Pertussis surveillance in a children hospital in Bangkok, Thailand

Objectives: To investigate the incidence, clinical characteristics and cost associated with pertussis in Thai children with persistent cough. Methods: A prospective study was conducted among children aged 0–18 years with persistent cough for ≥7 days with at least one of the following: paroxysm, inspiratory whooping, or post-tussive emesis. Nasopharyngeal swabs were obtained and tested for pertussis real time polymerase chain reaction (RT-PCR). Results: 19.6% of children (28 out of 143) had pertussis confirmed by RT-PCR, 75% of cases occurred in children who were too young to complete their primary series of vaccine. Paroxysm and post-tussive emesis were the most consistent clinical features, identified in 96% and 93% of cases, respectively, whooping was found in only 18%. Pertussis cases were more likely to have household cough contact (64% versus 30%, p < 0.001), be hospitalized (79% versus 58%, p = 0.048) and experience protracted duration of cough (47 vs. 20 days, p < 0.001) compare to their counterpart. Conclusion: Pertussis in Thai children is not infrequent and the common age group is young infant before completion of primary series of pertussis vaccine at six months of age, underline the importance of maternal pertussis immunization. Keyword: Pertussis, Thailand, Children, Whole-cell pertussis vaccine, Maternal immunizatio

Enhanced surveillance for severe pneumonia, Thailand 2010–2015

Abstract Background The etiology of severe pneumonia is frequently not identified by routine disease surveillance in Thailand. Since 2010, the Thailand Ministry of Public Health (MOPH) and US CDC have conducted surveillance to detect known and new etiologies of severe pneumonia. Methods Surveillance for severe community-acquired pneumonia was initiated in December 2010 among 30 hospitals in 17 provinces covering all regions of Thailand. Interlinked clinical, laboratory, pathological and epidemiological components of the network were created with specialized guidelines for each to aid case investigation and notification. Severe pneumonia was defined as chest-radiograph confirmed pneumonia of unknown etiology in a patient hospitalized ≤48 h and requiring intubation with ventilator support or who died within 48 h after hospitalization; patients with underlying chronic pulmonary or neurological disease were excluded. Respiratory and pathological specimens were tested by reverse transcription polymerase chain reaction for nine viruses, including Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and 14 bacteria. Cases were reported via a secure web-based system. Results Of specimens from 972 cases available for testing during December 2010 through December 2015, 589 (60.6%) had a potential etiology identified; 399 (67.8%) were from children aged < 5 years. At least one viral agent was detected in 394 (40.5%) cases, with the most common of single vial pathogen detected being respiratory syncytial virus (RSV) (110/589, 18.7%) especially in children under 5 years. Bacterial pathogens were detected in 341 cases of which 67 cases had apparent mixed infections. The system added MERS-CoV testing in September 2012 as part of Thailand’s outbreak preparedness; no cases were identified from the 767 samples tested. Conclusions Enhanced surveillance improved the understanding of the etiology of severe pneumonia cases and improved the MOPH’s preparedness and response capacity for emerging respiratory pathogens in Thailand thereby enhanced global health security. Guidelines for investigation of severe pneumonia from this project were incorporated into surveillance and research activities within Thailand and shared for adaption by other countries

Population-based bloodstream infection surveillance in rural Thailand, 2007–2014

Abstract Background Bloodstream infection (BSI) surveillance is essential to characterize the public health threat of bacteremia. We summarize BSI epidemiology in rural Thailand over an eight year period. Methods Population-based surveillance captured clinically indicated blood cultures and associated antimicrobial susceptibility results performed in all 20 hospitals in Nakhon Phanom (NP) and Sa Kaeo (SK) provinces. BSIs were classified as community-onset (CO) when positive cultures were obtained ≤2 days after hospital admission and hospital-onset (HO) thereafter. Hospitalization denominator data were available for incidence estimates for 2009–2014. Results From 2007 to 2014 a total of 11,166 BSIs were identified from 134,441 blood cultures. Annual CO BSI incidence ranged between 89.2 and 123.5 cases per 100,000 persons in SK and NP until 2011. Afterwards, CO incidence remained stable in SK and increased in NP, reaching 155.7 in 2013. Increases in CO BSI incidence over time were limited to persons aged ≥50 years. Ten pathogens, in rank order, accounted for > 65% of CO BSIs in both provinces, all age-groups, and all years: Escherichia coli, Klebsiella pneumoniae, Burkholderia pseudomallei, Staphylococcus aureus, Salmonella non-typhi spp., Streptococcus pneumoniae, Acinetobacter spp., Streptococcus agalactiae, Streptococcus pyogenes, Pseudomonas aeruginosa. HO BSI incidence increased in NP from 0.58 cases per 1000 hospitalizations in 2009 to 0.91 in 2014, but were higher (ranging from 1.9 to 2.3) in SK throughout the study period. Extended-spectrum beta-lactamase production among E. coli isolates and multi-drug resistance among Acinetobacter spp. isolates was common (> 25% of isolates), especially among HO cases (> 50% of isolates), and became more common over time, while methicillin-resistance among S. aureus isolates (10%) showed no clear trend. Carbapenem-resistant Enterobacteriaceae were documented in 2011–2014. Conclusions Population-based surveillance documented CO BSI incidence estimates higher than previously reported from Thailand and the region, with temporal increases seen in older populations. The most commonly observed pathogens including resistance profiles were similar to leading pathogens and resistance profiles worldwide, thus; prevention strategies with demonstrated success elsewhere may prove effective in Thailand

The 1^st EQAsia External Quality Assessment trial:<i>Escherichia coli</i> and <i>Salmonella </i>spp. – 2021

The EQAsia project was launched in 2020 aiming to strengthen the provision of External Quality Assessment (EQA) services across the One Health sector among National Reference Laboratories/ Centres of Excellence in South and Southeast Asia. EQAsia is supported by the Fleming Fund and strives to increase the quality of laboratory-based surveillance of WHO GLASS pathogens and FAO priority pathogens.The EQAsia Consortium includes the National Food Institute, Technical University of Denmark (DTU Food) as the Lead Grantee, the International Vaccine Institute (IVI) in South Korea, the National Institute of Health (NIH) in Thailand and the Faculty of Veterinary Science, Chulalongkorn University (CU) in Thailand.EQASIA provides a state of the art EQA program free of charge for the South and Southeast Asian region through existing local providers (NIH Thailand and CU Thailand). The program, referred to as a “One-Shop EQA program”, is designed to enable the laboratories to select and participate in relevant proficiency tests of both pathogen identification and antimicrobial susceptibility testing (AST), in line with the requirements of the WHO GLASS. The EQA program is supported by an informatics module where laboratories can report their results and methods applied.Three EQA trials are taking place during Feb 2021 – Feb 2022. The EQA trials focus on the WHO GLASS pathogens and FAO priority pathogens (see Section 7. References): Salmonella spp., Escherichia coli, Klebsiella pneumoniae, Shigella spp., Acinetobacter spp., Staphylococcus aureus, Streptococcus pneumoniae, Campylobacter (C. coli and C. jejuni), Enterococci (E. faecium and E. faecalis), Pseudomonas aeruginosa and Neisseria gonorrhoeae. In addition, a Matrix EQA is offered, aligning with the scope of WHO Tricycle and suggested from FAO, aiming to assess the veterinary laboratories’ ability to detect ampC beta-lactamases (ampC), extended-spectrum beta-lactamases (ESBL) and carbapenemase producing E. coli from animal caeca samples and food matrices.For a given organism, candidate strains are assessed and validated by DTU and the external partner (United States Food and Drug Administration, FDA). The validation includes both phenotypic minimum inhibitory concentration (MIC) determination by broth microdilution, and whole genome sequencing (WGS) to detect antimicrobial resistance (AMR) genes and chromosomal point mutations. The test strains are then selected based on the phenotypic AMR profile to include a heterogeneous panel, allowing for strain variation from almost pan-resistant to fully susceptible isolates.Each EQA trial encompasses the testing of a total of 11 test strains of a given organism. Of these, eight of the test strains are of the organism in focus (target organism), whereas three test strains are different from the targeted species (reported as non-[organism], e.g. non-Salmonella). For each of the 11 test strains, participants are requested to report which eight strains belong to the expected target organism. For the three organisms different from the expected, no further testing is required. For the remaining eight test strains of the target organism, results in relation to AST and serotyping (if relevant) are requested.This report contains results from the first EQA trial of the EQAsia project carried out in February-April 2021. This first EQA trial includes serotyping of Salmonella spp., as well as identification and AST of Salmonella spp. and Escherichia coli. The aim of this EQA trial is to monitor the quality of AST results produced by the participating laboratories and identify underperforming laboratories in need of assistance to improve their performance in AST.The evaluation of the participants’ results is based on international guidelines, namely the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Clinical and Laboratory Standards Institute (CLSI). Interpretative criteria referring to both disk diffusion and MIC determination are listed in the EQA protocol (Appendix 1) and allow for the obtained results to be interpreted into categories as resistant or susceptible depending on the method used. Results in agreement with the expected interpretation are categorised as ‘1’ (correct), while results deviating from the expected interpretation are categorised as ‘0’ (incorrect). This standardized interpretation of results is necessary to allow comparison of performance between laboratories. Laboratory performance is considered acceptable if there are &lt; 5% deviation from expected results.Evaluation of a result as “deviating from the expected interpretation” should be carefully analysed in a route cause analysis procedure performed by individual participants (self-evaluation) when the EQA results are disclosed. The methods applied have limitations in reproducibility, thus, on repeated testing, the same strain/antimicrobial combination can result in different MIC or Inhibition Zone Diameter values differing by one-fold dilution or ±3mm, respectively. If the expected MIC/Zone Diameter is close to the threshold for categorising the strain as susceptible or resistant, a one-fold dilution/±3mm difference may result in different interpretations. Since this report evaluates the interpretations of MIC/Zone Diameter and not the values, some participants may find their results classified as incorrect even though the actual MIC/Zone Diameter measured is only one-fold dilution/±3mm different from the expected MIC/Zone Diameter. In these cases, the participants should be confident about the good quality of their AST performance.In this report, results from laboratories affiliated with the Human Health (HH) or the Animal Health (AH) Sectors are presented separately. The laboratories are identified by codes and each code is known only by the corresponding laboratory and the organizers. The full list of laboratory codes is confidential and known only by the EQAsia Consortium.This report is approved in its final version by a Technical Advisory Group composed by members of the EQAsia Consortium, and by the EQAsia Advisory Board members Navin Karan (Pacific Pathology Training Centre, New Zealand), Monica Lahra (WHO Collaborating Center for STI and AMR, NSW Health Pathology Microbiology, New South Wales, Australia) and Ben Howden (The Peter Doherty Institute for Infection and Immunity, Australia).<br/

LAMP primers used for <i>bla</i>_oxa-23 and the ITS sequence.

<p>F3: outer forward primer; B3: backward inner primer; LF/LB: loop primersouter backward primer; FIP: forward inner primer; BIP:</p><p>LAMP primers used for <i>bla</i>_oxa-23 and the ITS sequence.</p

Pneumococcal colonization prevalence and density among Thai children with severe pneumonia and community controls.

BACKGROUND:Pneumococcal colonization prevalence and colonization density, which has been associated with invasive disease, can offer insight into local pneumococcal ecology and help inform vaccine policy discussions. METHODS:The Pneumonia Etiology Research for Child Health Project (PERCH), a multi-country case-control study, evaluated the etiology of hospitalized cases of severe and very severe pneumonia among children aged 1-59 months. The PERCH Thailand site enrolled children during January 2012-February 2014. We determined pneumococcal colonization prevalence and density, and serotype distribution of colonizing isolates. RESULTS:We enrolled 224 severe/very severe pneumonia cases and 659 community controls in Thailand. Compared to controls, cases had lower colonization prevalence (54.5% vs. 62.5%, p = 0.12) and lower median colonization density (42.1 vs. 210.2 x 103 copies/mL, p <0.0001); 42% of cases had documented antibiotic pretreatment vs. 0.8% of controls. In no sub-group of assessed cases did pneumococcal colonization density exceed the median for controls, including cases with no prior antibiotics (63.9x103 copies/mL), with consolidation on chest x-ray (76.5x103 copies/mL) or with pneumococcus detected in whole blood by PCR (9.3x103 copies/mL). Serotype distribution was similar among cases and controls, and a high percentage of colonizing isolates from cases and controls were serotypes included in PCV10 (70.0% and 61.8%, respectively) and PCV13 (76.7% and 67.9%, respectively). CONCLUSIONS:Pneumococcal colonization is common among children aged <5 years in Thailand. However, colonization density was not higher among children with severe pneumonia compared to controls. These results can inform discussions about PCV introduction and provide baseline data to monitor PCV impact after introduction in Thailand

Real-time turbidity assays under various conditions using a turbidimeter.

<p>(A) To determine the optimal reaction conditions, a LAMP assay was performed on extracted bacterial DNA at temperatures ranging from 62°C to 67°C. At 65°C, the reaction finished within the shortest period of time, and the negative control remained transparent after 60 minutes of incubation. (B) To determine the detection limit, the extracted DNA templates were serially diluted 10 times (from 2 pg to 2×10⁻⁶ pg) and used in the LAMP assay. The turbidity was evaluated with a turbidimeter every 5 minutes.</p