have than it would be possible clinically (Figure 2). the knowledge of microbiology. It is not surprising then, that in US almost half of the ICC chairs are laboratory Periodic reports also demonstrate trends of specific personnel. pathogens and can be very useful in planning preventive measures. Microbiology laboratory also participates in It is also important that the microbiologist is a routine process surveillance monitoring sterilization, medical doctor, because he/she will thus understand monitoring dialysis fluid. Sometimes it may be useful pathogenesis of infection as well as pathogenesis to routinely monitor some other processes, like of HAI, not only characteristics of an organisms, formula and instrument disinfection. will be able to understand pharmacokynetics and of antimicrobial agents - and will 5. Participation in resistance surveillance be able to communicate with clinical and nursing The surveillance of bacterial resistance to antimicrobial colleagues on the same level of understanding , agents is very important task of microbiological therapy and . laboratory. It serves to an antibiotic management team in hospitals, to make policies for antibiotic use with Only exceptionally, if there is no medical doctor the ultimate goal to decrease this resistance. Resistance available, a properly educated could be reports are usually periodical (yearly reports) and it is microbiologist too, but in that situation he/she has very useful to have resistance surveillance organised to be very closely connected with infectious disease on regional or country or even international level, to specialist. cope with the resistance development on a broader scale (for example European Conclusion Surveillance System). Microbiology laboratory is becoming an integral part of HAI prevention programmes. The emergence of 6. Education of HAI prevention personnel and other new pathogens, and new resistances in old pathogens, healthcare workers makes microbiology laboratory indispensable for Microbiologist acts also as an educator for infection successful prevention of HAI, not only outbreaks, but control personnel, first about characteristics of sporadic cases too. microorganisms that are important for epidemiology of infections, then about normal flora, difference between Different typing methods, available on site or in contamination, colonisation and infection with the central laboratory of the country, are necessary specific organisms, furthermore about interpretation of for outbreak management. As microbiology and microbiological reports and charts. laboratory methods are developing very fast, there is a sound need for a specialist microbiologist to be a Microbiology laboratory staff serves also as educators part of the infection control team, infection control to all other healthcare workers, about specimen taking committee and antibiotic committee. Only very and transport and also interpretation of microbiology close communication, collaboration and cooperation findings. Microbiology laboratory serves as education between microbiology laboratory and infection control point for basic clinical microbiology for medical and personnel can fulfil the duties of successful infection nursing students. prevention and control in healthcare institutions.

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