Hotspots sequences of gyrA, gyrB, parC, and parE genes encoded for fluoroquinolones resistance from local Salmonella Typhi strains in Jakarta.

BACKGROUND: Infection of Salmonella enterica subsp. enterica serovar Typhi is the primary etiology of typhoid fever globally and is common in many developing countries, especially those with dense populations and poor environmental sanitation. Antibiotic fluoroquinolones were used for the treatment in the 1980s due to the resistance to the first-line antibiotics. However, many cases of treatment failure of fluoroquinolones in typhoidal patients have been reported from numerous countries in Asia, Europe, Africa, and America. Mutations in quinolone resistance determining regions (QRDR) genes, gyrA, gyrB, parC, and parE, are found in fluoroquinolone-resistant Salmonella Typhi. Contrast reports came from the S. Typhi isolates in Indonesia, mainly Jakarta and the surroundings, obtained from patients with typhoid fever, with good sensitivity to the fluoroquinolones, i.e., nalidixic acid, ciprofloxacin, moxifloxacin, and levofloxacin. The present study, therefore, aimed to identify the hotspot sequences of gyrA, gyrB, parC, and parE genes of the local S. Typhi strains based on their susceptibility to fluoroquinolones from patients with typhoid fever in Jakarta and its satellite cities. RESULTS: A total of 28 isolates were identified as S. Typhi. All isolates were susceptible to nalidixic acid, levofloxacin, and moxifloxacin. Twenty-seven isolates (96.4%) were susceptible to ciprofloxacin, with one isolate (3.6%) being intermediate. The hotspot sequences of gyrA, gyrB, parC, and parE genes from all isolates were identical to the fluoroquinolone-sensitive reference sequence Salmonella enterica subsp. enterica serovar Typhi Ty2 (NCBI GenBank AE014613.1), including the isolate with intermediate susceptibility. The mutation was not found, and amino acid deduced from all hotspots in susceptible and intermediate isolates showed no replacement in all reported codons. CONCLUSIONS: This study showed that the local S. Typhi strains from Jakarta and surroundings were susceptible to fluoroquinolones (nalidixic acid, ciprofloxacin, levofloxacin, and moxifloxacin), and the hotspot sequences of the gyrA, gyrB, parC, and parE genes were all identical to the reference sequence. Thus, the hotspot sequences of the gyrA, gyrB, parC, and parE genes seemingly were conserved in Jakarta's local S. Typhi strains and could be considered wild type. The phenotypic susceptibility was consistent with the genotypic characteristic without non-synonymous mutations associated with drug resistance.

Diagnostic parameters of the AF Genital System® for detection of Mycoplasma hominis and Ureaplasma urealyticum.

OBJECTIVE: The prevalence of Mycoplasma hominis and Ureaplasma urealyticum (genital mycoplasma) amongst Indonesian women is poorly understood because of limited availability of diagnostic techniques. We sought to compare the diagnostic parameters of the AF Genital System® with those of culture methods and PCR as the gold standard for identification of M. hominis and U. urealyticum in vaginal swab specimens. METHODS: This was an observational diagnostic study. Eighty-eight specimens were collected from patients with abnormal vaginal discharge. Detection of M. hominis and U. urealyticum was performed using the AF Genital System®, culture methods, and PCR. RESULTS: Compared with PCR and culture methods, respectively, the AF Genital System® had sensitivities of 66.6% and 57% (M. hominis) and 55.5% and 77.8% (U. urealyticum). Compared with PCR and culture methods, respectively, the AF Genital System® had specificities of 82.9% and 86.5% (M. hominis) and 82.3% and 84.8% (U. urealyticum). CONCLUSION: The sensitivity of the AF Genital System® for detection of M. hominis and U. urealyticum from vaginal swab samples was lower than that of PCR, but specificity was reasonably good (82% to 83%).

Association of Acinetobacter Baumannii with invasive procedures in hospitalized patients in Jakarta.

INTRODUCTION: Acinetobacter baumannii, a multidrug-resistant Gram-negative opportunist has been known among the cause of nosocomial infection. Risk factors of infection related to A. baumannii have been reported elsewhere. This study aimed to find the association of A. baumannii positive culture and invasive procedures in patients hospitalized in the Intensive Care Unit and Hospital ward in Jakarta. METHODOLOGY: This study was a retrospective, 1:1 matched case-control study with total sampling method from in-patients in the ICU and the Internal Medicine Wards (IMW) of a Private Hospital, North Jakarta in 2015 - 2018. Data retrieved were positive culture of A. baumannii. Positive cultures of multi-sensitive bacteria were included as a control group. Antibiotic susceptibility test was carried out as recommended by Clinical and Laboratory Standards Institute. RESULTS: A total of 88 in-patients were studied, and A. baumannii isolates were identified from 44 patients. Most of A. baumannii showed resistant to almost all antibiotics tested, except for colistin. Bivariate analysis showed a significant association of A. baumannii positive culture and the use of ventilator in the ICU (p = 0,039), and with urinary catheters in the IMW (p = 0,022). Multivariate analysis showed that length of stay also has a significant association to A. baumannii positive culture in the ICU. CONCLUSIONS: The use of ventilators and urinary catheters showed a significant association with Acinetobacter baumannii positive culture in patients in the ICU and in the IMW respectively. All of the A. baumannii isolates were susceptible to colistin.

The molecular epidemiology of Salmonella Typhi across Indonesia reveals bacterial migration.

BACKGROUND: Typhoid fever remains a worldwide problem, but it is particularly common in Southeast Asia, including Indonesia. The causative agent Salmonella Typhi is known to have significant genome plasticity. METHODOLOGY: This study describes genetic fingerprints using restriction fragment length polymorphism with SpeI of chromosomal DNA and pulsed-field gel electrophoresis (PFGE) of S. Typhi isolated from different geographic areas spreading from west to east across Indonesia. RESULTS: A total of 33 SpeI digested S. Typhi chromosomal DNA gave 22 schizotypes, 20 pulsotypes, and 12 subtypes indicating genomic diversity and the presence of more than one clone of S. Typhi. Cluster analysis at a degree of similarity of >or=80% showed four clusters, three of which were associated with geographic area. One cluster (Dice coefficient 0.727-1.000) contained isolates from three different geographic areas (Jakarta, Makasar, Jayapura), spread across Indonesia. CONCLUSIONS: Genetic fingerprinting of S. Typhi in Indonesia showed the presence of endemic strains in localized geographic areas, as well as the movement of one strain type throughout the archipelago.

Trends in antimicrobial susceptibility of gram-negative bacteria isolated from blood in Jakarta from 2002 to 2008.

BACKGROUND: This study examined the susceptibility of Gram-negative bacteria in the bloodstream to antimicrobials with the aim of providing information relevant to the guidance of therapy. METHODOLOGY: Blood specimens received by the Laboratory of Clinical Microbiology, Faculty of Medicine, University of Indonesia, from 2002 to 2008, were analyzed for the presence of Gram-negative bacteria and their susceptibility to four antibiotic groups frequently administered in hospitals and community settings. RESULTS: During the seven-year period leading up to 2008, approximately 68% of Gram-negative bacteria were identified among all positive isolates from blood specimens. The eight most frequent species found were Acinetobacter anitratus (25.8%), Pseudomonas aeruginosa (19.5%), Klebsiella pneumoniae subsp. pneumoniae (14.5%), Enterobacter aerogenes (8%), Salmonella Typhi (7.5%), Escherichia coli (6.2%), Alcaligenes faecalis (5.6%) and Klebsiella oxytoca (3.2%). At 80% susceptibility or greater, Ceftriaxone and Cefotaxime were active only on E. coli and S. Typhi. Cefepime demonstrated activity on all eight species tested except K. pneumonia while Amikacin showed activity against five species, A. faecalis, E. aerogenes, E. coli, K. pneumoniae subsp. pneumoniae and S. Typhi. Gentamycin was active against three species: E. aerogenes, K. oxytoca and S. Typhi. Ciprofloxacin and Levofloxacin significantly differed in their spectrum: while Ciprofloxacin was active against four of the eight species tested (E. aerogenes, E. coli, K. oxytoca, and S. Typhi ), Levofloxacin was similar to Cefepime and was active against all eight species except K. pneumoniae subsp. pneumonia. CONCLUSIONS: Since antimicrobials are broadly used in Jakarta, it is important that the information captured in this study be disseminated.