2-Cholera-Outbreaks-and-Waterborne-Pathogens-Typhoid-fever (1).pdf

Advanced Microbiology and Parasitology
Case Study Analysis:
Cholera Outbreaks and Waterborne
Pathogens
Typhoid Fever
Destajo, Evan Dwight; Layawon, Dhaniel Marc;
Vergara, Angelita
Presenters
Section C
February 9, 2025

Introduction
Salmonella typhi is a Gram-negative, motile, rod-shaped bacterium that causes typhoid
fever, a serious illness primarily transmitted through contaminated food and water. This
bacterium is strictly adapted to humans and does not typically infect other animals
(Characteristics of Salmonella Typhi Bacteria, n.d.). In the year 2022, the Cordillera
Administrative Region (CAR) reported the highest number of typhoid fever cases, with Benguet
Province being particularly affected. Benguet Province reported 1,196 cases, accounting for
66% of all cases in the Cordillera region (2022-EDCS-Weekly-Surveillance-Report-No-34.pdf,
n.d.). This case study focused on the surveillance and response report from the municipality of
Buguias in the Province of Benguet, Philippines which covered January 1 to October 29, 2022
(Guzman et al., 2024). According to this report from the Buguias Municipal Health Office
Epidemiology and Surveillance Unit (unpublished), Buguias, primarily an agricultural town
known for its production of highland vegetables such as lettuce, cabbage, carrots and broccoli
with a total population of 44,877 as of 2020 (Philippine Statistics Authority, 2021), experienced
an unusual increase in the number of typhoid cases that surpassed the Philippines’ standard
epidemic threshold for several consecutive weeks (Guzman et al., 2024). This outbreak
investigation was conducted to confirm the existence of the outbreak and verify the cases,
identify the source of transmission, and recommend prevention and control measures.
Research Overview
Typhoid fever is a serious bacterial infection caused by Salmonella enterica serotype
Typhi, a Gram-negative, motile, rod-shaped bacterium which is strictly adapted to humans and
does not typically infect other animals. It is a facultative anaerobe, meaning it can survive with
or without oxygen, utilizing aerobic respiration in the presence of oxygen and fermentation in
anaerobic conditions, capable of invading epithelial cells and macrophages. It uses specialized
secretion systems to inject virulence factors into host cells, facilitating infection and evasion of
the immune response (Characteristics of Salmonella Typhi Bacteria, n.d.). Its’ primary route of
transmission is fecal-oral, often through contaminated food and water, making it a significant
public health concern in areas with poor sanitation. After ingestion, S. typhi traverses the
intestinal barrier, adheres to host cells, invades them, and can enter the bloodstream. This
systemic spread leads to the characteristic symptoms of typhoid fever (Typhoid Fever -
Symptoms & Causes - Mayo Clinic, 2023).
According to Newman (2023), the symptoms of typhoid fever typically develop gradually,
usually appearing 1 to 3 weeks after exposure to the bacteria. These include a sustained fever
that can reach up to 104°F (40°C), often rising progressively over several days; gastrointestinal
issues like abdominal pain, diarrhea or constipation, nausea, and loss of appetite; general
illness like headaches, muscle aches, fatigue, chills, and sometimes a cough; and rashes
characterized by flat, rose-colored spots on the abdomen and chest. If untreated, symptoms can

worsen over time, potentially leading to severe complications such as intestinal perforation
(intestinal wall tear) or sepsis (life-threatening condition that occurs when the body’s immune
system overreacts to an infection, leading to widespread inflammation, organ failure, and
potentially death) (Vyas, 2023).
Typhoid fever can be diagnosed through blood cultures, stool tests, and urine culture, or
other laboratory methods that identify S. typhi like serological tests (Widal test), rapid
immunochromatographic test (Typhidot) and rapid test (Tubex test). Early diagnosis is crucial
for effective treatment. The primary treatment for typhoid fever involves antibiotics such as
ciprofloxacin or ceftriaxone. However, antibiotic resistance has become a significant concern,
necessitating susceptibility testing for effective treatment. Patients may also require hydration
and electrolyte management to address fluid loss due to diarrhea and fever. Preventive
measures against this disease include vaccines; practicing of proper hygiene like regular
handwashing, safe food handling, and drinking clean water; and community efforts to enhance
sanitation infrastructure (Sheikh, 2024).
In the case study conducted between 1 January and 29 October 2022, the Philippine
Integrated Disease Surveillance and Response (PIDSR) system reported a total of 9,057 cases
of typhoid fever. PIDSR is the country’s national disease surveillance system established by the
Department of Health (DOH) to detect, monitor, and respond to infectious disease outbreaks
and other public health threats (GSMA & UKAid, 2022). This was a 121% increase in case
numbers relative to the same period in 2021, when 4,102 cases were reported. The Cordillera
Administrative Region reported the highest number of cases, with Benguet Province being
particularly affected. Benguet Province reported 1,196 cases, accounting for 66% of all cases in
the Cordillera region. According to a report from the Buguias Municipal Health Office
Epidemiology and Surveillance Unit (unpublished) in 2022, Buguias, a municipality in Benguet
Province, experienced an unusual increase in the number of typhoid cases that surpassed the
Philippines’ standard epidemic threshold for several consecutive weeks (2022-EDCS-Weekly-
Surveillance-Report-No-34.pdf, n.d.). In the Philippines, the epidemic threshold for typhoid fever
is typically based on surveillance data, using historical disease trends which is a five-year
moving average of reported typhoid cases. This epidemic threshold is the point at which cases
significantly exceed normal levels, indicating an outbreak and could help in detecting outbreaks
early, guide resource allocation, an prevent widespread transmission in communities (UNHCR
Emergency Handbook, 2024).
Buguias, with a total population of 44, 877 (as of 2020), is primarily an agricultural town
known for its production of highland vegetables such as lettuce, cabbage, carrots and broccoli
(Philippine Statistics Authority, 2021). Following a retrospective case review design, medical
records of cases captured by the PIDSR system were obtained from local hospitals and
reviewed to assess whether they met the PIDSR case definition and a slightly modified version
of the PIDSR case definition. The modified version was used in this investigation to avoid
missing cases that do not meet the stricter PIDSR definition, as not all symptoms were captured
in the medical records and most cases could not be interviewed retrospectively. The PIDSR
defined a suspected case as any person with an illness characterized by insidious onset of

sustained fever, headache, malaise, anorexia, relative bradycardia, constipation or diarrhoea,
and non-productive cough. The slightly modified version defined a suspected case as any
resident of Buguias, Benguet who developed symptoms including fever, headache, malaise and
any one or more of anorexia, constipation, diarrhoea, non-productive cough, vomiting,
abdominal pain or dizziness, and who had a positive rapid diagnostic test result (Typhidot or
Tubex) during the specified period (Guzman et al., 2024).
Suspected cases that met the modified case definition were interviewed using a
structured questionnaire designed to collect information about water sources and treatment, as
well as food preparation and storage practices. All cases gave their informed consent for the
interview. In addition, the houses and immediate surroundings of each interviewed case were
inspected and environmental samples (e.g. water, chicken manure, raw beef) were collected for
laboratory testing. The latter was cultured using Salmonella Shigella Agar, a selective and
differential medium for the isolation and enumeration of Salmonella and Shigella by means of
the direct plating method. After inoculation of samples on the agar, plates were incubated for
48–72 hours before screening. Positive cultures showing black centered colonies were
subjected to Phoenix automated identification and antibiotic sensitivity tests to confirm the
presence of bacterial pathogens. A profile of each suspected case was created and encoded in
Microsoft Excel. Key characteristics of cases were summarized using descriptive statistics:
categorical variables (such as sex) were described in terms of proportions, and continuous
variables (such as age) were reported using measures of central tendency and dispersion
(median and range). Weekly case numbers were compared with pre-defined alert and epidemic
thresholds, which were derived from disease incidence data collected over the previous 5 years
and calculated using the standard deviation method (Guzman et al., 2024).
The PIDSR system recorded 220 suspected cases of typhoid fever during the period
January 1 – October 29, 2022 for the municipality of Buguias, of which 208 (94.5%) were
reviewed using medical records to verify the diagnosis. Of the reviewed cases, 178 (85.6%) had
less than four symptoms, and 29 (13.9%) had only one symptom. Only 15 (7.2%) cases met the
modified case definition criteria used in this study, while none met the PIDSR case definition.
Of the 205 discarded cases (i.e. cases that did not meet the case definition criteria), 198 (96.6%)
had a positive serological test result, either through Typhidot (n = 177, 86.3%) or Tubex (n = 21,
10.2%). About half (n = 104, 50.7%) had an additional diagnosis other than typhoid fever such
as acute gastroenteritis (n = 31, 15.1%), respiratory tract infection (n = 30, 14.6%) or dengue (n
= 27, 13.2%). In terms of the symptoms presented, 77 (37.6%) did not manifest fever, while 16
(7.8%) only had fever as a symptom as shown in Table 1.

When the discarded cases were excluded, the number of typhoid cases breached the
alert threshold only once (in morbidity week 23). In comparison, when all 220 recorded cases
were considered, i.e. including the false positives that did not meet the modified case definition,
the epidemic threshold was breached in 15 out of the 43 morbidity weeks covered by this study,
as shown in Figure 1.
Of the 15 verified cases, just over half were male (n = 8, 53.3%). Cases ranged in age
from 14–66 years, with a median age of 31 years. The most common age group was 21–30
years (n = 5, 33.3%). Fourteen verified cases (93.3%) were interviewed. One third of the
interviewed cases were farmers (n = 5, 35.7%); all 14 said that they lived within 50 m of a farm
and 13 reported relying on springs as the main source of their drinking water (92.9%) (Guzman
et al., 2024).

Seven cases (46.7%) reported that, in addition to fever, headache and malaise, they had
experienced non-productive cough; five (33.3%) also experienced dizziness. Among the
interviewed cases, all 14 reported that they normally wash their hands prior to handling food.
Nine (64.3%) said that they sometimes ate raw vegetables. Most reported eating eggs at least
once a month (n = 9, 64.3%), but none ate raw or soft-boiled eggs. Beef and chicken were
seldom consumed by the majority of those interviewed (n = 13, 92.9%); only one person
consumed beef and chicken regularly and none consumed raw meat. All 14 interviewed cases
reported always seeing houseflies in their houses and self-reported that flies frequently land on
their food (Guzman et al., 2024).
According to the sanitary inspector, springs are the main source of water for many
households living in and around Buguias. It is also the most common source of drinking water
among farming communities. However, spring water is not always treated before use by some
of the population as they believe it is clean and safe to drink. The sanitary inspector identified
chicken manure as a possible source of water contamination, noting that compliance with an
ordinance mandating that farmers who use chicken manure keep it in a storage area is not
currently being adequately monitored. Across the municipality, chicken manure is widely used
as a fertilizer by farmers and thus flies are commonplace. Locally reared livestock products
(beef, chicken and pork) are sold within the community, typically from open, uncovered displays,
upon which flies are free to land (Guzman et al., 2024).
Of the 12 water samples that were taken from domestic taps and water storage tanks
and tested, two showed the presence of black colony formation. One out of six chicken manure
samples showed the presence of black colony formation. One sample of raw beef taken from a
beef store also showed the presence of black colony formation. Black colonies from a sample of
chicken manure fertilizer were subjected to a confirmatory culture and sensitivity test and tested
positive for Leminorella grimontii. No Salmonella species were detected. Confirmatory testing
was negative for all other samples with black colony formation (Guzman et al., 2024).
Analysis and Evaluation
Although 220 suspected cases of typhoid fever were reported in the municipality of
Buguias, Benguet between January and October 2022, this investigation showed that most of
them did not meet the modified case definition. Moreover, the pattern of case reporting revealed
that the disease reporting units relied heavily on the diagnosis recorded in the medical chart and
the results of Typhidot and Tubex rapid diagnostic testing. While Typhidot is a sensitive test for
early diagnosis of typhoid fever, it has low specificity just like the Widal test, and positive results
should be correlated with the clinical picture and other possible diagnoses (Guzman et al.,
2024). Tubex has its own share of limitations like inability to differentiate recent and active
infections (since IgM may persist for weeks). It may also cross react with other bacteria with
similar O – antigens (e.g. Salmonella enteritidis) and is less effective in late – stage typhoid
fever (Khanna et al., 2015). Nithya et al. (2022) demonstrated in their study that cross-reactivity
with other diseases can also cause false positive results in some cases. After verifying the

reported diagnoses, it was found out that the number of cases was aligned with historical
surveillance data and that typhoid cases had been overreported and the increase in case
numbers in 2022 represented a pseudo-outbreak.
Although the number of verified cases was above the alert threshold in morbidity week,
this increase is not inconsistent with, and generally follows, the endemic pattern. Routine
surveillance has shown that there has been steady but low-level transmission of typhoid fever
over a 5-year period and that known sources of transmission, including houseflies (Barreiro et
al., 2013) and consumption of untreated drinking water (Farooqui et al., n.d.), are likely present
in the municipality. It is notable that all the verified cases self-reported a constant presence of
houseflies in their houses, and that their food was frequently exposed to flies. While this implies
that the opportunity for flies to transmit the bacteria that cause typhoid fever does indeed exist in
this community, the findings do not prove a causal relationship between houseflies and typhoid
fever (Guzman et al., 2024).
This investigation also revealed that a high proportion of the verified cases relied on
untreated spring water as their main source of drinking water. The use of unsafe drinking water
has been linked to an increased rate of typhoid fever (Barreiro et al., 2013), and may be another
possible contributory factor for disease transmission in the municipality. This observation
highlights the need for proper water treatment and quality checks to ensure that the water
supply is safe for consumption and to prevent the spread of waterborne diseases including
typhoid.
Since doing confirmatory laboratory tests during clinical encounters is not included in the
normal practice in the Philippines, this study's primary weakness is its lack of such tests.
Another main concern is the reporting of false positives, causing public panic and
misinformation, loss of public trust, and psychological impact to patients. This could be
addressed through adherence to PIDSR protocols by training of surveillance officers, regular
evaluations of the surveillance system, and proper follow – up testing that are more sensitive
than the available rapid tests like bone marrow culture, PCR – based diagnostics (Bandhari et
al., 2024), and modified tests like Typhidot M. Bone marrow culture is the most sensitive method
for diagnosing typhoid fever. It involves collecting a small amount of bone marrow fluid from the
patient and culturing it to detect the presence of Salmonella typhi. It is more reliable than blood
culture (90 – 95% sensitivity), detects low bacterial load, and useful for long – term carriers
(Wain et al., 2001). PCR is a molecular diagnostic test used to detect Salmonella typhi DNA in
a patient's blood, stool, or urine. Bacterial DNA is first extracted from the sample and then the
DNA is amplified using specific S. typhi primers. The amplified DNA is visualized using gel
electrophoresis or real-time PCR (qPCR). Positive result is the detection of S. typhi DNA,
available within 3–5 hours (Facellitate, 2024). Typhidot M is a modified version of the Typhidot
test but specifically focuses on early detection of acute typhoid infection. Here, the serum is
placed on a test strip coated with S. typhi antigen and after 1 – 3 hours, positive results are
shown through the presence of antibodies (Beig et al., 2010). The most common concerns with
these tests are the costs and availability.
Current strategies in the country also include vaccination through typhoid conjugate

vaccines and targeted vaccination (World Health Organization: WHO, 2023), and water
treatment through boiling and chlorination (What Is Typhoid Fever?, n.d.). According to
Capeding et al. (2019), clinical trials have demonstrated the safety and immunogenicity of the
typhoid conjugate vaccines. For instance, a Phase II study conducted in Muntinlupa City,
Philippines, reported that all participants aged 6–23 months seroconverted after a single dose of
the Vi-DT vaccine, indicating a strong immune response. As of the latest available data, the
Philippines has not yet incorporated TCVs into its national immunization program. Given the
country's high incidence of typhoid fever, especially among vulnerable populations, adopting
TCVs could significantly reduce disease burden (World Health Organization: WHO, 2023).
Studies also indicate that boiling water reduces bacterial contamination by 99.9% and chlorine
effectively kills S. typhi in drinking water. Households using boiled or chlorinated water had
significantly lower infection rates compared to those relying on untreated water sources in
typhoid – endemic areas (Disaster Response Operations Management, Information and
Communication & Department of Social Welfare and Development, 2022), highlighting its
effectiveness.
Public health campaigns also emphasize food safety by avoiding street food, eating only
hot foods, peeling fruits personally, and avoiding raw vegetables unless properly washed
(Newman, 2023). Cooking food at temperatures above 70°C (158°F) kills S. typhi as households
following safe food preparation practices had significantly fewer cases (Bhandari et al., 2024).
Local governments distribute antibiotics, additional test kits, and chlorine granules as part of
initial responses (Disaster Response Operations Management, Information and Communication
& Department of Social Welfare and Development, 2022), and as always, community education
on hygiene practices is prioritized alongside vaccination efforts. As antibiotic resistance
becomes more prevalent globally, ongoing focus on preventive measures like better sanitation
facilities will be crucial to effectively control this disease among communities with risk (Newman,
2023).
Conclusion
This case study presented that most cases in Buguias, Benguet from the report done
last January 1 – October 29, 2022 were caused by the pseudo-outbreak of Typhoid fever since
most suspected cases did not meet the case definition criteria.
The main limitation of this study is the lack of confirmatory laboratory tests, as it is not
the standard to carry out these tests during clinical encounters in the Philippines, and could not
be conducted retrospectively. However, based on the clinical presentation of the suspected
cases and the epidemiological context, it was believed that the 205 cases that were excluded
were likely false positives.
Reporting false positive cases can also result in false outbreaks being declared and the
misallocation of resources to unnecessary response efforts. To prevent this, it is crucial for our
government to avail the proper confirmatory tests, enhance adherence to PIDSR protocols by

providing disease surveillance officers with training in case assessment to ensure cases meet
the case definition before they are included in the surveillance system report and by conducting
regular evaluations of the surveillance system. Given the apparent reliance on rapid diagnostic
test results for typhoid, it is also recommended that diagnostic algorithms be used with clinical
judgement and appropriate follow-up testing to ensure that fewer false positives are reported by
the PIDSR system. Finally, this study emphasizes the need to improve typhoid guidelines with
regards to diagnosis using rapid diagnostic tests and to investigate the cost-effectiveness of
making confirmatory laboratory tests for typhoid available in the Philippines.

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