Microbiology ananthanarayan ebook free download

Preface to the Tenth Edition viii

Preface to the First Edition ix
Acknowledgements xi
Special Acknowledgements xii

Part I General Microbiology

~ I n troduction and Bacterial Taxonomy 3

2.Morphology and Physiology of Bacteria 9
..a--s'terilisation and Disinfection 28
4Culture Media 39
5culture Methods 44
Vldentification of Bacteria 48
7 bacterial
Genetics 54

Part II Immunology

8 Infection 73
~ Immunity 80
,..-10(Antigens 89
11 Antibodies-lmmuno globulins 95
12 Antigen-Antibody Reactions 105
13 Complement System 122
1 4 s t r uand
c tFunctions
u r e of the Immune System 130
15 Immune Response 147
16 Hypersensitivity 163
17 Immunodeficiency Diseases 173
18 Autoimmunity 180
19 Immunology of Transplantation and Malignancy 185
20 lmmunohematology 193
 Contents

Part 111 Bacteriology

21 staphylococcus 201
22 streptococc us 210

23 pneumococcus 223
{1:/Neisseria 230
is,,-- Corynebacterium 239
26 Bacillus 248
_.:g,- Anaerobic Bacteria I: Clostridium 256
28 An
Anaerobic Bacteria II: Non-sporing Anaerobes / 273
29 Enterobacteriaceae I: Coliforms-Proteus ../ 279
,...JO' Enterobacteriaceae II: Shigella / 291
M Enterobacteriaceae Ill: Salmonella 296
32 vibrio v' 309
33 Pseudomonas 320
34 Yersinia, Pasteurella, Francisella 325
35 Haemophilus 333
36 Bordetella 339
37 Brucella 345
v31f Mycobacterium I: M.tuberculosis 351
J.9""' Mycobacterium II: Non-Tuberculous Mycobacteria (NTM) 366
Ill: M.leprae 371

4 ¥ • Spirochetes 377
42 Mycoplasma 393
43 Actinomycetes 398
44 Miscellaneous Bacteria 402
45 Rickettsiaceae 412
46 Chlamydiae 422

Part IV Virology

47 General Properties of Viruses 433

48 Virus-Host Interactions: Viral Infections 450
49 Bacteriophages 462
50 Poxviruses 467
51 Herpesviruses 472
52 Adenoviruses 486
53 Picornavi ruses 490
54 Orthomyxoviruses 502
 Contents vii

55 Paramyxoviruses 512
56 Arthropod- and Rodent-borne Viral Infections 522
57 Rhabdoviruses 534
58 Hepatitis Viruses 544
59 Miscellaneous Viruses 557
60 Oncogenic Viruses 568
61 Human Immunodeficiency Virus: AIDS 574

Medical Mycology
62 General Aspects 593
63 Superficial and Subcutaneous Mycoses 599
64 Systemic and Opportunistic Mycoses 609

Part VI Applied Microbiology

65 Normal Microbial Flora of the Human Body 625
66 Bacteriology of Water, Air, Milk and Food 629
67 Laboratory Control of Antimicrobial Therapy 639
68 lmmunoprophylaxis 643
69 Healthcare-associated Infections 648
70 Biomedical Waste Management 657
71 Emerging and Re-emerging Infections 660
72 Recent Advances in Diagnostic Microbiology 663

Part VII Clinical Microbiology

73 Bloodstream Infections 669
74 Respiratory Tract lnfections 672
75 Meningitis vs/' 675
76 urinary Tract Infections 678
77 Jsexually Transmitted Infections f 681
78 Diarrhea and Food Poisoning •• 684
79 Skin and Soft Tissue Infections 687
80 Pyrexia of Unknown Origin 689
81 Zoonoses 692
82 Principles of Laboratory Diagnosis of Infectious Diseases 694

Further Reading 698

Index 700
Preface to the Tenth Edition
authors
The tenth edition of Ananthanarayan and Paniker's Textbook of Microbiology upholds the vision of the pioneering
Previous editions brought in changes in the contents by including clinical cases
Dr R Ananthanarayan and Dr CK Jayaram Paniker.
relevant to individual organisms, and microbiology pertinent to infectious diseases . However, with the deluge of new information,
constant
compounded with the challenges in contending with infectious diseases and the rapid evolution of microorganisms, there is a
sed subject to the domain of infectious diseases,
need to revise existing knowledge. As microbiology moves from a laboratory-ba
relevant
students need to reorient themselves from the concept of microbiology as a non-clinical speciality to that of a clinically
from basic concepts in infectious diseases to healthcare-ass ociated and community-ac quired
subject, with applications ranging
infections, disease detection and prevention, outbreaks and epidemic management, and other public health challenges.
applied
The Medical Council of India has emphasised the need for integrated teaching, underscoring the requirement for
reviewed, while retaining their basic themes and concepts.
microbiology. Keeping this in mind, the chapters have been thoroughly
Some of the significant updates are listed below.
• ew concepts in sterilisation and disinfection, including plasma sterilisation and practices in healthcare settings
• ew and automated methods for identification of bacteria
• Updated molecular techniques as applied to microbiology
and their
• Simple diagrammatic presentations of current immunological techniques for antigen and antibody detection,
applications
• Clinical implications of bacterial organisms, current methods of detection, and suggested antibiotic treatment
• Salient features of the Revised National Tuberculosis Program (RNTCP)
• Strategies for diagnosis of MDR and XDR tuberculosis, and the STOP TB strategy of WHO
the Ebola
• New and emerging viral infections such as SARS, MERS-CoV, influenza epidemics, the Zika virus outbreak, and
outbreak
• NACO guidelines for HIV testing strategies for different categories of the population, and HIV exposure and source codes
and
• Latest vaccines for immunisation against childhood infections in India, including Rotavirus, Haemophilus influenzae
pneumococci
pictorial
• Healthcare-associated infections leading to CAUTI, VAP, HCA-BSI and SSI, and strategies for prevention with
representations
• Biomedical waste management rules (2016)
• Recent advances in diagnostic microbiology and the work flow in a clinical microbiology laboratory
• Quality control and accreditation of diagnostic tests performed by laboratories
• Easy-to-unde rstand line diagrams
• Flowcharts to make the conceptualisation of processes easy to comprehend by the undergraduat e student
• Relevant points boxed as highlights
• Recaps updated and retained for quick review by the students
right
Universities Press and its editorial team deserve special appreciation for the meticulous and methodical editing process
helped to fine-tune the rough edges of the book.
from the time I took up the assignment. Constant communication and interaction
valuable
My heartfelt thanks to Dr Sudha Ganesan for her timely feedback, and to Mr Madhu Reddy and Ms Aathira Varma for their
changes made in this revised edition will be helpful to the students of microbiology, and to those pursuing
inputs. It is hoped that the
infectious diseases.
We welcome suggestions for further improvement of the book in subsequent editions.
Reba Kanungo
Preface to the First Edition
Many of the health problems in developing countries like India are different from those of developed countries. Bacterial diseases
still play a considerable role in our country. Topics such as cholera and enteric diseases are important to us though only of less or
academic interest to the developed countries. The increasing importance of the newer knowledge in immunology to health and
disease is not adequately stressed in most of the extant textbooks. Virus diseases which are responsible for nearly 60 per cent of
human illness require wider coverage. The general approach to the teaching of microbiology in our country has also been rather
static. All these factors called for a textbook of microbiology more suited to countries like India.
We therefore undertook this endeavour based on our experience of teachi ng undergraduates and postgraduates for over two
decades. We omitted the discipline of parasitology from our book since we already have an excellent textbook on the subject published
in India.
This book has taken us over three years to write and over a year in publication. Naturally we would be out of date to a certain
and inevitable extent. We do not claim any perfection. On the contrary, we have requested medical students and teachers all over the
country to write to us about any shortcomings and give us suggestions as to how to improve the book. We shall spare no pains in
seeing that their valuable suggestions are given effect to in our second edition.

R Ananthanarayan
CK Jayaram Paniker
Acknowledgements
For kind permission to use photographs, the publishers are indebted to the following institutions and individuals:
Lister Metropolis Laboratory and Research Centre Pvt. Ltd., Chennai, for figures 32.2, 38.3, 43 .1a, 43. 1b, 4 7 .6, 64.8a; Sudha
Ganga! and Shubhangi Sontakke, for figures 10. la, 10.l b, 10.2, I 1.1, 11.2b, 11.3, 11.6, 12. lOb, 13 .1, 13.4, 14.6, 14.8, from
Textbook of Basic and Clinical Immunology (2013) published by Universities Press India Pvt Ltd. ; Department of Microbiology,
Nizam's Institute of Medical Sciences, Hyderabad, for figures 5.3a, 5.3b, 5.3c, 21.4, 23.1, 26.4, 28.1 , 61.4, 64.1O; Dr Ratna
Rao, Senior Consultant Microbiologist, Apollo Hospitals, Jubilee Hills, Hyderabad for figures 2.3a, 2.3b, 2.3c, 2.3d, 21.1 , 38.1,
64.9b; Dr Swarajya Lakshmi, Assistant Professor, Department of Microbiology, MNR Medical College, Andhra Pradesh for figure
64.9a; National Institute of Virology, Pune, for figures 56.1, 56.3; Dr Pallab Ray, Additional Professor, Department of Medical
Microbiology, PGIMER, Chandigarh, for figures 6.7, 27.3; Dr Asha Mary Abraham, Professor, Department of Clinical Virology,
Christian Medical College, Vellore, for figures 4 7. 7, 52.2a, 52.2b; Dr G Sasikala, Professor of Microbiology, STD Regional
Laboratory, Osmania General Hospital, Hyderabad, for figures 27.6, 27.2, 32.3, 33.1 , 38.2, 44.1, 58.1; Dr Subha Parameswaran,
Professor and Head, Department of Microbiology, K J Somaiya Medical College, Mumbai, for figures 36.1, 41.2, 51 .3, 51.4, 64.8b;
Dr Uma Tendolkar, Department of Microbiology, Lokmanya Tilak Municipal Medical College, Mumbai, for figure 51.5; Belnap,
D M, McDermott, 8 M, Jr, Filman, DJ, Cheng, N, Trus, 8 L, Zuccola, HJ, Racaniello, V R, Hogle, J M, and Steven, AC (2000),
for figure 53 . 1; World Health Organization, Global Programme for Vaccines and Immunization EPI, for figure 53.2; Centers for
Disease Control and Prevention Archives for figure 34.2; FA Murphy, University of Texas Medical Branch, Galveston, Texas, for
figures 59.2, 59.3 ; Prof. L. Dar, Department of Microbiology, Al/MS, New Delhi for figure 57.3; Prof. MC Sharma, Department of
Microbiology, Al/MS, New Delhi for figure 43.1 (a).
www.wikimedia.org for figures I.I, 1.2, 1.3, 1.4, 48.1 and 57.3; www.purifiers.co.za for figure 3.4a; www.pharmlabs.unc.edu for
figure 3.4b; www.healthessentials4you.com for figure 3.4c; www.tjclarkinc.com for figure 25.1 ; www.webak.upce.cz for figure 31.1;
www.home.kku.ac.th for figure 33.2; www.michigan.gov for figure 38.4; www.leprosyhistory.org for figure 40.1; www.bilkent.edu.tr
for figure 40.2b; www.granuloma.homestead.com for figure 40.2a; www.farm1.static.flickr.com for figure 52.2; www.umanitoba.ca
for figure 47.3 ; www.biochem.wisc.edu for figure 49.2; www.zunsanwong.blogspot.com for figure 59.4; www.med.ncku.edu.tw for
figure 63.2

Every effort has been made to contact holders of copyright to obtain permission to reproduce copyright material. However, if any
have been inadvertently overlooked, or have credited the wrong source, the publishers, on information, will be pleased to rectify the
error at the first opportunity. Images for which such permission was awaited at the time of publication will be replaced in subsequent
editions if such permission is not granted.
Special Acknowledgements

For their most helpful suggestions in the formulation of this edition, the publishers are grateful to Dr Anuradha Makkar,
Professor and Head, Department of Microbiology, Army College of Medical Sciences, New Delhi; Dr Prerna Bhalla, Professor,
Department of Microbiology, Hindu Rao Medical College, New Delhi (former Head, Maulana Azad Medical College, New Delhi) ;
Dr A K Praharaj, Professor and Head, Department of Microbiology, AIIMS , Bhubaneswar, Odisha; Dr Rajni Gaind, Professor
and Head, Department of Microbiology, VMMC, New Delhi; Dr Sai Leela Kondapanerti, Professor and Head, Department of
Microbiology, KIMS , Hyderabad.
For valuable feedback and help in developing the MCQs for the tenth edition, we are profoundly thankful to Dr Sarada
Devi K.L, Professor and Head, Department of Microbiology, GMC, Thiruvananthapuram, and her team members
Dr Deena Philomina, Professor and Head, GMC Kozhikode; Dr Anitha PM, Additional Professor, GMC Kozhikode and
Dr Shabina MB, Associate Professor, GMC Kozhikode.
Our special thanks are also due to Dr G Jyothi Lakshmi, Professor, Department of Microbiology, Osmania Medical College, Hyderabad;
Lieutenant Colonel Dr N andita Hazra, Sr Adv(Pathology and Microbiology) and Head, Department of Laboratory Medicine, Command
Hospital (Central Command) , Lucknow; Dr Thyagarajan Ravinder, Professor and Head, Department of Microbiology, Kilpauk
Medical College, Chennai; Dr S Manick Dass, Professor and Head, Department of Microbiology, Apollo Medical College, Hyderabad;
Dr G Jayalakshmi, Director and Professor, Department of Microbiology, Madras Medical College, Chennai; Dr Mary Mathews,
Retired Professor and Head, Department of Microbiology, Christian Medical College, Vellore.
Part I General Microbiology

1 Introduction and Bacterial Taxonomy 3

2 Morphology and Physiology of Bacteria 9
3 Sterilisation and Disinfection 28
4 Culture Media 39
5 Culture Methods 44
6 Identification of Bacteria 48
7 Bacterial Genetics 54
 Introduction and
Bacterial Taxonomy
attending on women in labour in the hospital and had
HISTORY prevented it by the simple measure of washing his
CLASSIFICATION, NOMENCLATURE AND TAXONOMY hands in an antiseptic solution, for which service to
Bacterial classification medicine and humanity, he was persecuted by medical
Nomenclature orthodoxy and driven insane.
Type cultures The development of microbiology as a scientific
discipline dates from Louis Pasteu.r 1822-95)
introduced techniques ot &_terilisatjon
and develope the d
steam steriliser, hot-air oven and
autoclave.3 e also established the d i f f e growth
ring
HISTORY
needs of different bacteria and contriEuted to the
Medical microbiology is the study of microbes that knowledge hy'crropho-
infect humans, the diseases they cause, and their bia. accidental observation that chicken -cholera
diagnosis, prevention and treatment. It also deals with
the response of the human host to microbial and other ~ ~
lost their
for
antigens.
to prot s
As microbes are invisible to the unaided eye, defini- t of th of attenuation
tive knowledge about them had to await the develop- and the developmentof live vaccinattenuated
es
ment of the microscope. The credit for having first cultures of the anthrax bacillus by incubation at high
observed and reported bacteria belongs to Antony temperature- (~43°C) and pr~d that inoculation
van Leeuwenhoek, a draper in Delft, Holland, whose of such cultures_in animals induced specific protec-
hobby was grinding lenses and observing diverse mate- tion against anthrax. It was Pasteur who coined the
rials through them (Fig. 1.1 ) . term vaccine for such prophylactic preparations to
In fact, even before the microbial cause of infections commemorate the first of such preparations, namely
had been established, Ignaz Semmelweis in Vienna cowpox, employed by Edward Jenne or protection
(1846) had independently concluded that puerperal against smallpox. The greatest impact on medicine
sepsis was contagious. Semmelweis also identified its was made by Pasteur's development of a vaccine for
mode of transmission by doctors and medical students hydrophobia.

Fig. 1.1 Antony van Leeuwenhoek Fig. 1.2 Louis Pasteur

 Part I GENERAL MICROBIOLOGY

An immediate application of Pasteur's work was specifically neutralised by their antitoxins. Paul Ehrlich
the introduction of antiseptic techniques in surgery by who studied toxins and antitoxins in quantitative terms
Joseph Lister (186 7) , effecting a pronounced drop in laid the foundations of biological standardisation
mortality and morbidity due to surgical sepsis. Lister's (Fig. 1.4) . Ernst Ru ska (1934) developed the electron
antiseptic surgery involving the use of carbolic acid microscope, enabling visualisation of the microbes we
was a milestone in the evolution of surgical practice, now call viruses. The development of tissue culture
from the era of 'laudable pus' to modern aseptic techniques has permitted the cultivation of viruses.
techniques. The causative agents of various infectious diseases
While Pasteur in France laid the foundations of were being reported by different investigators in such
microbiology, Robert Koch (184 3-1910) in Germany profusion that it became necessary to introduce criteria
perfected bacteriological techniques duringffjts stud for proving the claims that a microorganism isolated
ies on the culture and _life cycle pf the anthrax bacil- from a disease was indeed causally related to it. These
W.. (1876). He introduced.Stain ing techniques and criteria were enunciated by Koch and are known as
methods of obtaining bacteriajn pure culture using Koch's postulates. According to these, a microor-
solid media (Fig. 1.3). e discovered the bacillus of ganism can be accepted as the causative agent of an
tuberculosis ( 1882) and the cholera vibrio ( 1883). infectious disease only if the following conditions are
Roux and yersin (1888) identified a new mecha- satisfied
nism of pathogenesis when they discovered the diph- The bacterium should be constantly associated with
theria toxin. Similar toxins were identified in tetanus the lesions of the disease
and some other bacteria. The toxins were found to be It should be possible to isolate the bacterium in pyre
culture from the lesions .
inoculation of such pure culture into suitable
laboratory animals should reproduce lesions of the

---
disease.
--->1t should be possible to re-isolate the bacterium in
pure culture from the lesions produced in experi-
mental animals,
An additional criterion introduced subsequently
requires that specific antibodies to the bacterium
should be demonstrable in the serum of patients suf-
fering from the disease. Though it may not always be
possible to satisfy all the postulates in every case, they
have proved extremely useful in sifting doubtful claims
made regarding the causative agents of infectious
Flg. 1.3 Robert koch diseases.
The study of immunity had to await advances
in protein chemistry. The pioneering work of Karl
Landsteiner laid the foundations of immunochemistry.
In 1955, Niels Jerne proposed the natural selection
theory of antibody synthesis which attempted to explain
the chemical specificity and biological basis of antibody
synthesis, signifying a return to the original views of
antibody formation proposed by Ehrlich (1898).
Frank Burnet (195 7) modified this into the clonal
selection theory, a concept which, with minor altera-
tions, holds sway even now. The last few decades have
witnessed an explosion of conceptual and technical
advances in immunology. Immunological processes in
Fig. 1.4 Paul Ehrlich health and disease are now better understood following
 Introduction and Bacterial Taxonomy ' ,
,5 ,,
.
the identification of the two components of immu- manipulation and molecular engineering. They need
nity-humoral or antibody-mediated processes and to be used wisely and well for the benefit of all living
cellular or cell-mediated processes-which develop beings.
and manifest in separate pathways, The number of Nobel laureates in Medicine and
Alexander Fleming (1929) made the accidental dis- Physiology awarded the prize for their work in micro-
covery that the fungus Penicillium produces a substance biology, listed in Table I. l , is evidence of the positive
that destroys staphylococci. Work on this at Oxford by contribution made to human health by the science of
Florey, Chain and their team during the Second World microbiology.
War led to the isolation of the active substance penicil-
lin and its subsequent mass production, This was the
CLASSIFICATION, NOMENCLATURE
beginning of the antibiotic era, Other similar antibiotics
AND TAXONOMY
were discovered in rapid succession, With the sudden
availability of a wide range of antibiotics with potent All organisms are classified primarily to enable easy
antibacterial activity, it was hoped that bacterial infec- identification, all classification systems aim to group
tions would be controlled within a short period, But organisms with similar properties and to separate those
soon the development of drug resistance in bacteria that are different. The basic taxonomic unit in bacteria
presented serious difficulties, is the species; two species differ from one another in
With the development of a wide variety of antibiot- several features determined by genes.
ics active against the whole spectrum of pathogenic The method most widely adopted is presented in suc-
bacteria, and of effective vaccines against most viral cessive editions of Bergey's Manual of Determinative
diseases, expectations were raised about the eventual Bacteriology.
elimination of all infectious diseases. The global eradi- Bacterial taxonomy or systematics comprises three
cation of smallpox inspired visions of similar campaigns components:
against other major pestilences. However, when new • Classification, or the orderly arrangement of units.
infectious diseases began to appear, caused by hitherto A group of units is called a taxon (pl taxa) , irrespec-
unknown microorganisms, or by known microbes tive of its hierarchic level.
producing novel manifestations, it was realised that • Identification of an unknown with a defined and
controlling microbes was a far more difficult task than named unit.
was imagined , The climax came in 1981 when AIDS • Nomenclature, or the naming of units.
was identified in the USA and began its pandemic
spread, Unceasing vigil is essential to protect humans Bacterial classification
from microbes, A kingdom is divided successively into division, class,
Apart from obvious benefits such as specific meth- order, family, tribe, genus and species. An important
ods of diagnosis, prevention and control of infectious difference between the classification of bacteria and that
diseases, medical microbiology has contributed to of other organisms is that in the former, the properties
scientific knowledge and human welfare in many other of a population are studied, and not of an individual.
ways, Microorganisms constitute the smallest forms • A population derived by binary fission from a single
of living beings and, therefore, have been employed cell is called a clone.
as models of studies on genetics and biochemistry, As • A single bacterial colony represents a clone. Though
nature's laws are universal in application, information all the cells in a clone are expected to be identical in
derived from the investigation of microbes holds true, all respects, a few of them may show differences due
in the main, for humans as well, to mutation.
Studies on microorganisms have contributed, more • A population of bacteria derived from a particular
than anything else, to the unravelling of the genetic source, such as a patient, is called a strain.
code and other mysteries of biology at the molecular The general absence of sexual reproduction in
level. Bacteria and their plasmids, yeasts and viruses bacteria serves to keep their character constant. But
are routinely employed as vectors in recombinant bacteria possess several features that contribute to
DNA technology. They have made available precious some degree of heterogeneity in their populations.
information and powerful techniques for genetic Their short generation time and high rate of mutation
 Part I GENERAL MICROBIOLOGY

Table 1.1 Nobel laureates in Physiology and Medicine

1901 Emil Avon Behring Serum therapy

1902 Ronald Ross Malaria
1905 Robert Koch Tuberculosis
1907 CL A Laveran Role of Protozoa in causing diseases
1908 P Ehrlich and E Metchnikof Immunity
1913 Charles Robert Richet Anaphylaxis
1919 Jules Bordet Immunity
1926 Johannes Fibiger Spiroptera carcinoma
1928 Charles Nicolle Typhus
1930 Karl Landsteiner Discovery of human blood groups
1939 Gerhard Domagk Prontosil
1945 A Fleming, E Boris Chain and Howard Walter Florey Penicillin
1951 Max Theiler Yellow fever
1952 Selman A Waksman Streptomycin
1954 Franklin Enders, T H Weller and F C Robbins Poliomyelitis growth in tissue
1958 George Beadle & E L Tatum and J Lederberg Gene action and genetic recombination
1960 FM Burnet and P B Medawar Acquired immunological tolerance
1965 Francois Jacob, Andre Lwoff and Jacques Monod Genetic control of enzymes
1966 Peyton Rous Tumour-inducing viruses
1969 M Delbruck, AD Hershey and S E Luria Replication mechanism and the genetic struct ure
of vi ruses
1972 Gerald M Edelman and Rodney R Porter Chemical structure of antibodies
1975 D Baltimore, R Dulbecco and H Martin Temi n Interaction between tumour viruses and the
genetic material of the cell
1976 Baruch S Blumberg and D Carleton Gajdusek New mechanisms of infectious disease
dissemination
1978 Werner Arber, Daniel Nathans and Hamilton O Smith Restriction enzymes
1980 Baruj Benacerraf, Jean Dausset and George D Snell Immunological regulation by cell surface
1984 Niels K Jerne, Georges J F Kohler and Cesar Milstein Control of immune system and monoclonal antibodies
1987 Susumu Tonegawa Generation of antibody diversity
1989 J Michael Bishop and Harold E Varmus Origin of retroviral oncogenes
1996 Peter C Doherty and Rolf M Zinkernagel Specificity in cell mediated immune defence
1997 Stanley B Prusiner Prions
2005 Barry J Marshall and J Robin Warren Helicobacter pylori
2008 Harald Hausen and Francoise Barre-Sand L Montagnier Human papi lloma viruses, human immuno-
deficiency virus
2011 Bruce A Beutler, Jules A Hoffmann, Ralph M Steinman Activation of innate immunity,-and the dendritic
cell and its role in adaptive immunity
2012 Sir John B Gurdon, Shinya Yamanaka Mature cells can be reprogrammed to become
pl uripotent
2015 William C Campbell and Satoshi Omura Discoveries concerning a novel therapy against
infections caused by roundworm parasites
Youyou Tu Discoveries concerning a novel therapy against Malaria

lead to the presence, in any population, of cells with species. Here some characteristics are arbitrarily
altered characters. Methods of genetic exchange such given special weightage. Depending on the charac-
as transformation, transduction and conjugation cause teristic so chosen, the classification would give differ -
differences in character. Prophage and plasmid DNA ent patterns . While classification based on a weighted
can induce new properties. characteristic is a convenient method, it has the seri-
Phylogenetic classification: The hierarchical classifi- ous drawback that the characters used may not be
cation represents a branching tree-like arrangement, valid. Fermentation of lactose, in the example cited,
one characteristic being employed for division at each is not an essential and permanent characteristic.
branch or level. This system is called phylogenetic It may be acquired or lost, upsetting the system of
because it implies an evolutionary arrangement of arrangement.
 Introduction and Bacterial Taxonomy

Percentage similarity divided first into groups and then into types, as for
40 50 60 70 80 90 100 example, in streptococci.
Strains
Much greater discrimination in intraspecies typ-
A
ing has been achieved by the application of newer
B
E
techniques from immunology, biochemistry and
genetics. Investigations of epidemiology and patho-
..-+--+- C
genesis using these techniques have been collectively
.----t-----t- F
referred to as molecular epidemiology. The methods
-_
-- + - JG used are of two types: phenotypic (study of expressed
.___ _ _
characteristics) and genotypic (direct analysis of
genes, chromosomal and extrachromosomal DNA).
D
H
Molecular phenotypic methods include electrophore-
tic typing of bacterial proteins and immunoblotting.
X y Genotypic methods include plasmid profile analysis,
restriction endonuclease analysis of chromosomal
Fig. 1.5 Adansonian classification DNA with Southern blotting, PCR and nucleotide
sequence analysis.
Adansonian classification: This avoids the use of
weighted characteristics (Fig. 1.5) . It takes into Nomenclature
account all the characteristics expressed at the time of
The need for applying generally accepted names for
study. The availability of computers has extended the
bacterial species is self-evident. The scientific name
scope by permitting comparison of very large numbers
usually consists of two words, the first being the name
of properties of several organisms at the same time.
of the genus and the second the specific epithet (for
This is known as numerical taxonomy.
example, Bacillus subtilis). The generic name is usu-
Molecular or genetic classification: This is based on ally a Latin noun. The specific epithet is an adjective
the degree of genetic relatedness of different organ- or noun and indicates some property of the species
isms. Since all properties are ultimately based on the (for example, albus, meaning white), the animal in
genes present, this classification is said to be the most which it is found (for example, suis, means pig) , the
natural or fundamental method. DNA relatedness disease it causes (tetani , of tetanus) , the person who
can be tested by studying the nucleotide sequences discovered it (welchii, after Welch) or the place of its
of DNA and by DNA hybridisation or recombination isolation (London). The generic name always begins
methods. The nucleotide base composition and base with a capital letter and the specific epithet with a small
ratio (adenine-thymine: guanine-cytosine ratio) var- letter, even if it refers to a person or place (for example,
ies widely among different groups of microorganisms, Salmonella London).
though it is constant for members of the same species.
Molecular classification has been employed more with Type cultures
viruses than with bacteria. As a point of reference, type cultures of bacteria are
lntraspecies classification: For diagnostic or epidemi- maintained in international reference laboratories. The
ological purposes, it is often necessary to subclassify type cultures contain representatives of all established
bacterial species. This may be based on biochemical species. The original cultures of any new species
properties (biotypes) , antigenic features (serotypes) , described are deposited in type collections. They are
bacteriophage susceptibility (phage types) or produc- made available by the reference laboratories to other
tion of bacteriocins (colicin types). A species may be workers for study and comparison.
 Part I GENERAL MICROBIOLOGY

RECAP
• Over the centuries, the experiments and work of a number of individuals from many different countries
have provided a scientific basis to the study of diseases.
• Louis Pasteur (1822-1895) discovered methods of sterilisation and developed methods for culture of
microbes, showed that microorganisms cause disease and established the principles of immunisation.
• Joseph Lister (1827-1912) introduced 'antisepsis', wherein he sprayed the patient and operating field
with carbolic acid .
• Robert Koch (1843-1910) defined the criteria used to attribute a disease to an organism (Koch's
postulates):
❖ The organism must be found in all cases of the disease; the distribution in the body should cor-

respond to that of lesions observed.

❖ The organism should be cultured outside the body in pure culture for several generations.
❖ The organism should reproduce the disease in other susceptible animals.

❖ The organism should be isolated in pure culture from the lesion in animals.
(an additional postulate, not fo rmulated by Koch, is added-specific antibody to the organism should
develop during the course of the disease).
• Ruska (1934) developed the electron microscope enabling visualisation of the microbes we now call
viruses. The development of tissue culture techniques has permitted the cultivation of viruses.
• Roux and Yersin (1888) demonstrated that the harmful effects of diphtheria are caused by the exotoxin
produced by Corynebacterium diphtheriae during its growth.
• Paul Ehrlich (1854-1915) was a pioneer in the study of antitoxin and toxin neutralisation.
• Sir Alexander Fleming (1885-1955) discovered that the fungus Penicillium produces a substance, peni-
cillin, that destroys staphylococci; this discovery led to the formulation of other antimicrobials.
• Classification is t he arrangement of organisms into related groups or taxa; taxonomy is the science of
classification.
• Since all organisms are classified primarily to enable easy identification, all classification systems aim
to group organisms with similar properties and to separate those that are different. However, the bes_t
classification schemes are those that are based on evolutionary relatedness.
• The basic taxonomic unit in bacteria is the species; two species differ from one another in several fea-
tures determined by genes.

SHORT NOTES

1. Robert Koch
2. Louis Pasteur
3. Paul Ehrlich
4. Joseph Lister
5. Koch 's postulates
6. Bacterial classification
 Morphology and
Physiology of Bacteria
cation under the Plant and Animal kingdoms proved
MORPHOLOGY OF BACTERIA unsatisfactory; they were then classified under a third
SIZE OF BACTERIA kingdom, Protista. Based on differences in cellular
MICROSCOPY organisation and biochemistry, this kingdom has been
divided into two groups: prokaryotes and eukaryo-
STAINING TECHNIQUES
tes (Table 2.1 ). Bacteria and blue-green algae are
Gram stain
prokaryotes, while fungi, other algae, slime moulds
Acid fast stain
and protozoa are eukaryotes (Fig. 2.1 ) .
SHAPE OF BACTERIA Bacteria are prokaryotic microorganisms that do not
BACTERIAL ANATOMY contain chlorophyll. They are unicellular and do not
Cell wall show true branching, except in the so-called 'highi::r
Cytoplasmic membrane bacteria' (actinomycetales).
Cytoplasm
Ribosomes
Mesosomes (chondroids) MORPHOLOGY OF BACTERIA
lntracytoplasmic inclusions
Nucleus SIZE OF BACTERIA
Slime layer and capsule The unit of measurement used in bacteriology is the
Flagella .micron (micrometre, µm) .
Fimbriae
Spore
Prokaryote
Pleomorphism and involution forms
L forms Single, circular
Cell wall chromosome
PHYSIOLOGY OF BACTERIA
GROWTH AND MULTIPLICATION OF BACTERIA
Cell division
Plasmid
Growth
Bacterial growth curve Eukaryote
Bacterial counts
Mitochondrion *
(site of cellular respiration)

BACTERIAL NUTRITION
Factors that affect growth ~ - ~- --=:>t-"- Nuclear
membrane
BACTERIOCINS
Lysosome

Cytoplasm
Rough
endoplasmic Smooth
reticulum endoplasmic
(ribosomes) reticulum
INTRODUCTION
Golgi apparatus
Microorganisms are a heterogeneous grou_p of several
distinct classes of living beings. The original classifi- Fig. 2.1 prokaryote and eukaryote cells
 Part I GENERAL MICROBIOLOGY

Table 2.1 Some differences between prokaryotic and MICROSCOPY

eukaryotic cells
The morphological study of bacteria requires the use
of microscopes. Microscopy has come a long way
Nucleus
Nuclear membrane Absent Present since Leeuwenhoek first observed bacteria over three
nucleolus Absent Present hundred years ago using hand-ground lenses. The fol-
~xyribonucleoprot ein Ab_sent Present lowing types of microscopes are in use today:
Chromosome One (circular) More than
Optical or light microscope: Bacteria may be exam-
one (linear)
Mitotic diyision Absent Present ined under the compound microscope, either in the
living state or after fixation and staining. Examination
cytoplasm
ytoplasmic streaming Absent Present of wet films or 'hanging drops' indicates the shape,
pinocytosis Absent Present arrangement, motility and approximate size of the cells.
mitochondria Absent Present
But due to lack of contrast, details cannot be appreci-
\.j:ysosomes Absent Present
golgi apparatus Absent Present ated (Fig. 2.2a).
'--'Endoplasmic reticulum Absent Present Phase contrast microscopy: This improves the con-
Chemical composition trast and makes evident the structures within cells
Sterols Absent Present that differ in thickness or refractive index. Also, the
muramic acid Present abs ent
differences in refractive index between bacterial cells
and the surrounding medium make them clearly vis-
1 micron (µ) or micrometre (µm) = one thousandth ible. Retardation, by a fraction of a wavelength, of the
of a millimetre rays of light that pass through the object, compared
1 millimicron (mµ) or nanometre (nm) = one thou- to the rays passing through the surrounding medium,
sandth of a micron or one millionth of a millimetre produces 'phase' differences between the two types of