The development of multidrug resistance in Salmonella enterica serovar Typhi currently forms a major roadblock for the treatment of enteric fever. This poses a major health problem in endemic regions ...and extends to travellers returning from developing countries. The appearance of fluoroquinolone non-susceptible strains has resulted in use of ceftriaxone as drug of choice with azithromycin being recommended for uncomplicated cases of typhoid fever. A recent sporadic instance of decreased susceptibility to the latest drug regime has necessitated a detailed analysis of antimicrobial resistance genes and possible relationships with their phenotypes to facilitate selection of future treatment regimes. Whole genome sequencing (WGS) was conducted for 133 clinical isolates from typhoid patients. Sequence output files were processed for pan-genome analysis and prediction of antimicrobial resistance genes. The WGS analyses disclosed the existence of fluoroquinolone resistance conferring mutations in gyrA, gyrB, parC and parE genes of all strains. Acquired resistance determining mechanisms observed included catA1 genes for chloramphenicol resistance, dfrA7, dfrA15, sul1 and sul2 for trimethoprim-sulfamethoxazole and bla
/bla
genes for amoxicillin. No resistance determinants were found for ceftriaxone and cefixime. The genotypes were further correlated with their respective phenotypes for chloramphenicol, ampicillin, co-trimoxazole, ciprofloxacin and ceftriaxone. A high correlation was observed between genotypes and phenotypes in isolates of S. Typhi. The pan-genome analysis revealed that core genes were enriched in metabolic functions and accessory genes were majorly implicated in pathogenesis and antimicrobial resistance. The pan-genome of S. Typhi appears to be closed (B
= 0.09) as analysed by Heap's law. Simpson's diversity index of 0.51 showed a lower level of genetic diversity among isolates of S. Typhi. Overall, this study augments the present knowledge that WGS can help predict resistance genotypes and eventual correlation with phenotypes, enabling the chance to spot AMR determinants for fast diagnosis and prioritize antibiotic use directly from sequence.
Biofilm formation by
Acinetobacter baumannii
is one of the major cause of its persistence in hospital environment. Biofilm phenotypes are more resistant to physical as well as chemical stresses than ...their planktonic counterparts. The present study was carried in quest of biofilm-associated protein markers and their association with various biological pathways of
A. baumannii.
The study was designed with an aim to highlight the crucial common factor present in the majority of the
A. baumannii
strains irrespective of its resistance nature. A label-free proteome comparison of biofilm and planktonic phenotypes of
A. baumannii
was done using QExactive tandem mass spectrometry. Our investigation suggests key elevation of adhesion factors, acetate metabolism, nutrient transporters, and secretion system proteins are required for biofilm formation in
A. baumannii
. Elevation of biofilm-associated proteins revealed that biofilm is the unique phenotype with the potential to form robust matrix-embedded colonies and defeat stress condition. Further, core protein markers of biofilm phenotypes could be used as targets for new clinical interventions to combat biofilm-associated infections.
Enteric fever continues to be a major cause of mortality and morbidity globally, particularly in poor resource settings. Lack of rapid diagnostic assays is a major driving factor for the empirical ...treatment of enteric fever. In this work, a rapid and sensitive method 'Miod' 'has been developed. Miod includes a magnetic nanoparticle-based enrichment of target bacterial cells, followed by cell lysis and loop-mediated isothermal amplification (LAMP) of nucleic acids for signal augmentation along with concurrent measurement of signal via an in-situ optical detection system. To identify positive/negative enteric fever infections in clinical blood samples, the samples were processed using Miod at time = 0 hours and time = 4 hours post-incubation in blood culture media. Primers specific for the STY2879 gene were used to amplify the nucleic acids isolated from S. typhi cells. A limit of detection of 5 CFU/mL was achieved. No cross-reactivity of the primers were observed against 106 CFU/mL of common pathogenic bacterial species found in blood such as E. coli, P. aeruginosa, S. aureus, A. baumanni, E. faecalis, S. Paratyphi A and K. pneumonia. Miod was tested on 28 human clinical blood samples. The detection of both pre-and post-four-hours incubation confirmed the presence of viable S. typhi cells and allowed clinical correlation of infection. The positive and negative samples were successfully detected in less than 6 hours with 100% sensitivity and specificity.
There is a paucity of data on the epidemiology of sepsis in outborn neonates being referred to level-3 units in low- and middle-income countries (LMIC). The objective of the present study was to ...evaluate the prevalence of sepsis and outcomes of outborn neonates with sepsis, and to characterize the pathogen profile and antimicrobial resistance (AMR) patterns of common isolates in them.
In this prospective observational cohort study (2011-2015), a dedicated research team enrolled all neonates admitted to an outborn level-3 neonatal unit and followed them until discharge/death. Sepsis work-up including blood culture(s) was performed upon suspicion of sepsis. All the isolates were identified and tested for antimicrobial susceptibility. Gram-negative pathogens resistant to any three of the five antibiotic classes (extended-spectrum cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and piperacillin-tazobactam) were labeled multi-drug resistant.
Of the total of 2588 neonates enrolled, culture positive sepsis and total sepsis-i.e. culture positive and/or culture negative sepsis-was diagnosed in 13.1% (95% CI 11.8% to 14.5%) and 54.7% (95% CI 52.8% to 56.6%), respectively. The case fatality rates were 23.4% and 11.0% in culture-positive and total sepsis, respectively. Sepsis accounted for two-thirds of total neonatal deaths (153/235, 63.0%). Bacterial isolates caused about three-fourths (296/401; 73.8%) of the infections. The two common pathogens-Klebsiella pneumoniae (n = 50, 12.5%) and Acinetobacter baumannii (n = 46, 11.5%)-showed high degree of multi-drug resistance (78.0% and 91.3%, respectively) and carbapenem resistance (84.0% and 91.3%, respectively). About a quarter of infections were caused by Candida spp. (n = 91; 22.7%); almost three-fourths (73.7%) of these infections occurred in neonates born at or after 32 weeks' gestation and about two-thirds (62.1%) in those weighing 1500 g or more at birth.
In this large outborn cohort, we report high burden of sepsis, high prevalence of systemic fungal infections, and alarming rates of antimicrobial resistance among bacterial pathogens.
Pathogenic strains of Escherichia coli (EC) have emerged as a threat to public health due to its ability to contaminate food and water. Early detection of EC contamination in food products is of ...fundamental importance to avoid any severe medical situations associated with its infection. We herein report a rapid and facile; aptamer and NanoZyme-based assay for EC detection in fruit juice. The developed assay is highly rapid, sensitive, and affordable. The test can be completed within 5 min without any requirement of a sophisticated instrument and cost roughly $ 2. Moreover, the detection is visible to naked eyes. We have also adapted the aptamer on to an electrochemical sensing platform to evaluate its diagnostic utility. The aptamer performed impressively with both NanoZyme-based colorimetric and electrochemical assay and displayed a low-end detection limit of ~10 CFU. The approach presented in the current study is a generic strategy and in principle, may be used for the detection of various analytes, including other bacterial pathogens.
Acinetobacter baumannii has been identified by the Infectious Diseases Society of America as one of the six pathogens that cause majority of hospital infections. Increased resistance of A.baumannii ...even to the latest generation of β-lactams like carbapenem is an immediate threat to mankind. As inner-membrane fraction plays a significant role in survival of A.baumannii, we investigated the inner-membrane fraction proteome of carbapenem-resistant strain of A.baumannii using Differential In-Gel Electrophoresis (DIGE) followed by DeCyder, Progenesis and LC-MS/MS analysis. We identified 19 over-expressed and 4 down-regulated proteins (fold change>2, p<0.05) in resistant strain as compared to reference strain. Some of the upregulated proteins in resistant strain and their association with carbapenem resistance in A.baumannii are: i) β-lactamases, AmpC and OXA-51: cleave and inactivate carbapenem ii) metabolic enzymes, ATP synthase, malate dehydrogenase and 2-oxoglutarate dehydrogenase: help in increased energy production for the survival and iii) elongation factor Tu and ribosomal proteins: help in the overall protein production. Further, entry of carbapenem perhaps is limited by controlled production of OmpW and low levels of surface antigen help to evade host defence mechanism in developing resistance in A.baumannii. Present results support a model for the importance of proteins of inner-membrane fraction and their synergistic effect in the mediation of resistance of A.baumannii to carbapenem.
Antibiotics resistance is an paramount threat affecting the whole world but nowhere situation is as gloomy as in India. No study till date regarding epidemiology of hospital acquired infections in ...coronary care units(CCU) and cardiology wards from India. From Indian perspective it is the first observational study to analyse microbiological profile and antibiotic resistance in CCU. The purpose of this observational study is to explore the epidemiology and importance of infections in CCU patients.
After ethics committee approval, the records of all patients who were admitted in coronary care units, adult and pediatric cardiology wards surgery between January 2020 and December 2021 were reviewed retrospectively. The type of organism,source of infection ,age wise distribution and seasonal variability among patients who developed hospital acquired infection (HAI) were determined.
271 patients developed microbiologically documented HAI during from January 2020 to December 2021. Maximum number of organisms(78/271 28.78%) are isolated from urinary samples ,followed by blood stream(60/271 22.14%) and Endotracheal tube (54/271 19.92%). Acinetobacter baumanii (53/271, 19.5%) being the most common isolate among all the samples taken . Acinetobacter was the most frequent pathogens isolated in patients with LRTI and blood stream infection while E. coli was from urinary tract infection . In the adult population, infection with E. coli(24.6%) is the most common followed by Klebsiella pneumoniae (12.8%) and Acinetobacter baumanii (10.1%). In the pediatric population Acinetobacter baumanii (38.6%%) is the most common followed by Klebsiella pneumoniae (20.5%) and Methicillin Resistant Staphylococcus aureus, MRSA (6.8%). Commonly used antibiotics eg ciprofloxacin,ceftazidime and amikacin were found to be resistant against the top three isolates.
Urinary tract was the most common site of infection and Gram-negative bacilli, the most common pathogens in adult as well as pediatric population. Antibiotic resistance was maximum with commonly isolated microorganisms.
Office cystoscopy may be associated with urinary tract infection (UTI) in up to 10-20% of patients. Current practice of surgical part preparation in males with povidone-iodine excludes distal urethra ...in males, leaving a possibility for resident intra-urethral flora to cause post-procedural UTI. We designed this randomized study to assess whether additional cleaning of distal urethra with povidone-iodine solution can help reduce post-procedural incidence of UTIs in this setting. Additionally, urethral swab culture was done in the entire cohort to identify the prevalent microflora in the distal male urethra and to evaluate its role in causation of post-procedural UTI. Using a specialized urethral swab culture methodology, 85% males demonstrated some bacteria and 16% showed common uro-pathogens. 28 (14.5%) cases had post-procedure culture positive UTI. The incidence of UTI in control group (22%) was significantly more than the intervention group (7%) (p value <0.007). This result strongly supports inclusion of distal urethral irrigation with povidone-iodine in males before office cystoscopy, even when pre-procedure mid-stream urine culture is sterile.
High-risk hospital-associated multidrug-resistant (MDR) Enterococcus faecalis clonal complexes (CCs) such as CC2 and CC87 are enriched with virulence determinants that help to accumulate, colonize, ...and cause serious nosocomial infections. The aim of this study was to establish the epidemiology and clonal composition of 134 clinical E. faecalis isolates and to link molecular typing data with antimicrobial resistance and virulence determinants. All isolates were identified by conventional methods and confirmed by polymerase chain reaction (PCR) (16srRNA gene and ddl genes of E. faecalis/ E. faecium) in 5-years. Disc diffusion test was performed on all strains. We screened all E. faecalis for aac(6′)-aph(2″), vanA, and vanB resistance genes, and aggregation substance-asa1, cytolysin-cylA, collagen-binding protein-ace, enterococcal surface protein-esp, gelatinase-gelE, and hyaluronidase-hyl virulence genes by PCR. Representative isolates of E. faecalis were characterized by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Out of 539 patients with enterococcal infections, 134 (24.9%) had E. faecalis infections, 366 (67.9%) had E. faecium infections, and 39 (7.2%) had infections due to other enterococcal species. Of the 134 isolates, 79.1% and 61.9% isolates were high-level gentamicin resistant (HLGR) and MDR. In multivariate analysis, independent predictor for infection due to MDR E. faecalis strains was a surgical intervention (OR 2.41, 95% CI 1.17–4.96, P = 0·017). Overall, the observed rate of in-hospital mortality was 11.9%. The gelE, asa1, ace, cylA, esp and hyl genes were detected in 87.3%, 78.4%, 54.5%, 53.7%, 36.6% and 3.0%, respectively in E. faecalis isolates. The asaI, cylA, and gelE genes were significantly correlated with MDR E. faecalis. The PFGE analysis showed 28 clones with four major clones. MLST analysis revealed two sequence types-ST28 (CC87) and ST181 (CC2). This is the first Indian report on the emergence of the high-risk hospital-associated worldwide-disseminated ST28 (CC87) and ST181 (CC2), which have enriched with multiple virulence determinants and resistance to antibiotics, paticularly ampicillin. This report indicates serious health concern and calls for on-going surveillance, close monitoring, and improved infection control procedures to stop further spread of these isolates.
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•Aimes: To establish the epidemiology and clonal composition of 134 clinical E. faecalis isolates and to correlate antimicrobial resistance and virulence determinants.•A total of 539 enterococci, 134 (24.9%) were E. faecalis, 366 (67.9%) were E. faecium, and 39 (7.2%) were other enterococcal species. Of the 134 E. faecalis isolates, 79.1% and 61.9% isolates were HLGR and MDR.•The gelE, asa1, ace, cylA, esp and hyl genes were detected in 87.3, 78.4, 54.5, 53.7, 36.6 and 3.0% in E. faecalis isolates respectively.•This is the first report from India on the emergence of the high-risk hospital-associated worldwide-disseminated ST28 (CC87) and ST181 (CC2) enriched with multiple antibiotic resistance and virulence determinants.
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