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OBJECTIVE: Recent spoligotyping results in the island nation of Indonesia had revealed the existence of Mycobacterium tuberculosis complex lineage 3 (MTBC L3) or Central Asian (CAS) strains. In this work, whole-genome sequencing (WGS) - based methods were used to search for the presence of MTBC L3. RESULTS: Two unrelated Indonesian L3 strains discovered by WGS-based SNP phylogenomics are presented here for the first time. Assemblies of their genomes yielded 96.95% (MTBC strain Mtb_S6970) and 98.35% (Mtb_S19106) of the known reference strain H37Rv. Their respective constructed genome coverages are 45.38 ± 12.95x and 63.13 ± 21.10x. The two L3 genomes have 4062 and 4121 genes, respectively, which are well within the number of genes predicted in MTBC strains. Instead of having three rRNA genes usually, Mtb_S6970 possesses four. These L3 isolates exhibit cross-class antibiotic susceptibility. FadD26, fadE24, fbpA, lprO, and panC, which are thought to be important in the pathophysiology of MTBC, were discovered to have 3-7 times more loci in L3 than L2 or L4. The penetration of L3 in the nation, despite its antibiotic sensitivity, is a concerning indicator of borderless global spread that may eventually be overcome by the phenotypes of acquired drug resistance.
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Genoma Bacteriano , Mycobacterium tuberculosis , Secuenciación Completa del Genoma , Indonesia , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/efectos de los fármacos , Mycobacterium tuberculosis/aislamiento & purificación , Secuenciación Completa del Genoma/métodos , Genoma Bacteriano/genética , Filogenia , Humanos , Polimorfismo de Nucleótido Simple/genética , Tuberculosis/microbiologíaRESUMEN
Genomic sequencing has emerged as a powerful tool to enhance early pathogen detection and characterization with implications for public health and clinical decision making. Although widely available in developed countries, the application of pathogen genomics among low-resource, high-disease burden settings remains at an early stage. In these contexts, tailored approaches for integrating pathogen genomics within infectious disease control programs will be essential to optimize cost efficiency and public health impact. We propose a framework for embedding pathogen genomics within national surveillance plans across a spectrum of surveillance and laboratory capacities. We adopt a public health approach to genomics and examine its application to high-priority diseases relevant in resource-limited settings. For each grouping, we assess the value proposition for genomics to inform public health and clinical decision-making, alongside its contribution toward research and development of novel diagnostics, therapeutics, and vaccines.
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Corynebacterium diphtheriae (C. diphtheriae) is the causative agent of diphtheria. The main virulence factor of C. diphtheriae is diphtheria toxin, which is encoded by the tox gene and regulated by the dtxR gene. The tox and dtxR genes are used as genetic markers to identify bacteria causing diphtheria by PCR. Here, we present the whole-genome sequencing (WGS) data of 18 C. diphtheriae isolates from diphtheria outbreaks in different regions in Indonesia. We used these data to identify single nucleotide polymorphisms (SNPs) associated with the tox and dtxR genes to verify the accuracy of the PCR assay and performed molecular typing with a multilocus sequence typing (MLST) approach. The data can be used for further analyses, such as antimicrobial resistance and bacterial virulence factors.
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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 <1 year (55.5%), and 52.9% of them were aged <6 months. Similarly, 72.3% (68/94) of the laboratory-confirmed cases were infants. Both clinical cases and positivity rates tended to be higher in females (155 cases, 38.1%) than in males (119 cases, 29.4%). No confirmed cases were found in children aged ≥10 years, although positive results still occurred in close contact. Age-group and laboratory-confirmed cases were correlated (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.
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Tos Ferina , Bordetella pertussis , Niño , Femenino , Humanos , Indonesia/epidemiología , Lactante , Masculino , Tos Ferina/diagnóstico , Tos Ferina/epidemiología , Tos Ferina/prevención & controlRESUMEN
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.
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Técnicas de Tipificación Bacteriana/métodos , Infecciones por Corynebacterium/microbiología , Corynebacterium/aislamiento & purificación , Reacción en Cadena de la Polimerasa Multiplex/métodos , Proteínas Bacterianas/genética , Corynebacterium/clasificación , Corynebacterium/genética , Cartilla de ADN/genética , Difteria/microbiología , HumanosRESUMEN
Background/aim: The aim of this study was to find out characteristics and patterns of the spread of Corynebacterium diphtheriae isolated from Jakarta and the surrounding areas, using the whole genome sequencing (WGS) technique and multilocus sequence typing (MLST) approach. Materials and methods: The study samples consisted of 86 C. diphtheriae isolates, which were isolated from diphtheria patients and close contacts of patients. The DNA sequencing was carried out using the WGS technique. Data conversion applied the U-gene software. Molecular typing was conducted through the MLST approach, then followed by online data analysis. Results: The results showed that as many as 43 (50%) of all samples examined were new types with the same allele profile, namely 9-1- 13-4-3-3-4. New sequence type C. diphtheriae is registered in the MLST global database as ST534 based on the allele profile. The tox gene analysis in 43 isolates with ST534 indicated that there were three mutation positions, all of which were silent mutations. Conclusion: The main cause of diphtheria in Jakarta and the surrounding areas is a new sequence type of C. diphtheriae registered as ST534.