Uncommon pathogens causing infective endocarditis.

Infective endocarditis is caused by a wide range of aetiological agents. The microbiology, epidemiology, and treatment of this disease have changed considerably in the last two decades. Staphylococci and streptococci are known to be the classical causative agents; however, blood culture-negative endocarditis caused by fastidious and slow-growing organisms is now common. The list of uncommon pathogens causing endocarditis has expanded in recent years. This is a narrative literature review of the aetiological agents of endocarditis that are rarely encountered in clinical practice, their epidemiology, the characteristics of these pathogens, the clinical presentations of the cases, and their management.

Use of 16s rRNA Gene Sequencing for the Identification of Viridans Group Streptococci.

Streptococci belonging to the viridans group are gram-positive bacteria residing as commensals in the upper respiratory, gastrointestinal, and genital tracts in humans. Though they are largely known to be commensals, they may also cause life-threatening infections like infective endocarditis, septicemia, pyogenic infections, pneumonia, and meningitis. The viridans group streptococci (VGS) are usually identified by biotyping; however, species discrimination is not always possible by phenotypic characterization. We identified 53 isolates from blood cultures of patients with infective endocarditis and compared the results of biotyping with 16s rRNA gene sequencing for species identification. Organisms belonging to the mitis group were the most common. 16s rRNA gene polymerase chain reaction and sequencing were useful in identifying the etiological agents at the species level. S.oralis was the most common etiological agent.

The oral microbiota in patients undergoing coronary artery bypass graft surgery.

The oral cavity houses a diverse community of microorganisms which play an important role in maintaining the health of the individual. The coexistence of periodontal infections with coronary artery disease (CAD) has been shown in many studies. We investigated the presence and abundance of periodontitis-causing bacteria in patients with CAD. The oral microbiome of five patients admitted for coronary artery bypass graft (CABG) surgery was analysed by metagenomic sequencing of 16 s ribosomal ribonucleic acid (rRNA) gene amplicons. Two samples of oral mouthwash were collected 48-72 h apart when the patients were in the intensive care unit. Abundance and diversity of oral bacterial flora were analysed. The most abundant phyla were Firmicutes and Bacteroidetes. Less than 5% of the taxa in this group of patients belonged to the phylum Proteobacteria. Though there were variations in the abundance of the bacterial species in the immediate postoperative period, there was no major change in the overall diversity. High counts of periodontal pathogens such as Tannerella forsythia, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, and Treponema denticola were seen in most of the patients.

Culture-negative endocarditis caused by Stenotrophomonas maltophilia: a report of two cases.

Stenotrophomonas maltophilia, an aerobic, non-fermenting, Gram-negative bacterium, is an emerging nosocomial pathogen. It is considered to be a low-grade pathogen, and infections due to S. maltophilia are uncommon. However, in the recent past, S. maltophilia infections have been on the rise, particularly in patients who are either immunocompromised, aged or on long-term antibiotic therapy. Endocarditis due to S. maltophilia is extremely rare. This is a report of two patients with S. maltophilia endocarditis who were diagnosed by 16S rRNA gene sequencing.

Q fever endocarditis in India: A report of two cases.

Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella burnetii. Infective endocarditis is the most common form of chronic Q fever. Diagnosis of Q fever is difficult, as there are no pathognomonic symptoms. Methods of isolation of the organism in culture are tedious, hence serological and molecular techniques remain the mainstay of diagnosis. We report two cases of Q fever endocarditis diagnosed by IFA and real-time PCR.

Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016-2018.

Human metapneumovirus (hMPV) has emerged as a frequent cause of acute respiratory infections (ARI) among young children. The prevalence and genetic diversity of hMPV circulating in Chennai, Southern India, has not been studied yet. Hence, this study was aimed to investigate the prevalence, co-infection with other respiratory viruses like HRSV A and B, influenza A and B, hRV and HPIV 1-4 viruses, socio-demographic associations, and genotypes of hMPV among children in Chennai. A total of 350 nasal swab specimens were collected from children with ARI during April 2016 to August 2018 and tested for hMPV by real time PCR method. In this study, hMPV was detected in 4% (14/350) of the samples. One hMPV positive sample was found to be co-infected with influenza B virus. The mean and median ages of the children with hMPV infection were 61.5 months (5.1 years) and 83 months (6.9 years), respectively. Phylogenetic analysis of the partial F gene revealed the presence of A2c subcluster among the study strains as well as with B1 and B2 lineages. The prevalence data obtained in this study is important in evaluating the role of hMPV in childhood ARI and emphasizes the importance of routine viral diagnosis in hospitals. To the best of our knowledge, this is the first study to report the prevalence, seasonality, and genetic diversity of hMPV in Chennai as well as the first study to report A2c subcluster of hMPV among children in India.

Genetic diversity of human respiratory syncytial virus in children with acute respiratory infections in Chennai, South India.

Introduction: Human respiratory syncytial virus (HRSV) an RNA virus belonging to Pneumoviridae family, is an important cause of acute respiratory infections (ARIs) in young children. HRSV circulates as two subgroups A and B, which are further categorised into several genotypes. New genotypes may replace existing ones over successive epidemic seasons and multiple genotypes may cocirculate in the same community rendering it important to monitor them at the molecular level. The present study assessed the circulating genotypes of HRSV in Chennai. Materials and Methods: Two hundred and sixty-seven children with ARI were recruited during the study from April 2016 to March 2018 for detecting HRSV A and B by real-time reverse transcription-polymerase chain reaction. Phylogeny and selection pressure analysis were done. Results: Fifty-seven of the 267 samples (21.3%) were positive for HRSV, of which 7.1% and 14.2% were HRSV A and B, respectively, indicating that HRSV B was the major subgroup circulating in Chennai. Peak activity of HRSV was observed during the monsoon and winter months. Phylogenetic analysis of 2nd hypervariable region (HVR) of attachment glycoprotein gene (G gene) revealed that the HRSV A strains belonged to ON1 and HRSV B strains belonged to BA9 genotypes. Several unique amino acid substitutions were observed among the study strains. The Shannon entropy plot revealed that the HRSV A strains from our study have a high potential for amino acid substitutions in the 2nd HVR of G gene. Conclusion: This study underlines the genetic diversity of HRSV and emphasises the need for continued molecular surveillance for infection management and prevention strategies.

Comparison of nested polymerase chain reaction and real-time polymerase chain reaction targeting 47kda gene for the diagnosis of scrub typhus.

Introduction: Scrub typhus is a zoonotic infection caused by Orientia tsutsugamushi which is transmitted by Leptotrombidium mites. The disease manifests as a mild-to-severe illness with non-specific clinical symptoms. Rapid diagnosis and prompt treatment are essential for patient management. Both serological and molecular methods are used for the diagnosis of scrub typhus. The present study assessed the usefulness of detection of the gene encoding the 47kDa outer-membrane protein (OMP) for the laboratory diagnosis of scrub typhus. Materials and Methods: Nested polymerase chain reaction (nPCR) and real-time PCR targeting 47 kDa OMP antigen gene of O. tsutsugamushi were performed on ethylenediaminetetraacetic acid blood samples. Results: Six of the 103 (5.8%) patients showed the presence of 47kDa gene by nPCR. Seventy of 103 (67.9%) cases showed the presence of 47kDa gene by qPCR. Among the 70 positive cases, the majority of them were females (40/70, 57.1%). The highest number of positive cases was observed during October-February. Conclusion: Real-time PCR targeting O. tsutsugamushi-specific 47-kDa gene is more sensitive than nPCR and may be the assay of choice for the detection of the organism in patients with suspected scrub typhus.

Influenza Virus Among Children with Acute Respiratory Infections in Chennai, India.

Influenza is a major public health concern. Information on the prevalence of influenza virus in respiratory tract infections in Indian children is very sparse. In the present study, 267 nasal swabs were collected from children with acute respiratory infections in Chennai, India, out of which 22 (8.2%) and 6 (2.3%) samples were positive for influenza A and B virus respectively.

Coexistence of metallo-beta-lactamase-encoding genes in Pseudomonas aeruginosa.

BACKGROUND & OBJECTIVES: The emergence and rapid spread of carbapenem resistance mediated by metallo-beta-lactamase (MBL) in Pseudomonas aeruginosa is of major concern due to limited therapeutic options. This study was aimed at detecting the presence of MBL and its association with integrons in imipenem-resistant P. aeruginosa isolates and to determine their genetic relatedness. METHODS: A total of 213 P. aeruginosa isolates were collected from two tertiary care centres and tested against anti-pseudomonal antibiotics by antimicrobial susceptibility testing, followed by the detection of MBL production by combined disk method. Minimum inhibitory concentration (MIC) of meropenem was determined by E-test. Multiplex polymerase chain reaction (PCR) was performed for the detection of blaSPM, blaIMP, blaVIM, blaNDM, blaGIM and blaSIM. PCR was carried out to characterize the variable region of class 1 integron. Transcongujation assay was carried out for the confirmation of plasmid-mediated resistance. Enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR was performed for determining the genetic relatedness among P. aeruginosa isolates. RESULTS: Of the 213 P. aeruginosa isolates, 22 (10%) were found to be carbapenem resistant and these were from pus 18 (82%), urine 2 (9%), sputum 1 (5%) and tracheal wash 1 (5%). Among 22 isolates, 18 (81.8%) were found to be MBL producers by phenotypic method and MIC range of meropenem was 8 to >32 µg/ml. PCR amplification showed that 20 (91%) isolates carried any one of the MBL genes tested: blaVIM and blaNDM in seven (32%) and six (27%) isolates, respectively; blaVIM and blaNDMin three (14%); blaIMP and blaNDM in two (9%); blaVIM and blaIMP in one (5%) isolate. The blaVIM, blaIMP and blaNDM were found to co-exist in one isolate. None of the isolates were positive for blaSPM, blaSIM and blaGIM. All 22 isolates carried class I integron. Of the 20 MBL-positive isolates, transconjugants were obtained for 15 isolates. ERIC-PCR analysis showed all isolates to be clonally independent. INTERPRETATION & CONCLUSIONS: Our results showed 10.3 per cent of carbapenem resistance among P. aeruginosa isolates, and the coexistence of MBL-encoding genes among P. aeruginosa mediated by class I integron.

Native Valve Endocarditis Caused by Escherichia Coli.

Escherichia coli is a rare cause of infective endocarditis. This report describes a case of native valve endocarditis caused by Escherichia coli in a 58-year-old male renal transplant patient who had a concurrent urinary tract infection caused by the same organism. The patient was successfully treated with antibiotics and recovered without surgical intervention.

Genome sequence of an invasive strain of Streptococcus gordonii.

We report the genome sequence of IE35, a strain of Streptococcus gordonii isolated from the blood of a patient with prosthetic valve endocarditis. Whole-genome sequencing of S. gordonii IE35 strain by the combination of Illumina HiSeq2000 paired-end, Ion Torrent single-end sequencing and gap closing by Illumina NextSeq yielded a single, circular chromosome of 2,190,105 bp. It had 2106 predicted coding sequences, of which 2014 genes encoded proteins involved in various cellular processes and 66 genes coded for RNA. The predicted RNA genes were annotated up to pathway level and genes responsible for various metabolic processes and virulence were identified.

Emergence of rmtC and rmtF 16S rRNA methyltransferase in clinical isolates of Pseudomonas aeruginosa.

Occurrence of aminoglycoside (AG) resistance in clinical isolates of Pseudomonas aeruginosa is investigated in this study. Antimicrobial susceptibility test and minimum inhibitory concentration (MIC) for amikacin and gentamicin were performed followed by polymerase chain reaction amplifications of AG modifying enzyme genes (aac(6´)-I, aac(6´)-II, aac(3)-II/VI, ant(2´´)-I, aph(3´)-VI) and 16S methylases (rmtA-D, rmtF and armA). MIC50and MIC90were 64, 128 and > 256, >256 for amikacin and gentamicin, respectively. Four types of genes (aac(6´)-I, aac(3)-II/VI, ant(2´´)-I and aph(3´)-VI) were found in 53 (57.6%) isolates. ant(2´´)-I was the most predominant gene (28 isolates) followed by aac(6´)-I (23 isolates). Nineteen (20.6%) isolates were positive for 16S RMTases (rmtB, rmtC, rmtF and armA) and two isolates co-harboured rmtB + rmtC + rmtF.

Characterisation of the human oral microbiome in patients with coronary artery disease using next-generation sequencing of 16SrRNA amplicons.

INTRODUCTION: Oral health is suspected to be linked to heart disease since species of bacteria that cause periodontitis and dental caries have been found in the atherosclerotic plaque in arteries in the heart. OBJECTIVES: The aim of this study was to characterize the oral microbiome in patients with coronary artery disease (CAD) and in a patient with dental caries (DC) without any clinical symptoms of CAD. METHODS: DNA was extracted from the oral swabs collected from the patients and sequencing was performed by next generation sequencing method using Illumina (MiSeq) platform. The resulting sequencing data set was analysed using QIIME. RESULTS: A total of 31 phyla were found in all the samples. The predominant phylum found in both CAD and DC was Firmicutes (46.09% & 38.98%), Proteobacteria (17.73% & 9.79%), Fusobacteria (13.44% & 17.95%), Bacteroidetes (11.82% & 22.73%), Actinobacteria (8.33% & 7.71%) and TM7 (2.25% & 2.71%). We found a similarity in the bacterial diversity in the two groups of patients. CONCLUSION: A comparison of the oral microbiome in patients with CAD and DC shows a similarity in the composition of the oral microbiota with variations in the proportion of a few genera.

Molecular detection of Orientia tsutsugamushi from suspected scrub typhus cases.

CONTEXT: Scrub typhus is an acute febrile illness caused by Orientia tsutsugamushi. The disease is under-diagnosed in India, because of low index of suspicion and also due to its nonspecific presentation, and lack of confirmatory diagnostic tests. AIMS: This study was undertaken to diagnose scrub typhus in patients with undifferentiated fevers by serology and molecular methods. MATERIALS AND METHODS: A total of 68 blood samples were collected from patients clinically suspected to have scrub typhus. After transportation to the laboratory, the serum was separated from the blood and subjected to rapid card test. The ethylenediaminetetraacetic acid blood samples were subjected to DNA extraction using QIAamp DNA Mini Kit followed by nested polymerase chain reaction (nPCR). RESULTS: 24/68 (35.29%) cases showed the presence of antibody against scrub typhus by serology. 6/68 (8.8%) patients showed the presence of outer membrane protein antigen gene 56 kDa by nPCR. 5/24 serology positive cases showed the presence of 56 kDa outer membrane protein antigen gene by nPCR. A large number of cases positive by serology were negative by PCR which may indicate a low sensitivity of this test either due to low copy numbers or due to excess host DNA. CONCLUSION: Delay in treatment may increase disease severity and leads to higher mortality. Thus, molecular methods of diagnosis may aid in the early diagnosis of infection and enable prompt treatment. This is the first report on the diagnosis of scrub typhus in the suburbs of Chennai using molecular methods and reemphasizes the need for increased awareness of rickettsial infections in rural areas.

Analysis of Serum Th1/Th2 Cytokine Levels in Patients with Acute Mumps Infection.

BACKGROUND: The mumps virus is frequently the causative agent of parotitis. There has been no study on serum cytokine levels of acute mumps parotitis except for a few which document cytokine levels in cerebrospinal fluid of mumps meningitis. It is with this notion, our study aimed to find Th1/Th2 cytokine levels from patients with acute mumps parotitis. MATERIALS AND METHODS: Concentrations of mumps-specific IgM, mumps, measles, rubella-specific IgG antibody, and Th1/Th2 cytokines, namely interferon-γ (IFN-γ), interleukin-2 (IL-2), IL-4, and IL-10 were measured simultaneously in serum from 74 patients (42 pediatric and 32 adult cases), 40 healthy subjects (20 pediatric and 20 adults) and in the supernatant of peripheral blood mononuclear cells stimulated with mumps virus genotype C which served as the positive control. Statistical significance was analyzed between each group by means of Mann-Whitney U-test, Kruskal-Wallis test, and Spearman's rank correlation coefficient test. RESULTS: IgM positivity confirmed acute infection in all 74 patients and of these 67 were vaccinated cases; however, very few of them (10/67) were positive for mumps IgG. We found that IFN-γ, IL-2, and IL-10 showed a statistically significant increase in both pediatric and adult patients with acute mumps infection when compared to healthy controls and values were comparable to the positive control. CONCLUSION: The Th1 cells play important roles during the acute phase of mumps parotitis.

In vitro anti-HIV-1 activity of fucoidan from Sargassum swartzii.

Sargassum swartzii, a marine brown algae with wide range of biological properties belongs to the family Sargassaceae. Bioactive fucoidan fractions (CFF, FF1 and FF2) were isolated from S. swartzii and characterized by linear gradient anion-exchange chromatography and FT-IR. The characterized fucoidan fractions contained mainly sugars, sulfate and uronic acid. In the present study, anti-HIV-1 property of the fucoidan fractions was investigated. Fraction FF2 was found to exhibit significant anti-HIV-1 activity at concentrations of 1.56 and 6.25 µg/ml as observed by >50% reduction in HIV-1 p24 antigen levels and reverse transcriptase activity. Fucoidan fractions have no cytotoxic effects on PBMCs at the concentration range of 1.56-1000 µg/ml. These results suggest that fucoidan fractions could have inhibitory activity against HIV and has potential as an anti-HIV-1 agent.

Molecular Basis for Erythromycin Resistance in Group A Streptococcus Isolated From Skin and Soft Tissue Infections.

BACKGROUND: In recent years there has been an increase in the use of erythromycin in the treatment of infections caused by bacteria other than Group A Streptococcus (GAS), which has resulted in increased resistance to this antibiotic. Erythromycin and other macrolides are alternative agents for treating GAS infections in patients, who are allergic to penicillin and its derivatives. AIM: The main aim of this study was to identify frequency, pattern and genetic determinant of erythromycin resistance among the GAS isolated from skin and soft tissue infections. MATERIALS AND METHODS: A total 100 isolates of GAS were screened for erythromycin resistance by phenotypic and genotypic method. RESULTS: The results of the present study showed that 38% isolates were resistant to erythromycin. The iMLS (inducible macrolide-lincosamide-streptogramin) phenotype was predominant (55.26%) followed by M phenotype (26.32%) and cMLS (constitutive macrolide-lincosamide-streptogramin) (18.42%). CONCLUSION: Phenotypic and genotypic analysis showed that the MLSB phenotype with ermB mediated mechanism of resistance was found the most common (76.31%) followed by mefA (20.51%). The ermTR genes was absent in all the isolates.