Antimicrobial resistance heterogeneity among multidrug-resistant Gram-negative pathogens: Phenotypic, genotypic, and proteomic analysis.

Microbes evolve rapidly by modifying their genomes through mutations or through the horizontal acquisition of mobile genetic elements (MGEs) linked with fitness traits such as antimicrobial resistance (AMR), virulence, and metabolic functions. We conducted a multicentric study in India and collected different clinical samples for decoding the genome sequences of bacterial pathogens associated with sepsis, urinary tract infections, and respiratory infections to understand the functional potency associated with AMR and its dynamics. Genomic analysis identified several acquired AMR genes (ARGs) that have a pathogen-specific signature. We observed that blaCTX-M-15, blaCMY-42, blaNDM-5, and aadA(2) were prevalent in Escherichia coli, and blaTEM-1B, blaOXA-232, blaNDM-1, rmtB, and rmtC were dominant in Klebsiella pneumoniae. In contrast, Pseudomonas aeruginosa and Acinetobacter baumannii harbored blaVEB, blaVIM-2, aph(3'), strA/B, blaOXA-23, aph(3') variants, and amrA, respectively. Regardless of the type of ARG, the MGEs linked with ARGs were also pathogen-specific. The sequence type of these pathogens was identified as high-risk international clones, with only a few lineages being predominant and region-specific. Whole-cell proteome analysis of extensively drug-resistant K. pneumoniae, A. baumannii, E. coli, and P. aeruginosa strains revealed differential abundances of resistance-associated proteins in the presence and absence of different classes of antibiotics. The pathogen-specific resistance signatures and differential abundance of AMR-associated proteins identified in this study should add value to AMR diagnostics and the choice of appropriate drug combinations for successful antimicrobial therapy.

Effectiveness of antenatal screening of asymptomatic bacteriuria in reduction of prematurity and low birth weight: Evaluating a point-of-care rapid test in a pragmatic randomized controlled study.

BACKGROUND: Premature babies suffer higher mortality and life-long disabilities. Asymptomatic bacteriuria (ASB) is postulated to induce preterm labor. Routine antenatal screening for ASB using urine culture is not feasible in most developing countries due to long turn-around time, user-unfriendliness, and lack of resources. The current parallel-group superiority pragmatic randomized controlled trial evaluated the effect of screening and evidence-based treatment of ASB using an optical-sensor-based point-of-care rapid-test on the incidence of preterm birth and low birthweight (LBW). METHODS: 240 consenting asymptomatic pregnant women visiting an Indian tertiary public hospital for first antenatal check-up, irrespective of trimester/gravida, who had not consumed antibiotics in the preceding week, were enrolled from February-May 2017. Computer-generated concealed simple randomization allocation sequence was used to assign participants to intervention (120) and control arm (120). Usual hospital-care was provided in the control arm. In the intervention arm, urine samples were additionally screened for ASB using the rapid-test and the positive women were prescribed susceptible antibiotics. Blinded outcome assessors followed up with women post-delivery. The study was registered with the Clinical Trials Registry-India (CTRI/2016/09/007240). FINDINGS: 213 participants were analyzed (intervention: 103, control: 110). 21 women were found positive for ASB and prescribed pathogen-specific antibiotics. The incidence of preterm birth/LBW in intervention arm (n = 27) was lower than control arm (n = 45) by 14·7% (95% CI: 2·2-27·2); RR: 0.64, (95% CI: 0·43-0·95); p = 0·023, X2=5·13. INTERPRETATION: Rapid-test-guided treatment for ASB reduced the incidence of preterm birth/LBW in a pragmatic setting without any adverse event. FUNDING: Department of Biotechnology, Government of India.

Clinical and whole genome characterization of SARS-CoV-2 in India.

We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.

Plasmid-mediated antibiotic resistance among uropathogens in primigravid women-Hyderabad, India.

With the growing threat of antimicrobial resistance worldwide, uncovering the molecular epidemiology is critical for understanding what is driving this crisis. We aimed to evaluate the prevalence of plasmid-mediated-quinolone-resistance (PMQR) and extended-spectrum beta-lactamase- (ESBL) producing gram-negative organisms among primigravid women with bacteriuria. We collected urine specimens from primigravid women attending their first antenatal visit at Gandhi Hospital during October 1, 2015 to September 30, 2016. We determined antimicrobial susceptibility and ESBL and quinolone resistance using VITEK-2. We performed polymerase chain reaction amplification on resistant isolates for detection of ESBL-encoding genes (TEM, SHV, CTX-M) and PMQR genes (qnrA, qnrB, qnrD, qnrS, aac (6')-Ib-cr). Of 1,841 urine samples, 133 demonstrated significant bacterial growth with gram-negative bacilli accounting for 85% of isolates, including Escherichia coli (n = 79), Klebsiella pneumoniae (n = 29), Sphingomonas (n = 3), Enterobacter (n = 1), and Citrobacter (n = 1). We found 65% of E. coli isolates and 41% of K. pneumoniae isolates were ESBL positive. Of ESBL-positive isolates, the most common genes conferring resistance were TEM-1 (66.7%) followed by CTX-M-15 (33.3%). Fifty-seven percent of ESBL-positive E. coli also demonstrated resistance to quinolones with the most common PMQR genes being qnr-S (62.5%) and aac (6')-Ib-cr (37.5%). We did not find any resistance to quinolones among ESBL-positive K. pneumoniae isolates. Across different classes of antibiotics we found a strong clustering of multi-drug resistance in E. coli with over 45% of ESBL-positive isolates demonstrating resistance to at least three classes of antibiotics. This study emphasizes the high prevalence of plasmid-mediated ESBL and quinolone resistance in community-acquired urinary tract infections of primigravid women. The overall abundance of multi-drug-resistant isolates in this population is alarming and may present therapeutic challenges.

Clinical Validation of Innovative Optical-Sensor-Based, Low-Cost, Rapid Diagnostic Test to Reduce Antimicrobial Resistance.

The antibiotic susceptibility test determines the most effective antibiotic treatment for bacterial infection. Antimicrobial stewardship is advocated for the rational use of antibiotics to preserve their efficacy in the long term and provide empirical therapy for disease management. Therefore, rapid diagnostic tests can play a pivotal role in efficient and timely treatment. Here, we developed a novel, rapid, affordable, and portable platform for detecting uropathogens and reporting antibiogram to clinicians in just 4 h. This technology replicates the basic tenets of clinical microbiology including bacterial growth in indigenously formulated medium, and measurement of inhibition of bacterial growth in presence of antibiotic/s. Detection is based on chromogenic endpoints using optical sensors and is analyzed by a lab-developed algorithm, which reports antibiotic sensitivity to the antibiotics panel tested. To assess its diagnostic accuracy, a prospective clinical validation study was conducted in two tertiary-care Indian hospitals. Urine samples from 1986 participants were processed by both novel/index test and conventional Kirby Bauer Disc Diffusion method. The sensitivity and specificity of this assay was 92.5% and 82%, respectively (p < 0.0005). This novel technology will promote evidence-based prescription of antibiotics and reduce the burden of increasing resistance by providing rapid and precise diagnosis in shortest possible time.

Unmet Need of Antenatal Screening for Asymptomatic Bacteriuria: A Risk Factor for Adverse Outcomes of Pregnancy.

Recommended urine culture is unsuitable for screening pregnant women for asymptomatic bacteriuria due to long turn-around time, unaffordability, and user-unfriendliness. The objective of this review was to evaluate the suitability of various tests for this purpose. A PubMed-based systematic review of published articles irrespective of year and language was done. Search terms included asymptomatic bacteriuria, screening test, urinary tract infection, and diagnostic test. Diagnostic accuracy studies conducted on human populations comparing tests with urine culture were included. One author extracted predefined data fields, including quality indicators, another validated it. Of 78 records, 25 studies describing 15 tests were included. All tests were rapid, seven were valid and two of them were affordable and easy-to-use. No test provided comprehensive identification with antibiotic susceptibility. Despite publication bias, no test was found suitable for screening asymptomatic bacteriuria antenatally and providing evidence-based prescription. Further research is needed to develop tests which suit this purpose.

Poverty and Community-Acquired Antimicrobial Resistance with Extended-Spectrum ß-Lactamase-Producing Organisms, Hyderabad, India.

The decreasing effectiveness of antimicrobial agents is a global public health threat, yet risk factors for community-acquired antimicrobial resistance (CA-AMR) in low-income settings have not been clearly elucidated. Our aim was to identify risk factors for CA-AMR with extended-spectrum ß-lactamase (ESBL)-producing organisms among urban-dwelling women in India. We collected microbiological and survey data in an observational study of primigravidae women in a public hospital in Hyderabad, India. We analyzed the data using multivariate logistic and linear regression and found that 7% of 1,836 women had bacteriuria; 48% of isolates were ESBL-producing organisms. Women in the bottom 50th percentile of income distribution were more likely to have bacteriuria (adjusted odds ratio 1.44, 95% CI 0.99-2.10) and significantly more likely to have bacteriuria with ESBL-producing organisms (adjusted odds ratio 2.04, 95% CI 1.17-3.54). Nonparametric analyses demonstrated a negative relationship between the prevalence of ESBL and income.

Out-of-pocket health expenditures and antimicrobial resistance in low-income and middle-income countries: an economic analysis.

INTRODUCTION: The decreasing effectiveness of antimicrobial agents is a growing global public health concern. Low-income and middle-income countries are vulnerable to the loss of antimicrobial efficacy because of their high burden of infectious disease and the cost of treating resistant organisms. We aimed to assess if copayments in the public sector promoted the development of antibiotic resistance by inducing patients to purchase treatment from less well regulated private providers. METHODS: We analysed data from the WHO 2014 Antibacterial Resistance Global Surveillance report. We assessed the importance of out-of-pocket spending and copayment requirements for public sector drugs on the level of bacterial resistance in low-income and middle-income countries, using linear regression to adjust for environmental factors purported to be predictors of resistance, such as sanitation, animal husbandry, and poverty, and other structural components of the health sector. Our outcome variable of interest was the proportion of bacterial isolates tested that showed resistance to a class of antimicrobial agents. In particular, we computed the average proportion of isolates that showed antibiotic resistance for a given bacteria-antibacterial combination in a given country. FINDINGS: Our sample included 47 countries (23 in Africa, eight in the Americas, three in Europe, eight in the Middle East, three in southeast Asia, and two in the western Pacific). Out-of-pocket health expenditures were the only factor significantly associated with antimicrobial resistance. A ten point increase in the percentage of health expenditures that were out-of-pocket was associated with a 3·2 percentage point increase in resistant isolates (95% CI 1·17-5·15; p=0·002). This association was driven by countries requiring copayments for drugs in the public health sector. Of these countries, moving from the 20th to 80th percentile of out-of-pocket health expenditures was associated with an increase in resistant bacterial isolates from 17·76% (95% CI 12·54-22·97) to 36·27% (31·16-41·38). INTERPRETATION: Out-of-pocket health expenditures were strongly correlated with antimicrobial resistance in low-income and middle-income countries. This relation was driven by countries that require copayments on drugs in the public sector. Our data suggest cost-sharing of antimicrobials in the public sector might drive demand to the private sector in which supply-side incentives to overprescribe are probably heightened and quality assurance less standardised. FUNDING: National Institutes of Health.

Hemagglutination and biofilm formation as virulence markers of uropathogenic Escherichia coli in acute urinary tract infections and urolithiasis.

INTRODUCTION: Urinary tract infections (UTI) are a major public health concern in developing countries. Most UTIs are caused by E. coli, accounting for up to 90% of community-acquired UTIs (CAUTI). Recurrent UTI is considered as a major risk factor for urolithiasis. Virulence factors like adhesins and biofilm have been extensively studied by authors on UPEC isolated from recurrent UTI. The studies on isolates from infection stones in kidney are scanty. In a prospective study, we aimed to determine the expression of Haemagglutinins, (Type 1 and P fimbriae), Biofilm production and resistance pattern to common antibiotics of Uropathogenic E.coli (UPEC) isolates from Community acquired Acute Urinary Tract Infection(CAUTI) and Urolithiasis. MATERIALS AND METHODS: A total of 43 UPEC isolates, 23 mid-stream urine (MSU) samples from patients with CAUTI attending Out Patient Departments and 20 from renal calculi of urolithiasis patients at the time of Percutaneous nephrolithostomy (PCNL) were included in the study and the expression of Haemagglutinins,(Type 1 and P fimbriae), Biofilm production and resistance pattern to common antibiotics was assessed. RESULTS: A total of 43 UPEC isolates 23 from CAUTI and 20 from renal calculi were tested for production of biofilm and hemagglutinins. In CAUTI, biofilm producers were 56.52% and hemagglutinins were detected in all isolates 100%. In urolithiasis, biofilm producers were 100% but hemagglutinins were detected only in 70% of isolates. All isolates were resistant to multiple antibiotics used. CAUTI isolates were susceptible to 3(rd) generation cephalosporins, whereas urolithiasis isolates were resistant to 3(rd) generation cephalosporins and 25% were Extended Spectrum Beta Lactamases ESBL producers. CONCLUSIONS: HA mediated by type 1 fimbriae plays an important role in CAUTI (P < 0.001 highly significant), whereas, in chronic conditions like urolithiasis, biofilm plays an important role in persistence of infection and the role of hemagglutinins is less.

Prevalence of Cryptosporidium, Cyclospora cayetanensis and Isospora belli infection among diarrheal patients in South India

The emerging protozoan parasites <I>Cryptosporidium, Cyclospora cayetanensis and Isospora belli</I> have altered the etiological spectrum of diarrhea. The progressive decline in CD4 cell count in AIDS patients and lack of active immunity in the face of exposure to contaminated food and water in young children make these groups of persons particularly susceptible to protracted and severe diarrhea caused by the above parasites. Cryptosporidiosis is caused by human as well as several zoonotic species. The present study was undertaken to examine the prevalence of <I>Cryptosporidium</I> species, C. <I>cayetanensis</I> and <I>I .belli</I> among these two susceptible populations in comparison with adult immunocompetent individuals with diarrhea and to identify the <I>Cryptosporidium</I> species prevalent in these populations. A total of 447 children under the age of 5 years, 175 HIV-seropositive adults and 200 HIV seronegative adults with diarrhea attending tertiary care hospitals located in the twin cities of Secunderabad and Hyderabad in South India were included in the study. Single fecal samples were collected. Wet mounts and modified Ziehl Neelsen stained smears made from concentrated fecal specimens were screened microscopically for oocysts of <I>Cryptosporidium, Cyclospora cayetanensis and Isospora belli.</I> DNA extracted from fecal samples positive for <I>Cryptosporidium</I> was subjected to PCR RFLP for species identification. <I>Cryptosporidium</I> was detected in all the three groups, I.e. children (8.7%), HIV-seropositive adults (6.85%), and HIV-seronegative adults (1%). <I>Isospora and Cyclospora</I> were detected only among HIV- seropositive persons at a frequency of 16% and 1% respectively. <I>C. hominis</I> (71.7%) and <I>C. parvum</I> (18.9%) were the only 2 species of <I>Cryptosporidium</I> detected.