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Diphtheria is a vaccine-preventable disease. The clinical features and complications of diphtheria are associated with toxins produced by the causative bacteria. Diphtheria toxin synthesis is encoded by tox gene. This study aimed to provide an overview of the DNA sequences of the tox gene of Corynebacterium diphtheriae causing diphtheria in several region of Indonesia. A total of 65 Corynebacterium diphtheriae isolated from several provinces in Indonesia (2010-2017) were used as samples. Isolates recultured on blood agar medium (BA), incubated at 37 0 C overnight. DNA extraction conducted using the QiaAmp DNA Mini Kit. The DNA sequencing was carried out using the Whole Genome Sequencing (WGS) approach. The data conversion and analysis conducted using U-gene and BioEdit programs. Examination of 65 isolate C. diphtheriae with 1683 bp of tox gene sequences showed that there are 3 patterns of gene sequences with 3 mutation site. All mutations were silent mutation. The mutation sites were also not commonly used as 3’end binding site of the PCR primer. We concluded that tox gene of C. diphtheriae that causes diphtheria in some provinces in Indonesia have limited variations and these variations do not encode amino acid changes. This indicates that the vaccines used in Indonesia are still in accordance with the variations in circulating bacteria and PCR can be used for screening and predicting the toxigenicity of diphtheria-causing bacteria. Keywords: C. diphtheriae, gene tox, diphtheria, Indonesia Abstrak Difteri merupakan salah satu penyakit yang dapat dicegah dengan imunisasi (PD3I). Gambaran klinis dan komplikasi difteri dikaitkan dengan toksin yang diproduksi oleh bakteri penyebab. Sintesis toksin difteri dikode oleh gen tox. Penelitian ini bertujuan untuk memberikan gambaran sekuens DNA gen tox Corynebacterium diphtheriae penyebab difteri di beberapa wilayah Indonesia. Sebanyak 65 isolat C. diphtheriae tersimpan milik Badan Litbangkes yang diisolasi dari beberapa wilayah Indonesia tahun 2010- 2017 dijadikan sebagai sampel. Rekultur dilakukan pada medium agar darah (BA), diinkubasi pada suhu 37 o C selama sehari semalam. Ekstraksi DNA menggunakan kit QiaAmp DNA Minikit. Sekuensing DNA dilakukan dengan pendekatan Whole Genome Sequencing (WGS). Konversi dan analisis data menggunakan program U-gene dan BioEdit.Pemeriksaan 65 isolat C. diphtheriae dengan 1683 bp sekuens gen tox menunjukkan ada 3 pola sekuens gen dengan 3 lokasi mutasi. Seluruh mutasi bersifat silent mutation. Lokasi mutasi juga bukan merupakan tempat penempelan ujung 3’ primer PCR yang umum digunakan. Berdasarkan hasil penelitian dapat disimpulkan bahwa variasi gen tox yang ditemukan pada C. diphtheriae penyebab difteri di Indonesia memiliki variasi yang terbatas dan mutasi yang ada tidak mengkode perubahan asam amino. Hal ini mengindikasikan bahwa vaksin yang digunakan di Indonesia masih sesuai dengan variasi bakteri yang bersirkulasi. Hasil penelitian juga mengindikasikan bahwa PCR dapat digunakan untuk skrining dan memprediksi toksigenisitas bakteri penyebab difteri. Kata kunci : C. diphtheriae, gen tox, difteri, Indonesia

Identification of ESBL-E.coli from environment without selective medium will be challenging to do considering that E.coli mixes with various other microorganisms in the environment. This study aimed to determine the performance of TBX Agar supplemented with Cefotaxime as a selective medium for ESBL-E. coli screening from 138 water samples of environmental sampling obtained from rivers, open sewers in the market, poultry slaughterhouses and hospital waste water inlets and outlets around Jakarta. Laboratory examinations were carried out through the filtration stage, inoculation on the TBX Agar supplemented with Cefotaxime medium as well as species confirmation and ESBL with the indol test and double-disk test. The results showed that 87.08% (40-100%) of suspect colonies growing on TBX Agar supplemented with Cefotaxime medium were confirmed as E.coli and 82.51% (12-100%) were confirmed as ESBL-E.coli. However, there was no correlation between TBX Agar supplemented with Cefotaxime performance and sampling locations. Based on the results of the study, it can be concluded that the TBX supplemented with Cefotaxime medium can be used for ESBL-E.coli screening in the environment, but further confirmation is needed using the indole and double-disk tests. Keywords: Escherichia coli, ESBL, TBX Agar suplemented with Cefotaxime Abstrak Identifikasi ESBL-E.coli tanpa medium selektif akan sangat sulit dilakukan pada sampel lingkungan mengingat ESBL-E.coli bercampur dengan berbagai mikroorganisme lainnya. Tujuan penelitian ini yaitu untuk mengetahui performa TBX Agar yang disuplementasi Cefotaxime sebagai medium selektif untuk skrining ESBL-E.coli. Sampel penelitian sebanyak 138 sampel air lingkungan yang diambil dari sungai, saluran pembuangan terbuka di pasar, rumah pemotongan hewan unggas (RPHU) serta inlet dan outlet limbah rumah sakit di sekitar Jakarta. Pemeriksaan laboratorium melalui tahapan filtrasi, inokulasi pada medium TBX Agar dengan suplementasi Cefotaxime serta konfirmasi spesies dan ESBL dengan uji indol dan double-disk test. Hasil menunjukkan bahwa koloni tersangka yang tumbuh pada medium TBX Agar dengan suplementasi Cefotaxime sebanyak 87,08% (40-100%) terkonfirmasi sebagai E.coli dan 82,51% (12-100%) terkonfirmasi sebagai ESBL-E.coli. Namun, tidak ada hubungan antara performa TBX Agar dengan suplementasi Cefotaxime dengan lokasi pengambilan sampel. Berdasarkan hasil penelitian dapat disimpulkan bahwa medium TBX Agar dengan suplementasi Cefotaxime cocok digunakan untuk skrining ESBL-E.coli di lingkungan namun tetap diperlukan konfirmasi lanjut menggunakan uji indol dan double disk test. Kata kunci: Escherichia coli, ESBL, TBX Agar suplemented with Cefotaxime

Background: In Corynebacterium diphtheriae, the dtxR gene plays a role in regulating diphtheria toxin synthesis. The dtxR gene is often used as a marker for identifying C. diphtheriae by the polymerase chain reaction (PCR) method because it is present in all strains of this bacterium. Mutations in the dtxR gene can cause the over-synthesis of diphtheria toxin and reduce PCR assays' sensitivity. Objectives: This study aimed to describe the polymorphisms in the dtxR gene of C. diphtheriae isolated from a diphtheria outbreak in Indonesia. Methods: Forty-eight isolates of C. diphtheriae were obtained from clinical samples (throat/nasopharyngeal swabs) of diphtheria cases and close contacts. The isolates were revived on a blood agar plate (BAP), bacterial colonies were harvested, and deoxyribonucleic acid (DNA) was extracted. The DNA sequencing was carried out using a Whole-genome Sequencing (WGS) approach. The data were converted and analyzed with U-gene software. The dtxR gene analysis was performed with C. diphtheriae PW8 as references. Results: There were 59-point mutation locations in 48 isolates examined. None of these single nucleotide polymorphisms (SNPs) coded for amino acid changes. Based on the mutation pattern, seven clades/groups of the dtxR gene of 48 C. diphtheriae isolates were examined. Conclusions: At least seven types of DNA sequences and more than 50 SNPs of the dtxR gene were identified in 48 C. diphtheriae isolates from a diphtheria outbreak in Indonesia. Although all of them are silent mutations, they must be considered in the design of PCR examination in diphtheria laboratories.

Background: Corynebacterium diphtheriae, C. ulcerans, and C. pseudotuberculosis are known as diphtheria-causing bacteria. Although diphtheria therapy is administered based on the clinical manifestations, some cases are mild and atypical. The immediate and accurate identification of diphtheria-causing bacteria is of paramount importance to prevent the spread of the disease and provide case management as early as possible. Unfortunately, conventional methods as the gold standard are time-consuming. Objectives: This study aimed to develop and implement a multiplex real-time PCR with the dtxR and tox genes as the target to identify three species of diphtheria-causing bacteria and screen their toxigenicity quickly and accurately. Methods: The research sample encompassed seven reference strains, one synthetic DNA, 30 archived isolates, and 924 clinical specimens isolated from 311 diphtheria cases and 613 close contacts. The conventional methods as the gold standard and the established PCR assay were used to verify the results of multiplex real-time PCR developed in this study. Results: The multiplex real-time PCR could identify seven reference strains, one synthetic DNA, and 30 archived isolates as accurately as the conventional methods and the established PCR. Similar to established PCR, the multiplex real-time PCR identified diphtheria-causing bacteria in 120 (38.6%) out of 311 and 12 (2%) out of 613 clinical specimens from diphtheria cases and close contacts, respectively. Meanwhile, the conventional methods identified diphtheria-causing bacteria in 79 (25.4%) out of 311 and three (0.5%) out of 613 clinical specimens. Conclusions: The multiplex real-time PCR developed in this study can be used to identify three species of diphtheria-causing bacteria and screen their toxigenicity quickly and accurately. However, in this study, no diphtheria-causing bacteria other than C. diphtheriae was found in the clinical samples using the PCR or conventional methods. PCR is more sensitive than the conventional methods and can be used as an additional test in diphtheria laboratories.

Background: The World Health Organization reported Indonesia as one of the countries with the most prevalent cases of diphtheria worldwide. The microbiological aspects of diphtheria-inducing bacteria are of great significance in tracing disease transmission and case management. However, clinical aspects are critical for updating clinical features and case management in the field, which may sometimes differ from theoretical foundations. Objectives: This study aimed to identify the microbiological and clinical aspects, including molecular typing and case fatality rates, in diphtheria-confirmed cases from the capital city of Indonesia, Jakarta, and surrounding areas in 2017. Methods: The microbiological aspect of 40 diphtheria-confirmed cases were obtained by re-identify diphtheria-inducing bacteria isolated from the samples, while the clinical aspects of the cases were obtained from the medical records and epidemiological data. The chi-square test was used to examine the correlation between fatal cases and myocarditis and diphtheria antitoxin administration delay. In this study, P ≤ 0.05 was set as the significance level. Results: All 40 diphtheria confirmed cases were induced by toxigenic Corynebacterium diphtheriae with two biotypes, namely intermedius (60.0%) and mitis (40.0%). There are six sequence types of bacteria with two main sequence types, ie, ST534 (46.4%) and ST377 (35.7%). The proportions of cases that had a fever and sore throat were 72.5% and 77.5%, respectively; however, the prevalence rates of the cases with pseudomembrane and bull neck were 100% and 47%, respectively. Most cases were administered a combination of penicillin or erythromycin with other antibiotics (40%), and 22.5% of the cases only received penicillin. Myocarditis was noticed in three fatal cases, and their relationship was statistically significant (P = 0.000). All five fatal cases (12.5% of cases) received diphtheria antitoxin (DAT) lately or had not received it yet. Conclusions: Toxigenic C. diphtheriae with two biotypes (namely mitis and intermedius) and two main sequence types (ie, ST534 and ST377) was the causative agent of diphtheria-confirmed cases from Jakarta and surrounding areas in 2017. It was also concluded that those fatal cases were correlated with myocarditis complications.

Background: Indonesia is one of the five countries with the highest number of diphtheria cases worldwide. Diphtheria is caused by the toxigenic strains Corynebacterium diphtheriae, C. ulcerans, and C. pseudotuberculosis. The diphtheria-causing bacteria can be identified using conventional and molecular methods, including polymerase chain reaction (PCR) assay. We used the PCR assay as additional testing, because in island countries like Indonesia, specimen transport is a serious challenge to maintaining bacterial survival. Objectives: This study aimed to evaluate the PCR assay as additional testing to identify diphtheria-causing bacteria in the diphtheria laboratory. Methods: In this cross-sectional study, a total of 178 pairs of the throat and nasal swabs from diphtheria suspected cases and close contacts were collected from seven provinces in Indonesia in 2016. All samples were directly identified by the conventional method and multiplex PCR assay. Statistical analysis was conducted using the 2 × 2 tables to determine the sensitivity and specificity of both methods, while the χ2 test was used to examine the correlation between specimen examination delay and the differentiation of results. A P-value < 0.05 was considered as statistically significant. Results: Out of 178 examined samples, eight samples were identified as diphtheria-positive by both the conventional method and PCR assay, while nine samples were only detected by the PCR assay. All diphtheria-causing bacteria found in the positive samples were toxigenic C. diphtheriae. The diphtheria-causing bacteria were found in 27.6% of cases and 6.0% of close contacts using the PCR assay versus 13.8% of cases and 2.7% of close contacts using the conventional method. Statistical analysis showed that the PCR assay is about twice more sensitive than the conventional method. There was a significant correlation between the differentiation of results and > 72 hours’ specimen examination delay with a P-value of 0.04 (< 0.05). Conclusions: The PCR assay is more sensitive than the conventional method to identify diphtheria-causing bacteria and may be applied as additional testing to increase the positivity rate of diphtheria-confirmed cases in Indonesia as an archipelago country where geographical factors and specimen transport are real obstacles.

In diphtheria laboratory examinations, the PCR test can be applied to isolates and clinical specimens. This study aimed to develop a PCR assay to identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types. Seven reference isolates, four synthetic DNA samples, 36 stored isolates, and 487 clinical samples used for PCR optimization. The PCR results was confirmed by DNA sequence analysis. The results of the PCR examination of the 7 reference isolates and 36 stored isolates were similar to the results obtained using conventional methods as gold standard, both for diphtheria-causing and non-diphtheria-causing bacteria. The validation of the PCR results using DNA sequence analysis showed that there was no mispriming or misamplification. The multiplex PCR assay developed in this study could correctly identify the species and toxigenicity of diphtheria-causing bacteria, including the prediction of some NTTB types not yet covered by established PCR methods.

Pertussis cases have been reported most frequently in developed countries, but they are predicted to be the most prevalent in developing countries. Indonesia, a developing country, routinely conducts case-based surveillance for pertussis. We reviewed the data on pertussis cases and close contacts based on clinical sample documents examined in the National Reference Laboratory for pertussis, Indonesia (2016–2020). Our objective was to analyze the laboratory and epidemiological aspects of pertussis cases and close contacts, particularly to evaluate the implementation of a 5-year case-based surveillance of pertussis in Indonesia. Data were collected from sample documents and annual laboratory reports between January 2016 and December 2020. We analyzed the proportion of pertussis cases and close contacts by geographic region, year, age, and sex. We used the χ2 test to correlate the laboratory and epidemiological data. In total, 274 clinical cases of pertussis and 491 close contacts were recorded in 15 provinces. The peak number of cases occurred in 2019, with a positivity rate (percentage of laboratory-confirmed cases) of 41.23% (47/114). Clinical cases were dominated by infants aged p = 0.00). Clinical and confirmed cases of pertussis occurred mostly in the early age group and may be lower in those aged ≥10 years, especially in confirmed cases. New policies are needed for pertussis prevention at an early age, as well as the application of serology tests to increase laboratory-confirmed cases in children aged ≥10 years.