Indian Journal of Pathology and Microbiology

: 2010  |  Volume : 53  |  Issue : 2  |  Page : 217--221

Clinical microbiology: Should microbiology be a clinical or a laboratory speciality?

Sanjay Bhattacharya 
 Department of Microbiology, West Suffolk Hospital NHS Trust, Bury St. Edmund, United Kingdom

Correspondence Address:
Sanjay Bhattacharya
Locum Consultant Microbiologist, West Suffolk Hospital NHS Trust, Hardwick Lane, Bury St Edmunds, IP33 2QZ
United Kingdom


Clinical microbiology is a specific combination of knowledge, attitude and practice aimed at direct clinical involvement in infectious disease management using the core principles of medical microbiology and clinical medicine. In this article certain areas in microbiology, where a more proactive approach could make a significant difference in clinical outcome has been delineated. The article reiterates the role of a medical microbiologist in a hospital setting. The practices described are the norm in well-organized hospitals. These areas include management of positive blood cultures, management of patients in intensive care units (ICUs), hospital infection control and public health microbiology, development of hospital and community anti-infective policy, organization of clinical-microbiological meetings and provision of emergency out-of-hours service. The implementation of this clinical approach and increased engagement with direct patient care would require changes in existing training structure and working patterns of medical and technical staffs in microbiology.

How to cite this article:
Bhattacharya S. Clinical microbiology: Should microbiology be a clinical or a laboratory speciality?.Indian J Pathol Microbiol 2010;53:217-221

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Bhattacharya S. Clinical microbiology: Should microbiology be a clinical or a laboratory speciality?. Indian J Pathol Microbiol [serial online] 2010 [cited 2022 Dec 8 ];53:217-221
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India lacks critical infrastructure in infectious disease management and surveillance. Infection continues to be major killer in India; however, the infrastructure that is required to contain, manage and mitigate the problem either through well-equipped quality-assured laboratories or with trained healthcare workers (specialist in Infectious Diseases, Infection Control, Microbiology) is woefully lacking in large parts of the country. Although, significant strides in disease surveillance are being made through the Integrated Disease Surveillance Project (IDSP) launched in 2004, [1] there is hardly any systematic nationwide database about many important conditions such as bacteremia, antibiotic resistance or blood borne viruses. Most data available about the burden of infection-related mortality and morbidity in India are either from small-scale non-systematic studies or speculative projections. [2] A notable exception was the INCLEN multicentric study, which reported significant mortality from invasive bacterial infections (case fatality rate was 21 and 20%, respectively, for confirmed cases of invasive pneumococcal and Haemophilus influenzae disease). [3] Infrastructure development cannot happen overnight considering the multiplicity of factors involved (training, funding, quality assurance, human resources). Infectious disease is yet to be offered as a postgraduate course to doctors in India, and there are very few centers, which offer either diploma or masters course in allied specialties. [4] For example, there are 5 seats/year for MD Tropical Medicine at the School of Tropical Medicine in Kolkata (along with 12 seats for diploma in Tropical Medicine), 4 seats/year for diploma in medical virology at National Institute of Virology (Pune). In contrast, there are 499 seats in various medical colleges in India, which offer MD Microbiology as a postgraduate option. [4] In comparison, there are currently 145 infectious diseases and topical medicine consultants in the UK (population ~60 million or 5% of the Indian population) with another 110 trainees in infectious disease (some getting jointly trained in medical microbiology and virology). [5] The Royal College of Physicians of the UK recommends one infectious disease physician per district hospital (serving a population of ~200 000). [5] In contrast, we already have a shortfall of 50% in the number of community health centers (population served ~120 000; 2005 data) [6] not to speak of the number of trained healthcare workers that would be necessary to make them functional. It is obvious from these statistics that we face a daunting challenge. One of the solutions being proposed in this paper is the development of clinical microbiology as training and operating procedure within microbiology (the single biggest specialty dealing with infections in India). The strategic and operational characteristic of clinical microbiology is being outlined in this article.

Current status of medical microbiology training and practice in India

Historically, medical microbiology was practised as part of pathology till the late 1960s and the 70s (e.g. Department of Microbiology separated from Pathology at the Banaras Hindu University in 1968 and at the Armed Forces Medical College in 1979) when microbiology separated from the parent subject, but was relegated to a para-clinical group. In the Indian context, while the hospital microbiologists are largely medically qualified, the linkage with clinical medicine is not well developed. Generally, microbiology training and practice in India would be characterized by extensive hands-on technical work in diagnostic tests, result analysis followed by some interpretation. This would involve reading culture plates and biochemical reactions, observing slides for microscopic diagnosis and undertaking and analysing serologic tests. Besides, there would be a significant assignment for teaching students (undergraduates and postgraduate medical students, technicians), undertaking research and analysing data. While all these activities are essential and laudable there is not much effort to interface laboratory results with clinical management. This is both a lost opportunity as well as an important quality issue for training, practice and planning. The question is how can a medical laboratory, as important as microbiology, develop in isolation without effective interface with day-to-day clinical problems? The choice of tests, the communication of results, development of joint clinical-microbiological approaches to disease management and development of common policies (infection control, antibiotic policy, diagnostic algorithms) and even the selection of clinically important and relevant research projects is critically dependent on this very important interfacing opportunity that microbiologists can offer with respect to infection management within the hospital as well as in the community. Restricting microbiology within the confines of laboratory would sub-optimize patient care for the reasons described above. It would also be a lost opportunity to lead in infectious disease management, especially in the Indian context where infectious disease consultants/specialists are mostly nonexistent.

 Domains of Clinical Microbiology

A typical working day for a clinical microbiologist (as for example in the UK) would constitute getting involved clinically in positive blood culture management, offering consultation over a range of infectious disease issue (e.g. diagnosis and treatment of infective endocarditis, antibiotic therapy for orthopedic infections, empirical or directed therapy of various conditions such as neutropenic sepsis), hospital infection prevention and control (methicillin-resistant Staphylococcus aureus, multi-resistant Gram-negative bacilli, Clostridium difficile associated diarrhoea), besides providing expertise and leadership in laboratory diagnostic strategies, business planning, education and research. In this model, qualified technicians would do the day-to-day identification and analyses of pathogens and samples, and clinical microbiologists get involved once the results (preliminary or final) are available for clinical action. The clinical consultation may involve ward rounds (e.g. intensive care units) or telephonic advice with the clinical team responsible for the patient. Depending on the workload, clinical liaison may be organized on a daily/weekly/periodic interval with a rota of clinical microbiologist dividing a typical week or month as is convenient and possible. At each clinical interfacing opportunity, focus must be placed on the entire clinical context and not necessarily the microbiology/virology result related to the patient. As for example, during the application of clinical algorithms in the management of conditions such as swine influenza (novel H1N1), one has to take into account the context within which the algorithm is being applied, the limitations of the algorithm and consequences of error, and the other conditions (infectious or non-infectious), which might have similar clinical presentations. [7] Clinical microbiology is about managing the patient's infection-related diagnostic, therapeutic and infection control needs. A microbiology result forms an important but a small part in this clinical exercise.

 Management of Positive Blood Cultures

Blood cultures are taken when a bacteremic (or fungemic) infection is suspected many of which such as infective endocarditis, pneumonia, uro-sepsis and meningitis are potentially life-threatening. [8],[9] Therefore, management of positive blood cultures must be treated as a medical emergency with priority given to shortening test turn-around-time (TAT), early result communication and early intervention (appropriate anti-infective therapy, or other interventions as deemed necessary). In most modern laboratories, automated commercial blood culture machines such as the Bactec; or BacT/Alert; systems, which do continuous monitoring and automated flagging up of positive broths are used. This precludes the necessity of routine subculture, reduces contamination risk, shortens TAT and enables direct antimicrobial susceptibility testing from positive broth following Gram stain examination of it. [10] This microscopic examination of a Gram-stained smear of a positive blood culture broth is one of the most important diagnostic tests in microbiology, and rapid communication of Gram stain findings of a positive blood culture broth can be potentially lifesaving for many patients through the appropriate administration of antimicrobial therapy. [9],[10] The therapy can be rationalized further the following day when direct susceptibility test results are available along with preliminary identification of the pathogen following a direct biochemical testing from positive broths. Liasing with the clinician early in the positive blood culture scenario is crucial in order to understand possible significance, differentiation from contaminants and optimization of anti-infective management.

 Clinical Microbiology in the Intensive Care Unit

Ward rounds in intensive care unit (ICU) form an essential part of a clinical microbiologists' job schedule. ICU patients are significantly different from others because of their critical illness, altered physiology, need for organ support systems for one or more organ failure (ventilation, inotropic support, hemo-filtration, etc), significantly higher mortality and morbidity, shortened timescale for remedial action and significant financial implications for the hospital, patients and relatives. Infection (meningoencephalitis, sepsis, pneumonia) is a major cause of ICU admission. Significantly more samples are taken for microbiologic analysis from ICU patients than others. ICU ward rounds by microbiologists serve the crucial function of direct and regular liaison with intensive care specialists, [11] so that infection could be assessed and reviewed, and diagnostic tests and therapy could be augmented or optimized. ICU patients also receive significantly more antibiotics than other hospital inpatients (as measured by the Defined Daily Dose - DDD) and antimicrobial resistance [including multidrug resistant (MDR) pathogens such as MRSA, [12] ESBL-extended spectrum beta-lactamase producing Enterobacteriacae] [13] are commonly encountered. In addition, newly emerging MDR strains such as MDR Acinetobacter baumannii[14],[15] and metallo-betalactamase[16],[17] producing strains of Pseudomonas and other Gram-negative bacilli are beginning to appear in Indian hospitals including ICUs. All these organisms are capable of causing a variety of infections (notably blood stream infections, ventilator-associated pneumonia), which significantly endanger the patients' life. An ICU ward round would help control the spread of these nosocomial pathogens, provide antibiotic stewardship [18] but also help select appropriate therapy through early communication of preliminary results.

 Clinical-Microbiological Multidisciplinary Meetings

The objective of multidisciplinary team (MDT) meetings involving microbiology is to facilitate communication between clinicians and microbiologists in areas where infection is a major cause of morbidity and mortality. These include pediatrics, bone marrow or solid organ transplantation, HIV medicine, patients receiving chemotherapy (hematology, oncology), and tuberculosis and chest diseases. Although, it is possible to make this communication through ward rounds, or telephonically the MDT has the added advantage of acting as an educational forum, and may meet less frequently (once a week) with a structured list of patients and definite time table. Expertise in a specific area of clinical microbiology would require anatomical and physiological understanding of the subject (e.g. ocular microbiology), [19] in addition to detailed knowledge of varied clinical spectra and management strategies (e.g. immunosuppression strategies in transplantation, joint replacement strategies in orthopedics, [20] applications and limitations of prosthetic devices).

 Hospital Infection Control

Controlling the spread of infection within hospital between patients or to staffs, visitors have become an important issue in most developed countries. [21],[22],[23] Although multidrug resistant organisms such as MRSA or ESBL are important nosocomial pathogens, preventing the spread of other infections (norovirus, chickenpox, influenza, Group A Streptococcus, tuberculosis) is equally important. The clinical microbiologist is the key figure in infection control, and in the UK [24],[25] they are often the Infection Control Doctor (ICD) or the Director of Infection Prevention and Control (DIPC) for the hospital. However, it must be emphasized that infection control is everyone's responsibility and the ICD or the DIPC provides supervisory, leadership, planning, policy-making role to enable staffs, patients and visitors to achieve this objective. Although, the Infection Control Team constituting the microbiologists, infection control nurses is responsible for the day-to-day operational aspect, it is the Hospital Infection Control Committee comprising of ICD along with the lead nurse (nursing superintendent) and administrative head (medical superintendent), which is responsible for strategic aspects (policy making, business planning, procurements, target setting).

Hospital and community infection prevention and control is receiving significant media and public attention in many developed countries. Its importance in developing countries is also likely to grow, as awareness grows about infections in general and hospital infections in particular. In many cases, in addition to patients' well being, institutional reputation, health insurance securities are at stake. As health care becomes more and more privatized, hospitals and physicians may be judged by their meticillin-resistant S. aureus (MRSA) / Vancomycin resistant Enterococcus (VRE) / C. difficile / Extended Spectrum Beta Lactamase (ESBL) rates. This would inevitably mean a microbiologist becoming more proactive in clinical communication of nosocomial pathogens, implementation of infection control precautions (isolation, disinfection, cohorting and barrier nursing), and hospital policy making with regards to infection control, waste management and sterilisation-disinfection and outbreak management. In areas such as hematology-oncology, transplantation, orthopedic surgery and cardio-thoracic surgery, high standards of infection control would be necessary as the clinical, financial and scientific stakes get higher.

 Clinical Microbiology and Public Health

Clinical microbiologists can play a very important role in controlling the spread of infection in the community through early communication of clinically significant microbiology results (from outpatients' samples) to public health and community medicine specialists (tuberculosis, swine flu, Vibrio cholerae, food-borne salmonellosis, viral hepatitis, etc). In the UK, general practitioners in the community (most of who work under the National Health Service) are in regular communication with clinical microbiologists with regards to diagnostic interpretation, anti-infective therapeutic advice and prophylactic issues (vaccination). The importance of a clinical microbiologist in the field of public health has been amply demonstrated by numerous epidemics in India (pandemic Influenza A H1N1, poliomyelitis, cerebral malaria, plague, viral encephalitis, chikungunya). [1],[26],[27] At the moment, the situation seems somewhat disjointed with public health professionals from community medicine, and microbiologists seem to be working without significant structured coordination. If effective liaison is established between public health and other healthcare providers, as is being attempted through the IDSP, [1] many diseases in our national health programmes could be more effectively tackled.

 Development of a Hospital or Community Anti-Infective Policy

The way we use anti-infective therapy either for treatment of infections or prophylaxis determines not only the outcome of an individual case but also the long-term efficacy of the agent because of the possibility of development of anti-microbial resistance. Besides, there are significant cost and safety implications (anaphylaxis, antibiotic associated diarrhoea, selection of resistant strains) for the patient and healthcare system. A rational, evidence-based and cost-effective anti-infective policy [28],[29],[30] is a reference frame, which can help evaluate several parameters (patient outcome, nosocomial infection rate, cost of anti-infective therapy per patient). However, the anti-infective policy is not a tablet of stone and therapy may have to be individualized for atypical cases after discussion with clinical microbiologists. In recent years, there has been an attempt to initiate and institutionalize pharmaco-vigilance through antibiotic stewardship [18] to ensure appropriate selection and dosing of pharmaco-therapeutic agents and in the wider sense as an auditor of rational prescribing. This practice if institutionalized and performed with rigor, discipline and diligence on a wider scale, can benefit science, patient and community. The microbiologist is central to policy development of anti-infective agents. This is due to better chance to appreciate issues such as mechanism of action and resistance, microbiological spectrum and resistance epidemiology. This knowledge combined with pharmaco-dynamic and pharmaco-kinetic information is the backbone of any anti-infective policy. Inter- and intra-departmental consensus is essential for any policy to be effective. Multidisciplinary evidence based approach may help achieve this objective. Patience, perseverance, audits and re-audits may be needed to convince the sceptics. Education and visibility of the policy is as important as the accessibility and availability of the drugs. Periodic education in junior doctor induction program and enhanced visibility through antibiotic policy cards along with regular feedback (through clinical audit reports) can be low cost choices in the implementation process.

Emergency out-of-hours responsibility

Emergency out-of-hours on-call responsibility constitutes an important aspect of clinical microbiology service. In India, some centers provide this as a diagnostic service for processing cerebrospinal fluid samples in suspected cases of meningitis or encephalitis; however, a complete clinical microbiology on-call service has technical (diagnostic), clinical (augmentation and rationalization of anti-infective therapy; provision of diagnostic advice and interpretation) and infection control (e.g. outbreak management) components. The technical component of this service provision is generally performed by qualified technical staffs whereas the clinical and infection control aspects are dealt by medical microbiologists. The out-of-hours service is a vital lifeline between a sick patient or a critical situation (infection control risk) and the laboratory. Besides providing early presumptive diagnosis, out-of-hours clinical microbiology constitutes value addition to the overall clinical microbiology training experience. [31]

Defining features of clinical microbiology

The first step towards clinical microbiology should involve recognition and assessment of the clinical problem. Each result has a potential story hidden within the historical features and clinical presentation of the patient. Understanding the significance of any result (positive or negative) is not possible without knowing the patient. However, identification of clinical priorities is paramount since on a given day a microbiologist in a busy hospital is likely to encounter several clinically significant results. Distinguishing the etiologic pathogen from colonizers, commensals, contaminants is often not straightforward and a whole range of clinical features and diagnostic (e.g. imaging) or inflammatory markers (white cell count, C-reactive protein) may have to be evaluated before assigning possible clinical significance to an isolate or result. Moreover, 'no growth' or 'non-significant titres' in clinical microbiology is not necessarily a negative result and enquiry of the detailed clinical history in some cases may lead to the identification of more relevant tests as follow-up. Similarly interpretative comments, [32],[33] for instance with positive blood cultures, swab cultures, serology or antibiotic susceptibility can enhance reporting quality and patient care together with enhancing the clinical profile of microbiologists.

 Laboratory to Clinical Microbiology: A Road Map

Redefining the remit of microbiologists would entail several changes in education, training and management plans. [34] The typical job description of a clinical microbiologist has been outlined by the Royal College of Pathologists (UK) [35] and can provide a framework for training and operations. In order to make a difference in clinical management, the department has to work as a team with a sense of shared responsibility - defined by continuity of care. Since this work is intended to change clinical outcome and have medico-legal implications, documentation of clinical conversations between microbiologists and clinicians is essential, and steps taken to reduce turnaround time of clinically significant microbiology results. Implications for a clinical microbiology department could be profound in terms of change of working practices, and training issues with respect to microbiologists and microbiology technical staffs. Since this approach would mean considerable time being spent in clinical liaison by the microbiologists, the quality and standard of the technical services have to be greatly enhanced so that independent and reliable decisions could be taken at the technical level without the need of constant supervision by the medical staff. Microbiologists leaving the laboratory and going into the clinical areas does not mean the end of basic science, rather it would be an effort to better appreciate the value of basic science in patient care. In economic terms, clinical microbiology is about going out into the market place to find out what the customer (patient and clinicians) really want, and redesigning products and services in line with the market forces. In addition, the practice of clinical microbiology does not necessarily have to begin with a high investment on physical infrastructure or high technology. Even the most basic results based on microscopy, culture or serology can be given greater value by application of clinical-microbiological principles (viz. clinical liaison, infection assessment, therapeutic optimization, prevention of infection).


India is a country with relatively restricted material resources but with a significant pool of talented and educated human resource. Even with limited instrumentation and technology, the quantity and quality of clinically significant results generated by a microbiology laboratory in a teaching hospital is considerable. At present most of the medical staff in microbiology departments are involved in reporting of laboratory results, teaching medical students and in some cases research. Clinical responsibilities are being taken up gradually and engagement of the laboratory and the clinics can be accelerated if clinicians demand the right answers, and microbiologists pursue questions more pertinent to everyday clinical problems. There is scope of redesigning the work schedule in a more clinical, patient-centered manner so as to maximize the benefit to the patients in a hospital setting. The result of such a change in working practices can only be to the benefit of all concerned, not just the microbiologists. Apart from improving patient outcome, a clinical microbiology department would lead to better clinical training for microbiologists, better microbiological training for clinicians and redefining the micro-clinical boundaries. The idea is not to usurp the role of clinicians for the management of infection, but to support, complement and augment them with better diagnostics, greater interaction and enhanced role so that the benefits of laboratory advancements can be brought to the patient in a more effective manner. The burden of infection in the country is too great, and the resources available to combat them are too little to allow suboptimal use of men, materials, machines and methods.


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