Molecular Characterization of Escherichia coli Causing Urinary Tract Infections Through Next-Generation Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes.

Introduction An enormous increase in antimicrobial resistance (AMR) among bacteria isolated from human clinical specimens contributed to treatment failures. Increased surveillance through next-generation sequencing (NGS) or whole genome sequencing (WGS) could facilitate the study of the epidemiology of drug-resistant bacterial strains, resistance genes, and other virulence determinants they are potentially carrying. Methods This study included 30 Escherichia coli (E. coli) isolates obtained from patients suffering from urinary tract infections (UTIs) attending Prathima Institute of Medical Sciences, Karimnagar, India. All bacterial isolates were identified, and antimicrobial susceptibility patterns were determined through conventional microbiological techniques and confirmed by automated systems. All the isolates were investigated using NGS to identify genes coding for resistance, such as extended-spectrum beta-lactamases (ESBLs), metallo-beta-lactamases, and virulence genes. Multilocus sequence typing (MLST) was used to understand the prevalent strain types, and serotyping was carried out to evaluate the type of O (cell wall antigen) and H (flagellar antigen) serotypes carried by the isolates. Results The conventional antimicrobial susceptibility testing revealed that 15 (50%) isolates were resistant to imipenem (IPM), 10 (33.33%) were resistant to amikacin (AK), 13 (43.33%) were resistant to piperacillin-tazobactam (PTZ), 17 (56.66%) were resistant to cephalosporins, and 14 (46.66%) were resistant to nitrofurantoin (NIT). Among the isolates, 26 (86.66%) had revealed the presence of multiple antibiotic-resistant genes with evidence of at least one gene coding for beta-lactamase resistance. There was a high prevalence of blaCTX-M (19/30, 63.33%) genes, followed by blaTEM and blaOXA-1. The blaNDM-5 gene was found in three isolates (3/30, 10%). The virulence genes identified in the present study were iutA, sat, iss, and papC, among others. The E. coli serotype found predominantly belonged to O25:H4 (5, 16.66%), followed by O102:H6 (4, 13.33%). A total of 16 MLST variants were identified among the examined samples. Of the MLST-based sequence types (STs) identified, ST-131 (7, 23.33%) was the predominant one, followed by ST-167 (3, 10%) and ST-12 (3, 10%). Conclusions The study results demonstrated that the E. coli strains isolated from patients suffering from UTIs potentially carried antimicrobial resistance and virulence genes and belonged to different strain types based on MLST. Careful evaluation of bacterial strains using molecular analyses such as NGS could facilitate an improved understanding of bacterial antibiotic resistance and its virulence potential. This could enable physicians to choose appropriate antimicrobial agents and contribute to better patient management, thereby preventing the emergence and spread of drug-resistant bacteria.

Comparative Analysis of Enzyme-Linked Immunosorbent Assay and Immunochromatography for Rotavirus and Adenovirus Detection in Children below Five Years with Acute Gastroenteritis.

Introduction The most frequent etiologies of viral gastroenteritis among young children are rotavirus and enteric adenovirus. The clinical signs and symptoms of viral gastroenteritis are not distinct enough to allow for diagnosis. For the diagnosis and treatment of acute gastroenteritis, it is preferable to use quick, simple, and low-cost procedures. This study was undertaken to determine efficacy of immune-chromatography test (ICT) in comparison with enzyme-linked immunosorbent assay (ELISA) to detect rotavirus and adenovirus antigen in fecal specimen among children less than 5 years of age with acute gastroenteritis. Materials and Methods In a cross-sectional observational study, 314 fecal samples were collected from children aged less than 5 years with acute gastroenteritis attending or admitted to a tertiary care hospital during the 1 year study period. Samples were tested for rotavirus and adenovirus antigen using ICT and ELISA. Results Among the 314 children evaluated, 112 (35.66%) had rotavirus infection, nine (2.86%) had adenovirus infection, and three (0.95%) had both rotavirus and adenovirus infection. This study found that ICT is 98.20% sensitive and 100% specific for the diagnosis of rotaviral diarrhea and 100% sensitive and 99.7% specific for adenovirus diarrhea, compared to ELISA. Conclusion Immunochromatography tests used for the detection of rotavirus and adenovirus in the fecal sample showed a high degree of sensitivity and specificity. The ICT is easy to perform and rapid, and it does not require any special equipment. Hence, the ICT could be used as an alternative method for detecting viral pathogens in clinical practice.

Research Question, Objectives, and Endpoints in Clinical and Oncological Research: A Comprehensive Review.

Clinical research is a systematic process of conducting research work to find solutions for human health-related problems. It is applied to understand the disease process and assist in the diagnosis, treatment, and prevention. Currently, we are experiencing global unrest caused by the coronavirus disease (COVID-19) pandemic. The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) has been responsible for the deaths of more than 50 million people worldwide. Also, it has resulted in severe morbidity among the affected population. The cause of such a huge amount of influence on human health by the pandemic was the unavailability of drugs and therapeutic interventions to treat and manage the disease. Cancer is a disease condition wherein the normal cell function is deranged, and the cells multiply in an uncontrolled manner. Based on recent reports by the World Health Organization (WHO), cancer is the second leading cause of death globally. Moreover, the rates of cancers have shown an increasing trend in the past decade. Therefore, it is essential to improve the understanding concerning clinical research to address the health concerns of humans. In this review, we comprehensively discuss critical aspects of clinical research that include the research question, research objectives, patient-reported outcome measures (PROMs), intention-to-treat and per-protocol analysis, and endpoints in clinical and oncological research.

Assessment of SARS-CoV-2-Infected Patients and Their Clinical Outcomes During the Third Wave in India: A Single-Center Observational Study.

Background The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that emerged from the Chinese mainland has spread throughout the world affecting the normal lives of the people. Both developed and developing nations have been equally affected and coronavirus disease-19 (COVID-19) resulted in the death of millions of people worldwide. The virus is undergoing mutations and is evolving into variants that are responsible for wave after wave. This study was carried out to assess the clinical outcomes of people infected with the novel virus during the third wave of the COVID-19 pandemic in India. Methods The study was carried out between November 2021 and January 2022 and included 100 consecutive patients attending the hospital attached to the BLDE (Deemed to be University) Shri B.M. Patil Medical College, Bijapur, Karnataka, South India. All patients included in the study returned a positive report in a real-time polymerase chain reaction (RT-PCR). The patient details collected included age, sex, cycle threshold (Ct) values for envelope (E)/nucleocapsid (N), and Orf1b (open reading frame 1b) genes, hospitalization status, vaccine status, C-reactive protein (CRP), D-dimer, interleukin-6 (IL-6), and final clinical outcome. The data were entered into Microsoft Office Excel sheets, and statistical inferences were drawn using SPSS 24 (IBM Corp., Armonk, NY). Results Of the 100 patients included in the study, only 14 (14%) patients were vaccinated. The patient's mean age was 34.22±17.50. Among the vaccinated patients, the majority had taken COVISHIELD™ (85.71%) compared to COVAXIN® (14.29%). Only 14% of patients were symptomatic, and the mean Ct values among all the patients were 29.92±3.74 (E gene/N gene) and 27.6±4.78 (Orf1B gene). Eight (8%) patients were hospitalized, and all the patients recovered from the infection. Among the hospitalized patients, six (75%) were vaccinated. The mean age of the hospitalized patients was 43.8±14.25 years. The mean CRP, D-dimer, and IL-6 concentrations among the hospitalized patients were noted to be 22.375±16.58 mg/L, 654.325±577.24 ng/mL, and 5.075±2.15 ng/mL, respectively. Conclusion The study results demonstrate that despite unvaccinated status, most patients in the third wave had only suffered from asymptomatic infection. Moreover, people who developed a clinical infection and those who required hospitalization had an uneventful recovery irrespective of their vaccination status.

Breakthrough Infections: Clinical Profile and Outcomes of COVID-19 Vaccinated and Unvaccinated People From a Tertiary Care Hospital.

Introduction Despite the availability of a vaccine and extensive vaccination, breakthrough infections are commonly noted, which is jeopardizing the vaccine-based protection against COVID-19. The present study aims to evaluate COVID-19 breakthrough infections and to compare the clinical profile and outcomes of the vaccinated and unvaccinated populations.  Methods A retrospective observational study was conducted for two months (March-April 2021), and all cases reported during the study period were included in the study. Socio-demographic details, COVID-19 profiles, clinical outcomes, vaccination statuses, and types of vaccine were collected from the patients. Further, COVID-19-positive samples were screened for lineages using next-generation sequencing (NGS). Results Of the total 103 patients included in the study, 79 (76.7%) were symptomatic and 24 (23.3%) were asymptomatic. Only 32% were vaccinated and 68% were unvaccinated. 29.2% were hospitalized due to COVID-19 and all of them were unvaccinated. The mortality among hospitalized patients was extremely high (60%). The time to positivity after complete vaccination was noted to be 37.09±23.74 days. The unvaccinated study participants showed lower Cycle threshold (Ct) values (E Gene/N Gene: 17.38±4.53) as compared to the vaccinated people (E Gene/N Gene: 22±4.25). The Delta (B. 1.1. 629) (76.7%) was the predominant variant among the study population followed by AY.4 (20.4%) and Kappa (2.9%) variants. Conclusion Although the vaccination does not restrict/avoid infection, it appears to protect the vaccinated people from severe forms of COVID-19. Also, the higher Ct values among vaccinated people indicate that the viral load among such people may be lower and, therefore, minimizes viral transmission.

Traditional Widal Agglutination Test Versus Rapid Immunochromatographic Test in the Diagnosis of Enteric Fever: A Prospective Study From South India.

Introduction Early diagnosis and treatment are crucial to reducing the morbidity of patients with enteric fever/typhoid fever. Among the available diagnostic tests, the blood culture is considered a gold standard. However, in most of the developing and resource-limited settings, the diagnosis is made utilizing the traditional Widal test and rapid immunochromatographic test (ICT). This study was aimed to compare the diagnostic value and efficacy of ICT and traditional Widal test in the diagnosis of typhoid fever. Methods A prospective study was conducted, and 40 patients were included in the study. The Widal test and Salmonella enterica serovar Typhi IgM/IgG immunochromatographic test were performed for all the patients. The Widal is a tube agglutination test, and the rapid ICT utilizes the principle of enzyme-linked immunosorbent assay (ELISA). All the samples were also tested for the presence of antibodies (IgG and IgM) against the S. enterica serovar Typhi and the titers against 'O' and 'H' antigens of S. enterica serovar Typhi. An antibody titer of 1:80 or more against the 'O' and 'H' antigen was considered positive. Results In the ICT, 24 samples (60%) tested positive for the IgM antibodies, and only 15 samples tested positive and for IgG antibodies. In the Widal test, 27 samples (67.6%) returned positive for antibodies against the S. enterica serovar Typhi 'O' antigen. The sensitivity (90% vs 72.73%), specificity (81.25% vs 64%), and accuracy (82.12% vs 64.87%) for the Widal test were found to be more when compared to the ICT. Conclusion The results indicate that the traditional Widal agglutination test is superior to the rapid ICT in the diagnosis of enteric fever. However, both these tests cannot be considered as gold standards for the diagnosis owing to their low positive predictive values.

Immunological aspects and gender bias during respiratory viral infections including novel Coronavirus disease-19 (COVID-19): A scoping review.

The human immune system is not adequately equipped to eliminate new microbes and could result in serious damage on first exposure. This is primarily attributed to the exaggerated immune response (inflammatory disease), which may prove detrimental to the host, as evidenced by SARS-CoV-2 infection. From the experiences of Novel Coronavirus Disease-19 to date, male patients are likely to suffer from high-intensity inflammation and disease severity than the female population. Hormones are considered the significant pillars of sex differences responsible for the discrepancy in immune response exhibited by males and females. Females appear to be better equipped to counter invading respiratory viral pathogens, including the novel SARS-CoV-2, than males. It can be hypothesized that females are more shielded from disease severity, probably owing to the diverse action/influence of estrogen and other sex hormones on both cellular (thymus-derived T lymphocytes) and humoral immunity (antibodies).

Seroprevalence of Rubella Virus-specific Antibodies in Women and the Diagnostic Efficacy of Enzyme-linked Immunoassay and Rapid Immunochromatographic Tests.

Introduction Rubella is an infectious disease caused by the Rubella virus. The disease was previously called German measles and is transmitted through respiratory aerosols. Rubella causes both clinical and subclinical infections in children and young adults. Rubella virus has teratogenic capabilities and may cause severe complications in the fetuses of women who acquire Rubella viral infection during their pregnancy. The present study aims to evaluate the seroprevalence of anti-Rubella virus immunoglobulin (Ig) G and IgM antibodies in both pregnant and non-pregnant women and assess the diagnostic efficacy of enzyme-linked immunosorbent assay (ELISA) and rapid immunochromatographic tests. Methods The study included 240 females in the age range of 16-45 years. The study subjects included both pregnant women and non-pregnant women. After informed consent, 5 milliliters of blood was collected from each participant, and serum was separated and tested for the presence of antibodies (IgG and IgM) against the Rubella virus using both the traditional ELISA (Delta Biologicals, Pvt. Ltd., China) and a rapid ELISA-immunochromatographic test (ICT) (Span Biotech. Ltd., China). The data collected were systematically entered into Microsoft Excel sheets (Microsoft Corporation, Redmond, Washington) and were analyzed using SPSS Statistics for Windows, Version 17.0, 2008 (SPSS Inc., Chicago, Illinois). Results The study revealed an overall seroprevalence of 31.66% for Rubella-specific IgG and IgM antibodies. Out of the 125 pregnant women included in the study, 49 (39.20%) were seropositive for Rubella IgG antibodies, and among the 115 non-pregnant women tested, 24 (20.86%) were positive for Rubella IgG antibodies. Four (5.26%) of the 76 seropositive women revealed IgM antibodies. The sensitivities of both the ELISA (40.61%) and rapid immunochromatographic (39.20%) tests were observed to be low and the specificities of both methods were similar (79.13%). Conclusion The seroprevalence of Rubella-specific IgG antibodies was observed to be low as compared to the other regions of India. The low seroprevalence may predispose pregnant women to Rubella viral infection and may lead to increased incidences of congenital Rubella syndrome (CRS). Both the ELISA and immunochromatographic tests showed low sensitivity and similar specificities.

Recent trends in the spectrum of opportunistic infections in human immunodeficiency virus infected individuals on antiretroviral therapy in South India.

BACKGROUND: Opportunistic infections (OI) are the major cause of morbidity and mortality among human immunodeficiency virus (HIV) infected individuals. The pattern of OIs differs widely, hence it is necessary to correlate spectrum of OIs and CD4 counts among HIV infected individuals in specific localities. MATERIALS AND METHODS: The present study describes the clinical and laboratory profiles of different OIs among 55 HIV seropositive patients. CD4 count was estimated and antiretroviral therapy (ART) was started in 27 patients as per National Acquired Immunodeficiency Syndrome Control Organization guidelines. These 27 patients were classified into stage 1, stage 2 and stage 3 based on CD4 counts of >500 cells/µl, 200-499 cells/µl and <200 cells/µl respectively. The OIs presented by respective groups were documented. RESULTS: Pulmonary tuberculosis was found to be the most common OI constituting 43.6% of all cases followed by candidiasis (30.9%), cryptosporidial diarrhea (21.8%), herpes zoster (16.3%), cryptococcal meningitis (3.63%), Pneumocystis jirovecii pneumonia (1.81%), and other miscellaneous infections (23.6%). Only 1 patient was found in stage I while 13 patients each were grouped in stage II or stage III. The mean CD4 count in our study population who were on ART was 230 ± 150 cells/µl. CONCLUSION: The pattern of OIs among our study group did not differ significantly from patients not receiving ART. The effect of ART on CD4 count differs from patient to patient based on the degree of depletion of CD4 count before the initiation of ART, drug adherence, concomitant OIs and their treatment.

Clinico-Immunological Profile of Children Infected with HIV Through Vertical Transmission, in Southern India.

BACKGROUND: Karnataka, being "High Prevalent State" of southern India, the HIV infection among antenatal women has crossed 1%. There are very few reports available with CD4 count and stage wise clinical spectrum among children. The clinical spectrum among HIV infected infants and children vary in different areas of the world. Hence it is important to know the spectrum of opportunistic infections and their respective CD4 count among HIV infected children of our locality. MATERIALS AND METHODS: The opportunistic infections among 31 paediatric seropositive patients were evaluated. These all patients were classified as per CDC guide lines into stage I, stage II, and stage III based on CD4 counts of > 1000cells/µl, 500-999 cells/µl,<500cells/µl respectively. The opportunistic infections were diagnosed by standard laboratory investigations. Clinical spectrum presented by each stage children was documented. RESULTS: Children in stage I were 5(16.1%),stage II 14(45.1%) and stage III 12(38.7%). Oral candidiasis (29%) was the commonest, followed by recurrent respiratory tract infection (25.8%), tubercular lymphadenitis (16.1%) and chronic diarrhoea (12.9%). CONCLUSION: The present study showed the children with higher CD4 count had few infections and children with lower CD4 count presented with multiple opportunistic infections. This study also showed vertical transmission as the sole mode of transmission.

Lymphocutaneous nocardiosis caused by Nocardia otitidiscaviarum: A case report and review of literature.

Nocardia otitidiscaviarum is a rare clinical isolate of primary cutaneous infections. This report describes a case of lymphocutaneous nocardiosis caused by N. otitidiscaviarum. Analysis of 16S ribosomal RNA gene of the isolate and the type strain of N. otitidiscaviarum DSM 43242 showed 100% similarity. The partial gene sequence of 1439 bp was submitted to GenBank. (EU031786). The isolate was susceptible only to amikacin, minocycline, linezolid and resistant to remaining other routine anti-nocardial drugs. The patient was free of nocardiosis after 12 weeks of treatment with amikacin and linezolid. We reviewed four other cases of lymphocutaneous nocardiosis caused by N. otitidiscaviarum.

Clinicomicrobiological profile of children with acute pharyngitis with special reference to streptococcol grouping.

A total of 100 patients of acute pharyngitis were evaluated clinically and investigated microbiologically. Eighty patients proved culture positive acute pharyngitis, among them 17 patients proved positive for beta-haemolytic streptococci, 14 patients for Staphylococcus aureus, 24 for pneumococci, 13 patients for Streptococcus viridans, 3 for Brahmanella catarrhalis, 4 for coagulase negative staphylococci, 5 had mixed infection. Further streptococcal grouping was carried out on these isolates. Out of 17 isolates of beta-haemolytic streptococci 13 (76.47%) belonged to group A and 2 each (11.76%) belonged to group C and group G.

Rickettsial meningoencephalitis in a child--a case report.

Severe central nervous system involvement has been reported in adults with Rickettsia conorii infection but rarely in children. We report here a serologically documented case of meningoencephalitis in a child caused by spotted group R. conorii. Rickettsial infection is a relatively under-diagnosed entity in children with fever and rash, probably due to low index of suspicion and the lack of definitive diagnostic facilities. Rickettsial infections can be treated effectively with anti-microbials; if they remain undiagnosed and untreated, they are associated with significant morbidity and mortality. This differential diagnosis should be considered when a child is seen with fever and rash.

Effect of "HAART" on CD4+ T lymphocyte counts in HIV seropositive south-Indian individuals--a follow up study.

Because of the drastic cut down in the prices of antiretroviral drugs, the antiretroviral therapy has become more affordable in India. 16 HIV-1 infected individuals who were on HAART were followed up for 12 months. The CD4 + T Cell count estimation was done at mean intervals of 6 months and 12 months. Antiretroviral therapy showed good response in 14(87.5%) and deterioration in 2 (12.5%) cases.