Objectives Cases of nosocomial carbapenem-resistant Klebsiella pneumoniae (CRKP) have been increasing steadily since the 1990s. In this study, we sought to assess CRKP clonal diversity and patterns of dissemination at Hospital Canselor Tuanku Muhriz (HCTM), a tertiary university hospital located in Kuala Lumpur, Malaysia. Methods: From January 2022 to December 2023, all CRKP isolates from HCTM were included in the investigation. Associated patient demographic data and clinical histories were retrieved from hospital records. Antibiotic susceptibility data for the collected isolates were obtained from the HCTM diagnostic laboratory. Molecular typing was performed using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) to identify genetic clusters. Based on ERIC-PCR clustering results and epidemiological investigations, selected CRKP isolates were subjected to whole-genome sequencing (WGS) to validate clonal relatedness, identify antimicrobial resistance genes, and establish phylogenomic relationships. Results: During the study period, a total of 147 CRKP isolates were recovered from various wards across HCTM. All isolates exhibited resistance to imipenem, meropenem, or ertapenem, with 124 isolates confirmed as carbapenemase producers. ERIC-PCR identified 24 genetic clusters disseminated across 23 wards within HCTM. Twelve CRKP isolates were selected for WGS based on integrated epidemiological investigation and ERIC-PCR genotyping; sequence typing revealed ST17 as the dominant circulating CRKP lineage in the intensive care unit, ward 6E, and possibly across the hospital. The carbapenemase gene bla_NDM was detected in all WGS-analyzed CRKP isolates. Conclusion: Integrating epidemiological investigation, phenotypic testing, molecular typing, and WGS is essential to understand resistance dynamics, map transmission, and guide hospital infection prevention strategies.
Objectives Tuberculosis (TB) and drug-resistant TB (DR-TB) are national health burdens in Vietnam. In this study, we investigated the prevalence of rifampicin (RIF) and/or isoniazid (isonicotinic acid hydrazide, INH) resistance in patients with suspected TB, and applied appropriate techniques to help rapidly target DR-TB. Methods: In total, 1,547 clinical specimens were collected and cultured using the BACTEC MGIT system (Becton Dickinson and Co.). A resazurin microtiter assay (REMA) was used to determine the proportions of RIF and/or INH resistance. A real-time polymerase chain reaction panel with TaqMan probes was employed to identify the mutations of rpoB and katG associated with DR-TB in clinical isolates. Genotyping of the identified mutations was also performed. Results: A total of 468 Mycobacterium tuberculosis isolates were identified using the REMA. Of these isolates, 106 (22.6%) were found to be resistant to 1 or both antibiotics. Of the resistant isolates, 74 isolates (69.8%) were resistant to isoniazid (INH) only, while 1 isolate (0.94%) was resistant to RIF only. Notably, 31 isolates (29.24%) were resistant to both antibiotics. Of the 41 phenotypically INH-resistant isolates, 19 (46.3%) had the Ser315Thr mutation. There were 8 different rpoB mutations in 22 (68.8%) of the RIF-resistant isolates. The most frequently detected mutations were at codons 531 (37.5%), 526 (18.8%), and 516 (6.3%). Conclusion: To help prevent new cases of DR-TB in Vietnam, it is crucial to gain a comprehensive understanding of the genotypic DR-TB isolates.
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Objectives Real-time polymerase chain reaction is currently used as a confirmatory test for coronavirus disease 2019 (COVID-19). The test results are interpreted as positive, negative, or inconclusive, and are used only for a qualitative classification of patients. However, the test results can be quantitated using threshold count (Ct) values to determine the amount of virus present in the sample. Therefore, this study investigated the diagnostic usefulness of Ct results through various quantitative analyzes, along with an analysis of clinical and epidemiological characteristics.
Methods Clinical and epidemiological data from 4,642 COVID-19 patients in April 2021 were analyzed, including the Ct values of the RNA-dependent RNA polymerase (RdRp), envelope (E), and nucleocapsid (N) genes. Clinical and epidemiological data (sex, age, underlying diseases, and early symptoms) were collected through a structured questionnaire. A correlation analysis was used to examine the relationships between variables.
Results All 3 genes showed statistically significant relationships with symptoms and severity levels. The Ct values of the RdRp gene decreased as the severity of the patients increased. Moreover, statistical significance was observed for the presence of underlying diseases and dyspnea.
Conclusion Ct values were found to be related to patients’ clinical and epidemiological characteristics. In particular, since these factors are closely related to symptoms and severity, Ct values can be used as primary data for predicting patients’ disease prognosis despite the limitations of this method. Conducting follow-up studies to validate this approach might enable using the data from this study to establish policies for preventing COVID-19 infection and spread.
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Objectives Voluntary testing (VT) plays a crucial role in the prevention and control of infectious diseases. The present study investigated the perceptions and utilization of VT services for coronavirus disease 2019 (COVID-19) among the inhabitants of Saudi Arabia. Methods: In total, 3,510 adult participants from all provinces of Saudi Arabia were recruited via a national online survey. Results: Of the 3,510 participants, 88.9% were aware of the testing services available to them and of those, more than half (59.5%) had used the VT services and 96.1% were satisfied with the services. Contact with a positive COVID-19 case was the top reason for accessing VT, while a lack of awareness about the availability of VT services was the top perceived limiting factor. A history of chronic health conditions, anxiety and/or depression, and previous symptoms suggestive of COVID-19 were found to be predictors of the utilization of VT services (odds ratio [OR] 1.55, 95% confidence interval [CI] 1.22−1.96; OR 1.48, 95% CI 1.16−1.88; and OR 3.31, 95% CI 2.77−3.95), respectively. Conclusion: The awareness of voluntary COVID-19 testing services was satisfactory among the Saudi Arabian population, but can be improved. Sociodemographic and health history predictors of the utilization of VT services were identified.
<sec>
<title>Objectives</title>
<p>The emergence of resistant bacteria is being increasingly reported around the world, potentially threatening millions of lives. Amongst resistant bacteria, methicillin-resistant <italic>Staphylococcus aureus</italic> (MRSA) is the most challenging to treat. This is due to emergent MRSA strains and less effective traditional antibiotic therapies to Staphylococcal infections. The use of bacteriophages (phages) against MRSA is a new, potential alternate therapy. In this study, morphology, genetic and protein structure of lytic phages against MRSA have been analysed.</p></sec>
<sec>
<title>Methods</title>
<p>Isolation of livestock and sewage bacteriophages were performed using 0.4 μm membrane filters. Plaque assays were used to determine phage quantification by double layer agar method. Pure plaques were then amplified for further characterization. Sulfate-polyacrylamide gel electrophoresis and random amplification of polymorphic DNA were run for protein evaluation, and genotyping respectively. Transmission electron microscope was also used to detect the structure and taxonomic classification of phage visually.</p></sec>
<sec>
<title>Results</title>
<p>Head and tail morphology of bacteriophages against MRSA were identified by transmission electron microscopy and assigned to the <italic>Siphoviridae</italic> family and the <italic>Caudovirales</italic> order.</p></sec>
<sec>
<title>Conclusion</title>
<p>Bacteriophages are the most abundant microorganism on Earth and coexist with the bacterial population. They can destroy bacterial cells successfully and effectively. They cannot enter mammalian cells which saves the eukaryotic cells from lytic phage activity. In conclusion, phage therapy may have many potential applications in microbiology and human medicine with no side effect on eukaryotic cells.</p></sec>
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<sec><title>Objectives</title><p>Brucellosis is a major zoonotic disease that poses a significant public health threat worldwide. The classical bacteriological detection process used to identify <italic>Brucella</italic> spp. is difficult and time-consuming. This study aimed to develop a novel molecular assay for detecting brucellosis.</p></sec><sec><title>Methods</title><p>All complete sequences of chromosome 1 with 2.1-Mbp lengths were compared among all available <italic>Brucella</italic> sequences. A unique repeat sequence (URS) locus on chromosome 1 could differentiate <italic>Brucella abortus</italic> from <italic>Brucella melitensis</italic>. A primer set was designed to flank the unique locus. A total of 136 lymph nodes and blood samples were evaluated and classified by the URS-polymerase chain reaction (PCR) method in 2013–2014.</p></sec><sec><title>Results</title><p>Biochemical tests and bacteriophage typing as the golden standard indicated that all <italic>Brucella</italic> spp. isolates were <italic>B. melitensis</italic> biovar 1 and <italic>B. abortus</italic> biovar 3. The PCR results were the same as the bacteriological method for detecting <italic>Brucella</italic> spp. The sensitivity and specificity of the URS-PCR method make it suitable for detecting <italic>B. abortus</italic> and <italic>B. melitensis</italic>.</p></sec><sec><title>Conclusion</title><p>Quick detection of <italic>B. abortus</italic> and <italic>B. melitensis</italic> can provide the most effective strategies for control of these bacteria. The advantage of this method over other presented methods is that both <italic>B. abortus</italic> and <italic>B. melitensis</italic> are detectable in a single test tube. Furthermore, this method covered 100% of all <italic>B. melitensis</italic> and <italic>B. abortus</italic> biotypes. The development of this URS-PCR method is the first step toward the development of a novel kit for the molecular identification of <italic>B. abortus</italic> and <italic>B. melitensis</italic>.</p></sec>
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Objectives
Production of carbapenemase, especially <i>Klebsiella pneumoniae</i> carbapenemases (KPC), is one of the antibiotic resistance mechanisms of Enterobacteriaceae such as <i>Klebsiella oxytoca</i>. This study aimed to investigate and identify KPC-producing <i>K. oxytoca</i> isolates using molecular and phenotypic methods. Methods
A total of 75 isolates of <i>K. oxytoca</i> were isolated from various clinical samples, and were verified as <i>K. oxytoca</i> after performing standard microbiological tests and using a polymerase chain reaction (PCR) method. An antibiotic susceptibility test was performed using a disc diffusion method according to the Clinical and Laboratory Standards Institute guidelines. CHROMagar KPC chromogenic culture media was used to examine and confirm the production of the carbapenemase enzyme in <i>K. oxytoca</i> isolates; in addition, PCR was used to evaluate the presence of <i>bla</i><sub>KPC</sub> gene in <i>K. oxytoca</i> strains. Results
Of a total of 75 <i>K. oxytoca</i> isolates, one multidrug resistant strain was isolated from the urine of a hospitalized woman. This strain was examined to assess its ability to produce carbapenemase enzyme; it produced a colony with a blue metallic color on the CHROMagar KPC chromogenic culture media. In addition, the <i>bla</i><sub>KPC</sub> gene was confirmed by PCR. After sequencing, it was confirmed and deposited in GenBank. Conclusion
To date, many cases of KPC-producing Enterobacteriaceae, in particular <i>K. pneumoniae</i>, have been reported in different countries; there are also some reports on the identification of KPC-producing <i>K. oxytoca</i>. Therefore, to prevent the outbreak of nosocomial infections, the early detection, control, and prevention of the spread of these strains are of great importance.
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Objectives
<i>Escherichia coli</i> is regarded as the most important etiological agent of urinary tract infections. Fluoroquinolones are routinely used in the treatment of these infections; however, in recent years, a growing rate of resistance to these drugs has been reported globally. The aims of this study were to detect plasmid-mediated <i>qnrA</i>, <i>qnrB</i>, and <i>qnrS</i> genes among the quinolone-nonsusceptible <i>E. coli</i> isolates and to investigate their clonal relatedness in Qazvin and Zanjan Provinces, Iran. Methods
A total of 200 clinical isolates of <i>E. coli</i> were collected from hospitalized patients. The bacterial isolates were identified through standard laboratory protocols and further confirmed using API 20E test strips. Antimicrobial susceptibility was determined by the standard disk diffusion method. Polymerase chain reaction (PCR) and sequencing were used for detecting <i>qnrA</i>, <i>qnrB</i>, and <i>qnrS</i> genes and the clonal relatedness of <i>qnr</i>-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) method. Results
In total, 136 (68%) isolates were nonsusceptible to quinolone compounds, among which 45 (33.1%) and 71 (52.2%) isolates showed high- and low-level quinolone resistance, respectively. Of the 136 isolates, four (2.9%) isolates were positive for the <i>qnrS1</i> gene. The results from ERIC-PCR revealed that two (50%) cases of <i>qnr</i>-positive isolates were related genetically. Conclusion
Our study results were indicative of the presence of low frequency of <i>qnr</i> genes among the clinical isolates of <i>E. coli</i> in Qazvin and Zanjan Provinces, which emphasizes the need for establishing tactful policies associated with infection-control measures in our hospital settings.
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Objectives
Ebola and Marburg viruses (EBOVs and MARVs, respectively) are causative agents of severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. In 2014, there was a major Ebola outbreak in various countries in West Africa, including Guinea, Liberia, Republic of Sierra Leone, and Nigeria. EBOV and MARV are clinically difficult to diagnose and distinguish from other African epidemic diseases. Therefore, in this study, we aimed to develop a method for rapid identification of the virus to prevent the spread of infection. Methods
We established a conventional one-step reverse transcription-polymerase chain reaction (RT-PCR) assay for these pathogens based on the Superscript Reverse Transcriptase-Platinum <i>Taq</i> polymerase enzyme mixture. All assays were thoroughly optimized using <i>in vitro</i>-transcribed RNA. Results
We designed seven primer sets of nucleocapsid protein (NP) genes based on sequences from seven filoviruses, including five EBOVs and two MARVs. To evaluate the sensitivity of the RT-PCR assay for each filovirus, 10-fold serial dilutions of synthetic viral RNA transcripts of EBOV or MARV NP genes were used to assess detection limits of viral RNA copies. The potential for these primers to cross react with other filoviruses was also examined. The results showed that the primers were specific for individual genotype detection in the examined filoviruses. Conclusion
The assay established in this study may facilitate rapid, reliable laboratory diagnosis in suspected cases of Ebola and Marburg hemorrhagic fevers.
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Objectives
This study aimed to evaluate the specificity, sensitivity, cost, and turn-around time of three methods of gene polymorphism analysis and to study the relationship between IL28B rs12979860 and SVR rate to pegIFN-α/RVB therapy among patients with chronic hepatitis C. Methods
A total of 100 samples from chronic hepatitis C patients were analyzed in parallel using the three methods: direct sequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system (ARMS)-PCR. Results
The different profiles for IL28B rs12979860 alleles (CC, CT, and TT) obtained with PCR-RFLP, ARMS-PCR, and direct sequencing were consistent among the three methods. Prevalence of rs12979860 genotypes CC, CT and TT in HCV genotype 1a was 10(19.6%), 35(68.6%), and six (11.8%), respectively, and in HCV genotype 31, it was 13(26.5%), 31(63.3%), and five (10.2%), respectively. No significant difference was seen between rs12979860 genotype and HCV genotype (<i>p</i> = 0.710). Conclusion
Screening by ARMS – PCR SNOP detection represents the most efficient and reliable method to determine HCV polymorphisms in routine clinical practice.
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Objectives
This study was carried out in order to understand the behavior of dengue viruses through the entomological and laboratory surveillance of outbreaks. The aim of the study was to provide additional research to support current knowledge of epidemiological, clinical, and laboratory diagnosis of dengue virus and ultimately to use this information to forecast dengue as well as to justify intervention measures. Methods
Data on the presence of <i>Aedes</i> larvae in human dwellings during the entomological surveillance in Cuddalore, Nagapattinam, and Tirunelveli dengue outbreaks were taken to compute indices, namely the House Index (HI), Container index (CI), and the Breteau Index (BI). Standard procedures were followed for nonstructural Protein 1 (NS1) and immunoglobulin M enzyme linked immunosorbent assay for the confirmation of dengue. Serovar confirmation was made in the Kottayam field station of the Vector Control Research Center, Puducherry. Results
Larval indices HI < 2–3% and BI < 20 contributed to halting the outbreak. Incubation of the dengue viruses in humans was detected at 15 days, NS1 was identified as a tool for the early diagnosis of dengue cases and its presence indicated the need to implement all available interventions. It was also discovered that it is helpful to search for hidden habitats of <i>Aedes</i> when dengue cases have not been reduced even after the sustainable management of the larval indices, HI < 5% and BI < 20. Based on the observed incidences of stopping dengue outbreaks, it was learnt that neighborhood areas of the outbreak villages, around 400 m, should have permissible larval indices < 5% HI and BI < 20. Heterogeneous serovars that led to dengue hemorrhagic fever and Dengue Shock Syndrome (DSS) were identified using reverse transcription polymerase chain reaction and reconfirmed in the field as DEN-1 and DEN-3 viruses and were circulating in Tirunelveli during the outbreak. Conclusion
The behaviors of dengue viruses experienced in experimental, clinical, epidemiological, entomological, and laboratory surveillance did not deviate from observations in the field during dengue outbreaks in the Cuddalore, Nagapattinam, and Tirunelveli districts of Tamil Nadu, India.
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Objectives
A fast and accurate diagnosis is necessary to control and eliminate tuberculosis (TB). In Korea, TB continues to be a serious public health problem. In this study, diagnostic tests on clinical samples from patients suspected to have TB were performed and the sensitivity and specificity of the various techniques were compared. The main objective of the study was to compare various diagnostic tests and evaluate their sensitivity and specificity for detecting tuberculosis. Methods
From January 2013 to December 2013, 170,240 clinical samples from patients suspected to have TB were tested with smear microscopy, acid-fast bacilli culture, and real-time polymerase chain reaction (PCR). The test results were compared and data were analyzed. Results
A total of 8216 cultures tested positive for TB (positive detection rate, 4.8%). The contamination rate in the culture was 0.6% and the isolation rate of nontuberculous mycobacteria was 1.0%. The sensitivity and specificity of smear microscopy were 56.8% and 99.6%, respectively. The concordance rate between the solid and liquid cultures was 92.8%. <i>Mycobacterium</i> isolates were not detected in 0.4% of the cases in the liquid culture, whereas no <i>Mycobacterium</i> isolates were detected in 6.8% of the cases in the solid culture. The sensitivity and specificity of real-time PCR for the solid culture were 97.2% and 72.4%, respectively, whereas the corresponding data for the liquid culture were 93.5% and 97.2%. Conclusion
The study results can be used to improve existing TB diagnosis procedure as well as for comparing the effectiveness of the assay tests used for detecting <i>Mycobacterium tuberculosis</i> isolates.
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In December 2011, a 42-year-old male farmer was admitted to a hospital in Sanandaj (Western Iran) with fever and anemia in order to check whether he suffered from some infectious diseases. During the first 3 days after admission, the patient gradually developed progressive oliguria, fever, abdominal pain in the right upper quadrant, leukocytosis with toxic granulation, petechiae and ecchymosis, oral bleeding, and vomiting. The sonographic findings revealed splenomegaly and an increase in the thickness of the gall bladder wall. In order to manage the patient and taking into consideration the most probable differential diagnoses, diagnostic tests were performed on two blood samples collected from him, and real-time polymerase chain reaction for human cytomegalovirus was positive.
Objectives
The resistance of <i>Streptococcus pneumoniae</i> to the recently available antibiotic treatment has been a growing problem. The aim of the study was to determine the quinolone-resistant strains and detect the presence of mutations in the quinolone resistance-determining regions of the <i>gyrA</i>, <i>parE</i>, and <i>parC</i> genes. Methods
In this study, for the first time in Iran, the polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method was used to investigate the presence of mutations at quinolone resistance-determining regions of topoisomerase IV and DNA gyrase on 82 <i>S. pneumoniae</i> strains, among them 45 clinical samples were from patients and 37 from healthy carriers (control group). Results
In clinical samples, 34 (75.56%) strains contained mutations in the <i>parC</i> gene, 31 (68.89%) carried mutations in the <i>gyrA</i> gene, and 14 (31.11%) had <i>parE</i> gene mutations. Antibiotic susceptibility test was performed using the CLSI (Clinical and Laboratory Standards Institute) criteria on three different generations of quinolone family, with nalidixic acid (82.22%) showing the highest resistance and levofloxacin (42.22%) the least resistance. Conclusion
Results indicated that there is a significant correlation between quinolone resistance development and mutations in the <i>parE</i> gene as well as in the <i>parC</i> and <i>gyrA</i> genes.
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Objectives
Chikungunya (CHIK) has been classified as a communicable disease group IV in South Korea since late 2010. Based on this, we investigated the extent of imported cases of CHIK in dengue-suspected individuals returning from dengue-endemic regions. Methods
A total of 486 dengue-suspected serum samples were screened for CHIK by enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Further RT-PCR-positive samples were used for the viral culture, and CHIK was subsequently confirmed by sequence analysis of the culture samples. Results
Five out of 107 dengue-positive samples were found to be positive for CHIK and 15 out of 379 dengue-negative samples were found to be positive for CHIK by immunoglobulin M ELISA. Further, a CHIK virus was isolated from one of the two RT-PCR-positive sera by cell culture and confirmed by sequence analysis. Conclusion
The present study documents the first evidence of travel-associated CHIK infection in South Korea. Considering the intense international traffic between countries, our finding emphasizes the urgent need for active patient and vector surveillance for timely response to reduce the introduction of CHIK in Korea.
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Objectives
To date, no indigenous dengue virus (DENV) transmissions have been reported in Korea. However, imported dengue infections have been diagnosed in travelers returning from endemic areas. This study presents the first virological evidence of travel-associated DENV importation into South Korea. Methods
From January 2004 to June 2006, a total of 278 serum samples from 245 patients with suspected dengue fever were tested using the Panbio Dengue Duo IgM/IgG Rapid Strip Test. We selected 11 of the early symptomatic-phase sera that were negative for IgM and retrospectively studied them by virus isolation and reverse transcription-polymerase chain reaction. Results
All 11 serum samples were found to be DENV positive by reverse transcription-polymerase chain reaction and viruses were successfully isolated from seven of the 11 serum samples. All the isolates were identified as DENV serotype-1. Conclusion
We successfully isolated seven DENV serotype-1 strains for the first time in South Korea from imported infections. Considering that the vector mosquito, <i>Aedes albopictus</i>, already exists in South Korea, we propose that a vector surveillance program for dengue is urgently needed.
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