The Bulletin of the Sri Lanka College of Microbiologists
The Bulletin of the Sri Lanka College of Microbiologists is the annual publication of the Sri Lanka College of Microbiologists issued along with the Annual Scientific Sessions of the College. The Bulletin includes the summaries of the speeches/lectures/symposia and abstracts of oral/ poster presentations to be made during the Annual Scientific Sessions in addition to reviews, research articles and case reports relevant to microbiology and infectious diseases sent by the membership. The aims of the bulletin are to encourage the membership to conduct and publish good quality research to support and improve the practice of microbiology in Sri Lanka and to share experiences to enrich and upgrade the professional standards.
PP21 - Demographic and Clinical Features of Leptospirosis Among Febrile Patients Admitted to the District General Hospital, Kilinochchi
Introduction Leptospirosis, a zoonotic disease caused by spirochetes, remains a significant public health concern in developing countries, presenting with a wide spectrum of symptoms ranging from mild illness to severe, life-threatening complications. Objectives This study aimed to detect anti-Leptospira IgM using an ELISA kit and describe the demographic and clinical characteristics of leptospirosis among clinically suspected patients admitted to the District General Hospital, Kilinochchi. Design, Setting, and Methods A hospital- and laboratory-based descriptive, cross-sectional study was conducted from July to September 2022 among clinically suspected leptospirosis patients admitted to the District General Hospital, Kilinochchi. Blood samples (3 mL) were collected, and demographic, clinical, and risk factors were obtained using an interviewer-administered questionnaire. Ethical clearance was obtained from the Faculty of Medicine at the University of Jaffna. Serum samples were tested for anti-Leptospira IgM using an ELISA kit (Abbexa, UK). Results A total of 66 patients with suspected leptospirosis were recruited, predominantly males (80.3%; n = 53), with the highest representation in the 26–35 (25.8%; n = 17) and 36–45 (21.2%; n = 14) year age groups. Among them, 11 (16.7%) tested positive for anti-Leptospira IgM by ELISA, including eight males (72.7%). All seropositive cases were from rural areas, had a history of animal contact, and responded to doxycycline. Fever and headache were present in all cases (100%; n = 11), followed by myalgia (90.9%; n = 10), jaundice (45.5%; n = 5), conjunctival suffusion (45.5%; n = 5), and shaking chills (36.4%; n = 4). Only 66.7% (n = 44) had a fever lasting 5 days or longer. Conclusions IgM ELISA detected leptospirosis only in 16.7% of clinically suspected cases. Limitations of this study include the fact that the gold standard, MAT, was not performed to confirm the suspected cases, and the low sensitivity of IgM ELISA for detecting leptospira, which varies depending on the serovars included in the ELISA kit.
Copyright (c) 2025 The Bulletin of the Sri Lanka College of Microbiologists 2025
PP1 - Bacterial pathogens & their antibiotic susceptibility pattern of community-acquired bacteremia in adult diabetic patients at a Base Hospital in Gampaha District Sri Lanka
Introduction Poorly controlled diabetes increases the risk of bacteremia and sepsis, causing high morbidity and mortality if untreated. Antibiotic resistance varies geographically, making it essential to understand local susceptibility patterns for effective patient care. Objectives To assess the causative bacterial pathogens, antibiotic susceptibility, and related 30-day mortality in community-acquired bacteremia in adult diabetic patients at a base hospital (BH) in Gampaha District, Sri Lanka. Methodology A hospital-based, prospective, descriptive, cross-sectional study was conducted at BH Wathupitiwala from November 21, 2022, to March 20, 2023. Blood cultures were collected from all adult diabetic patients admitted to medical and surgical wards with suspected or documented infections who met qSOFA criteria within 48 hours of hospital admission and before starting antibiotics. Data were gathered using an interviewer-administered questionnaire and structured record sheets. Blood cultures were processed manually or using the BACT/ALERT automated system. Identification and antibiotic susceptibility testing were done according to standard operating procedures for positive cultures. Data analysis was performed using SPSS version 26. Results Among 129 eligible patients, 28 (21.7%) had significant positive blood cultures. Blood cultures that did not yield a positive result after 5 days of incubation were considered negative (n=101). The most common pathogens were Enterobacterales (n = 20, 71%) and Staphylococcus aureus (n = 6, 21.4%). The main focus was urinary tract infections (n=19, 67.8%), followed by skin and soft tissue infections (n=7, 25%) and respiratory infections (n=7, 25%). A significant association between blood culture positivity among diabetic patients with UTI was noted (OR:3.8; 95% CI: 1.56 – 9.29; p=.002). Extended-spectrum beta-lactamases (ESBL) producers comprised (n=9)45% of Enterobacterales. All Enterobacterales were 100% sensitive to carbapenems and amikacin. All S. aureus isolates, including MRSA (n=4,11%), were 100% sensitive to vancomycin, teicoplanin, and linezolid. The 30-day mortality rate among diabetic bacteremia patients was 28.5%. (n=8). Conclusion Among the studied adult diabetic patients, community-acquired bacteremia was predominantly caused by Enterobacterales, with urinary tract infection identified as the primary source. A notably high rate of ESBL-producing Enterobacterales was observed. The 30-day mortality was 28.5%. Prompt initiation of effective antibiotics after blood culture collection in suspected sepsis patients is crucial.
Invasive Salmonella Saintpaul Infection in an Immunocompromised Adult: Unusual Presentation Following a Suspected Snake Bite.munocompromised Patient: A Case of Salmonella Saintpaul bacteraemia
Introduction Non-typhoidal Salmonella (NTS) infections are typically foodborne and cause self-limiting gastroenteritis. However, in immunocompromised individuals, these infections can become invasive and life-threatening. We describe a case of Salmonella Saintpaul bacteremia in an immunocompromised patient who developed septic shock following a suspected snake bite. Salmonella Saintpaul is a serotype of Salmonella enterica subsp. enterica, and while it is most often linked to contaminated food, reptiles are recognized as potential reservoirs. of the disease (1, 2) Although a clear causal relationship between the snake bite and subsequent infection cannot be firmly established, the temporal sequence raises the possibility of reptile-associated transmission. However, given the epidemiology of NTS, a foodborne source remains equally plausible. This case highlights the diagnostic uncertainty that can arise in complex presentations and emphasizes the importance of considering both common and uncommon transmission routes in immunocompromised patients presenting with sepsis. Case Report A 53-year-old male who was diagnosed with type 2 diabetes mellitus, hypertension, and autoimmune hepatitis and was on mycophenolate mofetil and prednisolone (>20 mg/day for 3 weeks) presented to Colombo North Teaching Hospital (CNTH) with a history of loose stools (5 episodes), vomiting, abdominal pain, and drowsiness. He was treated at a local hospital five days before for an unknown snake bite on the dorsum of his right thumb and discharged with analgesics and oral co-amoxiclav. He neither had a history of outdoor food consumption nor contact with diarrhoeal disease. On admission, the GCS was 14/15, the pulse rate was greater than 100 bpm, blood pressure was 84/52 mmHg, respiratory rate was 20 breaths per minute, and saturation on air was 97%. He was afebrile, and Figure 01 displays the patient's fever chart during hospitalization. There were bilateral coarse crepitations on auscultation. Initial laboratory findings revealed leucocytosis and elevated inflammatory markers, while blood culture confirmed the presence of an invasive Salmonella Saintpaul. The isolate was identified through biochemical and agglutination testing at CNTH, followed by serotyping at the National Reference Laboratory. In the ward, he was initially managed for hepatic encephalopathy and lower respiratory tract infection with intravenous ceftriaxone. As he did not improve, ICU care was given for a duration of 5 days (Figure 1 and Figure 2). Due to clinical deterioration, antibiotics were escalated to IV meropenem and azithromycin. Despite early administration of appropriate antibiotic therapy and supportive care, the patient succumbed to death on the 8th day of hospital admission. Table 01 depicts the patient's investigation summary, as shown below. Day 1 WBC-11.7x103/µL Total bilirubin-94.6µmol/L Neutrophil- 9.27 x103/µL Direct bilirubin- 62.5 µmol/L C-reactive protein- 202mg/L Serum creatinine- 120 µmol/L Urine full report-Normal Chest X-ray - Figure 02 illustrates the chest X-ray with bilateral acute inflammatory changes and probable bronchopneumonia. Day 3 ESR-49mm/1st hour C-reactive protein- 178.7mg/L Serum amylase 591 U /L Blood culture – Isolate was identified as Salmonella spp. at the CNTH by biochemicals and agglutination test and confirmed as Salmonella Saintpaul by serotyping at the National Reference Laboratory. Stool culture- Salmonella not isolated Ultrasound scan KUB – unremarkable Day 6 WBC-10.42x103/µL INR- 2.44 Neutrophil- 7.19 x103/µL Platelets- 54 x103/µL Sputum Xpert MTB/RIF- Negative Day08 C-reactive protein- 110mg/L Serum creatinine- 116µmol/L Table 01: Investigation summary of the patient. Figure :01 Fever chart during the hospital admission Figure:02 Chest X-ray Discussion Salmonella Saintpaul typically causes gastroenteritis and is commonly associated with foodborne outbreaks, but in rare cases, it can lead to invasive infections, including bacteremia and sepsis. Salmonella Saintpaul sepsis is an uncommon but serious manifestation of infection. It primarily affects elderly and immunocompromised individuals. Invasive forms of Salmonella infection could be associated with high morbidity and require prompt intervention. Symptoms of Salmonella Saintpaul sepsis is non-specific, often resembling other bacterial infections; hence, blood culture remains the gold standard for diagnosing bacteraemia, though isolation of Salmonella from other sterile sites or stool can also confirm the infection. Salmonella is recognized as a part of the normal reptile gut microbiota, and the majority of Salmonella strains identified in reptiles belong to Salmonella enterica subspecies 1, followed by subspecies 111b and subspecies 11 (1,3). Even though the definitive causal relationship between reptile exposure and the infection could not be conclusively established, the temporal association and the known zoonotic potential of reptiles as reservoirs for Salmonella species strongly suggest a plausible link. Reptile-associated salmonellosis (RAS) has been well-documented, particularly in children and immunocompromised adults. Salmonella Saintpaul has been reported as one of the serotypes isolated from reptiles, including geckos, lizards, and other exotic pets (1, 4). However, in Sri Lanka, no literature is found related to RAS. Most often, supportive therapy is the main treatment for salmonella infections. However, severe or immunocompromised cases may need antibiotics. Recommended antibiotics include third-generation cephalosporins (e.g., ceftriaxone), quinolones (e.g., ciprofloxacin, levofloxacin), and macrolides. Unfortunately, rising bacterial resistance, especially for the quinolone group, has rendered treatment more challenging (2, 5). Conclusion This case highlights the importance of considering Salmonella species as potential causes of sepsis, especially in high-risk patients with recent exposure to reptiles. RAS cases can resemble other forms of salmonellosis, making the link to reptiles go unperceived. Therefore, it is important to inquire about any contact with reptiles in Salmonellosis. Management of Salmonella Saintpaul sepsis involves prompt administration of appropriate antibiotics, as guided by antibiotic susceptibility testing. Common first-line antibiotics for invasive Salmonella infections in our setting include ceftriaxone and azithromycin.
CP3 - Generalized tetanus following a deep foot njury: A Case report
Introduction Tetanus is a life-threatening but vaccine-preventable disease caused by the neurotoxin of Clostridium tetani. Despite global eradication efforts, sporadic cases still occur, particularly in areas with incomplete immunization coverage. Case Report We report a case of generalized tetanus in a previously healthy 48-year-old male who sustained a deep puncture wound to his right foot while working in a field contaminated with goat excreta. He received wound care and a dose of tetanus toxoid at a peripheral hospital, and there was no documentation of prior tetanus immunization. Three days post-injury, he developed trismus, generalized muscle rigidity, risus sardonicus, and painful spasms. On admission, he was treated with intravenous metronidazole and tetanus immune globulin (TIG) and received intensive care, including sedation, muscle relaxants, and magnesium sulfate for autonomic instability. Wound debridement was also performed. Despite the severity of symptoms, mechanical ventilation was not required. The patient gradually improved and underwent physiotherapy, completing a full course of tetanus vaccination prior to discharge. Discussion This case underscores the importance of thorough wound assessment and proper post-exposure prophylaxis, particularly in adults with unknown vaccination status. Conclusion: Prevention through vaccination, timely prophylaxis, appropriate wound management, and increased awareness among healthcare providers are critical to reducing the morbidity and mortality associated with tetanus.
PP22 -Genomic surveillance and prevalence of RSV in children under three years of age : preliminary data of WHO RSV pilot project phase III
Introduction Respiratory syncytial virus(RSV) causes significant morbidity and mortality in children. WHO has extended global RSV surveillance in children under 2 years of age to elucidate the disease burden. Genetic clades circulating in Sri Lanka have not been reported, which is important for surveillance and vaccine introduction initiatives. Objectives To determine the observed prevalence of RSV, circulating subtypes, and genetic diversity and to assess the association between demographic details and clinical symptoms with laboratory results. Design, setting, and methods A retrospective study was conducted with selected samples sent between July 2024 and February 2025 from in-ward children under 3 years of age having acute respiratory infections. The fusion (F) gene, attachment glycoprotein (G) gene, and whole genome of the positive samples were sequenced, and Nextclade software was used to determine the clades. Results Forty samples were tested using the Altona RSV PCR assay 55.6% of whom were from males and 16 (40%) tested positive for RSV, with 07(43.8%) for RSV A and 09(56.2%) for RSV B. Age groups included: birth to 6 months (56%), 7 to 12 months (24%), 13 to 18 months (0%), 19 to 24 months (12.5%), and more than 24 months (6.5%). Two newborns from the ICU and a deceased 3-year-old tested positive for RSV A. Only three (03) RSV A samples yielded successful sequences, and all of them were Clade A.D.3, and G clade was GA2.3.5. All RSV B samples did not yield productive sequencing data. Conclusions Respiratory syncytial virus showed a high prevalence; RSV A and RSV B were equally distributed in this cohort. Only a few samples yielded sequences that did not convey meaningful diversity. Further surveillance with a larger cohort is needed to elucidate disease burden and genetic diversity. This is the first report of RSV clades in Sri Lanka.
PP18 -Comparison of conventional manual blood culture bottle with in-house prepared biphasic blood culture bottle for the isolation of bacteria
Introduction Blood cultures, which enable the accurate identification of the pathogen, are the gold standard method for diagnosing septicemia. Although automated methods are available to process blood cultures, modified manual blood culture bottles (BCs) are still necessary in low-resource settings. Objectives To develop a biphasic blood culture bottle and compare it with a conventional manual blood culture bottle using simulated blood samples inoculated with selected bacteria. Design,s etting,s and Methods Biphasic blood culture bottles (BCB) were prepared using Brain Heart Infusion (BHI) agar slant and the BHI broth. The volume of agar and the slanting angle were newly optimized using 8 mL of agar and broth, and the mixture was kept at an angle of 6º for 15 minutes until solidification. Conventional blood culture bottles (CBC) were used as the control. Simulated blood samples were prepared as neat, 1/10 and 1/20 compared to McFarland turbidity by inoculating the blood samples with Pseudomonas aeruginosa (ATCC 27853), Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 25923) as pure and mixed (1:1 ratio) inoculums. Simulated samples were inoculated into BCs and incubated at 37°C overnight. The slants of BCB were tilted once a day. Colonies of the subcultured positive broths were counted using the pour plate method and manually on the slant. Appearance was compared using the Gram staining. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated. Data were analyzed using Statistical Package for the Social Sciences version 26. Results There was no significant difference in colony counts of S.aureus and mixed broth of S.aureus and E.coli between CBC and BCB. All Gram stain appearances in BCB were similar to those of CBC. The sensitivity, specificity, positive predictive value, and negative predictive value of the BCB are 93.75%, 96.875%, 96.77%, and 3.23%, respectively. Isolated colonies were recovered using a slant one day earlier in BCB. Conclusion BCB could be used to identify blood pathogens S.aureus, P.aeruginosa, and mixed cultures of S.aureus and E.coli with a reduced turnaround time compared to the CBC.
PP14 -Patient demographics and the varying clinical presentation of invasive salmonellosis with positive blood cultures: An analysis of a decade-long database
Introduction Salmonella is an enteric pathogen that causes both intestinal and extraintestinal disease, ranging from self-limiting gastroenteritis to invasive disease complicated with empyema, abscess, or other serious illnesses. Objectives To assess patient demography and to determine the clinical presentations, risk factors, and laboratory parameters in blood culture (BC) positive salmonellosis. Design, setting, and methods Anonymized data from 97 reference laboratory confirmed Salmonella blood culture-positive patients from December 2014 to February 2025 were accessed retrospectively and analyzed. Fisher's exact test was used to determine any statistical association between variables, and a p-value of less than 0.05 was taken as significant. Results The majority were females (52, 54%), and 22 (23%) were <5 years, while 30 (31%) were >60 years. Clinical presentation varied from acute gastroenteritis (28) to intra-abdominal infections (22) and severe sepsis requiring inotrops on admission (25). There were 14 enteric fever patients whose blood cultures were positive for S. Typhi (12) or S. Paratyphi (2). Other non-typhoidal entities were pyelonephritis (4), meningitis (2), septic arthritis (2), splenic abscess (2), and pleural effusion (1). Risk factors like cirrhosis, steroid use, chronic kidney disease, or chemotherapy were found in 50 (51%), but no statistical significance was found with any. Most BCs became positive within 18 hours (65), and 7 took more than 48 hours. All salmonellae were sensitive to ceftriaxone, while 25% were resistant to ciprofloxacin (58% Typhi, 100% Paratyphi A, and 18% non-typhoidal). The majority of patients had leukocytosis (49%), with neutrophil predominance (73%), while 39% had counts within the normal range, and 17% had counts below normal. Additionally, 36% had normal or marginally elevated CRP levels. No statistically significant association was found between intestinal or extraintestinal disease and ciprofloxacin resistance. Mortality within 24 hours was recorded in 6/97 (6%), all of which were by non-typhoidal species. Conclusions Invasive salmonellosis can occur in any age group, but it predominantly affects extremes, with varying clinical presentations. Patients can have normal or near-normal leukocyte counts and CRP levels even with a positive BC. Patients with risk factors may be more prone to get invasive disease.
PP8 -Viral and atypical bacterial Etiology of community-acquired respiratory infections in children at two tertiary care hospitals in Peradeniya
Introduction Acute respiratory tract infections (ARTIs) in children impose a significant healthcare burden worldwide. Despite the availability of international data on the etiology of pediatric ARTIs, there is a lack of information on the pathogens causing these conditions in Sri Lanka, necessitating this study. Objective To analyze viral and atypical bacterial etiology of ARTIs among pediatric patients in two tertiary care hospitals in Peradeniya. Design, setting, and methods A prospective descriptive study was conducted in two tertiary care hospitals in Peradeniya. Multiplex PCR testing was conducted on nasopharyngeal swabs (NPS) from 75 randomly selected subjects with acute respiratory tract infections to detect 20 viruses and four atypical bacteria. Additionally, all 75 NPS were processed utilizing SARS-CoV-2 RT-PCR assay. Data analysis was performed using IBM SPSS Statistics 25.0. Descriptive statistics summarized the dataset, with mean ± SD for normally distributed continuous variables. Categorical variables were compared using the Pearson Chi-squared test, with statistical significance set at p < 0.05. Results To analyze the viral and atypical bacterial pathogens as the etiology of ARTIs, a cohort of 523 patients admitted to the hospital was studied. Among them, 445 (85%) presented with respiratory symptoms, and 73.4% (384/523) of those with symptoms were diagnosed with ARTIs. Of the 75 samples tested systematically, 82.6% (62/75) were positive for at least one viral pathogen. Of these, 85.4% (53/62) exhibited the presence of a single viral pathogen, while 14.5% (9/62) demonstrated the presence of dual viral pathogens. None of the samples tested positive for the atypical bacterial pathogens. The most commonly detected viral group was influenza (19/62, 30.6%), followed by the human parainfluenza virus (HPIV) group (14/62, 22.5%) and Respiratory syncytial virus (RSV) group (12/62, 19.3%). Among pneumonia patients, influenza viruses were the most commonly detected (12 out of 25, 48%). RSV was frequently detected among patients diagnosed with bronchiolitis, followed by HPIV. The study revealed no significant differences in PCR positivity and the number of viruses detected, regardless of demographic and clinical parameters. Conclusion Acute respiratory infections, predominantly viral, accounted for the majority of admissions.
PP9 -Audit of peripheral intravenous cannula (PIVC) site maintenance practices and PIVC associated phlebitis occurrence at selected government hospitals in Sri Lanka.
Introduction Peripheral intravenous catheters (PIVCs) are the most used invasive medical devices in hospitals. Peripheral intravenous cannula site phlebitis is one of the healthcare-associated infections that can be prevented by correct cannula insertion and maintenance practices. Objectives The study was designed to assess the PIVC site maintenance practices and associated phlebitis occurrence at selected government hospitals in Sri Lanka. Design, setting, and methods The audit was conducted among patients at five hospitals: District General Hospital Avissawella, Teaching Hospital Batticaloa, District General Hospital Embilipitiya, Teaching Hospital Polonnaruwa, and Base Hospital Puttalam, from February 2025 over a period of five days. All patients in the ward at the time of the audit were included, excluding those sent in for referrals and investigations. Data on the number of patients who were cannulated, number of cannulas with written inserted date, number of dates from the insertion of a cannula, number of well-kept cannulas (cleaned, well attached), number of the cannulas with signs of cannula site infection (pain, erythema, swelling, warmth, tenderness) and number of cannula sites with features of infection once removed, were collected using a paper-based worksheet. Results Of the 2,556 patients audited, 77.07% (n = 1,970) were cannulated at the time of the audit. Out of 1999 cannulas (from 1970 patients), 81.69% of PIVCs (n = 1633) were dated, and 88.04% (n = 1760) were well-maintained. Of the dated cannulas, 11.70% (n = 191) were kept for more than three days. There were 4 in situ cannulas with signs of cannula site infection, and 151 (7.66%) patients had cannula sites with signs of phlebitis. Conclusion PIVC use among the study population is noted to be high. While documentation of insertion dates was good, 11.70% of cannulas remained in situ for more than three days, potentially increasing the risk of complications. Maintenance practices varied across hospitals, although the overall percentage of well-maintained cannulas was high. The results highlight the need for standardized PIVC maintenance protocols to improve patient safety.
A Comparative Analysis of CLSI and EUCAST Interpretations of Intermediate Antimicrobial Susceptibility: Navigating the Gray Zone
Antimicrobial susceptibility testing (AST) is fundamental to the effective management of infectious diseases. Accurate interpretation of AST results guides clinicians in selecting appropriate antimicrobial agents and optimizing dosing regimens. Central to this process are the interpretive categories assigned to antimicrobial-organism combinations, which translate in vitro data into clinically relevant predictions of therapeutic success. However, the interpretation of intermediate susceptibility, particularly concerning the concepts of "Susceptible, Dose-Dependent" (SDD) employed by the Clinical and Laboratory Standards Institute (CLSI) and "Susceptible, Increased Exposure" favored by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), has been a source of ongoing debate and refinement within clinical microbiology. This essay presents a comparative analysis of these two interpretive approaches, exploring their historical context, underlying principles, clinical implications, and the ongoing evolution of AST interpretation.
Enhancing Safety in Antibiotic Administration: Avoiding Anaphylaxis and Medication Errors
Abstract Patient safety, “first, do no harm” should be the most vital goal of any healthcare service. The harm that is caused by unsafe medication practices and medication errors should be avoided or minimized by improving knowledge and awareness. Antibiotics are one of the most commonly over-prescribed and irrationally used medicines, particularly in low and middle income countries (LMIs). Therefore, errors in prescription and administration could have a significant impact on patient outcomes and healthcare costs. Allergies and anaphylaxis are off target adverse drug reactions that occur with any antibiotic, more commonly reported with beta-lactams. Frequently, patients are loosely labeled as having an “antibiotic allergy”. Most are “erroneous labels” which are rarely evaluated or questioned in clinical practice. On the other hand, any patient who is prescribed an antibiotic could develop a severe allergic reaction at any given time, which should be managed appropriately. In view of the recent events with increased number of reported cases of anaphylaxis associated fatalities due to antibiotics in the country and to ensure patient safety when administering antibiotics, this review aims at identifying effective interventions to avoid or reduce medication errors and fatalities associated with severe allergic reactions when administering antibiotics.
Artificial intelligence in medical microbiology: revolutionizing diagnostics and beyond: A brief review
Artificial intelligence (AI) is rapidly transforming various fields, and medical microbiology is no exception. This review explores the current applications of AI in medical microbiology, including its role in diagnostics, drug discovery, and public health management. AI has the potential to enhance the efficiency, accuracy, and speed of microbiological testing, ultimately leading to improved patient outcomes. However, problems related to data quality, algorithm interpretability, and clinical integration must be acknowledged and dealt with for widespread implementation.
CP4 -Non-typhoidal salmonella meningitis in an infant: A case report
Introduction Non-typhoidal Salmonella (NTS) typically causes gastroenteritis but rarely leads to invasive disease, including meningitis. We report a case of NTS meningitis in a 5-month-old female infant caused by Salmonella paratyphi B var Java, highlighting the importance of microbiological diagnosis and antimicrobial susceptibility testing in clinical management. Case Report A previously healthy 5-month-old girl presented with one day of fever followed by focal convulsions and three days of profuse diarrhea. Her mother and sibling had concurrent diarrheal illness, and there was a recent history of flooding in their residential area. Despite exclusive breastfeeding, the infant received supplementary boiled water via spoon daily. Initial examination revealed fever and irritability with normal hydration status. Laboratory investigations showed leukocytosis (WBC 20,000/μL with 82% neutrophils) and elevated C-reactive protein (154 mg/dL). Lumbar puncture findings were consistent with partially treated bacterial meningitis, including elevated CSF protein (339 mg/dL), pleocytosis (50 polymorphs/mm³, 240 lymphocytes/mm³), and low CSF glucose (22 mg/dL). Blood culture yielded Salmonella paratyphi B var. Java, which was susceptible to multiple antibiotics, including cefotaxime, but showed intermediate susceptibility to ciprofloxacin. CSF culture remained sterile, and stool culture was negative for Salmonella. Following initial empiric treatment with cefotaxime, therapy was briefly escalated to meropenem due to persistent fevers but later de-escalated back to cefotaxime based on susceptibility results. The patient completed a 21-day course of antibiotics with significant clinical improvement and normalization of CSF parameters. Discussion This case highlights the importance of considering NTS in the differential diagnosis of bacterial meningitis in infants, particularly in developing regions with poor sanitation or following environmental contamination events, such as flooding. The successful outcome underscores the value of blood cultures prior to antibiotic initiation, appropriate antibiotic selection based on susceptibility testing, and extended treatment courses for invasive NTS infections. Public health measures, including improved sanitation and exclusive breastfeeding without supplementary water in young infants, are crucial preventive strategies against this potentially devastating infection
Meningitis and renal abscess by Streptococcus chicken group D; 2 case reports
Introduction Enterococcus gallinarum, nicknamed Streptococcus chicken group D, is a motile, Gram-positive facultative anaerobic bacterium that is rarely found in human clinical specimens but frequently encountered in the gastrointestinal tract in poultry. It is an opportunistic pathogen which causes infections in humans rarely. These infections present a significant therapeutic challenge due to their intrinsic resistance to vancomycin and other antibiotics typically used to treat Enterococcus infections. These two case reports aim to contribute to the limited literature on this pathogen in the causation of meningitis and renal abscesses. Case report 1 A two-month-old baby boy with a history of mild left ventricular dilatation, possibly secondary to evolving cardiomyopathy combined with a stormy postnatal period, presented with a fever for two days with poor weight gain. The baby was febrile, tachycardic, and tachypneic but maintained saturation. He was active and alert without nuchal rigidity. Laboratory investigations on admission revealed a neutrophilic leukocytosis, anemia, and CRP of 292mg/dL. The CSF full report revealed an elevated polymorph count, with significantly low glucose and high protein levels. An ultrasound scan (USS) of the abdomen showed a possibility of a right-sided renal lump. Further investigations revealed persistently elevated inflammatory markers. Both CSF and Urine cultures remained sterile, while the blood culture grew a motile Enterococcus species, which was confirmed as Enterococcus gallinarum by the Vitek® automated identification system. It was sensitive to linezolid and ampicillin while resistant to vancomycin. Empirical cefotaxime was switched to IV ceftriaxone 340mg daily, and IV Ampicillin 170mg every 6 hours was added following culture results. Repeat USS abdomen revealed right-sided pyelonephritis with abscess formation at the lower pole of the right kidney. The cranial USS was unremarkable. Infective endocarditis was excluded. Aspiration of the renal abscess was not performed, as the response to the current treatment regimen was satisfactory. He was treated for a total of three weeks, and one month review after discharge disclosed no relapses ultrasonically. Case report 2 A 50-year-old man with diabetic ketoacidosis presented with fever, dysuria, and backache for several days. He was septic and in acute kidney injury with rising creatinine of 174 µmol/L, and USS revealed bilateral pyonephrosis and renal abscesses. His white cell count was 7x103 /mm3 with neutrophils at 80%, CRP of 247 mg/L, and urine culture was sterile. On admission, his blood culture grew Enterococcus gallinarum. Endocarditis was excluded. He was treated with IV meropenem initially and later combined with linezolid after the sensitivity. Treatment was continued for three weeks until a satisfactory clinical, biochemical, hematological, and radiological response was achieved. Interestingly, it was revealed retrospectively that he is keeping a chicken farm and working there himself with the others. Discussion In addition to enterococcal meningitis, the first patient had pyelonephritis complicated with abscess formation, which is likely due to hematogenous spread. The second patient had renal abscesses. Due to its uncommon etiology, high clinical suspicion, proper and timely bacteriological diagnosis, and targeted antibiotic use with adequate duration of therapy were of paramount importance in treating infections caused by this pathogen. Once blood culture becomes positive, it is necessary to exclude endocarditis and deep-seated abscesses to ensure adequate duration of antibiotics. Avoiding unnecessarily prolonged antibiotic regimens and enhancing immunity are of great value in reducing the incidence of infections in hospital settings.
PP17 -Enhancing infection prevention and control practices among intern medical officers: A targeted awareness program
Introduction Healthcare-associated infections (HAIs) are a major global concern, leading to increased morbidity, mortality, and healthcare costs. Infection prevention and control (IPC) practices are essential to mitigate these risks. Intern medical officers, as frontline healthcare providers, must be proficient in IPC principles to ensure patient safety and safeguard their own occupational health. This service evaluation aimed to assess the effectiveness of a structured awareness program in improving the knowledge and skills of intern medical officers related to three key IPC components: safe blood culture collection, needlestick injury (NSI) prevention, and hand hygiene compliance. Objectives The objectives were to evaluate improvements in knowledge and skills regarding aseptic blood culture collection, to assess awareness enhancement regarding NSI prevention and post-exposure management, and to assess improvements in knowledge and compliance with WHO hand hygiene guidelines. Design, setting, and methods This service evaluation was conducted at the base hospital Tangalle using a structured multimodal training program. The program included PowerPoint presentations, interactive discussions, case-based discussions, and practical demonstrations. A total of 25 intern medical officers participated in the study. Pre-test and post-test assessments (15 single-best-answer questions) were used to evaluate knowledge improvement across the three IPC components. Results The mean pre-test score was 9.64/15, which significantly improved to 13.56/15 post-training (p < 0.05). The highest pre-test score was 13/15, increasing to 15/15 post-test, while the lowest score improved from 6/15 to 9/15. Topic-wise improvements included Safe blood culture collection, showing a 123.4% increase in correct responses; hand hygiene, with a 47.4% improvement; and NSI prevention, where pre-test knowledge of 95.2% improved to 100%. Conclusions This structured awareness program significantly enhanced the knowledge and skills of intern medical officers in IPC, with statistically significant improvements in all key areas. The highest knowledge gap was in safe blood culture collection, highlighting the need for further hands-on training. Future programs should include more practical assessments, periodic refresher sessions, and compliance monitoring to sustain IPC adherence in clinical practice.
PP16 -Screening urine cultures for presence of antibiotics – Internal quality audit in a base hospital in Sri Lanka
Introduction Urine culture is a crucial test for determining the etiology of urinary tract infections (UTIs). The presence of antibiotics in urine can reduce the bacterial load in positive urine cultures, leading to an inaccurate interpretation. Objectives This study was conducted to determine the prevalence of unreported antibiotic use prior to urine culture and its effect on the culture reports. Design, setting, and methods The study was conducted over a two-week period, using both inpatient and clinic urine samples. The urine anti-bacterial substance assay (UABA) described in the literature was performed for each sample using Mueller-Hinton agar plates inoculated with a lawn of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923. The presence of an inhibition zone was taken as a positive UABA test. Urine cultures were performed according to the standard operating procedure. Details on the request forms and the culture results were compared with the study's findings. Results Out of the total 92 samples, 60 (65.2%) were positive for UABA, indicating the presence of antibiotics. Among these UABA-positive samples, 85% (51/60) showed no growth in the urine culture, while 3.3% (2/60) showed ‘no significant growth’. Among UABA negative samples, 62.5% (20/32) showed no growth in the urine culture. Fisher’s exact test gave a p-value of 0.039, indicating a significant association between UABA test results and culture outcomes. Out of UABA-positive samples, 80% (48/60) had clinical details provided, but only 51.6% (31/60) included clinical history suggestive of UTI in the request forms. Antibiotic usage was mentioned only in 21.7% (13/60) of the request forms. In UABA-negative samples, 53.1% (17/32) included clinical history, and 46.8% (15/32) had UTI-suggestive history in the request forms. Conclusion The majority of urine samples showed the presence of antibiotics; however, the documentation on the request form was inadequate. The presence of antibiotics has significantly impacted the culture results, resulting in increased reports of 'no growth' and 'no significant growth.' Periodic auditing of the presence of antibiotics in urine can serve as a method to enhance laboratory quality.
PP11 - Antimicrobial resistance patterns of colonizing Escherichia coli and Klebsiella pneumoniae from urine samples of pregnant women as an indicator for antimicrobial resistance in a rural community in Sri Lanka
Introduction Antimicrobial resistance (AMR) in bacteria causing common community-acquired infections is increasing gradually worldwide and has a significant impact on mortality, morbidity, and treatment costs. Asymptomatic gut colonization with these resistant bacteria serves as a reservoir for the spread of AMR in the community. Most available AMR data originate from hospital-based settings and may not reflect AMR rates at the community level. This research aims to address the gap in community-level AMR data. Objectives This study was conducted to assess antibiotic resistance patterns, determine the prevalence of extended-spectrum beta-lactamase (ESBL) production among colonizing Escherichia coli and Klebsiella pneumoniae, and describe the factors associated with AMR Enterobacteriaceae colonization. Design, setting and methods In this descriptive cross-sectional study, urine samples were collected from pregnant mothers attending antenatal clinics in the Kalutara District and cultured using a semi-quantitative method. E. coli and K. pneumoniae isolates with colony counts between 10³ and <10⁵ CFU/mL were further processed for antibiotic sensitivity testing according to the Clinical and Laboratory Standards Institute (CLSI) M100, 33rd Edition. The combined disc method was used to detect ESBL production. Results A total of 252 pregnant women were included in the study. A total of 69 isolates were identified, comprising 31 (44.9%) E. coli and 38 (55.1%) K. pneumoniae. Of these, 63 (91.3%) isolates exhibited resistance to at least one antibiotic from the 13-antibiotic panel tested. ESBL producers were recovered from the urine of 5.2% (13, n=252) women. Multi-drug resistance (MDR) was identified in 8.7% (6, n=69) of isolates. No isolates showed carbapenem resistance. None of the studied factors were significantly associated with colonization by ESBL-producing E. coli or K. pneumoniae. Conclusions A considerable proportion of resistance to at least one antibiotic was observed, with a notable ESBL prevalence of 5.2%, highlighting the growing concerns of community-related antimicrobial resistance (AMR). Although carbapenem resistance was not detected, the presence of MDR highlights the importance of vigilant surveillance and timely targeted interventions to prevent AMR.
PP15 -A REVIEW OF THE PATTERN OF ANTIMICROBIAL RESISTANCE AT TEACHING HOSPITAL BATTICALOA DURING 2021 – 2024
Introduction Antimicrobial resistance (AMR) is a global concern. Appropriate AMR surveillance is an essential strategy to combat it. Teaching Hospital Batticaloa (THB) is the largest tertiary care hospital in the Eastern province. Therefore, we analyzed the AMR pattern of the selected clinical isolates of THB during the past four years from 2021 to 2024. Objectives To analyze the rate of isolation of selected pathogens and their AMR pattern at Teaching Hospital Batticaloa during 2021 – 2024. Design, setting, and methods This is a laboratory-based, cross-sectional, descriptive study where data were collected from WHONET and analyzed using Microsoft Excel. Results A total of 22664 blood samples, 22374 urine samples, and 582 pus samples were processed during this period. Around 10% (2194/22664) of blood, 16% (3599/22374) of urine, and 25% (145/582) of pus samples revealed a significant growth of a pathogen, and 23% (5216/22374) of urine samples and 8.6% (1947/22664) of blood samples revealed contamination. Coliforms are the predominant pathogens in all three samples, contributing to 35% (769/2194), 70% (2509/3599), and 48% (71/145) of the significant positive blood, urine, and pus samples, respectively. Third-generation cephalosporin susceptibility data were available for approximately 60% (2037/3349) of the total coliforms, out of which 49.8% (1015/2037) revealed resistance. Carbapenem susceptibility data was available for 55% (1866/3349)) of the total coliforms, out of which 5.4% (100/1866) revealed carbapenem resistance. Around 59% of (2008/3349) of total coliforms were tested against Ciprofloxacin, and 55% (1109/2008) revealed resistance to it. Fifty-one percent (1693/3349) of coliforms were tested against Amikacin, and 23% (387/1693) revealed resistance to it. Cefoxitin susceptibility data were available for 88.4% (313/354) of Staphylococcus aureus isolates, out of which 65.8% (206/313) were identified as MRSA. Conclusions Nearly half of the coliforms for which 3rd generation cephalosporin susceptibility data was available were resistant to 3rd generation cephalosporins, which are one of the significant classes of antibacterials used in Sri Lanka. Nearly two-thirds of Staphylococcus aureus isolates, for which cefoxitin susceptibility data were available, were MRSA, indicating the possibility of treatment failure with the common empiric therapy of flucloxacillin. Continuous monitoring is essential to detect the AMR trends of common clinical isolates and to implement effective measures to rationalize antimicrobial usage.
PP6 -Retrospective study on the prevalence of human metapneumovirus in samples from the National Respiratory Reference Laboratory (Feb. 2022-Feb. 2024)
Introduction Human metapneumovirus (HMPV) causes upper and lower respiratory infections, primarily affecting infants, young children, the elderly, and immunocompromised individuals. This retrospective analysis evaluated HMPV detection in samples from patients with clinically suspected acute respiratory tract infections referred for multiplex respiratory testing. Objectives To determine the HMPV positivity rate and to assess the association between demographic characteristics, clinical presentation, and laboratory findings. Design, Setting, and Methods A retrospective analysis was conducted on 131 respiratory samples collected via oropharyngeal and nasopharyngeal swabs from hospitalized patients with suspected acute respiratory infections (Feb 2022–Feb 2024). Clinical and demographic data were extracted from request forms. Samples were tested using the validated, CE/IVD-certified FastTrack® Respiratory Pathogens 21 multiplex PCR. The chi-square test (p < 0.05) was used to assess the associations between categorical variables and HMPV positivity. Results The age of participants ranged from newborn to 81 years (mean: 15 years), with 52.6% being male. HMPV positivity was 7.6% (10/131; 95% CI: 3.7%–13.5%). Positive cases ranged from 10 months to 73 years (mean 20.8 years), with the distribution as follows: <1 year (1), 1–10 years (3), 11–45 years (3), 46–65 years (1), and >66 years (2). Three patients had upper respiratory tract infections, and seven had lower respiratory tract infections. Four required ICU admissions (10 months, 13, 68, and 73 years); elderly patients had comorbidities (diabetes, hypertension). Influenza B co-infection was seen in a 13-year-old. No statistically significant correlation was present between HMPV positivity and age group, comorbidity status, ICU admission, or presentation. Conclusion Human metapneumovirus showed a low positivity rate, with cases spanning all age groups, highlighting its potential to infect across the spectrum. Lower respiratory tract infection was common in positive cases. Detection among ICU admissions and comorbid individuals indicates possible severity in risk groups. However, findings are limited by selection bias and are not generalizable to population incidence. Further research is needed to clarify the relationship between age, clinical severity, and outcomes and to guide prevention and clinical management.
PP20 -Post pandemic period circulation and seasonality of SARS-CoV-2 : Analysis of samples from National Respiratory Reference Laboratory, Jan 2023- Dec 2024
Introduction SARS-CoV-2, the causative agent of the COVID-19 pandemic, continues to circulate globally following the lifting of the status of Public Health Emergency of International Concern (PHEIC) by the World Health Organization on 5th May 2023. The National Influenza Centre (NIC), serving as the national reference laboratory for respiratory viruses, has maintained extensive testing for SARS-CoV-2, providing a comprehensive picture of seasonality and trends for public health measures. Objectives To determine the observed prevalence of SARS-CoV-2, seasonality/trend, and compare them with influenza seasonality from the samples received from January 2023 to December 2024. Design, setting, and methods A retrospective analysis was conducted on 7,831 respiratory specimens received between January 2023 and December 2024 from OPD, inpatient, and sentinel surveillance sites nationwide. Testing was performed using the CDC Influenza SARS-CoV-2 multiplex and Altona SARS-CoV-2 PCR assays. Monthly positivity trends were analyzed using the Chi-square test and compared with 2022 data. SARS-CoV-2 and influenza were tested simultaneously on the same samples following WHO surveillance protocols. Results A total of 7,831 samples were analyzed, comprising 2,469 in 2023 (with a monthly average of 205) and 5,362 in 2024 (with a monthly average of 447). There were two clear SARS-CoV-2 peaks during the post-pandemic period: a primary peak from April to June, with the highest positivity in May (8% in 2023; 17.6% in 2024), and a secondary peak from November to early January, highest in December (5.6% in 2023; 5.8% in 2024). These findings were statistically significant (p < 0.05). For comparison, 2022 data, analyzed separately, showed major pandemic-phase peaks: 41% in January and 35% in August, with a smaller rise in December (10%). Influenza displayed consistent bimodal seasonality from March to June and November to February across 2023–2024. Conclusion From 2023 to 2024, SARS-CoV-2 demonstrated low prevalence with two seasonal peaks: April to June and November to January. These periods overlap with the established bimodal seasonality of influenza. These findings are crucial for tailoring public health interventions and preparedness strategies.
OP6 -Antiviral susceptibility of seasonal influenza A and B strains to neuraminidase inhibitors (oseltamivir, zanamivir, peramivir and laninamivir) from 2013– 2024 in Sri Lanka
Introduction Neuraminidase inhibitors (NAIs) are the main antiviral medications for influenza worldwide. Antiviral susceptibility monitoring has become an integral part of influenza surveillance conducted by laboratories participating in the Global Influenza Surveillance Response System. Phenotypic assays for determining 50% inhibitory concentrations (IC50) for NAIs are commonly fluorescence-based. Objectives To report antiviral susceptibility to NAIs (oseltamivir, zanamivir, peramivir and laninamivir) among seasonal influenza A and B viruses circulating from 2013–2024 in Sri Lanka. Design, setting and methods Representative samples from patients on antiviral from routine surveillance (geographically), clinical samples (ward, ICU), post-mortem samples, different age groups, and tissue culture isolates were sent to the WHO Collaborating Centre (WHO CC), Australia, for NAI susceptibility testing from 2013–2024. Samples were subjected to Sanger/whole-genome sequencing, and where virus isolates were available, these were tested for susceptibility to NAIs using the 2′-(4-Methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUNANA) substrate phenotypic assay. IC50 values for viruses were compared to the median IC50 of viruses of the respective type/subtype/lineage known to be susceptible to the NAIs. Three categories of inhibition were determined: normal inhibition, reduced inhibition, and highly reduced inhibition. Results Of 1402 samples, 217 strains were cultured and tested in phenotypic assays. From the years 2013 to 2024, 20, 13, 19, 20, 39, 17, 20, 08, 30, 13, 0, and 18 strains that were isolated were tested, respectively. All influenza A, pandemic H1N1 2009 (n=78), H3N2 (n=88) strains and influenza B (n=51) strains showed normal inhibition to oseltamivir, zanamivir, peramivir and laninamivir, and no genetic markers associated with reduced/highly reduced inhibition were identified. Conclusions All isolated strains of seasonal influenza virus showed normal inhibition to oseltamivir, zanamivir peramivir and laninamivir. Due to cost and logistic constraints, a limited number of samples were sent for testing. National Influenza Centres and WHO CCs should monitor as many samples as possible for genetic markers for antiviral resistance, with a subset being selected for phenotypic testing. This is the first report of antiviral susceptibility of peramivir and laninamivir in Sri Lanka.
PP5 -Prevalence of co-infection with influenza A, influenza B and SARS-CoV-2 viruses among samples referred to the national laboratory in 2024
Introduction Co-infection with respiratory pathogens, such as influenza and SARS-CoV-2, poses a significant challenge in clinical diagnosis and treatment. Understanding the prevalence and clinical characteristics of such cases is crucial for guiding effective healthcare interventions. The National Influenza Centre/Laboratory adopted testing all surveillance samples for both viruses, as recommended by the WHO, which was later expanded to include all clinical samples. This provides prevalence data from a larger sample and reflects the co-circulation of the viruses. Objectives To determine the prevalence of co-infection with influenza and SARS-CoV-2 viruses among patient samples referred to the National Reference Respiratory Laboratory, Colombo. Design, setting, and methods All samples sent from OPD and in-ward patients from all over the country between January and December 2024 were tested using CDC in-house multiplex PCR, and Altona Diagnostics (IVD, CE) assays to detect influenza A/B and SARS-CoV-2. The analysis included patient demographics and clinical symptoms. Co-infection was defined as the simultaneous detection of both viruses in the same sample, and all those were sent to the WHO reference laboratory in Australia for confirmation. Results Out of the 5,364 samples analyzed, 23(0.42%) were confirmed as co-infected with SARS-CoV-2 and influenza A/B. Twelve were from the OPD, three from the intensive care/emergency treatment units, and eight from wards. This co-infected group consisted of 15 females and eight males, with ages ranging from 1 to 81 years (mean age: 32.5 years). The age groups were 1-12 years (5), 13-45 years (7), 46-65 years (6), and over 66 years (5). Most co-infected patients presented with fever 65% (15), cough 69% (16), sore throat 39% (9), shortness of breath 17% (4). The request forms did not mention the co-morbid factors of the co-infected patients. Twenty patients were co-infected with influenza A and SARS-CoV-2, and three with influenza B and SARS-CoV-2. The influenza A subtypes were H1 (13), H3 (4), and not typed (3). All influenza B cases (3) were of Victoria lineage. Conclusion The study highlights a very low prevalence of co-infection among this cohort. Continued routine testing for both viruses raises questions in a low-resource setting due to the significant costs involved.
PP19 -The occurrence of morbidity and mortality among patients experiencing respiratory symptoms at Teaching Hospital, Kurunegala, in April 2024
Introduction Respiratory tract infections (RTIs) remain a major global health burden, contributing to significant morbidity and mortality across all age groups. Their etiology includes viral, bacterial, and fungal pathogens, with outbreaks often influenced by seasonal patterns and environmental factors. This study investigates an increased incidence of RTIs among patients admitted to the Teaching Hospital in Kurunegala between the second and fourth weeks of April 2024. The study aims to identify contributing factors, determine causative agents, assess clinical presentations, and evaluate management and preventive strategies. Design, setting, and methods This observational study was conducted at the Teaching Hospital in Kurunegala and the Medical Research Institute (MRI) in Colombo, Sri Lanka. It included patients presenting with severe acute respiratory distress or those who developed respiratory complications during hospitalization. Respiratory specimens underwent bacterial culture, antibiotic sensitivity testing, and molecular diagnostics (real-time PCR and respiratory multiplex PCR) to identify viral and bacterial pathogens. Fungal testing was performed selectively. All laboratory assays followed strict quality control measures, and results were promptly shared with clinicians for timely intervention. Results Of the 12 patients analyzed, 7/12 were over 60 years old, and 10/12 had pre-existing comorbidities. The most common symptoms included fever, cough, and shortness of breath. Mechanical ventilation was required in 7/12 patients, and 8/12 patients succumbed to the illness. Laboratory findings revealed SARS-CoV-2 in 4 of 12 patients, influenza A in 2 of 12, and Parainfluenza 1 in 1 of 12. One patient had a secondary bacterial (Staphylococcus aureus) and fungal (Candida spp.) co-infection. Oseltamivir was administered to 7 of 12 patients, but no SARS-CoV-2-specific antiviral treatments were administered. Conclusion This investigation highlights the critical impact of respiratory tract infections among elderly and comorbid patients during the April 2024 outbreak at the Teaching Hospital in Kurunegala. The predominance of SARS-CoV-2 and influenza A, along with a high requirement for mechanical ventilation and a mortality rate of 67%, underscores the severity of these infections in vulnerable populations. The lack of SARS-CoV-2-specific antiviral therapy and delayed clinical recognition likely contributed to the poor outcomes. Furthermore, the absence of pathogen detection in postmortem samples emphasizes the need to strengthen specimen collection protocols and enhance diagnostic capabilities. Strengthening surveillance systems, ensuring timely access to laboratory testing, and optimizing therapeutic interventions are vital to reducing morbidity and mortality in future outbreaks.
CP2 - Staphylococcus aureus urine culture leading to diagnosis of psoas abscess; a case report
Introduction Staphylococcus aureus is the commonest pathogen causing psoas abscesses by hematogenous spread or local inoculation. Although commonly found in immunocompromised individuals, our case involves an immunocompetent patient who was diagnosed following a positive urine culture. Case report A 63-year-old male, previously unevaluated, presented in January 2025 with lower back pain worsening over one and a half months, interfering with his daily routines. More recently, the pain had started radiating along the right leg from the right buttock. He denied trauma or fever. His appetite had reduced, but he denied weight loss. He developed dysuria over the past two weeks, with poor urine flow and reduced output. His right inguinal lymph nodes were palpable, and he could not raise his right leg above 80o due to pain. His WBC count was 12.3 × 103/ µL with 83% neutrophils. His CRP was 67 mg/L, and ESR was 68mm/1st hour. X-ray L-S spine and Ultrasound scan (USS) abdomen were unremarkable. His urine culture became positive for >105 CFU/mL of methicillin-sensitive Staphylococcus aureus (MSSA), and he was started on IV ceftriaxone 2g daily. Blood cultures were subsequently requested, and two became positive for the same organism, despite being collected after antibiotics were commenced. IV flucloxacillin 2g was administered 6 hourly. His repeat USS revealed a right-sided psoas abscess; however, guided aspiration failed. Therefore, both antibiotics were continued, as the pathogen causing the abscess could not be confirmed. MRI of the L-S spine revealed paravertebral inflammation at the L3–L4 level, accompanied by a psoas abscess. The echocardiogram excluded infective endocarditis. His pain gradually improved, and inflammatory markers decreased. We continued treatment for three weeks, monitoring the response clinically, biochemically, and radiologically. He was discharged on oral flucloxacillin with follow-up arranged through medical, microbiological, and neurosurgical reviews. Discussion Staphylococcus aureus can be a skin colonizer, and positive urine culture is often overlooked as a contaminant. However, it may indicate infective endocarditis or a deep-seated abscess and always warrants further investigation to rule out major pathology. In our patient, the presence of MSSA in the urine culture led to the diagnosis of a psoas abscess in the context of ongoing lower back pain, as it was properly investigated even in the absence of fever.
OP5 -Parasitic helminth stages isolated from soil samples of selected public areas in Gampaha and Colombo, Sri Lanka.
Introduction Sri Lanka has successfully controlled soil-transmitted helminthiases affecting humans through mass deworming and improved sanitation. However, soil contamination with animal excreta is widespread, allowing the ova of gut-dwelling geohelminths in canines and felines to develop into infective ova or larvae in the soil. Such contaminated soil poses a public health hazard for toxocariasis and cutaneous larva migrans. Objective This study aimed to determine the prevalence of soil contamination with parasitic helminth ova and larvae in selected public areas of the Gampaha and Colombo districts. Design, setting and methods Study locations were selected randomly from Gampaha and Colombo districts. Sampling was conducted at four sites in each location from May 2024 to January 2025. A 15x15cm square wooden template was placed, and approximately 200g of soil was collected into labeled zip-lock bags after scraping off the topsoil using a clean spade. The samples were processed using the Magnesium sulfate floatation and Baermann funnel technique for the detection of helminth ova and larvae, respectively. Identification of parasitic helminth stages was based on morphology on light microscopy at 40x10 magnification. Results A total of 140 soil samples were analyzed from Colombo (n=56) and Gampaha (n=84). Study sites included parks (n = 12), temples (n = 20), university grounds (n = 12), side roads (n = 12), beaches (n = 4), school grounds (n = 28), hospital grounds (n = 4), and home gardens (n = 48). The overall prevalence of parasitic helminth stages in soil, determined by Magnesium sulfate flotation, was 32.1% (45/140), with rates of 39.3% (22/56) and 27.4% (23/84) in Colombo and Gampaha districts, respectively. Ova of Toxocara spp. were detected in 31.1% (14/45), Ascaris lumbricoides in 8.9% (4/45), and hookworm in 4.4% (2/45) of positive samples through the floatation method. Hookworm larvae, probable Ancylostoma spp., were detected in 24.3% (34/140) by the Baermann technique. The highest contamination rates were observed in parks at 41.7% (5/12) and temple grounds at 40.0% (8/20). Conclusions Soil contamination with parasitic helminth stages was widespread in Colombo and Gampaha districts. The high prevalence in children's parks and temples indicates risks to children while they are playing or walking barefoot. Health education, regular deworming of pets, and controlling stray animal populations are recommended. Acknowledgments Financial assistance by the University of Kelaniya Research grant RP/03/04/06/01/2023.
PP13- Effectiveness of Sri Lankan sweet potato varieties (reddish and whitish) as an alternative media for potato dextrose agar to isolate Candida albicans.
Introduction Candida albicans are commonly isolated using Sabouraud Dextrose Agar (SDA), Potato Dextrose Agar (PDA), and Potato Dextrose Broth (PDB), which remain expensive. Exploring alternative, cost-effective media is crucial in Sri Lanka. Objectives The objective was to determine the minimum effective concentration (MEC) of sweet potato infusions (SPI) required to prepare sweet potato agar (SPA) and sweet potato broths (SPB) with and without the addition of dextrose, compared to PDA and PDB. Design, setting, and methods Six SPI concentrations (10, 50, 100, 200, 300, and 400 g/L) were prepared from both reddish and whitish sweet potatoes, with and without dextrose, and used to formulate SPA and SPB following the PDA preparation method. Candida albicans (ATCC 10231) was inoculated at McFarland 0.5. All media were incubated at 25°C for 48 hours. Colony count, macroscopic and microscopic appearance, and germ tube formation were assessed and compared with PDA and PDB. Each concentration was tested in triplicate and repeated. Data were analyzed using an ANOVA test. Results The mean colony count for PDA was 550 mL⁻¹. For SPA, the MECs were 200 g/L (whitish, without dextrose), 100 g/L (whitish, with dextrose), 300 g/L (reddish, without dextrose), and 200 g/L (reddish, with dextrose), with colony counts of 548, 542, 532, and 528 mL⁻¹, and corresponding p-values of 0.99, 0.85, 0.63, and 0.11, indicating no significant difference from PDA. The mean direct germ tube count for PDB was 3.92 x 10⁴ mL⁻¹. Similar MECs to those observed in SPA were found in SPB, compared to PDB. For these MECs, corresponding direct germ tube counts were 4.0 x 10⁴ mL⁻¹, 3.83 x 10⁴ mL⁻¹, 4.0 x 10⁴ mL⁻¹, and 3.96 x 10⁴ mL⁻¹, with p-values of 0.782, 0.851, 0.428, and 1.00, respectively. Colonies on all media were round, creamy-white, smooth, and 1–3 mm in diameter. Microscopically, cells showed true hyphae, pseudohyphae, and clustered blastospores. Germ tube tests confirmed C. albicans. Conclusion Both reddish and whitish sweet potato varieties can serve as alternatives to potato and dextrose in the preparation of PDA and PDB for culturing Candida albicans. However, the whitish variety shows effectiveness at lower concentrations compared to the reddish variety.
PP12-Comparison of antibiotic sensitivity in Escherichia coli isolated from natural water and ground water in Gampaha District
Introduction Antimicrobial resistance in water sources poses a risk to both human and animal health. Therefore, surveillance of water sources is essential. Objective Compare the antimicrobial sensitivity patterns of Escherichia coli in surface and groundwater sources of the Gampaha District. Design, setting, and methods Two water samples were collected by the author using a water collection tool from each of the 52 major surface water bodies (SWB) marked on Google Maps and the Department of Census, as well as 161 groundwater (GW) samples in the Gampaha District. All samples were processed according to the standard single-membrane-filtration method using nitrocellulose membranes. They were inoculated onto Membrane-Lactose-Glucuronide agar. E. coli colonies were further confirmed biochemically. Antibiotic susceptibility tests were performed on E. coli isolates using the disc diffusion method (CLSI M100, vol. 34, 2024). In case of a similar ABST pattern from the same source, one isolate was used for analysis. Results There were 93 E.coli isolates selected from 104 SWB isolates and 84 E.coli from 161 GW samples. The contamination was 100% in SWBs and 52.17% in GW. The coliform counts were greater than 200 CFU/100 mL in 68.2% of SWB compared to 67.85% of GW. Highest resistance rates of E. coli were noted for ampicillin in both types (54.8% in SWB, 45.2% GW). None of the isolates were resistant to ertapenem. Slightly higher resistance rates in SWBs compared to GW were noted for co-amoxiclav (19.4% vs. 17.9%), gentamicin (18.3% vs. 13.1%), and cefotaxime and ceftazidime (8.6% vs. 7.1%). A higher rate of resistance was noted for trimethoprim-sulfamethoxazole (9.7% vs. 14.3%) and tetracycline (15.1% vs. 17.9%). ESBL was detected in 5 isolates (5.37%) in SWB, and one isolates in GW. Amp-C beta-lactamases were detected with two isolates from GW. Multidrug resistance was observed in 19% of GW and SWB. However, there was no statistically significant difference in the antibiotic susceptibilities between the isolates from the two sources. Conclusion Our findings reveal high rates of antibiotic resistance in NWBs and GW, which humans access for their daily needs. The implications of these findings highlight the critical need for urgent interventions against AMR in aquatic settings.
PP4 -Bacterial identification, their ABST patterns, and associated factors in suspected ear infection patients attending ENT Clinic, Teaching Hospital, Jaffna.
Introduction Ear infections are a common health issue across all ages and a leading cause of preventable hearing loss. Accurate pathogen identification and understanding of associated factors are critical for effective management and prevention. Empirical antibiotic use without sensitivity testing contributes to the development of antimicrobial resistance. However, recent data on bacterial isolates and antibiotic susceptibility in Sri Lanka, particularly Jaffna, remain limited. Objectives This study aimed to identify bacterial pathogens, assess their antibiotic susceptibility, and explore factors associated with ear infections among patients attending the ENT clinic at the Teaching Hospital in Jaffna. Design, setting and methods An institution-based descriptive cross-sectional study using convenience sampling was conducted from May 31 to July 30, 2024, among patients with ear discharge and clinically suspected bacterial infections, verified by physicians. Bacterial identification and antibiotic susceptibility testing followed the Sri Lanka College of Microbiologists’ Laboratory Manual and CLSI guidelines (26th edition). Socio-demographic, behavioral, and clinical data were collected through interviewer-administered questionnaires with patients and attending physicians. Statistical analysis was performed using Chi-square tests (p < 0.05). Results Among 155 patients, 81(52.3%) were male, and 43(27.7%) were pediatric. The culture positivity rate was 89.7%, yielding 143 bacterial pathogens. The most common pathogens were Pseudomonas spp. (48.3%), Enterobacteriaceae (28.7%), Staphylococcus aureus, and Acinetobacter spp. (5.6% each). Pseudomonas spp. showed high susceptibility to Polymyxin B (98.6%) but lower to Ciprofloxacin (79.7%). MRSA was detected in 52.0% (13/25) of Staphylococcus aureus isolates. Multidrug resistance (defined as resistance to ≥3 antibiotic classes) was detected in 22.4% (32/143) of bacterial isolates. Otitis media (OM) accounted for 71.6% of cases, with chronic suppurative OM (57.7%) being the most common, and 59.9% of otitis externa (OE) cases were acute. OM was significantly associated with pediatric and elderly age groups, the use of sharp objects, hearing impairment, and a history of prior infections. OE was associated with the pediatric age group, swimming, water exposure, and passive smoking (p < 0.05). Conclusions The high culture positivity with Pseudomonas spp. and the observed antibiotic resistance patterns highlight the need for antimicrobial stewardship programs. The identified associated factors suggest the importance of targeted prevention strategies for better control of ear infections.
PP3 - An analysis of Streptococcus pneumoniae isolates observed at a paediatric tertiary care hospital in Sri Lanka
Introduction Invasive pneumococcal disease is associated with significant morbidity and mortality, especially among children below 5 years in developing countries. Pneumococcal infections caused by antibiotic-resistant strains complicate treatment. Objectives This analysis describes the sources and antibiotic susceptibility patterns of Streptococcus pneumoniae isolates from diagnostic cultures performed at the Lady Ridgeway Hospital for Children in Colombo (LRH) in 2024. Design, setting, and methods A retrospective descriptive analysis was conducted on all Streptococcus pneumoniae isolates from routine samples received at the LRH microbiology laboratory from January 1, 2024, to December 31, 2024. The age and sex of patients, specimen types, and clinical information were extracted from the request forms. Pneumococci were identified using bile solubility and optochin susceptibility tests. Antibiotic susceptibility (AST) was tested with disc diffusion methods. Isolates from sterile sites were sent to the reference laboratory for determination of the minimum inhibitory concentration (MIC). The data was analyzed using SPSS (version 22.0). Results A total of 136 Streptococcus pneumoniae isolates were identified. Among the patients, 75% (102/136) were under the age of five, and 64.7% (88/136) were boys. The majority, 51.5% (70/136), were respiratory specimens, including 48 sputum, nine nasopharyngeal aspirates, six endotracheal aspirates, three bronchoalveolar lavage, two gastric aspirates, one lung tissue, and one nasal swab. Ear swabs accounted for 44.9% (61/136), and there was one pus sample. Four blood culture isolates were from one meningitis and three pneumonia patients, all of whom were under 5 years old. AST by disc diffusion test for all the isolates revealed high rates of non-susceptibility to penicillin (88.4%), co-trimoxazole (73.2%), erythromycin (62.3%), and clindamycin (40%). Susceptibility to vancomycin (100%) and chloramphenicol (99%) was excellent. MIC testing of the four blood culture isolates at the reference laboratory showed 100% susceptibility to penicillin, cefotaxime, vancomycin, and levofloxacin. Conclusion Of the pneumococcal infections studied, a greater proportion was among children below 5 years. Higher rates of non-susceptibility to penicillin, cotrimoxazole, and erythromycin were evident. These findings highlight the importance of preventing pneumococcal disease among children antibiotic resistant strains complicate the treatment.
OP2 -Identification of Anaerobic Bacteria in Herniated Lumbar Discs of Patients Undergoing Microdiscectomy
Introduction Although studies have indicated that vertebral discs are sterile, emerging evidence suggests the presence of low-virulent anaerobes in herniated discs. This finding indicates that the presence of anaerobes could be attributed to the disease's pathophysiology and post-surgical effects in lumbar disc herniation (LDH), apart from traditional causative factors. Objective This study aimed to identify the presence of anaerobes in herniated lumbar discs in patients undergoing lumbar microdiscectomy. Design, setting, and methods A cross-sectional study was conducted from 2022 to 2024 in patients with LDH (n=101) undergoing lumbar microdiscectomy at selected hospitals in Sri Lanka. Anaerobic bacterial cultures were performed on all surgically excised discs and transported separately in both enrichment media [Robertson cooked meat media (RCM) and thioglycolate (TG) broth]. To rule out bacterial contamination, skin scrapings and muscle biopsies were collected as controls and processed concurrently with the disc cultures. Discs collected within RCM were directly sub-cultured. TG specimens were homogenized using a Seward 400 Stomacher machine and subsequently inoculated onto brucella blood agar and bacteroides bile esculin agar. The cultures were incubated under an anaerobic glove box, and culture negatives were confirmed after 14 days of incubation. Isolates were screened by colony morphology, Gram stain, and aerotolerance and then confirmed with the Rapid ID 32A kit. Results Of the total LDH cases (29/101), 28.71% yielded positive results for anaerobic culture, with 19/29 cultures testing positive in RCM and 14 in TG media, while four discs showed bacterial growth in both media. The study identified a diverse range of anaerobic bacterial isolates, including Actinomyces meyeri (7/29) 24.14%, Parvimonas micra (6/29) 20.69%, Gemella morbillorum (5/29) 17.24%, Capnocytophaga sputigena (4/29) 13.79%, Parabacteroides distasonis, Propionibacterium propionicum (2/29 each) 6.9%, Actinomyces naeslundii, Propionibacterium acnes and Veillonella spp. (1/29 each) 3.45%. None of the controls generated any anaerobic bacterial growth throughout the study. Conclusions This study revealed diverse anaerobes in excised herniated lumbar discs, with Actinomyces meyeri as the predominant isolate, followed by other facultative and obligate anaerobes. Higher culture positivity in RCM than in TG indicates media-specific differences in anaerobe yield. The presence of anaerobes may implicate their role in LDH pathophysiology. Acknowledgment: Grant No: ASP/01/RE/AHS/2021/87.