Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis.

BACKGROUND: Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery. OBJECTIVES: The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model. METHODS: Vaginal samples obtained from reproductive-age group women with (n = 40) and without BV (n = 40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy. RESULTS: Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84 ± 0.21 and accuracy of 0.79 ± 0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97 ± 0.07 and an accuracy of 0.92 ± 0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97 ± 0.07 and accuracy of 0.94 ± 0.08 with diagnostic performance only slightly superior to the metabolite-based model. CONCLUSION: Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.

Coagulase-negative staphylococci causing blood stream infection at an Indian tertiary care hospital: Prevalence, antimicrobial resistance and molecular characterisation.

INTRODUCTION: Recent years have seen a rise of coagulase-negative staphylococci (CoNS) from common contaminants to agents of nosocomial blood stream infections (BSI's). Molecular typing and establishing a correlation with antibiotic resistance is essential particularly in countries like India where genotyping studies for drug-resistant CoNS are sparse. METHODS: A prospective study was done over 18 months, wherein 42,693 blood samples were received, and 59 patients with BSI due to CoNS were evaluated. The isolates recovered were identified by a biochemical test panel and matrix-assisted laser desorption ionization - time of flight mass spectrometry followed by antimicrobial susceptibility testing by Kirby-Baur disc diffusion method and E-test strips. Staphylococcal chromosomal cassette mec (SCCmec) element was characterised by multiplex polymerase chain reaction for all methicillin-resistant (MR) isolates. RESULTS: The majority of CoNS isolated were constituted by Staphylococcus haemolyticus (47.5%) followed by Staphylococcus epidermidis (33.9%), Staphylococcus hominis (11.86%), Staphylococcus cohnii (5.08%) and Staphylococcus warneri (1.69%). Among all isolates 57.6% were MR with statistically significant higher resistance versus methicillin sensitive-CoNS. This difference was significant for erythromycin (76% vs. 44%, P = 0.011), rifampicin (50% vs. 12%,P= 0.002) and amikacin (26.5% vs. 4%, P = 0.023), ciprofloxacin (64.7% vs. 20%, P = 0.001) and cotrimoxazole (55.9% vs. 20%, P = 0.006). SCCmec type I was predominant (61.8%, P = 0.028) and exhibited multidrug resistance (76.2%). Coexistence of SCCmec type I and III was seen in 8.82% MR isolates. CONCLUSION: CoNS exhibit high antimicrobial resistance thereby limiting treatment options. The presence of new variants of SCCmec type in hospital-acquired CoNS may predict the antibiotic resistance pattern. This is the first evaluation of the molecular epidemiology of CoNS causing BSI from India and can serve as a guide in the formulation of hospital infection control and treatment guidelines.

Application of real-time quantitative polymerase chain reaction assay to detect Legionella pneumophila in patients of community-acquired pneumonia in a tertiary care hospital.

Legionella pneumophila is one of the important pathogen responsible for community -acquired pneumonia attributing for 1-5% of cases. Since early and accurate therapy reduces mortality, rapid and reliable diagnostic methods are needed. A total of 134 samples of blood, urine and respiratory tract fluids were collected. Blood was tested for IgG, IgM and IgA antibodies using commercially available kits. A total of 8 (6%) samples were found to be positive for L. pneumophila by quantitative reverse transcription polymerase chain reaction (qRT-PCR), compared to conventional PCR where 6 (4.4%) samples were positive. Serology was positive in a total of 32 (23%) cases though only 3 (2.2%) of the PCR-positive cases were positive by serology as well. These results suggest that real-time PCR can detect Legionella infection early in the course of the disease before serological response develops.

The changing face of community-acquired methicillin-resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of infection, both in hospitalised patients with significant healthcare exposure and in patients without healthcare risk factors. Community-acquired methicillin-resistant S. aureus (CA-MRSA) are known for their rapid community transmission and propensity to cause aggressive skin and soft tissue infections and community-acquired pneumonia. The distinction between the healthcare-associated (HA)-MRSA and CA-MRSA is gradually fading owing to the acquisition of multiple virulence factors and genetic elements. The movement of CA-MRSA strains into the nosocomial setting limits the utility of using clinical risk factors alone to designate community or HA status. Identification of unique genetic characteristics and genotyping are valuable tools for MRSA epidemiological studies. Although the optimum pharmacotherapy for CA-MRSA infections has not been determined, many CA-MRSA strains remain broadly susceptible to several non-ß-lactam antibacterial agents. This review aimed at illuminating the characteristic features of CA-MRSA, virulence factors, changing clinical settings and molecular epidemiology, insurgence into the hospital settings and therapy with drug resistance.

Prosthetic joint infection due to Lysobacter thermophilus diagnosed by 16S rRNA gene sequencing.

We report the first case of prosthetic joint infection caused by Lysobacter thermophilus which was identified by 16S rRNA gene sequencing. Removal of prosthesis followed by antibiotic treatment resulted in good clinical outcome. This case illustrates the use of molecular diagnostics to detect uncommon organisms in suspected prosthetic infections.

Ureaplasma: current perspectives.

Ureaplasma species are the most prevalent genital Mycoplasma isolated from the urogenital tract of both men and women. Ureaplasma has 14 known serotypes and is divided into two biovars- Ureaplasma parvum and Ureaplasma urealyticum. The organism has several genes coding for surface proteins, the most important being the gene encoding the Multiple Banded Antigen (MBA). The C-terminal domain of MBA is antigenic and elicits a host antibody response. Other virulence factors include phospholipases A and C, IgA protease and urease. Besides genital tract infections and infertility, Ureaplasma is also associated with adverse pregnancy outcomes and diseases in the newborn (chronic lung disease and retinopathy of prematurity). Infection produces cytokines in the amniotic fluid which initiates preterm labour. They have also been reported from renal stone and suppurative arthritis. Genital infections have also been reported with an increasing frequency in HIV-infected patients. Ureaplasma may be a candidate 'co factor' in the pathogenesis of AIDS. Culture and polymerase chain reaction (PCR) are the mainstay of diagnosis. Commercial assays are available with improved turnaround time. Micro broth dilution is routinely used to test antimicrobial susceptibility of isolates. The organisms are tested against azithromycin, josamycin, ofloxacin and doxycycline. Resistance to macrolides, tetracyclines and fluoroquinolones have been reported. The susceptibility pattern also varies among the biovars with biovar 2 maintaining higher sensitivity rates. Prompt diagnosis and initiation of appropriate antibiotic therapy is essential to prevent long term complications of Ureaplasma infections. After surveying PubMed literature using the terms 'Ureaplasma', 'Ureaplasma urealyticum' and 'Ureaplasma parvum', relevant literature were selected to provide a concise review on the recent developments.

Dissemination of methicillin-resistant Staphylococcus aureus SCCmec type IV and SCCmec type V epidemic clones in a tertiary hospital: challenge to infection control.

Two-hundred MRSA strains from inpatients with healthcare-associated (HA) and 100 MRSA strains from outpatients with community-associated (CA) skin and soft tissue infections (SSTIs) were tested for antimicrobial susceptibility, staphylococcal cassette chromosome mec (SCCmec) typing, Panton-Valentine leucocidin (PVL) toxin, seh and arcA genes. Based on SCCmec typing, HA-MRSA isolates were further divided into HA-SCCmec I/II/III MRSA and HA-SCCmec IV/V MRSA, and CA-MRSA isolates into CA-SCCmec I/II/III MRSA and CA-SCCmec IV/V MRSA. SCCmec types were further characterized by pulsed-field gel electrophoresis, spa typing and multi-locus sequence typing. Seventy-five (37·5%) HA-MRSA isolates and 83/100 CA-MRSA isolates were SCCmec IV/V genotype. HA-SCCmec IV/V MRSA was associated with malignancy (P = 0·03) and bone fractures (P = 0·02) compared to CA-SCCmec IV/V MRSA. HA-SCCmec IV/V MRSA was associated with PVL gene carriage compared to HA-SCCmec I/II/III MRSA (P < 0·001). ST22-MRSA-IV (EMRSA-15), ST772-MRSA-V, and ST36-MRSA-IV and ST239:EMRSA-I:III were the major clones identified. Our study documents the emergence of SCCmec IV and SCCmec V MRSA clones in an Indian hospital.

Anti-Viral Activity of Indian Plants.

Plants continue to be a major source for new chemical entities to develop novel therapeutic agents. Large number of plants has been shown to be active in vitro against a variety of human pathogenic viruses or their near congeners. In several cases the active compounds have been isolated and characterized. Very few of them, however, have been investigated in detail in vivo or taken to the clinic. Pure compounds like andrographolide, curcumin and glycyrrhizic acid as well as extracts of Azadirachta indica have shown activity against several viruses and should be investigated further for their therapeutic potential. An analysis of available data from several hundred species indicates that antiviral activity is more likely to be found in plants belonging to certain families. It is necessary to screen more plants of these families which are available in India to obtain further leads.

Burden of healthcare-associated infections in a paediatric intensive care unit of a developing country: a single centre experience using active surveillance.

Healthcare-associated infections (HAIs) are an important cause of morbidity and mortality among critically ill patients of all age groups. This prospective surveillance study was performed to estimate the burden of HAIs in a paediatric intensive care unit (PICU) of a developing country. During the 12-month study, 187 patients were treated in the PICU for ≥48h, of whom 36 patients had 44 episodes of HAIs. The crude infection rate and incidence density (ID) of HAI were 19.3/100 patients and 21/1,000 patient-days, respectively. Of the 44 episodes of HAI, 27 (61%) were healthcare-associated pneumonia (HAP), 12 (27%) were bloodstream infections (HA-BSI) and four (9%) were urinary tract infections. Mean length of stay and mortality were significantly higher in patients who developed an HAI [25 vs 7 days (P<0.0001) and 50% vs 27.8% (P<0.005), respectively]. Acinetobacter spp. were the commonest infecting bacteria in both HAP and HA-BSI. For developing countries, active surveillance is essential to reduce the burden of HAIs in high risk groups.

Clinical and molecular characteristics of nosocomial meticillin-resistant Staphylococcus aureus skin and soft tissue isolates from three Indian hospitals.

We analysed risk factors for nosocomial meticillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infections (SSTIs) in three Indian hospitals. We also determined antimicrobial resistance patterns and genotypic characteristics of MRSA isolates using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and staphylococcal cassette chromosome (SCCmec) typing. Medical records of 709 patients admitted to three tertiary hospitals with nosocomial S. aureus SSTIs were clinically evaluated. Antimicrobial susceptibility testing of patient isolates was performed in accordance with Clinical and Laboratory Standards Institute guidelines, with meticillin and mupirocin resistance confirmed by multiplex polymerase chain reaction. PFGE analysis of 220 MRSA isolates was performed, followed by MLST and SCCmec typing of a selected number of isolates. MRSA was associated with 41%, 31% and 7.5% of infections at the three hospitals, respectively. Multiple logistic regression analysis identified longer duration of hospitalisation [odds ratio (OR): 1.78; OR: 2.83 for >or=20 days], intra-hospital transfer (OR: 1.91), non-infectious skin conditions (3.64), osteomyelitis (2.9), neurological disorders (2.22), aminoglycoside therapy (1.74) and clindamycin therapy (4.73) as independent predictors for MRSA SSTIs. MRSA isolates from all three hospitals were multidrug resistant, with fifteen clones (I-XV) recognised. A majority of the strains possessed type III cassette. The common sequence type (ST) 239 was considered the signature MLST sequence for PFGE clone III. This major MRSA clone III was closely related to the UK EMRSA-1 and was significantly more resistant to antibiotics. Dissemination of multidrug-resistant MRSA clones warrants continuous tracking of resistant genotypes in the Indian subcontinent.

Incidence and characterization of Clostridium perfringens isolated from antibiotic-associated diarrhoeal patients: a prospective study in an Indian hospital.

Clostridium perfringens has been reported as causing between 2-15% of all cases of antibiotic-associated diarrhoea (AAD), and may be diagnosed by detection of enterotoxin in faeces. A prospective study comprising 150 diarrhoeal patients and 100 non-diarrhoeal controls was undertaken to assess the incidence of C. perfringens-associated diarrhoea in an Indian hospital. Methods used included C. perfringens culture, reverse passive latex agglutination (RPLA) and enzyme-linked immunosorbent assay (ELISA) for detection of enterotoxin, and polymerase chain reaction (PCR) assay for the presence of enterotoxin gene. Attempts were made to type the isolates by multiplex PCR. Of the 150 diarrhoeal stool samples tested, 13 were culture positive. Of these, four were positive for C. perfringens enterotoxin by RPLA, two were positive by PCR and two were positive by RPLA and ELISA. Twenty-seven samples were positive for culture of C. perfringens in non-diarrhoeal controls but none were positive for enterotoxin either by RPLA or by PCR. The average incidence of C. perfringens AAD using these methods was 2.6%. Toxin typing showed that all the isolates belonged to type A. To conclude, the relatively low incidence of toxigenic C. perfringens suggests that enterotoxigenic C. perfringens is not a major cause of AAD in this population.

Bacteriological and antimicrobial susceptibility profile of soft tissue infections from Northern India.

BACKGROUND: Soft tissue infections require a judicious combination of antimicrobial therapy in addition to surgical debridement to limit tissue loss and preserve life. AIMS: To study the bacterial etiology of soft tissue infections and their antimicrobial susceptibility pattern. SETTINGS AND DESIGN: A single institutional retrospective study of one year duration from January to December 2002. MATERIALS AND METHODS: A total of 5039 consecutive pus samples received in the Bacteriology Laboratory was analyzed from the records. RESULTS: There were a total of 2783 bacterial isolates comprising of 1504 gram negative bacilli and 1279 gram positive cocci. Staphylococcus aureus was the commonest isolate followed by Escherichia coli and Pseudomonas species. Methicillin resistance in S. aureus was found to be 38.56%, high level aminoglycoside resistance was observed in 53.3% enterococci and 66.75% of the gram negative bacilli were extended spectrum beta-lactamase producers. Rifampicin and vancomycin showed best activity for S. aureus; for gram-negative bacilli, piperacillin-tazobactam combination showed best activity. CONCLUSIONS: Continuous monitoring of antimicrobial susceptibility pattern in individual settings together with their judicious use is emphasized to minimize emergence of drug resistant bacteria.

Antimicrobial resistance profile of nosocomial uropathogens in a tertiary care hospital.

A retrospective analysis was done of the resistance pattern of urinary tract pathogens isolated over a 4 months period in a tertiary care hospital. There were a total of 871 clinical isolates comprising of 793 gram negative bacilli and 78 gram positive cocci obtained from 5477 consecutive urine samples. Extended spectrum beta lactamase production was observed in 71.5% of the gram negative bacilli; of these 6.18% were also inhibitor resistant. High level aminoglycoside resistance was observed in 70.17% of Enterococcus isolates while methicillin resistance was documented in 23.8% of the Staphylococcus isolates. A high level of resistance was also noted for ciprofloxacin. Multidrug resistance is a common problem in hospitals which emphasizes the need for judicious use of antimicrobial agents and their continuous in vitro monitoring.