In the era of healthcare, and its related research fields, the dimensionality problem of high dimensional data is a massive challenge as it contains a huge number of variables forming complex data ...matrices. The demand for dimension reduction of complex data is growing immensely to improvise data prediction, analysis and visualization. In general, dimension reduction techniques are defined as a compression of dataset from higher dimensional matrix to lower dimensional matrix. Several computational techniques have been implemented for data dimension reduction, which is further segregated into two categories such as feature extraction and feature selection. In this review, a detailed investigation of various feature extraction and feature selection methods has been carried out with a systematic comparison of several dimension reduction techniques for the analysis of high dimensional data and to overcome the problem of data loss. Then, some case studies are also cited to verify the better approach for data dimension reduction by considering few advances described in the technical literature. This review paper may guide researchers to choose the most effective method for satisfactory analysis of high dimensional data.
Each year, infectious diseases are responsible for millions of deaths, most of which occur in the rural areas of developing countries. Many of the infectious disease diagnostic tools used today ...require a great deal of time, a laboratory setting, and trained personnel. Due to this, the need for effective point-of-care (POC) diagnostic tools is greatly increasing with an emphasis on affordability, portability, sensitivity, specificity, timeliness, and ease of use. In this Review, we discuss the various diagnostic modalities that have been utilized toward this end and are being further developed to create POC diagnostic technologies, and we focus on potential effectiveness in resource-limited settings. The main modalities discussed herein are optical-, electrochemical-, magnetic-, and colorimetric-based modalities utilized in diagnostic technologies for infectious diseases. Each of these modalities feature pros and cons when considering application in POC settings but, overall, reveal a promising outlook for the future of this field of technological development.
Biofilm and wound healing: from bench to bedside Goswami, Aakansha Giri; Basu, Somprakas; Banerjee, Tuhina ...
European journal of medical research,
04/2023, Letnik:
28, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The bubbling community of microorganisms, consisting of diverse colonies encased in a self-produced protective matrix and playing an essential role in the persistence of infection and antimicrobial ...resistance, is often referred to as a biofilm. Although apparently indolent, the biofilm involves not only inanimate surfaces but also living tissue, making it truly ubiquitous. The mechanism of biofilm formation, its growth, and the development of resistance are ever-intriguing subjects and are yet to be completely deciphered. Although an abundance of studies in recent years has focused on the various ways to create potential anti-biofilm and antimicrobial therapeutics, a dearth of a clear standard of clinical practice remains, and therefore, there is essentially a need for translating laboratory research to novel bedside anti-biofilm strategies that can provide a better clinical outcome. Of significance, biofilm is responsible for faulty wound healing and wound chronicity. The experimental studies report the prevalence of biofilm in chronic wounds anywhere between 20 and 100%, which makes it a topic of significant concern in wound healing. The ongoing scientific endeavor to comprehensively understand the mechanism of biofilm interaction with wounds and generate standardized anti-biofilm measures which are reproducible in the clinical setting is the challenge of the hour. In this context of "more needs to be done", we aim to explore various effective and clinically meaningful methods currently available for biofilm management and how these tools can be translated into safe clinical practice.
Amebiasis, caused by Entamoeba histolytica (E. histolytica), is a significant cause of morbidity and mortality in developing countries. Mortality due to amebiasis is mostly by extra intestinal ...infections, amebic liver abscess being the most common one. This study was conducted to determine the current epidemiological status, risk factors, associated microflora and strain variation of E. histolytica causing liver abscesses.
A total of 115 liver abscess cases comprising of 107 (93%) males and 8 (6.9%) females were included in the study. Microscopic examination of pus samples from the abscesses and species discrimination using nested multiplex PCR showed the presence of E. histolytica in 101 (87.5%) cases. Data collected by face to face interviews using a pre tested questionnaire suggested intake of untreated drinking water (ORs: 6.4, p = 0.002), habit of alcohol consumption (ORs: 4.0, p = 0.019) and lack of urban services (ORs: 0.08, p = 0.017) to be major risk factors associated with E. histolytica infections. The study of associated bacterial flora through aerobic culture of liver aspirates and conventional PCR for detection of anaerobes revealed the presence of Fusobacterium (19, 25.5%), Peptococcus (19, 25.5%), Prevotella (18, 24.3%), Bacteroides (8, 10.8%), Staphylococcus aureus (3, 4%), Escherichia coli (2, 2.7%), Peptostreptococcus (2, 2.7%), Clostridium (2, 2.7%) and Klebsiella pneumoniae (1, 1.3%). Further to study the clonality, genotyping of E. histolytica targeting six tRNA-linked polymorphic STR loci (A-L, D-A, N-K, R-R, STGA -D and S-Q) was carried out which showed the presence of 89 different genotypes in the liver aspirate samples.
The findings highlight the high prevalence of genetically diverse E. histolytica from the liver abscess cases in this geographical region. Low socio-economic status and habit of alcohol consumption were important predictors of amebic liver abscess.
The emergence of multidrug-resistant tuberculosis (MDR-TB) has complicated the situation due to the decline in potency of second-line anti-tubercular drugs. This limits the treatment option for ...extensively drug-resistant tuberculosis (XDR-TB). The aim of this study was to determine and compare the minimum inhibitory concentration (MIC) by agar dilution and resazurin microtiter assay (REMA) along with the detection of mutations against linezolid and clofazimine in confirmed XDR-TB clinical isolates. A total of 169 isolates were found positive for Mycobacterium tuberculosis complex (MTBC). The MIC was determined by agar dilution and REMA methods. The isolates which showed non-susceptibility were further subjected to mutation detection by targeting rplC gene (linezolid) and Rv0678 gene (clofazimine). The MIC for linezolid ranged from 0.125 microg/ml to > 2 microg/ml and for clofazimine from 0.25 microg/ml to > 4 microg/ml. The MIC.sub.50 and MIC.sub.90 for linezolid were 0.5 microg/ml and 1 microg/ml respectively while for clofazimine both were 1 microg/ml. The essential and categorical agreement for linezolid was 97.63% and 95.26% and for clofazimine, both were 100%. The sequencing result of the rplC gene revealed a point mutation at position 460 bp, where thymine (T) was substituted for cytosine (C) while seven mutations were noted between 46 to 220 bp in Rv0678 gene. REMA method has been found to be more suitable in comparison to the agar dilution method due to lesser turnaround time. Mutations in rplC and Rv0678 genes were reasons for drug resistance against linezolid and clofazimine respectively.
Entamoeba infections have major impact on millions of the people worldwide. Entamoeba histolytica has long been accepted as the only pathogenic species. However, recent reports of other Entamoeba ...spp. in symptomatic cases have raised questions on their pathogenicity.
Total 474 stool samples and 125 liver aspirates from patients with intestinal and extra intestinal manifestations and from community were included. Sewage samples from the hospital and the city were also included. Microscopic examination and molecular detection were performed to detect presence of E. histolytica/ dispar/ moshkovskii/ bangladeshi. The associated demographic and socioeconomic factors were statistically analyzed with the presence of Entamoeba. Microscopy detected Entamoeba spp. in 5.4% stool and 6.4% liver aspirate samples. Through nested multiplex PCR, prevalence of Entamoeba spp. in intestinal and extra-intestinal cases was 6.6% (20/301) and 86.4% (108/125) respectively and in asymptomatic population was 10.5% (13/123). Sewage samples did not show presence of any Entamoeba spp. Uneducated subjects, low economic conditions, untreated drinking water, consumption of raw vegetables and habit of not washing hands before meals were significantly associated with presence of Entamoeba spp.
E. histolytica still remains the only Entamoeba spp. in invasive extra intestinal infections. E. dispar was detected in both asymptomatic and symptomatic intestinal infections. Routine identification of Entamoeba spp. should incorporate PCR based detection methods.
Infections by Entamoeba histolytica (E. histolytica) lead to considerable morbidity and mortality worldwide and treatment is reliant on a single class of drugs, nitroimidazoles. Treatment failures ...and intermittent reports of relapse from different parts of world indicate towards development of clinical drug resistance. In the present study, susceptibility testing of clinical isolates of E. histolytica was carried against metronidazole and tinidazole. Additionally, anti-amoebic property of active compounds of Andrographis paniculata was also evaluated. Prevalence of metronidazole resistance gene (nim) in patients attending hospital was also done to get comprehensive insight of present situation of drug resistance in E. histolytica. Mean inhibitory concentration 50 (IC50) value of E. histolytica isolates against metronidazole and tinidazole was 20.01 and 16.1 µM respectively. Andrographolide showed minimum mean IC50 value (3.06 µM). Significant percentage inhibition of E. histolytica isolates by andrographolide was seen as compared to metronidazole (p = 0.0495). None of E. histolytica isolates showed presence of nim gene. However, in stool samples from hospital attending population, prevalence of nimE gene was found to be 76.6% (69/90) and 62.2% (56/90) in diarrheal and non-diarrheal samples respectively. Inhibitory concentration of commonly used nitroimidazoles against clinical isolates of E. histolytica are on rise. Percentage inhibition of E. histolytica isolates by andrographolide was significantly higher than control drug metronidazole.
Background
The rapid emergence of carbapenem resistant
Acinetobacter baumannii
(CRAB) has resulted in an alarming situation worldwide. Realizing the dearth of literature on susceptibility of CRAB in ...genetic context in the developing region, this study was performed to determine the susceptibility profile against standard drugs/combinations and the association of
in-vitro
drug synergy with the prevalent molecular determinants.
Methods and findings
A total of 356 clinical isolates of
A. baumannii
were studied. Confirmation of the isolates was done by amplifying
recA
and ITS region genes. Susceptibility against standard drugs was tested by Kirby Bauer disc diffusion. Minimum inhibitory concentration (MIC), MIC
50
and MIC
90
values against imipenem, meropenem, doripenem, ampicillin/sulbactam, minocycline, amikacin, polymyxin B, colistin and tigecycline was tested as per guidelines. Genes encoding enzymes classes A (
bla
GES
,
bla
IMI/NMC-A
,
bla
SME
,
bla
KPC
), B (
bla
IMP
,
bla
VIM
,
bla
NDM
) and D (
bla
OXA-51,
bla
OXA-23
and
bla
OXA-58
) were detected by multiplex polymerase chain reaction. Synergy against meropenem-sulbactam and meropenem-colistin combinations was done by checkerboard MIC method. Correlation of drug synergy and carbapenemase encoding genes was statistically analyzed.
Results
Of the total, resistance above 90% was noted against gentamicin, ciprofloxacin, levofloxacin, ceftazidime, cefepime, ceftriaxone, cotrimoxazole and piperacillin/tazobactam. By MIC, resistance rates from highest to lowest was seen against imipenem 89.04% (n=317), amikacin 80.33% (n=286), meropenem 79.49% (n=283), doripenem 77.80% (n=277), ampicillin/sulbactam 71.62% (n=255), tigecycline 55.61% (n=198), minocycline 14.04% (n=50), polymyxin B 10.11% (n=36), and colistin 2.52% (n=9). CRAB was 317 (89.04%), 81.46% (n=290) were multidrug resistant and 13.48% (n=48) were extensively drug resistant. All the CRAB isolates harboured
bla
OXA-51
gene (100%) and 94% (n=298)
bla
OXA-23
gene. The
bla
IMP
gene was most prevalent 70.03% (n=222) followed by
bla
NDM,
59.62% (n=189). Majority (87.69%, 278) were co-producers of classes D and B carbapenemases,
bla
OXA-23
with
bla
IMP
and
bla
NDM
being the commonest. Synergy with meropenem-sulbactam and meropenem-colistin was 47% and 57% respectively. Reduced synergy (
p
= <0.0001) was noted for those harbouring
bla
OXA-51
+bla
OXA-23
with
bla
NDM
gene alone or co-producers.
Conclusion
Presence of
bla
NDM
gene was a significant cause of synergy loss in meropenem-sulbactam and meropenem-colistin. In
bla
NDM
endemic regions, tigecycline, minocycline and polymyxins could be viable options against CRAB isolates with more than one carbapenemase encoding genes.
Extensive drug resistance in Klebsiella pneumoniae (K. pneumoniae) causing major outbreaks in large hospitals is an emerging challenge. We describe a near fatal outbreak of colistin resistant, ...carbapenem resistant K. pneumoniae (CRKp) producing metallo beta-lactamases (bla
) and bla
in the neonatal intensive care unit (NICU) at the background of a larger outbreak involving multiple parts of the hospital and the challenges in its containment.
Following identification of an outbreak due to colistin resistant CRKp between April to June 2017 in the NICU, a thorough surveillance of similar cases and the hospital environment was performed to trace the source. All the isolated K. pneumoniae were tested for susceptibility to standard antibiotics by disc diffusion and microbroth dilution methods. Molecular detection of extended spectrum beta lactamases (ESBLs) and carbapenemases (classes A, B, D) genes was done. Enterobacterial repetitive intergenic consensus (ERIC) PCR and multi-locus sequence typing (MLST) was done to determine the genetic relatedness of the isolates. Characteristics of different sequence types were statistically compared (Student's t-test).
A total of 45 K. pneumoniae isolates were studied from NICU (14 cases of neonatal sepsis), ICU (18 cases), other wards (7 cases) along with 6 isolates from hospital environment and human colonizers. The primary case was identified in the ICU. All the K. pneumoniae from NICU and 94.4% from the ICU were colistin resistant CRKp. Majority (59.37% and 56.25%) harbored bla
/bla
and bla
genes, respectively. Two distinct sequence types ST5235 and ST5313 were noted with colistin resistance, distribution within the NICU and mortality as significant attributes of ST5235 (p < 0.05). The outbreak was contained with strengthening of the infection control practices and unintended short duration closure of the hospital.
Large hospital outbreaks with considerable mortality can be caused by non-dominant clones of colistin resistant CRKp harboring bla
and bla
carbapenemases in endemic regions. The exact global impact of these sequence types should be further studied to prevent future fatal outbreaks.
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