COMMUNITY MEDICINE

CHS KEY POINTS FOR
CLINICAL YEARS
Prepared by: Dr. Dipendra Jung Shahi
Special contributors: Dr. Anish Dhakal, Jyoti shah
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1. DIET, NUTRITION AND CHRONIC DISEASES
METABOLIC SYDROME
3

Chronic disease : DCHS
 Diabetes
 Cancer
 Hypertension
 Stroke
DASH : Fruits, Vegetable, low fat, reduced
saturated fat
4

3. Food Security, Food Hygiene, Sanitation
Food Security
“Food security exists when all people, at all times, have
physical, social and economic access to sufficient, safe and
nutritious food to meet their dietary needs and food
preferences for an active and healthy life” (FAO,2002)
USA
Utilization- safe and nutritious food which meets their dietary needs
Stability- at all times
Availability- sufficient
Access- access to food
Utilization
6

Food Insecurity
“ a situation where some people do not have access to
sufficient quantities of safe and nutritious food and
hence do not consume the food that they need to
grow normally and conduct an active and healthy
life” (FAO)
7
Food insecurity may be due to:
lack of food
 lack of resources
 improper use
Changes in time:
no availability
no access
no proper utilisation
no stability

Reasons for Food insecurity (Availability)
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Access: reason for Food insecurity
9

Utilization: reason for Food insecurity
10

Stability: reason for Food insecurity
11

List of Agencies working on Food security
and nutrition
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Food Hygiene and Sanitation
Types of Food Contaminants
a) Biological Contaminants (B/V/F/P, biological toxins)
b) Physical Contaminants (Hair, Staple wire, Dust)
c) Chemical Contaminant (Pesticides, Sanitizers)
13

Main Causes of Food Borne Illness
1. Cross- Contamination
Hand to Food (When and how to wash hands? )
Food to Food
Equipment to Food
2. Time-Temperature Abuse
(41⁰F - 140⁰F) for more than 4 hrs.
3. Poor Personal Hygiene
17

Methods of pasteurization
• Holder method: Milk is kept at 63-66 °C for at
least 30 minutes, then quickly cooled to 5 °C
• HTST method (High temperature short time): Milk
rapidly heated to 72 °C, held at this temperature
for 15 seconds and rapidly cooled to 4 °C. This is
the widely used method
• UHT (Ultra high temperature) method: Milk
rapidly heated to 125 °C for a few seconds, then
rapidly cooled and bottled as quickly as possible
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Tests of pasteurized milk
• Phosphatase test
• Standard plate count
• Coliform count
19

Meat hygiene
• Meat includes various tissues of animal origin
• Diseases transmitted by eating contaminated meat
are
– tape worm infestation (T. solium, T. saginata),
– bacterial infections (anthrax, actinomycosis,
tuberculosis and food poisoning)
• Characteristics of good meat:
– Neither pale, pink nor a deep purple tint, firm and
elastic to touch, should not be slimy and have an
agreeable odour
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Fish hygiene
• Fish deteriorates and loses freshness because
of autolysis after death and bacterial
colonization
• Signs of fresh fish:
1. It is in a state of stiffness or rigor mortis
2. Gills are bright red
3. Eyes are clear and prominent
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Types of Food Fortification
o Biofortification (genetic engineering)
o Microbial biofortification and synthetic biology
o Commercial and industrial fortification (i.e. flour, rice, oils)
o Home fortification (Sprinkle of MNP- Baalvita)
22

Legal provision against food
adulteration in Nepal (Food Act 2023)
• Any person who produces, sells, exports or imports the Adulterated
Food may be punished with a fine from Rs.5,000/- to Rs. 10,000/- or
with imprisonment for a term from one year to two years or with
both
• If, after consuming any adulterated food, any person is likely to die or
dies or suffers an irreparable bodily damage or is likely to suffer such
damage, the producer or seller of such adulterated food may be
punished with a fine from Rs. 10,000/- to Rs. 25,000/- and
imprisonment for a term not exceeding three years;
• And such producer or seller has to provide a compensation in a sum
from Rs. 25,000/- to Rs. 100,000/- to the person affected from that
adulterated food or his heir
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4.Multi sector nutritional plan
Breast feeding should be: 3E
1. Early initiation
2. Exclusive
3. Extended
Micronutrient deficiency control program
Vitamin A supplement, Bal vita program
Iodine, Iron, deworming, flour fortification
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5. CMAM
Principle and component of CMAM - (CMAT)
1.Care for as long as needed
2.Maximum access and coverage
3.Appropriate medical and nutritional care
4. Timeliness
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• Sarbottam pitho ko lito - 2:1:1
(pulse:maize/rice: wheat/millet)
• Posilo pitho-1:1:1
• MUAC
measurement malnutrition Color coding
>13.5 Normal Green
12.5 -13.5 mild yellow
11.5-12.5 moderate Red
<11.5 severe
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6. Food and Drug interaction
• Antacids can lower stomach acidity which can may interfere with
iron, folate and vitamin B12 absorption
• Dietary calcium can bind to the antibiotic tetracycline making it
unavailable for absorption
• Amino acids compete for absorption with levodopa
• Some anticonvulsants can compete for absorption with folate
resulting in decreased folate absorption
– Isoniazid: similar in structure to vitamin B6 and induces
vitamin B6 excretion
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Food and Drug interaction
• Absorption of iron from supplements ↓↓ 50% when taken with
food
Best absorbed when taken with 250ml of water on empty stomach
• High fiber diet may decrease the absorption of tricyclic
antidepressants such as amitriptyline (Triad)
• Contain a chemical called tyramine that interacts with a medication,
monoamine oxidase inhibitor, which can result in dangerously high
blood pressure
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8.Maternal and child nutrition
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Interventions in women of reproductive
age and during pregnancy
• Folic acid supplementation
• Iron and folic acid supplementation
• Maternal multiple micronutrient
supplementation
• Maternal calcium supplementation
• Maternal iodine supplementation or fortification
• Addressing maternal wasting and food insecurity
with balance energy and protein
supplementation
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Nutrition interventions in neonates
• Delayed cord clamping
• Neonatal vitamin K administration
• Neonatal vitamin A supplementation
• Kangaroo mother care
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Nutrition interventions in infants and
children
• Promotion of breastfeeding and supportive
strategies
• Promotion of dietary diversity and
complementary feeding
• Vitamin A Supplementation in children
• Iron supplementation in infants fand children
• Preventive zinc supplementation in children
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1. Introduction to Family Health
What is Family?
• A primary unit of all societies.
• Group of related individuals living
together, sharing common physical
and social environment including
kitchen
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Family Vs Household
Household Family
• May contain only one person Must contain at least two members
• Need not be related to each other Must relate to each other by blood,
adoption or marriage
• Can contain more than one family Cannot comprise more than one
household
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Phases of NORMAL family life cycle
Phases Events characterizing
No. Description Beginning of phase End of phase
I. Formation Marriage Birth of first child
II. Extension Birth of first child Birth of last child
III. Complete extension Birth of last child 1st child leaves
home
IV. Contraction 1st child leaves home Last child leaves
home
V. Extended contraction Last child left home Death of spouse
VI. Dissolution Death of 1st spouse Death of survivor
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How Family affects health?
• The political, social and technological contexts
influence family structure and process vary across
place and over time.
• Processes by which families affect the health of
individuals:
 Micro-level processes
 Macro-level processes
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Micro level processes (within family)
• Resource Distribution
• Socialization
• Social Support
• Reciprocal effects
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Macro-level processes
• Demographic factors: e.g Fertility and
Mortality, Divorce and non – marital child-
bearing, Maternal age.
• Technological factors: e.g contraception,
neonatal care, assisted reproduction,
prenatal care.
• Economic and political factors: e.g Increase
female in labor force, abortion laws etc. 44

Parenting styles:
1. Authoritarian: -
 Give orders and expect them to be obeyed
 Children of these parents rate low on social
competence
 self esteem, intellectual curiosity, spontaneity
 Perform well in schools, but have higher level of
depression
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2. Authoritative;
 Parents set clear boundaries and expectations,
but are also loving and supportive, explain their
reasoning, allow children to explain themselves
 Children of authoritative parents are the most
well adjusted with high social competence
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3. Permissive;
 Parents do not expect their children to act maturely, allow them to
follow their own impulses.
 Children of these parents have difficulty with impulse control, take
less responsibility.
 But they have higher self esteem, better social skills, and lower
levels of depression.
4. Uninvolved
 Respond with little attention, frequency or effort;
 Children perform worse in all areas.
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2. Disability and Health
Defination
The constitution of Nepal defines a disabled person as
one who is mentally or physically unable to lead a normal
life.
Disabled Protection and Welfare Act defined disability as
The condition of difficulty in carrying out daily activities
normally and in taking part in social life due to problems
in parts of the body and the physical system as well as
obstacles created by physical, social and cultural
environments, and by communication
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Disability: To define
• Disability is an impairment that may be
– cognitive
– developmental
– intellectual
– mental
– physical
– sensory,
– or some combination of these.
49

ICF
 International Classification of Disease
 Talk about “bio-psycho-social model” and
1. Functioning
2. Disability
3. Body functions
4. Body structures
5. Impairments
6. Activity
7. Participation
8. Activity limitations
9. Participation restrictions
10. Environmental factors
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Classification of Disability in Nepal
• The 2011 Census Report of Nepal (CRN) has classified disability into
seven distinct groups:
1. Physical disability- Polio, Cerebral palsy, absence of a body part
2. Vision-related disability - cannot read the first line of Snellen chart
(3/60)
3. Hearing-related disability- cannot even hear sound above 80
decibels is deaf
4. Mental Disability - Intellectual disability/Mental retardation, Mental
illness, Autism
5. Deaf-Blind
6. Voice and speech-related disability
7. Multiple disabilities
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The government has granted facilities and rights
for the disabled in 9 areas
• Identity cards
• Free education
• Scholarships
• Medical care
• Workforce : reserve 5% of all jobs
• Transportation: A 50% discount
• Accessibility
• Income tax and customs: An income tax
exemption
• Social welfare and Shelter: NPR. 1000 per month
as social welfare allowances
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I.D CARD WITH COLOR CODING
According to the nature of disability
1. Red
2. Blue
3. yellow
• White
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3. Ageing and Rehabilitation
Senior Citizen Act 2063, Nepal
• Economic Aspect
• Social Security
• Health Services and Nutrition
• Participation and Engagement
• Educational and Entertainment Aspects
• Legislation Enactment
• Miscellaneous
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Health Services and Nutrition
• Geriatric wards shall be established and run along with
trained health professionals/manpower in central, regional
zonal hospitals
• Awareness programs shall be conducted to develop a
healthy state via preventive measures and healthy behavior
in senior citizens (2062/63 onwards, continuously)
• Free clinics and health camps
• Health related materials shall be freely distributed
• Training shall be provided to elderly care takers in elderly
homes/day care centers
• Concept of health insurance system)
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4. HIV /AIDS
• HIV is a retrovirus; this means that
it: converts RNA to DNA.
• the enzyme reverse transcriptase: converts RNA
to DNA.
• HIV is an enveloped virus; this means that it: is
covered by cell membrane.
• The diameter of HIV is about: 140nm
• Prevention of mother-to-child transmission
(PMTCT) programmes provide antiretroviral
treatment (ART) to HIV-positive pregnant women
to stop their infants from acquiring the virus
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A costume designer namedMarc
Happel
The red ribbon, as an awareness
ribbon is used as the symbol for
the solidarity of people living
with HIV/AIDS and for the
awareness and prevention of drug
abuse and drunk driving
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The start of the epidemic (4-H-Club)
• hemophiliacs, who received contaminated
blood transfusions
• homosexual men, who reported higher
incidences of the disease
• heroin users, and people who used drugs via
injection
• Haitians or people of Haitian origin, many
cases of AIDS were reported in Haiti
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Transmission
• The 'hunter' theory
• The oral polio vaccine (OPV) theory
• The contaminated needle theory
• The colonialism theory
• The conspiracy theory
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ALMA-ATA
• The landmark event for primary health care was
the International Conference on Primary Health
Care that took place at Alma-Ata from September
6 - 12, 1978.
• Alma-Ata was the capital of the Soviet Republic
of Kazakhstan, located in the Asiatic region of the
Soviet Union.
63

What is Primary Health Care?
Definition:
PHC is essential health care made universally
accessible to individuals and acceptable to them,
through their full participation and at a cost the
community and country and afford.
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Principles of PHC
1. Equitable distribution
2. Community participation
3. Intersectoral coordination
4. Appropriate technology
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Elements
• E – Education for Health
• L – Locally endemic disease prevention and control
• E – Expanded program for immunization
• M – Maternal and Child Health including responsible
parenthood
• E – Essential drugs
• N – Nutrition
• T – Treatment of communicable and non-communicable
diseases
• S - Safe water and sanitation 66

KEY AREAS TO REVITALIZE PHC
• Leadership and governance
• Human resources
• Multi sectoral collaboration
• Managing financial resources
• Knowledge generation
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6.Family planning
Definition
It is the planning that allows individuals and
couples to anticipate and attain their desired
number of children and the spacing and timing
of their births
 Family Planning Association of Nepal (FPAN)
established in 1958
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Why FP is important
high birth rate with a corresponding high
death rate result in slow increase in
population size
High birth rates and disproportionally low
death rates result in rapid population growth
 both a low birth rate and a low death rate
result in well controlled and increase only slowly.
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Family planning counseling GATHER
• G Greet the client respectfully.
• A Ask them about their family planning needs.
• T Tell them about different contraceptive options
and methods.
• H Help them to make decisions about choices of
methods.
• E Explain and demonstrate how to use the
methods.
• R Return/refer; schedule and carry out a return visit
and follow up.
71

7. Sustainable Development Goals
Definition
 Sustainable development has been defined as
development that meets the needs of the
present without compromising the ability of
future generations to meet their own needs.
 SDG has 17 Goals with 169 targets and 300
indicators
 The central principle of the SDGs is to “Leave
no one behind”
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Why SDG Is needed
Despite many successes, the poorest and most
vulnerable people are being left behind
1. Gender inequality persists
2. Big gaps exist between the poorest and richest
households, and between rural and urban areas.
3. Conflicts remain the biggest threat to human
development.
4. Millions of poor people still live in poverty and
hunger, without access to basic services
74

Issues and Challenges in SDGs
Implementation
SDGs are
• comprehensive,
• ambitious and
• challenging goals and require huge resources
75

1. International health agencies
WHO (194 Member Countries)
77

Work of WHO
1. Prevention and Control of specific Diseases
2. Development of Comprehensive Health Services
3. Family Health
4. Environmental Health
5. Health Statistics
6. Bio-Medical Research
7. Health Literature and Information
8. Cooperation with Other Organization
78

Six diseases malaria, schistosomiasis, trypanosomiasis
filariasis, leishmaniasis and leporsy
STRUCTURE Of WHO
79

Structure
1. World Health Assembly “Health Parliament” of Nations and the supreme governing body of the
organization. Meets annually at headquarters Geneva.
Functions:
To determine international health policy and programmes
To review the work of the past, To approve the budget for following year
To elect Member States to serve for 3 yrs on the Executive Board
2. The Executive Board
• 30-31 members designated as “Member State”. At least 3 persons from each WHO regions
• Has power to take decision  emergencies eg. Earthquakes, floods etc.
3. The Secretariat
Headed by Director General (chief technical and administrative officer of the organization)
Function:
To provide technical and managerial support for their national health development programme
80

2. Evaluation
Definition
Evaluation is defined as a process of
determining the appropriateness of
programme planning, assessing degree of
effectiveness and progress of programme
implementation, and measuring the final
achievements of the programme.
81

Why is evaluation done?
• Importance
– Evaluation helps in understanding the success and
weakness of the programme.
– It encourages the community people to take part in
different educational and health-related programmes.
– It helps to know the condition of the community
people and what type of programme they really need
for their overall development.
– Helps in the improvement of community participation
as per situation.
– Helps the local people to understand the importance
of their participation.
82

A. Time of evaluation
• Beginning of
programme
• Middle of programme
• End of programme
B. WHO Criteria of
evaluation- (AREA)
– Adequacy
– Relevancy
– Efficiency
– Appropriateness
C. Types of evaluation
• Diagnostic evaluation
• Formative evaluation
• Summative evaluation
D. Types of economic evaluation
• Cost identification ( cost
minimization)
• Cost-effectiveness analysis
• Cost-utility analysis
• Cost benefits analysis
83

E. Ways of doing
evaluation
• Self evaluation
• Participatory
evaluation
• Rapid participatory
appraisal
• External evaluation
• Interactive
evaluation
F. Evaluation phases
• Process evaluation
• Outcome evaluation
• Impact evaluation
G. Methods of evaluation
– Interview
– Observation
– Study office records and
reports
– Meeting and discussion
84

FOR MCQ
- If outcomes of the interventions are equal
→ use cost minimization method
- If outcomes of the interventions are in natural units
→ use cost effectiveness method
- If outcomes of the interventions are in the change in
quality of life of patients or their family
→ use cost utility method
- If the overall value created from the interventions
are measured in monetary terms
→ use cost benefit method
85

3. INTERNATIONAL INITIATIVES
Some Milestones on Path to Global Health
• 1920, League of Nations Health Organization
• 1945, World Bank Group founded
• 1946, U.N. Infant and Child Emergency Fund, UNICEF
• 1948, World Health Organization founded
• 1977, Eradication of smallpox
• 2002, Global Fund to Fight AIDS, Tuberculosis and Malaria
• 2005, Millennium Development Goals established
86

Evolution of Primary Health Care
The Alma-Ata Conference
• International conference on primary health care
• Conducted from 6-12th September 1978 at Alma Ata
• Mile stone in the history of public health
• Key to the attainment of the goal of the Health for All
87

Primary Health Care
“Primary Health Care is essential health care
made universally accessible to individuals &
acceptable to them, through their full
participation & at a cost the community &
country can afford”
88

Origins of MDGs
 In 2001, group of expert in UN
Secretariat selected 18 targets from Sept
2000 Millennium Declaration and
grouped them into 8 goals
 Objective – to reshape UN Development
Agenda
 Accepted by all Heads of State at
Millennium Summit
 The 8 goals refocused UN Development
Agenda around poverty reduction and
other ‘social goals’
89

UN Millennium Development Goals
• Eight goals for 2015 -- Goals set in 2005 at World
Summit of UN General Assembly (three are
primarily health-sector related)
1. Eradicate extreme poverty & hunger
- Reduce by half those living on <$1/day
- Reduce by half % suffering from hunger
2. Achieve universal primary education
3. Promote gender equality and empower
women
4. Reduce by 2/3rds child mortality for < fives
5. Reduce by 3/4ths maternal mortality ratio
6. Combat HIV/AIDS, malaria & other diseases
7. Ensure environmental sustainability
8. Develop a global partnership for
development
2
90

Strengths Weaknesses
Framework integrating various
dimensions of human
development
Lack of consultation has
limited G77 national
ownership due to perception
of donor agenda
Simple, transparent, and easy-
to-communicate
Excluded some important
issues in Millennium
Declaration and elsewhere
Provided bases for converging
advocacy
Inadequate incorporation of
other issues e.g. climate
change & econ development
Later recognised special needs
of Africa, LDCs, LLDCs, and
SIDS
Limited consideration of
enablers of development
Strengths and Weaknesses of MDGs
91

Sustainable Development Goals
From MDGs
(2000-2015)
to SDGs, changing the world in 17
steps
(2016-2030)
Ban Ki-Moon clustered
SDGs into six “essential
elements”: dignity,
prosperity, justice,
partnership, planet, people.
Resulted in 17 Goals and 169 targets for 2016
to 2030
92

MDGs SDGs
Mainly for developing
countries
Universal – for ALL countries
8 solid goals for
development
17 goals, 169 targets, integrating
3 dimensions (ecological,
environmental and social) of SD
From UN Secretariat Negotiated by Member States
with stronger country ownership
Means of Implementation
(MoI), monitoring and
follow-up not defined in
advance
MoI inter-governmentally
negotiated, global architecture
and monitoring system being
shaped
What’s new with SDGs
94

The SDGs versus MDGs
Key Strengths of the proposed SDGs include:-
 The notion of leaving no one behind – with many targets
aspiring zero/fully coverage (raising the ambition of the MDGs)
 Stand alone goal of Inequality (within and between countries)
 Stand alone goal on gender inequality , including ending of all forms of
violence, discrimination, child marriages, and female genital
mutilations
 Participatory/Inclusiveness Process in formulation of the SDGs: The
participation and buy in of a wide range of stakeholders including
member states and non governmental organizations
 Environmental issues are strongly represented
 Governance - for the first time
95

4. Planning of Health Services
Health planning- WHO
is an orderly process of defining community health
problems, Identifying unmet needs, surveying of
resources to meet them, establishing priority goals that
are realistic and feasible and projecting administrative
action to accomplish the purpose of the proposed
program
Ad-hoc Planning -Prepared during epidemic or for
special health programs like health camps, awareness
campaign etc.
96

Characteristics of Planning
1. It is a process
2. It is future oriented
3. It is universal in nature
4. It is goal focused- planning not only sets goal but
also selects actions to achieve it.
5. It is decision oriented, meaning that it is a result
of decision making
6. Planning is always directed towards increasing
efficiency
97

Types of Planning
A. On the basis of Time
1. Long term plan or Perspective Plan
• Long term visionary plan tentatively
covering 15-20 years.
• E.g: Second Long Term Health Plan
(1997-2017), MDG, etc
2. Medium term or Periodic Plan
• Generally of 3-5 years.
• E.g: Five year plan, Three year interim
plan
3. Short term
• Generally of one year
E.g: Annual plan, quarterly plan,
etc.
B. On the basis of Managerial Hierarchy
1.Strategic Planning or Corporate
Planning
2. Tactical Planning or divisional Planning
3. Operational Planning or Functional
Planning
C. On the basis of Use
1. Single use plan
2. Standing Plan
98

Planning Cycle (PIE)
Implementation
Evaluation
Planning
99

Steps of planning (PBQ)
• Analysis of the Health Situation
• Data Analysis and Need Prioritization
• Setting goals and objectives
• Identification of resources
• Development of detail implementation plan
• Plan for monitoring and evaluation
• Prepare budget
100

Planning process in Nepal
• National: Baisakh 15
• Regional: Falgun 13
• District: Magh 15
• PHCC/HP: Mangsir 30
• VDC : Mangsir 1
101

5. Strategic planning
• A strategy is path you choose to walk
towards the achievements of your aim or to
solve a particular problem.
• Strategic planning is a visionary process that
results in major, long-range and far-reaching
strategic directions or goals for the future
102

Internal Analysis:
Strengths and Weaknesses
External Analysis:
Opportunities and Threats
SWOT Analysis
104

Components of log frame/project
matrix:
1) Intervention logic or Narrative summary
2) Objectively verifiable indicators(OVI)
3) Means of Verification
4) Assumptions
105

6. BUDGETING
• Budget is derived from French word
“bougette” which means small leather bag
• “Budget is an estimate of future needs
arranged according to an orderly basis
covering some or all activities over given
period of time of an enterprise for a definite
period of time”
106

Characteristics of Budgeting
It is
• Constitutional
• Simplicity and flexibility (cost control)
• Yearly plan
• Future programme (on the basis of past)
• Guidelines
107

Types of budget
• Capital budget: generating capital goods e.g.
construction of dams, roads & equipments
• Recurrent Budget: generally the administrative
costs and costs on soft programs e.g. health
service extension , educational and others
• Financing: Principal and interest paid by the
government (Nepal)
108

Challenges of Health care financing in Nepal
• High out-of-pocket payments,
• Higher but still limited revenue-raising
capacities,
• Purchasing arrangements pose significant
constraints to universal coverage and
• No risk pooling mechanism
• High poverty and income inequality
109

Tuberculosis
• Chronic granulomatous disease caused by
Mycobacterium tuberculosis
• Rarely by M. bovis, M. africanum, M. canetti,
M. microti.
• Distnguishbetween tuberculosis and non-
tuberculousmycobacteria
• SYNONYMS: consumption, pthisis, scrofula,
Pott’sdisease, yaksma, shaky oncay, white
plague.
111

Tuberculosis
• Non motile, non spore-forming, aerobic, rod-shaped
bacteria 2-4 um in length
• Lipid-rich cell wall which gives the acid-fast property.
Pathogen
• Mycobacterium tuberculosis complexM.Tuberculosis,
M. canetti, M. microti, M. africanum, M. bovis
• Diabetics have 2-3 times higher risk of developing
tuberculosis
112

Tuberculosis
• Diagnosis: Smear Microscopy
:Mycobacterial Culture
:Nucleic Acid Amplification Tests
First-Line ATT: 2HRZE+ 4HR
• Isoniazid prophylaxis
• Isoniazid and rifampicin Prophylaxis for MDR/XDR
exposed
113

Enteric Fever
• Typhoid is a systemic infection with the
bacterium Salmonella enterica subspecies
enterica serotype Typhi
Bacterium
• From the family Enterobacteriacea
• Lipopolysachharideantigens O9 and O12
• Protein flagellar antigen Hd
• Polysaccharide capsular antigen Vi
114

Enteric Fever
• Incubation period 7-15 days.
• Gallbladder dissemination directly from blood or
retrogradelyfrom bile
Outbreaks
• Tajikistan, 1997: 8000 people in a six-month period with
150 deaths
• Chitwan
• Pokhara
• Kathmandu
115

Enteric Fever
Clinical Features
• Febrile Illness which is often non-specific
• Headache, Abdominal pain, diarrhoea, anorexia
• Coated tongue, hepatomegaly, splenomegaly
• Ilealperforation, GI bleeding
Diagnosis
• Blood culture
• Bone marrow culture
• PCR and other DNA based test
116

Enteric Fever
Treatment
• Fluoroquinolones
• Third generation cephalosporins
• Macrolides
Control
• Safe drinking water
• Effective Sewage Disposal
• Hygienic Food Preparation
Vaccine
• Parenteral Whole cell typhoid vaccine
• Vi polysachharide:
• Conjugate Vi 92% Efficacy
117

Hepatitis A
• Non-enveloped single-stranded linear RNA virus
• Transmitted via the fecal/oral route
• Ingestion or Direct contact
• Strong correlation of incidence with socioeconomy
• Mostly affects young or older
Diagnosis
• Nucleic Acid Amplification and Sequencing
• Serology --IgM(anti-HAV)
118

Hepatitis B
• Enveloped double-stranded linear RNA virus
• Hepadnaviridaefamily
Incubation period 30-180 days (avg75) days
Outcome
• Asymptomatic Infection
• Acute Hepatitis
• Chronic Hepatitis
• Cirrhosis, HCC
119

Hepatitis B
Diagnosis
• Serology --HBsAg--IgM(anti-HBcAg)--HBeAg--
Anti-HBs (anti-HBsAg) appears after a few
weeks
• Anti-HBs is a marker of immunity and used for
passive immunization
VaccinesRecombinant HepB vaccine
120

Hepatitis E
• Hepeviridaefamily
• 4 main genotypes
• Genome has 3 main parts
Transmission
• Fecal contamination of drinking water Genotypes1 and 2
• Zoonotic transmission undercooked meat Genotype 3 and 4
• In pregnancy from mother to fetus
121

Japanese Encephalitis
• Transmitted by Culexmosquitoes
• Enzootic cycle in pigs and wading birds
• Humans are dead end hosts
• Transmitted April to October in temperate regions, less
seasonal in colder areas.
• Single stranded RNA virus
• Flaviviridae family
Diagnosis JEV-specific IgMantibody in CSF
Cause of Death: Aspiration, Seizures, Raised ICP and
Hypoglycaemia
122

Dengue
• Transmission by Aedes aegypti and A.
albopictus
• Single stranded positive-sense RNA virus
Serotypes Types 1 to 4
• Flaviviridae family
• Diagnostic Tests:IgG and IgG
123

Malaria
• P. falciparum, P. vivax, P. ovaleand P. malariae
Diagnostic Tests
• Microscopy:Thick SmearThin Smear
• Rapid Tests:Histidinerich protein-2 (HRP-2)
Treatment
• Uncomplicated chloroquine resistant -
Artemether, Quinine sulfate plus Doxycycline,
Tetracycline
124

Malaria
• Uncomplicated chloroquine sensitive malaria- Chloroquine
phosphate
• Severe malaria- Artesunate
Mosquito repellent and avoidance advice:
• N-diethyl-meta-toluamide(DEET)
• Wearing permethrin-treated clothing
• Wearing clothes and footwear to cover as much skin as
possible
• Sleeping under insecticide treated bed-nets
• Staying in housing with a/c or well screened areas
• Refraining from outdoor activity during peak biting ho
125

Diagnostic Tests
+ -
+ a
(True positives)
b
(False positives)
- c
(False negatives)
d
(True negatives)
Disease
Test
126

Diagnostic Tests
• A sensitive test identifies correctly those who have the
disease
• A specific test identifies correctly those who do not have
the disease
Q. Assume a population of 1,000 people with the
prevalence of disease of 20%
• Test A Sensitivity=80% Specificity=60%
• Test B Sensitivity=90% Specificity=90%
127

Test A Sensitivity=80% Specificity=60%
Result of
Test-A True
Characteristic
Disease No Disease Total
Positive 160 320 480
Negative 40 480 520
Total 200 800 1000
128

Test B Sensitivity=90% Specificity=90%
Result of
Test-B True
Characteristic
Disease No Disease Total
Positive 180 80 260
Negative 20 720 740
Total 200 800 1000
129

Attack Rate (Risk)
• Attack rate for exposed= a/a+c
• Attack rate for unexposed= c/c+
Rate ratio = Rate for group of primary interest/ Rate for comparison
group
Odds ratio =ad/bc
Vaccine Efficacy/Effectiveness=Risk among unvaccinated group –Risk
among vaccinated group/Risk among unvaccinated group
=1 -risk ratio
130

• Vaccine efficacy/effectivenssis interpreted as the
proportionate reduction in disease among the vaccinated
group.
• Thus a VE of 90% indicates a 90% reduction in disease
occurrence among the vaccinated group, or a 90% reduction
from the number of cases you would expect if they have not
been vaccinated.
131

Station question- Graph
interpretation
132

Hill's criteria for causation,
133

Basic Concepts in
Biostatistics
Created by:
Anish Dhakal (Aryan)

Normal Distribution
• This is the standard
normal bell shaped curve
• Features of distribution
a) Continuous
b) Symmetric
c) Bell-shaped
• Mean is Zero (0) and
Standard Deviation is
One (1)
• Total area: 1.00 or 100%

• Chebyshev’s theorem
gives the formula 1-1/k2
• That is for any
distribution of data.
• In normal distribution,
more data is
concentrated. For
example, the theorem
states 75% of data
within 2 S.D. In normal
curve, the number is
above 95%

Skewness
• If data is perfectly
symmetrical, skewness=
Zero
• Positive skewness: Right
side of the curve is longer or
fatter
(Mean>Median>Mode). As
you can see majority of data
is on the right side: Right
skewed)
• Negative skewness: Left
side of the curve is longer or
fatter
(Mean<Median<Mode). As
you can see majority of data
is on left side: Left skewed)

Kurtosis
• Kurtosis is
nothing but
the
tailedness
of the
distribution
.

Distribution of Sample Means
• Samples are vital as we cannot go and measure
the data from large population every time.
• Now, let’s take many random samples from one
population each of size “n”.
• Calculate mean of all the samples taken from that
population.
• Now calculate the mean of all the mean of the
samples.
• That’s exactly what sampling distribution of
sample means is all about.

Distribution of Sample Means (taken
with replacement)
I. Mean will be same as population mean (µ)
II. Standard Deviation of Sample (from mean)
= Standard error of mean
= SD of
population/ 𝑁𝑜. 𝑜𝑓 𝑠𝑎𝑚𝑝𝑙𝑒𝑠
= σ/ 𝒏

Central Limit Theorem
• When sample size “n” increases without limit,
the distribution of sample means approaches
the normal distribution.
• If original population is not normally
distributed, we need n≥30.
• If sample size is less than 30, it must be
already normally distributed.

Z-score
• (Value-Mean)/S.D
• For population:

X− µ
σ
• Hence, for sample means:

𝑿 −µ
σ/ 𝒏

Confidence Interval of 90%, 95% & 99%
• Remember the Critical Value Numbers (two-
tailed tests):
 90%: 1.65
 95%: 1.96
 99%: 2.58

Margin of Error
𝑿- Z (σ/√𝒏) < µ < 𝑿 + Z (σ/√𝒏)
If population standard deviation (σ) is not known, use t v
(standard deviation of sample). In such cases, n-1 would
of freedom. As degree of freedom increases further, t dis
approach normal distribution among many family of curv
degrees of freedom.
• Here, Z (σ/√𝑛) is the margin of error or maximum erro
• Maximum error of estimate (E) = Z (σ/√𝒏)
𝒑𝒒

Minimum Sample Size
n=
Z2 pq
E2 (for proportions)
n =
Z2σ2
E2
The same can also be deduced from the previous formu
of error where,
• E = Z (σ/√𝒏) or Z
𝒑𝒒
𝒏

Null and Alternate Hypothesis
Null: H0: µ=k
Alternate: H1
I. H1: µ ≠ k (two-tailed test)
II. H1: µ > k (right-tailed test)
III. H1: µ < k (left-tailed test)
Null hypothesis Errors:
1) Reject when H0 true: Type I Error
2) Do not reject when H0 not true: Type II Error
Maximum probability of committing Type I Error (rejection of null
hypothesis when it is true) is equal to the level of significance ().
Confidence level = 1-. 1-ß (Type II Error) is the power of the test.

p value
• p value denotes how much of your result can
occur due to chance/sampling error
• If the p value is less than the level of significance
(), the hypothesis test is statistically significant
• In other words, if your p value is less than the ,
then your confidence interval will not contain the
null hypothesis value. Hence you can safely reject
the null hypothesis (value in critical or rejection
region)

Confusion Corner: , Z-scores, Critical Region & Area Under
the Curve
 The first aspect is to consider whether it is left, right or
two-tailed curve we are dealing with. If someone says
you that the critical value for 95% confidence interval is
1.96, it assumes that it is a two tailed test (hence the
notation Z /2 i.e. zee sub alpha over 2).
 When you get  (in this case 0.025 on first point), that
would give the area of the curve that we are concerned
about. By convention, while you search for the nearest
area in the body of z-table, it is area to the left of the
point. Look for corresponding z-scores (critical values).
 Alternatively, if you are given z-scores like in figure
alongside, trace for the area in the table. The first point
at -1.96 gives area 0.0250 (blue shaded area on left) and
the point +1.96 gives area 0.9750 (blue shaded area on
left + non-shaded area in middle).
 The blue shaded area on the right also have area of
0.0250 (its same as the left side only to be on positive
side). If you need area of the middle portion, that would
be 0.9750 - 0.0250 = 0.9500 (95% confidence level on a
two-tailed test with critical region 2.5% on left and 2.5%
on left)

Traditional Z-Test for Hypothesis
Testing
1. State null hypothesis and identify the claim (null or alternate
hypothesis)
2. Find the critical value (Z-value) on table with  given (based
on whether it is left-tailed: critical value corresponding to ,
right-tailed: critical value corresponding to 1-  or two-tailed:
critical value corresponding to /2 and 1- /2 on left and right
side respectively)
3. Compute the test value (Z-value)
4. Compare the critical value(s) and computed value in Step 2 &
Step 3. Make a decision about the location of computed value.
Does the computed value fall in the critical region or not? If it
falls in critical region, reject the null hypothesis. Note that here
we are comparing z-values based on  and based on what we
calculate. We cannot compare the areas as that would be same
for both positive and negative z-values.

P-value Test for Hypothesis Testing
1. State the hypothesis and identify the claim
2. Compute the test value (Z-value)
3. Find the p-value. Find value corresponding to z-value on the table
(area). If this is a left-tailed test, that corresponding value is your p-
value. If this is a right tailed test, you need to find the rightmost area
beyond the point of z value so use 1-corresponding value. If this is a two-
tailed test, your final p-value would be either double the corresponding
value or double of (1-corresponding value) depending on whether your
z-value is negative or positive respectively.
4. Now all you need to do is compare your p-value with the level of
significance (). On a 5% level of significance, reject null hypothesis (the
difference is significant) if p-value<0.05. If p-value is greater than or
equal to 0.05, there is not enough evidence to reject the null hypothesis.

How to state the acceptance and
rejection of claims?
• Claim is Ho (Null hypothesis):
A. Reject Ho: There is enough evidence to reject null hypothesis
B. Do not reject Ho: There is not enough evidence to reject null
hypothesis
• Claim is H1 (Alternate Hypothesis):
A. Reject Ho: There is enough evidence to support alternate
hypothesis
B. Do not reject Ho: There is not enough evidence to support
alternate hypothesis

Concept of Hypothesis Testing
• While you test a hypothesis, never simply say that null
hypothesis is true or false. You do not know that!
• The only thing you know is that based on evidence
provided, there is enough evidence to reject the null
hypothesis or not. To state with 100% certainty
whether that is true or false, whole population needs
to be tested.
• When a null hypothesis is rejected at a level of
significance , the confidence interval computed at 1-
would not contain the value of mean stated by the null
hypothesis and vice versa.

Probability
• Classical probability: all outcomes equally
likely to happen (sample spaces)
• Empirical probability: actual experiments to
determine probability (frequency distribution)
• Conditional probability: The probability that
second event B occurs given that the first
event A has occurred can be found by:
P(B|A) = P(A and B)/P(A)

Fundamental of Counting Rule
I. If repetitions are permitted, the numbers stay the
same going from left to right. For example if a
number of 5 digits is to be selected the total number
of possibilities = 10*10*10*10*10 = 100000
possibilities of selecting a 5 digit number.
II. If repetitions are not permitted, we got one less
choice every time. The numbers decrease by one for
each place left to right. Total number of possibilities
in the above example = 10*9*8*7*6 = 30240
possibilities of selecting a 5 digit number.

Permutation and Combination
• Permutation of ‘n’ objects taking ‘r’ objects at a
specific order):
𝒏 𝑷 𝒓=
𝒏!
𝒏−𝒓 !
• Combination of ‘r’ object selected from ‘n’ objec
nCr =
𝒏!
𝒏−𝒓 !𝒓!
• Hence,nCr = nPr
𝒓!
(r! removes the duplicates whichAnish Dhakal (Aryan)

Mean of random variable with
discrete probability distributions:
µ = X1.P(X1) + X2.P(X2) + ………………………………... +
Xn.P(Xn) = Σ[X.P(X)]
where,
X1, X2……………….Xn are the outcomes
P(X1), P (X2)………P(Xn) are the corresponding
probabilities

Binomial Distribution of Probability
• Condition for binomial probability experiment:
i. Fixed number of trials
ii. Two outcomes or results can be reduced to two outcomes
iii. Outcomes of each trial independent of each other
iv. Probability of success remains the same for each trial
P(x=k) = b(k; n,p) =
𝒏!
𝒏−𝒌 !𝒌!
.pk.qn-k = C(n,k).pk.qn-k
where,
p= probability of success
q= probability of failure
n= number of trials
k= number of success (at x=k) (0≤x≤n)

Multinomial Distribution
P(x)
=
𝒏!
x1!x2!x3!....................xk!
. 𝐩1
x1.p2
x2……….pk
xk
where,
x1,x2,x3…………………..xk are number of occurrence
of events
p1, p2, p3………………..pk are the corresponding
probabilities
x1+x2+x3………………….xk= n (total number ofAnish Dhakal (Aryan)

Poisson Distribution
P(x, λ)=
e−ʎ.ʎx
𝒙!
where,
n: sufficiently large
probability of success: sufficiently small
ʎ= mean number of occurrence per unit time, length
volume
x= number of occurrence of the event
e= 2.7183

Correlation Vs. Regression
• Correlation:
simply determines whether two variables are
correlated and to what extent.
• Regression:
determines nature of relationships, estimate
dependent variable based on independent variable
(functional relationship/projection of events).

Line of Best Fit
• Choose a straight line which best represents the
scatter plot and you have line of best fit.
• Sum of squares from each point to the line is
minimum.
Equation of the line (Regression line equation):
Predicted value (y’)= a+bx
where,
a= y-intercept
x= slope of line
Closer the observed value (y) is to the predicted value
(y’), the better is the fit and the closer ‘r’ is to +1 or -1.Anish Dhakal (Aryan)

Total variation = Explained variation + Unexplained variation
=Σ(y’-y)2 + Σ(y-y’)2
= Σ(y-y)2
y-y’ is the unexplained deviation or residuals. Sum of the square of res
the least possible value gives rise to line of best fit.

Coefficient of determination
• r2=
explained variation
total variation
=
Σ(y’−y)2
Σ(y−y)2
• This is the percentage of total variation
explained by the regression line using the
independent variable.
• 1-r2: coefficient of non-determination: due to
chance

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