Otogenic Cerebellar Abscess with Polymicrobial Anaerobic Infection in a Young Female- A Rare Presentation.

Brain abscess is a serious clinical condition caused by a localized collection of pus within the brain tissue. This typically occurs as a result of an infection that originates from a nearby area, such as an ear, sinus, or dental infection, or an infection in the bloodstream. Streptococcus and Staphylococcus species are the most common organisms implicated in brain abscesses. Apart from aerobic growth, cases of mixed infections of both aerobic and anaerobic organisms are also commonly reported in the literature. Herein we report a 23-year-old immunocompetent female with chronic otitis media who presented with cerebellar abscess where the aerobic growth was sterile and anaerobic culture revealed pure growth of dual anaerobes viz… Peptostreptococcus and Bacteroides thetaiotaomicron. This case highlights the importance of prompt diagnosis and management of polymicrobial anaerobic infection in cases of brain abscess.

Cycle threshold values of SARS-CoV-2 RNA in conjunctival swabs and nasopharyngeal secretions: a comparative study from a tertiary care center in India.

PURPOSE: To detect the viral RNA load of SARS-CoV-2 in conjunctival swabs of COVID-19 patients, and compare with nasopharyngeal swabs. METHODS: Conjunctival swabs of COVID-19 patients (with PCR positive nasopharyngeal swabs) were subjected to quantitative reverse transcription-polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2 RNA. The cycle threshold (Ct) values of Open Reading Frame 1 (ORF 1 Ab gene) and nucleoprotein (N gene) PCRs were used to assess the viral RNA load, and compare them with the baseline values of nasopharyngeal swabs. RESULTS: Of 93 patients, 17 (18.27%) demonstrated SARS-CoV-2 RNA in conjunctival swabs. Baseline nasopharyngeal swabs were collected at a median of 2 days; while, the conjunctival swabs were collected at median 7 days, from onset of illness (p < 0.001). Despite a significant delay in conjunctival swab collection than nasopharyngeal swabs, the Ct values (ORF or N gene PCRs) were comparable between nasopharyngeal swab and conjunctival swab samples. Subsequently, during the recovery period, in four of these 17 patients (with conjunctival swab positivity), when the second nasopharyngeal swab was 'negative', the conjunctival swab was 'positive'. CONCLUSION: The conjunctival swabs demonstrated SARS-CoV-2 RNA in 17 (18.27%) of 93 COVID-19 patients. Our results may suggest a delayed or a prolonged shedding of the virus/viral RNA on the ocular surface than in nasopharyngeal mucosa.

Salmonella enterica serovar Give causing brain abscess and bacteremia: A case report.

Non-typhoidal Salmonellosis are an important cause of gastroenteritis and invasive disease in developing countries, with increase resistance and mortality in paediatric age group. We report here, a rare case of bacteremia and brain abscess in a 3year old female child with Salmonella enterica serovar Give as a causative organism.

Real-time loop-mediated isothermal amplification (real-time LAMP) assay for rapid diagnosis of amoebic liver abscess.

Among the parasitic diseases, amoebic liver abscess (ALA) ranks second to malaria in terms of mortality. Due to the poor sensitivity of conventional diagnostic methods, there is a need for the development of effective and rapid diagnostic methods for ALA. Thus, the purpose of this work was to develop a real-time loop-mediated isothermal amplification (RT-LAMP) assay specific to Entamoeba histolytica. Further, we compared the performance of real-time LAMP with conventional and real-time PCR (RT-PCR) targeting 18S small subunit ribosomal RNA (18S SSU rRNA) gene of E. histolytica in patients with ALA. A total of 126 liver samples were obtained for the study. Of these, 96 aspirated pus samples were obtained from patients suffering from an ALA (serology confirmed, anti-amoebic immunoglobulin IgG positive), 19 aspirated pus samples from patients with pyogenic liver abscess (PLA, 16S RNA gene positive) and 11 autopsy liver tissues. The results showed that the DNA of E. histolytica was detected in 81 samples by conventional PCR, 93 by RT-PCR and 95 by RT-LAMP. The analytical sensitivity of the RT-LAMP assay was much higher than the other two techniques. RT-LAMP assay was able to amplify up to one copy of the targeted gene of E. histolytica while conventional PCR and RT-PCR could amplify up to 103 and 102 copies of the targeted gene of E. histolytica, respectively. In conclusion, RT-LAMP proved to be a sensitive, specific and rapid test which can be utilised as an effective tool for the diagnosis of ALA.

A fatal case of Aeromonas jandaei necrotizing fasciitis.

Introduction: Necrotizing soft tissue infections (NSTIs) are associated with a fulminating course because of their rapid destruction of tissue planes underlying the skin. Aeromonas -associated monomicrobial NSTIs are usually associated with exposure to fresh water, particularly among agricultural workers and fish handlers. Albeit uncommon in incidence, urgent medical and surgical intervention are required once a diagnosis has been made. Case report: A 40-year-old male patient, a known case of alcoholic liver disease, presented to the emergency department with pain and diffuse swelling of bilateral lower limbs, which quickly progressed to form blackish discolouration and blebs. Blood for preliminary haematological and biochemical investigations, as well as fluid draining from blebs, were sent for microbiological investigation. The Gram stain revealed occasional neutrophils and Gram-negative bacilli, and pure growth in aerobic culture was identified as Aeromonas jandaei by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The patient was started on empirical antimicrobials, although lesions continued to progress and he ultimately succumbed within 12 h of hospital admission. Conclusion: As appropriate antimicrobial therapy and early surgical intervention are required for management of the same, occupational exposure and the fulminant course should raise suspicion of Aeromonas -associated infections.

No role of common NOD2 gene variants in predicting sepsis related outcomes in Indian patients undergoing hematopoietic stem cell transplant.

Background: High-risk single nucleotide polymorphisms (SNPs) in nucleotide-binding oligomerization domain-2 (NOD2) gene are associated with high susceptibility for infections and inflammation due to risk of inappropriate cytokine production and NF-κB activation. We studied the incidence of three high-risk NOD2 gene SNPs (8, 12 and 13) among BM-transplant (BMT) recipients. Methods: Sequential patients undergoing BMT over 1-year period were prospectively studied. Patients were tested with MspI/HhaI or NlaIV restriction-endonucleases (Euryx, Gdansk, Poland) for NOD2 gene SNPs 8, 12, and 13, respectively. Regimen-related organ toxicity was graded using the Seattle-Bearman criteria. Results: Forty patients were enrolled, their median age was 38 years (range 3-64), and 52.5% were males. Twenty patients each (50%) underwent autologous and allogeneic BMT. Majority of the patients (n = 38, 95%) developed febrile-neutropenia in the post-transplant period and 4 patients died due to overwhelming sepsis within day +100. Acute graft-versus-host disease (GVHD) [grade I-II (n = 3) and grade III-IV (n = 6)] was observed in 9/20 allogeneic HSCT recipients. None of our 40 patients showed presence of any of the three NOD2 gene SNPs. Conclusion: The 3 commonly observed high risk SNPs (8,12, and 13) of NOD2 genes were not present in study population. It is quite likely that due to geographical and racial variations these polymorphisms are completely absent in North India. NOD2 gene is highly diverse and polymorphic variants can be absolutely different in various populations. Larger studies targeting sequencing of the whole NOD2 gene can convincingly rule out or confirm the role of NOD2 gene variants in Indian population.

Microbial cell-free DNA detection: Minimally invasive diagnosis of infectious diseases.

BACKGROUND: Detection of infectious diseases, especially among immunocompromised and patients on prolonged anti-microbial treatment, remains challenging, limited by conventional techniques with low sensitivity and long-turnaround time. Molecular detection by polymerase chain reaction (PCR) also has limited utility as it requires a targeted approach with prior suspicion of the infecting organism. Advancements in sequencing methodologies, specifically next-generation sequencing (NGS), have presented a promising opportunity to identify pathogens in cases where conventional techniques may be inadequate. However, the direct application of these techniques for diagnosing invasive infections is still limited by the need for invasive sampling, highlighting the pressing need to develop and implement non-invasive or minimally invasive approaches to improve the diagnosis of invasive infections. OBJECTIVES: The objectives of this article are to explore the notable features, clinical utility, and constraints associated with the detection of microbial circulating cell-free DNA (mcfDNA) as a minimally invasive diagnostic tool for infectious diseases. CONTENT: The mcfDNA detection provides an opportunity to identify micro-organisms in the blood of a patient. It is especially beneficial in immunocompromised patients where invasive sampling is not possible or where repeated cultures are negative. This review will discuss the applications and constraints of detecting mcfDNA for diagnosing infections and the various platforms available for its detection.

Mycobacterium abscessus Complex-Associated Chronic Meningitis: Time to Think Beyond Tuberculosis.

Background: Mycobacterium abscessus complex (MabC) has emerged as an important cause of human infections, including meningitis. In the absence of correct microbiological identification, cases of MabC meningitis are treated with conventional anti-tubercular therapy, thereby worsening the outcome. Objective: The current study was conducted to determine the clinical features, antimicrobial susceptibility, and outcome of patients with MabC meningitis. Material and Methods: Cerebrospinal fluid specimens processed between 2011 and 2021 were subjected to smear, culture, MALDI TOF identification, hsp65 gene sequencing, and susceptibility testing using Sensititre™ RAPMYCOI plates along with a literature review. Results: 12 cases of MabC meningitis were identified between 2011 and 2021, 11 of which were M. abscessus subspecies abscessus on hsp65 gene sequencing. A pioneer case of meningitis with M. abscessus subspecies bolletii was also identified. The common predispositions were TB elsewhere, HIV positivity, and head injury. Two patients had dual infections, both MabC and TB. Ten patients succumbed to infection with a mean survival of 11 months. All isolates were susceptible to amikacin and tigecycline and subspecies bolletii had a higher minimum inhibitory concentration (MIC) than subspecies abscessus. A combined analysis with the available literature, reporting 19 more cases, revealed that the overall mortality of MabC meningitis was 61.3% (19/31) and that of shunt-associated/neurosurgical intervention-related MabC meningitis was 66.7% (12/20). To date, out of 20 MabC meningitis isolates in which subspecies identification was carried, 13 were M. abscessus, six were M. massiliense, and one was M. bolletii. Conclusion: MabC is an important differential diagnosis of chronic meningitis. Prompt identification and speciation are imperative for targeted therapy, thus improving the overall patient outcome.

Characteristics and outcome of infectious complications after autologous hematopoietic cell transplantation in multiple myeloma patients.

BACKGROUND: Infections are a significant cause of morbidity and mortality after autologous hematopoietic cell transplantation (AHCT) in multiple myeloma (MM) patients. There has been a rapid advancement and evolution in MM treatment landscape in the last decade. There is limited information on post-AHCT infectious complications among MM patients with or without levofloxacin prophylaxis from developing countries. MATERIALS AND METHODS: We performed a retrospective study to explore the incidence, pattern, and clinical outcome of infections following AHCT in MM patients from 2010 to 2019 at our center. Patient-specific, disease-specific, and transplant-specific details were retrieved from the case files. The characteristics of infectious complications (site, intensity, organism, treatment, and outcomes) were analyzed. All patients who underwent transplantation from 2010 to 2016 received levofloxacin antibiotic prophylaxis. Common terminology criteria for adverse events (CTCAE) criteria (v5.0) were used for the grading of infections and regimen-related toxicity. International Myeloma Working Group updated criteria were used for the assessment of disease response before transplant and at day +100. RESULTS: Ninety-five consecutive patients with newly diagnosed multiple myeloma (NDMM) (n = 85), RRMM (n = 7), plasma cell leukemia (n = 2), and Polyneuropathy, Orgaomegaly, Endocrinopathy, Monoclonal gammopathy, skin abnormalities (POEMS) syndrome (n = 1) underwent AHCT during the study period. Their median age was 55 years (range 33-68); 55.8% were males. Immunoglobulin IgG kappa was the most common monoclonal protein (32.6%), International Staging System stage III disease was present in 45.3%, and 84.2% of patients achieved more than very good partial response before AHCT. The median time from diagnosis to AHCT was 10 months (range 4-144). Eighty-nine patients (93.7%) developed fever after AHCT. Fever of unknown focus, microbiologically confirmed infections, and clinically suspected infections were found in 50.5%, 37.9%, and 5.3% of patients, respectively. Clostridiodes difficile-associated diarrhea was observed in eight patients (8.4%). Neutrophil and platelet engraftment occurred after a median of 11 days (range 9-14) and 12 days (range 9-23), respectively. The median duration of hospital stay was 16 days (range 9-29). Only two patients (2.1%) required readmission for infections within 100 days of AHCT. Transplant-related mortality (TRM) in the study population was 4.2% (n = 4). The levofloxacin prophylaxis group (n = 32, 33.7%) had earlier neutrophil engraftment (day +10 vs. day +11) and platelet engraftment (day +11 vs. day +12), but time to fever onset, duration of fever, hospital stay, TRM, and day +100 readmission rates were not significantly different from those of patients without levofloxacin prophylaxis. There was no significant difference in the spectrum of infections between patients with and without levofloxacin prophylaxis. The overall survival and progression-free survival of the study population at 5 years were 72.7% and 64.8%, respectively. CONCLUSION: This study shows that the incidence of infections and TRM are higher in MM patients from lower-middle income countries after AHCT than in those from developed countries. The majority of such patients lack clinical localization and microbiological proof of infection. There was no significant difference in the spectrum of infections and their outcomes in patients with and without levofloxacin prophylaxis.

Burden, risk factors, and outcomes of multidrug-resistant bacterial colonisation at multiple sites in patients with cirrhosis.

Background & Aims: The reported burden of multidrug-resistant organism (MDRO) infections is highest in patients with cirrhosis from India. We evaluated whether colonisation at multiple barriers predisposes to such infections and poor outcomes in patients with cirrhosis. Methods: We prospectively performed swab cultures, antimicrobial susceptibility testing (AST), and genotype testing for MDROs from various sites (rectum, nose, composite-skin, and central-line) in patients with cirrhosis (2020-2021) on admission and follow-up at a tertiary institute. We analysed clinical data, risk factors for MDROs, and patient outcomes. Results: Of 125 patients aged 49 years, 85.6% males, 60.8% with acute-on-chronic liver failure, 99 (79.2%) were identified as 'colonisers'. MDRO-colonisation at rectum, nose, skin, or central line was observed in 72.7% (88/121), 30.0% (36/120), 14.9% (18/121), and 3.3% (4/121) patients, respectively. Patients were colonised with the following types of bacteria: extended-spectrum beta-lactamase (71/125), carbapenem-resistant Enterobacterales (67/125), MDR-Enterococcus (48/125), MDR-Acinetobacter (21/125), or methicillin-resistant Staphylococcus aureus (4/125). Multiple precipitants of acute-decompensation (odds ratio [OR]: 3.4, p = 0.042), norfloxacin prophylaxis (OR: 3.9, p = 0.008), and MDRO infection at admission (OR: 8.9, p = 0.041) were the independent predictors of colonisation. Colonisation increased the risk of infection by MDROs at admission (OR: 8.5, p = 0.017) and follow up (OR: 7.5, p <0.001). Although any-site colonisers were at greater risk of cerebral failure and poorer Child-Pugh scores, the nasal and skin colonisers were at higher risk of cerebral and circulatory failures than non-colonisers (p <0.05).Patients with more than one site colonisation (prevalence: 30%) developed multi-organ failure (p <0.05), MDRO infection (OR: 7.9, p <0.001), and poorer 30-day survival (hazard ratio: 2.0, p = 0.005). Conclusions: A strikingly high burden of MDRO colonisation among patients with cirrhosis in India necessitates urgent control measures. Multiple-site colonisation increases the risk of MDR-infections, multi-organ failure, and mortality in patients with cirrhosis. Impact and Implications: Infections by bacteria resistant to multiple antibiotics are an emerging cause of death in cirrhosis. We showed that ∼70-80% of critically ill hospitalised patients with cirrhosis carry such bacteria with the highest rate in the rectum, nose, skin, and central line port. Carbapenem-resistant and vancomycin-resistant bacteria were amongst the most common colonising bacteria. The presence of these bacteria at multiple sites increased the risk of multidrug-resistant infections, multiple organ failures, and death in patients with cirrhosis.

Role of fluoroquinolone prophylaxis in allogeneic hematopoietic cell transplantation in regions with a high prevalence of fluoroquinolone resistance.

Introduction: The role of fluoroquinolone (FQ) prophylaxis in preventing gram-negative bacilli (GNB) bacteremia, graft-versus-host disease (GVHD), and overall survival (OS) after allogeneic hematopoietic cell transplantation (allo-HCT) is debatable and may differ in settings with low and high prevalences of FQ resistance. In this study, we aimed to answer this question in regions with high FQ resistance. Methods: This single-center retrospective study included all consecutive allo-HCT recipients aged ≥12 years from 2012 to 2021. Allo-HCT recipients until 2016 were administered FQ prophylaxis (levofloxacin). After 2016, the institutional protocol was modified to no antibiotic prophylaxis. Data were retrieved from patient records for disease and transplant characteristics, the incidence of GNB bacteremia, duration of parenteral antibiotics, hospitalization duration, acute GVHD, and OS. Results: A total of 135 allo-HCT recipients (43 in the FQ-prophylaxis cohort and 92 in the no-antibiotic prophylaxis cohort) were analyzed in this study. The two cohorts were matched for age (median, 26 vs. 24.5 years; p = 0.8). The no-antibiotic prophylaxis cohort had a higher proportion of malignant diagnoses (80% vs. 58%, p = 0.01), haploidentical transplants (46% vs. 14%, p = 0.004), and posttransplant cyclophosphamide exposure (46% vs. 14%, p = 0.003) than did the FQ cohort. Despite this, the incidence of GNB bacteremia was not significantly different between the two cohorts (37% vs. 34%, p = 0.6). There were no differences in parenteral antibiotic use or hospitalization duration, as well as the incidence of acute GVHD (53% vs. 53%, p = 0.3). The 1-year OS was similar between the two cohorts (66% vs. 67%, p = 0.6). Conclusion: This study shows that FQ prophylaxis did not affect the incidence of GNB bacteremia, parenteral antibiotic use, hospitalization duration, acute GVHD, and OS post-allo-HCT.

Isolation of Multidrug-Resistant Organisms in Surveillance Stool Culture at Diagnosis Fails to Predict Mortality or Subsequent Sepsis due to Multidrug-Resistant Organisms in Children with Acute Leukemia: A Single-Center, Prospective, Observational Study.

The utility of surveillance stool culture (SSC) to guide antibiotics for febrile neutropenia (FN) is unresolved in non-transplant settings. The prospective study explored the prevalence of multidrug-resistant organisms (MDRO) in SSCs, its correlation with mortality, and the concordance of SSCs with cultures obtained during subsequent episodes of FN amongst children with acute leukemia. SSCs were obtained at presentation and 2 mo into chemotherapy. Seventy-nine patients (mean age: 5.9±3.2 y) with acute lymphoblastic leukemia (ALL) (80%), acute myeloid leukemia (AML) (16%), or biphenotypic leukemia (4%) were enrolled. MDROs were isolated from 14 (17.5%) patients in the first SSCs, including E.coli (80%), K. pneumoniae (10%), and E. faecium (10%). Three (3.8%) patients developed MDRO sepsis; none concorded with the SSCs. Eleven (14%) patients died; 4/14 (28.5%) with MDRO-colonization vis-à-vis 7/66 (10.6%) without MDRO-colonization (OR: 3.37, 95% CI: 0.8-13.6; p = 0.095). MDRO-colonization failed to predict MDRO-sepsis, bloodstream infection, or mortality. SSC failed to guide the choice of antibiotics for FN in children with acute leukemia.

How can lessons from the COVID-19 pandemic enhance antimicrobial resistance surveillance and stewardship?

COVID-19 demanded urgent and immediate global attention, during which other public health crises such as antimicrobial resistance (AMR) increased silently, undermining patient safety and the life-saving ability of several antimicrobials. In 2019, WHO declared AMR a top ten global public health threat facing humanity, with misuse and overuse of antimicrobials as the main drivers in the development of antimicrobial-resistant pathogens. AMR is steadily on the rise, especially in low-income and middle-income countries across south Asia, South America, and Africa. Extraordinary circumstances often demand an extraordinary response as did the COVID-19 pandemic, underscoring the fragility of health systems across the world and forcing governments and global agencies to think creatively. The key strategies that helped to contain the increasing SARS-CoV-2 infections included a focus on centralised governance with localised implementation, evidence-based risk communication and community engagement, use of technological methods for tracking and accountability, extensive expansion of access to diagnostics, and a global adult vaccination programme. The extensive and indiscriminate use of antimicrobials to treat patients, particularly in the early phase of the pandemic, have adversely affected AMR stewardship practices. However, there were important lessons learnt during the pandemic, which can be leveraged to strengthen surveillance and stewardship, and revitalise efforts to address the AMR crisis.

Anaerobic Gram-Negative Bacteria: Role as a Reservoir of Antibiotic Resistance.

BACKGROUND: Anaerobic Gram-negative bacteria (AGNB) play a significant role as both pathogens and essential members of the human microbiota. Despite their clinical importance, there remains limited understanding regarding their antimicrobial resistance (AMR) patterns. This knowledge gap poses challenges in effectively managing AGNB-associated infections, as empirical treatment approaches may not adequately address the evolving resistance landscape. To bridge this research gap, we conducted a comprehensive study aimed at exploring the role of human AGNB as a reservoir of AMR. This can provide valuable insights for the prevention and management of anaerobic infections. METHODS: We studied the prevalence of AMR and AMR determinants conferring resistance to metronidazole (nimE), imipenem (cfiA), piperacillin-tazobactam (cepA), cefoxitin (cfxA), clindamycin (ermF), chloramphenicol (cat) and mobile genetic elements (MGEs) such as cfiAIS and IS1186 associated with the cfiA and nim gene expression. These parameters were studied in Bacteroides spp., Fusobacterium spp., Prevotella spp., Veillonella spp., Sutterella spp., and other clinical AGNB. RESULTS: Resistance to metronidazole, clindamycin, imipenem, piperacillin-tazobactam, cefoxitin and chloramphenicol was 29%, 33.5%, 0.5%, 27.5%, 26.5% and 0%, respectively. The presence of resistance genes, viz., nim, ermF, cfiA, cepA, cfxA, was detected in 24%, 33.5%, 10%, 9.5%, 21.5% isolates, respectively. None of the tested isolates showed the presence of a cat gene and MGEs, viz., cfiAIS and IS1186. The highest resistance to all antimicrobial agents was exhibited by Bacteroides spp. The association between resistant phenotypes and genotypes was complete in clindamycin, as all clindamycin-resistant isolates showed the presence of ermF gene, and none of the susceptible strains harbored this gene; similarly, all isolates were chloramphenicol-susceptible and also lacked the cat gene, whereas the association was low among imipenem and piperacillin-tazobactam. Metronidazole and imipenem resistance was seen to be dependent on insertion sequences for the expression of AMR genes. A constrained co-existence of cepA and cfiA gene in B. fragilis species was seen. Based on the absence and presence of the cfiA gene, we divided B. fragilis into two categories, Division I (72.6%) and Division II (27.3%), respectively. CONCLUSION: AGNB acts as a reservoir of specific AMR genes, which may pose a threat to other anaerobes due to functional compatibility and acquisition of these genes. Thus, AST-complying standard guidelines must be performed periodically to monitor the local and institutional susceptibility trends, and rational therapeutic strategies must be adopted to direct empirical management.

Molecular diagnosis of Tuberculous meningitis: sdaA-based multi-targeted LAMP and GeneXpert Ultra.

SETTING: Nucleic acid amplification techniques like GeneXpert and GeneXpert Ultra (Xpert Ultra), the first-line tests for diagnosing Tuberculous meningitis (TBM), are expensive and depend on sophisticated equipment. OBJECTIVE: The diagnostic potential of multitargeted loop-mediated isothermal assay (MLAMP), a low-cost simple test using novel gene combination, was evaluated for TBM. DESIGN: 300 CSF specimen (200 TBM patients, 100 controls) processed between January 2017 and December 2021 were subjected to MLAMP (using sdaA, IS1081 and IS6110 gene targets), sdaA PCR and Xpert Ultra. The performance was evaluated against uniform case definition as per Marais criteria, and against culture. RESULTS: Uniform case definition classified 50 as definite TBM and 150 as probable or definite TBM. Against this uniform case definition, the sensitivity and specificity of MLAMP was 88% and 100%, respectively. The sensitivity was 96% against culture-positive cases and 85.3% against culture-negative cases. The sensitivity of sdaA-LAMP, IS1081-LAMP, IS6110-LAMP, Xpert Ultra and sdaA-PCR was 82.5%, 80.5%, 85.3%, 67% and 71%, respectively against uniform case definition. sdaA-LAMP detected additional two cases and IS1081-LAMP detected nine. 11 of 134 (8.2%) cases were reported rifampicin resistant by Xpert Ultra. CONCLUSION: MLAMP, incorporating sdaA and IS1081, is a cheap, easy and accurate first-line diagnostic test for TBM.

Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages.

Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.

Emerging Bacterial Pathogens in the COVID-19 Era: Chryseobacterium gleum -A Case in Point.

Introduction In the ongoing severe acute respiratory syndrome coronavirus 2 pandemic, a long hospital stay and empirical broad-spectrum antibiotics make the patients prone to acquire nosocomial infections especially with unconventional organisms, and Chryseobacterium gleum is one such rare nosocomial pathogen. Methods The given study is a case-series-based study conducted from September 2020 to April 2021 in which clinically suspected pneumonia patients who recovered from coronavirus disease 2019 (COVID-19) were included. Results Seventeen C. gleum isolates were obtained in pure culture from the tracheal aspirates of nine COVID-19 patients (including repeat samples to rule out colonization) within a period of eight months (September 2020-April 2021). Our records showed that there has been an increase in the number of isolates of C. gleum obtained in respiratory samples in 2020. We also did a review of literature of all the cases of C. gleum pneumonia reported till now. Conclusion To the best of our knowledge, this is the first study reporting the isolation of this rare pathogen from COVID-19 patients with clinical significance in a large cohort of patients. Therefore, it becomes important to consider this pathogen as a significant cause of respiratory infections, especially in patients recovered post COVID-19.

Bifunctionalized nanobioprobe based rapid color-shift assay for typhoid targeting Vi capsular polysaccharide.

Typhoid fever is an acute illness caused by Salmonella Typhi and the current diagnostic gap leads to inaccurate, over-diagnosis of typhoid leading to excessive use of antibiotics. Herein, to address the challenges we describe a new rapid color-shift assay based on a novel bifunctional nanobioprobe (Vi-AgNP probe) that is functionalized with specific biomarker Vi polysaccharide and also has the co-presence of Ag as urease inhibitor. The immunoreactions between the Vi with specific antibodies (Abs) present in typhoid patient sample forms a shielding barrier over Vi-AgNP probe rendering the urease to be active, generating colored output. Vi polysaccharide coating on the AgNP was visualized using HRTEM. TEM was performed to get insight into shielding barrier formation by the Abs. MST (microscale thermophoresis) data showed less binding Kd of 7.43 µM in presence of Abs whereas probe with urease showed efficient binding with Kd 437 nM. The assay was validated using 53 human sera samples and proven effective with 100% sensitivity. The assay showed relative standard deviation (RSD) of 4.3% estimated using rabbit anti-Vi Abs. The entire procedure could be completed within 15 min. Unlike lateral flow based assays, our assay does not require multiple combination of Abs for detection. The assay format was also found compatible in paper strip test that provides promising opportunities to develop low-cost on-spot assay for clinical diagnostics.

Can beta-lactamase resistance genes in anaerobic Gram-negative gut bacteria transfer to gut aerobes?

The study was conceived with the hypothesis that human aerobic gut flora could act as a reservoir of ß-lactamases and contribute to the emergence of ß-lactam resistance by transferring ß-lactamase genes to resident anaerobes. Thus, we studied the repertoire of ß-lactam resistance determinants (ß-lactamases associated with aerobes and anaerobes) in Gram-negative anaerobes. The phenotypic resistance against ß-lactams and the presence of aerobic and anaerobic ß-lactamases were tested in Gram-negative anaerobic isolates (n = 200) by agar dilution method and targeted PCR, respectively. In addition, whole-genome sequencing (WGS) was used to study the ß-lactam resistance determinants in 4/200 multi-drug resistant (MDR) strains. The resistance to ß-lactams was as follows: imipenem (0.5%), cefoxitin (26.5%), and piperacillin-tazobactam (27.5%). None of the isolates showed the presence of ß-lactamases found in aerobic microorganisms. The presence of anaerobic ß-lactamase genes viz. cfiA, cepA, cfxA, cfiAIS [the intact segment containing cfiA gene (350 bp) and upstream IS elements (1.6-1.7 kb)] was detected in 10%, 9.5%, 21.5%, and 0% isolates, respectively. The WGS data showed the presence of cfiA, cfiA4, cfxA, cfxA2, cfxA3, cfxA4, cfxA5 in MDR strains. The study showed a distinct dichotomy in repertoires of ß-lactamases between aerobes and anaerobes.

Mycotic aneurysm by Bacteroides fragilis presenting as fever of unknown origin.

A mycotic aneurysm is an infection of the vessel wall which can be bacterial, fungal, or viral in origin. It is invariably a fatal infectious disease if appropriate treatment is not done. We describe the case of a forty-six years male who presented with complaints of high-grade fever and lower back pain with worsening symptoms with the passage of the illness. An infrarenal lobulated abdominal aortic aneurysm was confirmed by CT angiography. He underwent aneurysmorrhaphy and metronidazole was started following the culture report (Bacteroides fragilis). He was discharged successfully from the hospital.