FROM MICROBIOLOGY TO CLINICAL MICROBIOLOGY CAN WE MAKE IT? Dr.T.V.Rao MD The Curriculum in Microbiology in the Indian contest remained static for severaldecades; the training in MD (Microbiology) under Medical Faculty remained without clinicalapproaches in Diagnosis and treatment. Much of Medical Microbiology remained to the Laboratorywith little interest in the Hospital practice. Every Medically qualified Microbiologist spends Majoryears of life in a speciality without much productivity and newer innovations. Thanks to severalcurricular changes in efforts to make subject, as par with a Clinical Speciality. Fewer allocations fromboth Government and Private Institutions in funding and shortage of qualified technicians havebrought the speciality to brink of deterioration. The Pandemic of AIDS awakened the Society andDoctors that spread of AIDS cannot be controlled with Laboratories, but our continuousunderstanding of the Society, and greater understanding of the disease with clinical knowledge. Ithink it is time that we should become active to make Microbiology as Clinical Microbiology with ourunited efforts. At present we all study in-depth Microbiological aspects dealing particularly withtheoretical and little practical knowledge of medical diagnostics. It also focuses on molecular andconventional techniques for isolating, identifying and characterizing bacterial, viral, fungal andparasitic pathogens, as well as prevention and control of infectious diseases, epidemiology, anddetails of specimen collection, handling, examination and interpretation of results. However a littleinteractions with our knowledge of Medicine make greater contributions. At present curriculum iselaborate and wide without much specificities, creates greater confusion. My little experience asqualified in MD from reputed Government Institution make me to realize that I do not practice even10% of the knowledge gained in my post-graduation, and Post graduate degrees make you aundergraduate teachers at the most a postgraduate examiner after years of our service. It isquestionable how much we are productive to the society. The reasons are many clinicians go ontheir own way thinking antibiotics can solve all problems, which has led to growing concerns onAntibiotic multidrug, pan drug resistant strains. We can make a change in thinking with practice offew good ideals as ………1 Make use of suitable range of diagnostic, investigative and/or monitoring procedures whenundertaking investigations, which can give optimal, care of the patients.2 Communicate complex and technical information to patient’s, colleagues and those with limitedtechnical knowledge in terms that facilitate understanding of issues.3 Accept the responsibilities of the role of the scientist-trained person in relation to other healthcare professionals and with empathy and sensitivity to patients, and families.4 Ensure validations of data, through use of appropriate sources of information including relevantdatabases and consultation with senior colleagues.5 Use laboratory Information Technology, WHONET systems for handling, processing and storage ofpatient data.
CLINICAL EXPERIENTIAL LEARNINGThe recommended examples of clinical microbiology learning are• Prepare a portfolio of significant clinical cases reported in your hospital and be able to list clinicaloutcomes and main learning points.• Participate in multidisciplinary review meetings at which bacteriology and other diagnostic resultsare presented as part of the clinical record.• Critically appraise the internal quality control and external quality assessment of different routinebacteriology methods and draw conclusions about method performance and quality.Our Postgraduate Students should be, familiar with• The clinical impact of important bacterial and viral infections and of the appropriate clinicaland laboratory investigations.• The interpretation and reporting of laboratory results in the context of important bacterialand other Microbial infections.• The partnership between the clinical microbiology laboratory and other clinical specialties inthe investigation of common bacterial infections. As we are aware many specimens sent toMicrobiology are sent for Histopathological and biochemical examination too, our constant touchwith our colleagues makes our reports acceptable and causes no confusion among the Clinicians.• Perform and critically evaluate the results from a range of assays used to investigate viralinfection including: immunoassay; agglutination; immunofluorescence; neutralization;Immmunoblotting, electrophoresis and gel diffusion. Many rapid tests we do in the laboratory areinconclusive, and may not be specific, and Microbiologists should accept the limitations and try forbetter and newer generation of tests, or else we become static in progress of the patients care.• Clinical practice guidelines if followed by Clinical microbiologists, have several potentialbenefits, including better patient care at lower costs and, when applied properly, the potential toprotect health care providers from legal claims. There are several potential reasons we are failing tofollow, many standard guidelines, due lack of coordination at many levels of administration,resources and funding crunch as in most of the Developing countries. Still we can do better beingaware of clinical practice guidelines. It is not surprising that clinical microbiologists might not beaware of a specific aspect of clinical practice guidelines.Many of us are confused with different conflicting interpretative criteria; there are over 1,000clinical practice guidelines in the National Guidelines Clearinghouse database, all of which makerecommendations that directly affect laboratory practice.• Overcoming the challenges, remains a challenge to all upcoming Microbiologists, until theMedical fraternity realizes, Microbiology is not an armchair job as in the past but active Life SavingClinical Specialty.
Changing role of Microbiologists – Simple Measures to Improve our Laboratories - Now the Societyrealises that Antibiotic Resistance is a concern to everybody’s health and a future concern for even aHealthy person, We should be proactive and prove that we are leaders to handle the situation, witheven little developments in our Laboratories, will prove useful to the Medical profession. HospitalMicrobiology laboratories should follow standard protocols for susceptibility testing, possible withfollowing with CLSI guidelines and reporting on WHONET software 5.6 which also can be changedfrom default to the currently accepted zone sizes in reporting, Must generate and distributeAntibiograms at regular intervals (Quarterly) to the Clinicians so they can be made aware howineffective some antibiotics have become. Hospitals to send antimicrobial susceptibility testing (AST)to standardized labs to avoid erroneous reporting of organisms and their susceptibility pattern. Pan-drug-resistant Gram-negatives, carbapenem-resistant Gram-Negatives, Vancomycin- resistantEnterococcus and MRSA should be made notifiable. We can create collaborating laboratories aroundus and strive to improve the quality control of isolates for identification emerging trends in antibioticresistance.Know your Antibiotics; Testing for Cephamycins in Diagnostic Laboratories - Cephamycins are agroup of beta-lactam antibiotics. They are very similar to cephalosporins, and the Cephamycins aresometimes classified as cephalosporins. They are characterized by the presence of a 7-α-methoxylgroup, which confers unusually high resistance to β-lactamases. Cefoxitin, the first semisyntheticCephamycin, is resistant to almost all β-lactamases. Like cephalosporins, Cephamycins are basedupon the cephem nucleus. Unlike most cephalosporins, Cephamycins are a very efficacious antibioticagainst anaerobic microbes. Semisynthetic, Cephamycins are produced by Streptomyces spp.;includes cefoxitin sodium, cefmetazole and cefotetan. The significant resistance to β-lactamasedisplayed by the Cephamycins is reflected in the kinetics of enzyme activity (Km and Vmax) that arereported for the cephalosporins and the Cephamycins. Resistance to β-lactamase is probably one ofthe reasons that many cephalosporin-resistant cultures are susceptible to Cephamycins. Activeagainst many cephalothin-resistant gram-negative bacteria; cefoxitin demonstrates a very broadspectrum that includes indole-positive Proteus and many strains of Serratia. In contrast to that ofthe cephalosporins, cefoxitins spectrum of activity against anaerobic pathogens includesBacteroides fragilis. Cefoxitin is bactericidal and almost devoid of any inoculum effect. We have totest for the susceptibility patterns for Cephamycins independent of 3rd generation Cephalosporins,and report for the utility of these drugs.Know your Microbes - Threat of Multidrug-Resistant Gonorrhoea, -- Gonorrhoea has affectedhumans for centuries and remains common Sexually transmitted Infection Worldwide, an estimated106.1 million cases occur annually. Many patients infected with Gonococcus infections approachunqualified, even chemists and few times a family physician for a treatment, and patients may notgive the proper history and will be subjected to very unscientific approaches with ineffectiveantibiotics. A major challenge to monitoring emerging antimicrobial resistance of N. gonorrhoea isthe substantial decline in capability of laboratories to perform essential gonorrhoea culturetechniques required for antibiotic susceptibility testing. Specific diagnosis of infection with N.gonorrhoea can be performed by testing endocervical, vaginal, urethral (men only), or urinespecimens. Culture, nucleic acid hybridization tests, and NAATs are available for the detection ofgenitourinary infection with N. gonorrhoea. Since antibiotics were first used for treatment of
gonorrhoea on empirical basis, N. gonorrhoea has progressively developed resistance to theantibiotic drugs prescribed to treat it: sulfonilamides, penicillin, tetracycline, and ciprofloxacin.When bacteria become resistant to an antibiotic, they no longer can be killed by that medicinesprescribed; there is no reliable technology that allows for antibiotic susceptibility testing from non-culture specimens; Antimicrobial resistance in Neisseria gonorrhoea may arise by selection ofresistant mutants from endogenous flora produced by spontaneous chromosomal mutations, or itcan be acquired from other bacteria by plasmid-mediated transfer or DNA transformation andrecombination. Plasmid-mediated resistance to tetracycline and penicillin, and chromosomallymediated resistance to tetracycline, penicillin, and spectinomycin can occur. As of recently,increased resistance to fluoroquinolones has also been observed. This can happen by alteration ofdrug targets, restriction of access to bacterial targets, or both; thus, fluoroquinolone potency isdetermined by its ability to reach and act on their target enzymes, DNA gyrase and topoisomeraseIV, which are both required for bacterial DNA replication . However we are rarely getting a specimenfor culturing Gonococcus in majority of our laboratories. In those who fail initial treatment, cultureshould be done to determine sensitivity to antibiotics. Clinicians many times take decision to treatthe disease with accumulated experience, Fluoroquinolones such as ciprofloxacin or Ofloxacin are nolonger recommended as first-line therapies for gonococcal infections. Patients infected with N.gonorrhoea frequently are coinfected with C. trachomatis; this finding has led to therecommendation that patients treated for gonococcal infection also be treated routinely with aregimen that is effective against uncomplicated genital C. trachomatis infection .Therapy forgonorrhoea is often given before the susceptibility of the infecting organism is known, the Centresfor Disease Control and Prevention recommends that uncomplicated gonorrhoea be treated onlywith the antibiotic ceftriaxone — given as an injection — in combination with either azithromycin ordoxycycline — two antibiotics that are taken orally. Many times the partner of the patient is missedfor diagnosis and treatment, one should remember the partner also should undergo testing andtreatment for gonorrhoea, even if he or she has no signs or symptoms. Partner receives the sametreatment; you give to the infected partner. Even if youve been treated for gonorrhoea, one can bereinfected if his/her partner isnt treated. Untreated gonococcus infection can lead to pelvicinflammatory disease, ectopic pregnancy, and infertility in women and can facilitate transmission ofhuman immunodeficiency virus. Childhood blindness still affects infants born to mothers infectedwith gonorrhoea, particularly in resource-limited countries. NIAID is studying new ways to treatcephalosporin-resistant infections by using existing antibiotic therapies in combination (i.e.,gentamicin and azithromycin vs. Gemifloxacin and azithromycin).Know your Microbes - Challenges in treating Enterococcus Infections --Enterococcispecies can cause a variety of infections, including urinary tract infections, bacteraemia,endocarditis, and meningitis. The combination of high-level resistance to ampicillin, Vancomycin,and aminoglycosides is now fairly common among hospital-acquired Enterococcus faecium has amajor impact on therapeutic options. Compared with most streptococci, enterococci are relativelyresistant to penicillin and ampicillin; even when these cell wall-active agents inhibit enterococci, theyoften do not kill them, and Vancomycin is even less bactericidal. And imipenem has some activityagainst E. faecalis. Cell wall-active agents with limited or no activity against enterococci includenefcillin, oxacillin, Ticarcillin, Ertapenem, most cephalosporins, and aztreonam. Enterococci are alsorelatively impermeable to aminoglycosides, and the serum concentrations of aminoglycosidesrequired for bactericidal activity are much higher than can be achieved safely in humans. The
simultaneous use of a cell wall-active agent is needed to raise the permeability of the cell so that anintracellular bactericidal aminoglycoside concentration can be achieved without excessive toxicity.Enterococcus isolates are usually tested for susceptibility to ampicillin, penicillin, and Vancomycin.Prior to using penicillin or ampicillin for endocarditis or other life threatening enterococcusinfections, such as meningitis, the isolate should also be screened for beta-lactamase productionwith nitrocefin, a chromogenic cephalosporin, even if ampicillin susceptible. Although found onlyrarely, the presence of beta-lactamase confers resistance to penicillin and ampicillin when largenumbers of organisms are present (eg, endocarditis vegetation’s), even though the organism maytest susceptible using standard laboratory inoculum. Isolates from life threatening infections shouldalso be tested for high-level resistance to gentamicin and streptomycin. If the organism is reportedas susceptible to high levels of an aminoglycoside ("SYN-S" indicates "susceptible to synergism"),then it is assumed that synergism will be achieved with that aminoglycoside. Strains that areresistant to high levels of gentamicin are resistant to synergism with tobramycin, netilmicin, andamikacin as well as gentamicin, but some of these strains lack high-level resistance to streptomycinand will demonstrate synergism with that agent. Newer antibiotics (eg, quinupristin-dalfopristin,linezolid, Daptomycin, Tigecycline) with activity against many VRE strains have improved thissituation, but resistance to these agents has already been described. A mutation (G2576U) in thedomain V of the 23S rRNA is responsible for linezolid resistance, whereas resistance to quinupristin-dalfopristin may be the result of several mechanisms: modification of enzymes, active efflux, andtarget modification. Resistance of E faecalis and E faecium to Daptomycin, a newer cyclic lipopeptideantibiotic that acts on the bacterial cell membrane, has also been reported. Think before treatingand suggesting treatment for Enterococcus infection.Know your Microbe Community-Associated MRSA (CA-MRSA) Refers to an MRSAinfection with onset in the community in an individual lacking established MRSA risk factors, such asrecent hospitalization, surgery, residence in a long-term care facility, receipt of dialysis, or presenceof invasive medical devices. CA-MRSA isolates commonly possess genes for the Panton-ValentineLeukocidin (PVL) toxin, rarely identified in HA-MRSA isolates. Presence of PVL genes in S.aureusisolates has been associated with primary skin infections. From a clinical management standpoint,awareness of local resistance patterns for pathogens in the differential diagnosis of specific clinicalsyndromes is more important than formally categorizing possible MRSA infections as CA-MRSA orHA-MRSA; Factors common to these settings that facilitate the spread of infection include crowding,frequent skin-to-skin contact between individuals, participation in activities that result incompromised skin surfaces, sharing of personal items that may become contaminated with wounddrainage, and challenges in maintaining personal cleanliness and hygiene. Community outbreakshave been reported in sports teams, child care attendees, prison inmates, and diverse populationswhere habitation is relatively concentrated. Isolates obtained from these patients with MRSAinfections described as CA-MRSA based on epidemiologic criteria have been noted to possessbacteriologic characteristics distinct from those of isolates from patients meeting epidemiologiccriteria for HA-MRSA, although this situation is evolving. CA-MRSA isolates tend to be resistant tofewer antimicrobial classes, possess different toxin genes, and carry a different type of the genecomplex. Unlike HA-MRSA isolates, which are usually resistant in vitro to multiple classes ofantimicrobial agents, many CA-MRSA isolates to date have been resistant only to beta-lactams (theantimicrobial class that includes penicillins and cephalosporins) and macrolides / azalides (e.g.,erythromycin, clarithromycin, azithromycin). However, resistance to other classes of antimicrobial
agents, such as fluoroquinolones and tetracycline’s, occurs and may be increasing in prevalence.Most CA-MRSA isolates to date have been susceptible to trimethoprim-Sulphmethoxazole(TMP/SMX), gentamicin, tetracycline, and clindamycin; although some S. aureus isolates that appearerythromycin-resistant and clindamycin-susceptible by routine susceptibility testing by disc diffusionmethods exhibit in vitro resistance to clindamycin during therapy (“inducible resistance”) called theD-zone test. S. aureus strains with the inducible resistance phenotype, termed “inducible macrolide-lincosamide-streptogramin B resistance” (iMLS), have a high rate of mutation to constitutiveclindamycin resistance, a trait which would confer a selective advantage during clindamycin therapy.Although erythromycin is used to induce clindamycin resistance in the D-zone test, pre-treatment orco-treatment with erythromycin is not needed for iMLS strains to express clindamycin resistance invivo during a course of therapy. If empiric Clindamycin therapy has been initiated and inducibleclindamycin resistance is detected, response to therapy should be assessed. Clinicians shouldconsider changing to another agent if response to therapy has been unsatisfactory and shouldmonitor the patient closely to assure resolution of the infection, if clindamycin therapy is continued.The problem to identify CA-MRSA continues to be difficult in most of Laboratories as we routinely donot do Genotyping for differentiating between HA-MRSA and CA-MRSA. An optimal clinical filling ofthe request from with all relevant details can be able to give some clues to identify at least few withAntibiogram patterns. Too much dependence of empirical treatment by Clinicians can lead toincreased morbidity and Mortality as CA-MRSA can produce life threating complications if noteffectively treated. Only vigilant prevention and implementation of the most current treatmentprotocols will provide an increased margin of safety.Know your Antibiotics - Aztreonam is the first member of a new class of beta-lactam antibiotics,the Monobactams. It was originally isolated from Chromobacterium violaceum. It is a syntheticbactericidal antibiotic. The Monobactams, having a unique monocyclic beta-lactam nucleus, arestructurally different from other beta-lactam antibiotics (eg, penicillins, cephalosporins,Cephamycins). The sulfonic acid substituent in the 1-position of the ring activates the beta-lactammoiety; an aminothiazolyl oxime side chain in the 3-position and a methyl group in the 4-positionconfer the specific antibacterial spectrum and beta-lactamase stability. It is resistant to some beta-lactamases, but is inactivated by extended-spectrum beta-lactamases. Aztreonam has strong activityagainst susceptible gram-negative bacteria, including Pseudomonas aeruginosa. It has no usefulactivity against gram-positive bacteria or anaerobes. It is known to be effective against a wide rangeof laboratory isolates of bacteria including Citrobacter, Enterobacter, E. coli, Haemophilus, Klebsiella,Proteus, and Serratia species. In 2010 the Clinical and Laboratory Standards Institute (CLSI) loweredthe susceptibility breakpoints of some cephalosporins and aztreonam for Enterobacteriaceae andeliminated the need to perform screening for extended-spectrum β-lactamases (ESBLs) andconfirmatory tests. Widespread resistance in Enterobacteriaceae and Pseudomonas aeruginosa tocephalosporin and Monobactam antibiotics due to extended -spectrum beta-lactamases hasresulted in the need for reassessment of the interpretative criteria (breakpoints) established forthese agents over 2 decades ago. Breakpoints need to be revised due to changing resistancemechanisms and bacterial population distributions, changing science leading to a betterunderstanding of the pharmacologic determinants of clinical response, and adoption of “bestpractices” by clinicians. The breakpoints were revised in order to better represent the effect theseagents might have when they are used to treat infections caused by contemporary isolates withcurrently recommended dosage regimens. Knowledge gained from ESBL-producing organisms played
a major role. From Clinical point of view based on therapeutic trials have shown aztreonam to beeffective in Gram-negative infections including complicated infections of the urinary tract, in lowerrespiratory tract infections and in gynaecological and obstetric, intra-abdominal, joint and bone, skinand soft tissue infections, uncomplicated gonorrhoea and septicaemia. In comparisons with otherantibiotics, aztreonam has been at least as effective as or more effective than Cefamandole inurinary tract infections and similar in efficacy to tobramycin or gentamicin. All the Diagnosticlaboratories should not forget to test the resistance and sensitivity pattern of aztreonam as it is anequally effective Antibiotic like several 3rd Generation Cephalosporins.Know your Antibiotics Clindamycin facts to Know – Clindamycin continues to be less used morefeared Antibiotic, in the daily practice. Clindamycin is a semisynthetic derivative of lincomycin, anatural antibiotic produced by the actinobacterium Streptomyces lincolnensis. It is obtained by It isusually used to treat infections with anaerobic bacteria, but can also be used to treat some protozoaldiseases, such as malaria. Community-acquired MRSA isolates are often susceptible to several non–b-lactam drug classes, although they are usually not susceptible to macrolides. Several newerantimicrobial agents and a few older agents are available for treatment of systemic Staphylococcalinfections, but use may be limited by the relatively high cost of these agents or the need forparenteral administration. Inexpensive oral agents for treatment of localized, community-acquiredMRSA infection include clindamycin, trimethoprim-Sulphmethoxazole, and newer tetracycline’s.Clindamycin is used primarily to treat anaerobic infections caused by susceptible anaerobic bacteria,including dental infections, and infections of the respiratory tract, skin, and soft tissue, andperitonitis. In patients with hypersensitivity to penicillins, clindamycin may be used to treatinfections caused by susceptible aerobic bacteria. It is also used to treat bone and joint infections,particularly those caused by Staphylococcus aureus. Topical application of clindamycin phosphatecan be used to treat mild to moderate acne. It is most effective against infections involving thefollowing types of organisms: Aerobic Gram-positive cocci, including some members of theStaphylococcus and Streptococcus (e.g. pneumococcus) genera, but not enterococci, Anaerobic,Gram-negative bacteria, including some Bacteroides, Fusobacterium, and Prevotella, althoughresistance is increasing in Bacteroides fragilis. Clindamycin is commonly used in the treatment oferythromycin resistant Staphylococcus aureus causing skin and soft tissue infections. In vitro routinetests for clindamycin susceptibility may fail to detect inducible clindamycin resistance due to ermgenes resulting in treatment failures, thus necessitating the need to detect such resistance by asimple D test on routine basis.Why we do D test for Clindamycin susceptibility -When testing a Gram-positive bacteria forsensitivity to clindamycin, it is common to perform a "D-Test" to determine if there is a macrolide-resistant subpopulation of bacteria present. This test is necessary because some bacteria express aphenotype known as MLSB, in which susceptibility tests will indicate the bacteria are susceptible toclindamycin, but in vitro the pathogen displays inducible resistance.How to perform D test. In this test, an agar plate is inoculated with the bacteria in question andtwo drug-impregnated disks (one with erythromycin, one with clindamycin) are placed 15–20 mmapart on the plate. If the area of inhibition around the Clindamycin disk is "D" shaped, the test resultis positive and clindamycin should not be reported as sensitive due to the possibility of resistantpathogens and therapy failure. If the area of inhibition around the clindamycin disk is circular, thetest result is negative and clindamycin can be reported as sensitive. The Physicians are warned
clindamycin, may cause overgrowth of dangerous bacteria like C.difficle in the large intestine. Thismay cause mild diarrhoea or may cause a life-threatening condition called colitis. Clostridium difficleassociated diarrhoea (CDAD) has been reported with use of nearly all antibacterial agents, includingClindamycin and may range in severity from mild diarrhoea to fatal colitis. Treatment withantibacterial agents alters the normal flora of the colon leading to overgrowth of C.difficle.Clindamycin is more likely to cause this type of infection than many other antibiotics, so it shouldonly be used to treat serious infections and patients are asked report adverse effects to theconcerned Physicians. Why all are afraid of use of Clindamycin as it causes overgrowth of C.difficilewhich produces toxins A and B which contribute to the development of CDAD. Hyper toxin producingstrains of C. difficile cause increased morbidity and mortality, as these infections can be refractory toantimicrobial therapy and may require colectomy. CDAD must be considered in all patients whopresent with diarrhoea following antibiotic use. Careful medical history is necessary since CDAD hasbeen reported to occur over two months after the administration of antibacterial agents.Note – The above published articles are contributed to various WEB resources for benefit of YoungGeneration of MicrobiologistsDr.T.V.Rao MD, Professor of Microbiology. Travancore Medical College,Kollam, Kerala IndiaEmail email@example.com