SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia.

Objectives: To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. Methods: A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. Results: Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). Conclusion: The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.

The trend of paediatric cases during the first year of the COVID-19 pandemic in North Sumatra, Indonesia.

Objective: The aim of the study was to describe the epidemiology of coronavirus disease 2019 (COVID-19) cases in children in North Sumatra Province during the period June 2020 to July 2021. Methods: This study included samples from children in North Sumatra Province aged 0-17 years, suspected to have COVID-19. A case of COVID-19 was confirmed by RT-PCR in the Microbiology Laboratory, Faculty of Medicine, Universitas Sumatera Utara, Indonesia. Data were collected from June 2020 to July 2021. Demographic data including age, sex, and date of diagnosis were collected. A descriptive statistical analysis was performed, and ratios or percentages were compared. Results: A total of 117 650 people were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and 2222 (1.9%) children were positive. The age group 6-11 years had the highest proportion of cases with 679/2222 cases (30.6%). Overall, the number of positive COVID-19 cases peaked in July 2021, with 650 cases and a positivity rate of 3.0%. In 2020, the greatest proportion of cases occurred in the age group of 12-14 years; however, this changed to the age group 6-11 years in 2021. Conclusions: COVID-19 was detected in all paediatric age groups in North Sumatra during the study period. Incidence peaks occurred due to mass gatherings, public holidays, and the introduction of a new variant in Indonesia. Children accounted for a much higher proportion of SARS-CoV-2 infection compared to those reported in other studies and could have played a role as the source of transmission in society.

Use of saliva as an alternative diagnostic method for diagnosis of COVID-19.

Background: Mass population testing has been recommended to contain the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the use of nasopharyngeal swab specimens has caused many logistic challenges. This study investigated the sensitivity and specificity of saliva as a non-invasively-obtained specimen for molecular detection of SARS-CoV-2 RNA. Methods: In total, 153 patients with confirmed coronavirus disease 2019 (COVID-19) who had been admitted to the regional referral hospital or who self-isolated at home were included in this study. Nasopharyngeal swab specimens and saliva samples were collected on the same day, and were tested for SARS-CoV-2 infection using reverse transcriptase polymerase chain reaction. Results: The sensitivity and specificity of saliva samples were 81.5% and 76.4%, respectively, in cases that had been confirmed as COVID-19 using nasopharyngeal swab samples. Positive predictive values and negative predictive values were 92.3% and 54.1%, respectively. The highest detection rates were found among samples collected 4-7 days since symptom onset. Conclusion: Saliva samples showed comparable performance to nasopharyngeal swab specimens for the diagnosis of COVID-19 in adults. The performance of saliva as a diagnostic specimen for COVID-19 testing is particularly significant during the first week of symptoms.

Sensitivity of nasopharyngeal swab and saliva specimens in the detection of SARS-CoV-2 virus among boarding school girls.

Objectives: With the reopening of schools, the detection of coronavirus disease 2019 (COVID-19) in children is very important in order to prevent outbreaks in schools and to reduce the risk of more severe post-COVID-19 complications. Various specimens can be used to detect the SARS-CoV-2 virus, and saliva has been considered as an alternative specimen in adults. However, data in children are lacking, especially among the female population. This study compared the efficacy of saliva specimens with nasopharyngeal swab specimens for the detection of severe acute respiratory syndrome coronavirus-2 using reverse transcriptase polymerase chain reaction. Methods: This study evaluated the diagnostic performance of saliva among boarding school girls at three time points: diagnosis, and days 7 and 14 since first confirmation using a nasopharyngeal swab specimen. Eighty-four paired samples from 36 individuals were compared. Nasopharyngeal samplings were carried out by trained health officers, while saliva samplings were performed independently by children. Results: The overall percentage agreement (OPA) between saliva and nasopharyngeal swabs was 50.2%. The OPA was 52.8% at diagnosis, and this increased slightly to 54.2% at day 7, and subsequently decreased to 45.8% at day 14. Saliva specimens had sensitivity of 44.6%, specificity of 80.0%, positive predictive value of 94.2% and negative predictive value of 16.3% compared with nasopharyngeal swab specimens for the diagnosis of COVID-19. Conclusions: The use of saliva as an alternative specimen for the diagnosis of COVID-19 in children should be considered carefully. Thorough sampling instructions should be given in order to minimize bias in the findings.

A comparative pilot study on Gram-negative bacteria contaminating the hands of children living in urban and rural areas of Indonesia versus Germany - A suitable monitoring strategy for diarrhea risk assessment?

Diarrhea is the second leading cause of death mainly effecting young children. Often it is the result of fecal-oral pathogen transmission. We aimed to investigate whether monitoring the prevalence of Gram-negative bacteria on the hands of asymptomatic children is suitable as an indicator of fecal contamination of the environment in their playground. We compared the prevalence of Gram-negative bacteria on the hands of children, who live in the German city of Göttingen, an urban area in a high-income country, with the situation in Medan as an urban area and Siberut as a rural area both in the middle-income country Indonesia. A total of 511 children at the age of 3 months to 14 years were asked to put their thumb print on MacConkey agar, which was used to screen for the presence of Gram-negative bacteria. These were subsequently identified by using MALD-TOF mass spectrometry and classified into the order Enterobacterales, Pseudomonadales, and others. The highest burden of hand contamination was found in children from rural Siberut (66.7%) followed by children from urban Medan (53.9%), and from urban Göttingen (40.6%). In all three study sites, hand contamination was lower in the youngest (<1 year) and oldest age groups (10-14 years) and highest in the age group 5-9 years. Bacteria of the order Enterobacterales possibly indicating fecal contamination were most prevalent in Siberut (85.1%) followed by Medan (62.9%) and Göttingen (21.5%). Most facultative and obligate gastrointestinal pathogens such as Escherichia coli (n = 2) and Providencia rettgeri (n = 7), both being members of the order Enterobacterales, as well as Aeromonas caviae (n = 5), and Vibrio cholerae (n = 1) both belonging to other orders were nearly exclusively identified on the hands of children in Siberut. This result was not surprising, because hygienic conditions were lowest in Siberut. Only one isolate of A. caviae was found in Medan, and no facultative gastrointestinal pathogen was identified on the hands of children from Göttingen. Our pilot study therefore indicates that investigating hands of children for the prevalence of Gram-negative bacteria using selective media are a helpful method to monitor hygienic conditions, and thereby assess the risk for diarrhea-causing bacterial pathogens in the environment.

Missing Cases of Bacteriologically Confirmed TB/DR-TB from the National Treatment Registers in West and North Sumatra Provinces, Indonesia.

This study aimed to assess the percentage of confirmed drug-sensitive (DS) TB and drug-resistant (DR) TB patients who were missing in the national treatment registration in North Sumatra and West Sumatra, where treatment services for DR-TB in North Sumatra are relatively well established compared with West Sumatra, where the system recently started. Confirmed DS/DR-TB records in the laboratory register at 40 government health facilities in 2017 and 2018 were traced to determine whether they were in the treatment register databases. A Jaro-Winkler soundexed string distance analysis enhanced by socio-demographic information matching had sensitivity and specificity over 98% in identifying the same person in the same or different databases. The laboratory data contained 5885 newly diagnosed records of bacteriologically confirmed TB cases. Of the 5885 cases, 1424 of 5353 (26.6%) DS-TB cases and 133 of 532 (25.0%) DR-TB cases were missing in the treatment notification database. The odds of missing treatment for DS-TB was similar for both provinces (AOR = 1.0 (0.9, 1.2), but for DR-TB, North Sumatra had a significantly lower missing odds ratio (AOR = 0.4 (0.2, 0.7). The system must be improved to reduce this missing rate, especially for DR-TB in West Sumatra.

Prevalence of Panton-Valentine leucocidin ( pvl) and exfoliative toxin A ( eta) gene within methicillin resistant and susceptible Staphylococcus aureus in an urban tertiary hospital: A molecular epidemiology pilot study.

Background: Staphylococcus aureus is well known to cause a multitude of clinical manifestations, from mild to severe bloodstream infections that could lead to death. Infections are common, either in community-acquired or hospital-acquired settings, and treatment remains a challenge due to methicillin-resistant Staphylococcus aureus (MRSA). The pathogenesis of S. aureus is mediated by several cell-surface and secreted virulence factors. The virulence factors discussed in this study are Panton-Valentine leucocidin ( pvl) and exfoliative toxin A ( eta). Identifying both pvl and eta gene may help in studying bacterial pathogenesis and biology thus creating possible therapeutic pathway or intervention.Our pilot study aimed to observe pvl and eta as virulence gene prevalence in a North Sumatera tertiary referral health center. Methods: Our study was a descriptive-analytical observational study with a cross-sectional design in which we collected isolates over a single time period. The frequency of genes is reported as a percentage comparison between MRSA and methicillin-susceptible S. aureus (MSSA). Qualitative gene prevalence analysis was carried out using the polymerase chain reaction (PCR). Results: Our results showed that from 38 MRSA sample isolates, 32 samples were found to be pvl-positive, or 84,3% of the total samples. From 40 MSSA sample isolates, one sample was found to be pvl-positive MSSA, or 97,5%. Regarding eta, from 38 MRSA sample isolates, 81,6% of the total sample did not have eta, while from 40 MSSA sample isolates, all samples were found to be positive for eta. We found that both pvl and eta were significantly more likely to be expressed in the MSSA strain. Conclusions: Our study shows that pvl and eta are more likely expressed in MSSA strains than in MRSA strains in Indonesia.

Clinical Epidemiology of Pediatric COVID-19 Delta Variant Cases From North Sumatra, Indonesia.

The Delta variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) dominated the coronavirus disease 2019 (COVID-19) pandemic in 2021. Here we report the Delta variant among pediatric cases in North Sumatra, Indonesia, from June to July 2021. Whole-genome sequencing (WGS) from 18 new COVID-19 pediatric patients showed that six were B.1.459 and six were B.1.466.2, known variants in Indonesia in clade 20A. Six were the Delta variant B.1.617.2 of clade 21A, with five on one branch and one on a distant branch consistent with that patient's geographic separation, suggesting at least two introductions to the region. Variants tended to be spatially clustered, and four children with Delta variant had an adult infected household member, all of whom had lower real-time polymerase chain reaction cycle threshold (Ct) values compared with the child. No temporal trends were observed for Ct. These data support a paradigm shift with children being highly susceptible to the Delta variant and a priority for vaccination.

Performance of Xpert MTB/RIF and sputum microscopy compared to sputum culture for diagnosis of tuberculosis in seven hospitals in Indonesia.

Introduction: Tuberculosis (TB) is a major public health concern in Indonesia, where the incidence was 301 cases per 100,000 inhabitants in 2020 and the prevalence of multi-drug resistant (MDR) TB is increasing. Diagnostic testing approaches vary across Indonesia due to resource limitations. Acid-fast bacilli (AFB) smear is widely used, though Xpert MTB/RIF has been the preferred assay for detecting TB and rifampicin resistance since 2012 due to higher sensitivity and ability to rapidly identify rifampicin resistance. However, <1,000 Xpert instruments were available in Indonesia as of 2020 and the Xpert supply chain has suffered interruptions. Methods: We compared the performance of Xpert MTB/RIF and AFB smear to facilitate optimization of TB case identification. We analyzed baseline data from a cohort study of adults with pulmonary TB conducted at seven hospitals across Indonesia. We evaluated sensitivity and specificity of AFB smear and Xpert MTB/RIF using Mycobacterium tuberculosis (Mtb) culture as the gold standard, factors associated with assay results, and consistency of Xpert MTB/RIF with drug susceptibility test (DST) in detecting rifampicin resistance. Results: Sensitivity of AFB smear was significantly lower than Xpert MTB/RIF (86.2 vs. 97.4%, p-value <0.001), but specificity was significantly better (86.7 vs. 73.3%, p-value <0.001). Performance varied by hospital. Positivity rate for AFB smear and Mtb culture was higher in subjects with pulmonary cavities and in morning sputum samples. Consistency of Xpert MTB/RIF with DST was lower in those with rifampicin- sensitive TB by DST. Discussion: Additional evaluation using sputa from primary and secondary Indonesian health centers will increase the generalizability of the assessment of AFB smear and Xpert MTB/RIF performance, and better inform health policy. Clinical trial registration: [https://clinicaltrials.gov/], identifier [NCT027 58236].

Appropriateness of diagnosis and antibiotic use in sepsis patients admitted to a tertiary hospital in Indonesia.

OBJECTIVE: To evaluate the diagnostic and antibiotic treatment strategies for patients suspected of sepsis, in a tertiary hospital in Indonesia. This can identify areas for improvement in care provided, and inform diagnostic and antimicrobial stewardship activities within the hospital. METHODS: Retrospective review of medical records with regards to the diagnosis and management of adult patients with sepsis admitted to a tertiary hospital in Indonesia. We assessed the diagnostic process, and whether or not the antibiotic treatment provided was appropriate for the diagnosis. Appropriateness of antibiotic treatment was classified as being definite appropriate, probable appropriate, inappropriate, or unknown. RESULTS: The study included 535 adult patients, of whom 295 (55%) were diagnosed with a community-acquired sepsis, and 240 (45%) with a hospital-acquired sepsis. A specimen for culture and antimicrobial susceptibility testing was collected from three out of four patients (392/535). All but 10 patients had information on antibiotic treatment at the time of sepsis diagnosis. Of those, nearly 50% (257/525) of the patients received antibiotic treatment with unknown appropriateness because no cultures were taken (n = 141) or all cultures were negative (n = 116). Just 3.4% and 9.1% of the patients received definite or probable appropriate antibiotic treatment, respectively. CONCLUSIONS: There is a clear need in encouraging attending physicians to obtain the much-required blood cultures, or cultures from the suspected source of infection before empirical antibiotic treatment is started. This will improve the use of appropriate antibiotic treatment strategies, and contribute to antimicrobial stewardship.

Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia.

Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia.Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant Mycobacterium tuberculosis in Java, Indonesia.Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared.Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS-MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33-76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population.Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.

Laboratory-based versus population-based surveillance of antimicrobial resistance to inform empirical treatment for suspected urinary tract infection in Indonesia.

Surveillance of antimicrobial resistance (AMR) enables monitoring of trends in AMR prevalence. WHO recommends laboratory-based surveillance to obtain actionable AMR data at local or national level. However, laboratory-based surveillance may lead to overestimation of the prevalence of AMR due to bias. The objective of this study is to assess the difference in resistance prevalence between laboratory-based and population-based surveillance (PBS) among uropathogens in Indonesia. We included all urine samples submitted to the laboratory growing Escherichia coli and Klebsiella pneumoniae in the laboratory-based surveillance. Population-based surveillance data were collected in a cross-sectional survey of AMR in E. coli and K. pneumoniae isolated from urine samples among consecutive patients with symptoms of UTI, attending outpatient clinics and hospital wards. Data were collected between 1 April 2014 until 31 May 2015. The difference in percentage resistance (95% confidence intervals) between laboratory- and population-based surveillance was calculated for relevant antibiotics. A difference larger than +/- 5 percent points was defined as a biased result, precluding laboratory-based surveillance for guiding empirical treatment. We observed high prevalence of AMR ranging between 63.1% (piperacillin-tazobactam) and 85% (ceftriaxone) in laboratory-based surveillance and 41.3% (piperacillin-tazobactam) and 74.2% (ceftriaxone) in population-based surveillance, except for amikacin and meropenem (5.7%/9.8%; 10.8%/5.9%; [laboratory-/population-based surveillance], respectively). Laboratory-based surveillance yielded significantly higher AMR prevalence estimates than population-based surveillance. This difference was much larger when comparing surveillance data from outpatients than from inpatients. All point estimates of the difference between the two surveillance systems were larger than 5 percent points, except for amikacin and meropenem. Laboratory-based AMR surveillance of uropathogens, is not adequate to guide empirical treatment for community-based settings in Indonesia.

Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes.

Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool.

Rethinking Antimicrobial Resistance Surveillance: A Role for Lot Quality Assurance Sampling.

Global surveillance of antimicrobial resistance (AMR) is a key component of the 68th World Health Assembly Global Action Plan on AMR. Laboratory-based surveillance is inherently biased and lacks local relevance due to aggregation of data. We assessed the feasibility, sensitivity, and affordability of a population-based AMR survey using lot quality assurance sampling (LQAS), which classifies a population as having a high or low prevalence of AMR based on a priori defined criteria. Three studies were carried out in Medan and Bandung, Indonesia, between April 2014 and June 2017. LQAS classifications for 15 antibiotics were compared with AMR estimates from a conventional population-based survey, with an assessment of the cost of a single LQAS classification using microcosting methodology, among patients suspected of urinary tract infection at 11 sites in Indonesia. The sensitivity of LQAS was above 98%. The approach detected local variation in the prevalence of AMR across sites. Time to reach LQAS results ranged from 47 to 138 days. The average cost of an LQAS classification in a single facility was US$466. The findings indicate that LQAS-based AMR survey is a feasible, sensitive, and affordable strategy for population-based AMR surveys, providing essential data to inform local empirical treatment guidelines and antimicrobial stewardship efforts.

Predictive value of the urinary dipstick test in the management of patients with urinary tract infection-associated symptoms in primary care in Indonesia: a cross-sectional study.

OBJECTIVE: To assess the test characteristics of a urine dipstick test in predicting a positive urine culture in an outpatient setting in Indonesia. DESIGN: Cross-sectional study. SETTING: Two outpatient clinics in Medan, Indonesia. PARTICIPANTS: 616 consecutively enrolled participants suspected of having a urinary tract infection. OUTCOME MEASURES: The primary outcome is the estimates of accuracy (sensitivity, specificity, predictive values) where urine culture is the reference test. The secondary outcome is the post-test probability of a positive urine culture. RESULTS: The optimal test characteristics were obtained when index test positivity was defined as any leucocyte esterase reaction and/or a nitrite reaction and reference test positivity was defined as a urine culture with a growth of at least 103 colony-forming units/mL (sensitivity: 88.2% (95% CI 81.6 to 93.1), negative predictive value: 93.0% (95% CI 88.9 to 95.9)). The post-test probability of a positive urine culture after a negative urinary dipstick test was 7% in the obstetric/gynaecology clinic and 8% in the internal medicine clinic. CONCLUSION: The use of a urine dipstick test in a rule-out strategy can reduce the need for urine culture and avoid the prescription of (ineffective) antibiotics in a non-urology outpatient setting.

Antimicrobial resistance in uropathogens and appropriateness of empirical treatment: a population-based surveillance study in Indonesia.

Objectives: Urinary tract infections (UTIs) are a common reason for empirical treatment with broad-spectrum antibiotics worldwide. However, population-based antimicrobial resistance (AMR) prevalence data to inform empirical treatment choice are lacking in many regions, because of limited surveillance capacity. We aimed to assess the prevalence of AMR to commonly used antimicrobial drugs in Escherichia coli and Klebsiella pneumoniae isolated from patients with community- or healthcare-associated UTIs on two islands of Indonesia. Methods: We performed a cross-sectional patient-based study in public and private hospitals and clinics between April 2014 and May 2015. We screened patients for symptoms of UTIs and through urine dipstick analysis. Urine culture and susceptibility testing were supported by telemicrobiology and interactive virtual laboratory rounds. Surveillance data were entered in forms on mobile phones. Results: Of 3424 eligible patients, 3380 (98.7%) were included in the final analysis, and yielded 840 positive cultures and antimicrobial susceptibility data for 657 E. coli and K. pneumoniae isolates. Fosfomycin was the single oral treatment option with resistance prevalence <20% in both E. coli and K. pneumoniae in community settings. Tigecycline and fosfomycin were the only options for treatment of catheter-associated UTIs with resistance prevalence <20%, whilst the prevalence of resistance to meropenem was 21.3% in K. pneumoniae . Conclusions: Patient-based surveillance of AMR in E. coli and K. pneumoniae causing UTIs indicates that resistance to the commonly available empirical treatment options is high in Indonesia. Smart AMR surveillance strategies are needed to inform policy makers and to guide interventions.