Antimicrobial efficacy of eravacycline against emerging extensively drug-resistant (XDR) Acinetobacter baumannii isolates

PURPOSE

Drug-resistant Acinetobacter baumannii is an emerging threat. This study has been conducted to observe the efficacy of eravacycline along with the RND-efflux pump system.

METHODS

A cross-sectional study was done collecting 48 clinical isolates of Acinetobacter baumannii. MICs of 15 antibiotics were detected along with BMD of tigecycline and eravacycline. PCR products of drug-resistant regulatory genes were sequenced and analyzed.

RESULTS

Of the total 48 Isolates, 35 (72.91%) were XDR and 13 (27.08%) were MDR. Out of all, 60.41% of isolates were found to be susceptible to eravacycline by BMD according to both FDA and EUCAST guidelines. A 2-fold decline of MIC50/90 was observed with the use of eravacycline compared to tigecycline. RND-efflux genes like AdeC in 30 (62.5%) isolates and Regulatory gene AdeS in 29 (60.41%) isolates were detected, explaining the existing resistance mechanism.

CONCLUSIONS

XDR Acinetobacter poses an escalating threat due to its resistance to multiple antibiotics, raising serious concerns in healthcare settings. Eravacycline is an encouraging new drug for empirical use in severe infection caused due to the same. Molecular investigation and strict antimicrobial stewardship should be followed to control the emergence, and a better understanding of mechanisms of resistance to prevent the spread of drug-resistant isolates.

Deciphering Intermediate Nugent scores: Utility of Real-time PCR for Bacterial Vaginosis diagnosis

PURPOSE

To optimize real-time PCR assays for diagnosis of Bacterial Vaginosis (BV) and determine cut-off loads by ROC analysis for Gardnerella vaginalis, Atopobium vaginae and Lactobacillus spp. as compared to Nugent scoring (Gold standard) in clinical samples.

RESULTS

Out of 125 women, 34 were positive, 26 intermediate and 65 negative for BV by Nugent scoring. All three real-time PCR assays were found to be highly sensitive & specific and AUC suggested excellent diagnostic accuracy. An optimal cut-off was >9.45 × 103 copies/ ml, >3.34 × 103 copies/ ml & ≤ 18.63 × 103 copies/ ml for G. vaginalis, A. vaginae and Lactobacillus spp. respectively, in BV positives. Gram staining and qPCR were discordant only in patients with intermediate scores (n = 26) where qPCR identified 15 (57.69%) as positive and 11 (42.3%) as negative.

CONCLUSION

PCR-based molecular BV diagnosis is more accurate and can be used for deciphering intermediate Nugent scores.

Detection of Aminoglycoside Modifying Enzyme (AME) genes in Acinetobacter baumannii isolates and the inhibitory effect of efflux pump activity on drug susceptibility pattern

INTRODUCTION

The development of aminoglycoside modifying enzymes (AMEs) and increased efflux activity are considered important aminoglycosides resistance mechanisms.

AIM

This study is focused on the detection of the AMEs gene and assessing the effect of efflux pump inhibitor on the reversal of A. baumannii drug susceptibility.

METHODOLOGY

Bacterial DNA was amplified using AMEs gene-specific primers. Isolates were also investigated for efflux pump activity using efflux pump inhibitor (EPI) i.e. Carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and the impact of both mechanisms was analyzed.

RESULTS

Among A. baumannii isolates, 55% isolates (n ​= ​22/40) were identified to have aminoglycoside modifying enzymes genes; ant(3')-I gene (50%, 11/22), aac(6')-Ib gene (45.4%, 10/22), aph(3')-I gene (18.1%, 4/22) and aac(3)-I (9.1%, 2/22). Total 70% isolates have shown MIC alteration in different classes of drugs in response to EPI-CCCP. Such alteration was found in 100% amikacin sensitive and 58.6% amikacin resistant, 93.7% and 57.1% gentamicin sensitive and resistant isolates respectively.

CONCLUSION

The presence of aminoglycosides modifying enzymes was frequent among aminoglycosides resistant A. baumannii isolates and the coexistence of efflux pumps activity also plays an important role to increase drug resistance.

REPOSITORIES

Genbank and their accession numbers are MT903331[aac(3)-I], MT903332 MT903333 [ant(3')-I], MT903334, MT903335 [aph(3')-I)] and MT903336, MT940242 [ aac(6')-Ib].

Ceftriaxone-resistant Salmonella Typhi isolated from paediatric patients in north India: Insights into genetic profiles and antibiotic resistance mechanisms

PURPOSE

To investigate the antibiotic resistance and genetic profile of ceftriaxone-resistant Salmonella Typhi isolated from the blood culture of two paediatric cases of typhoid fever and one from the stool culture of their household contact, in North India.

METHODS

In this study, whole-genome sequencing was carried out with paired-end 2 ​× ​150 bp reads on Illumina MiSeq (Illumina, USA) employing v2 and v3 chemistry. To check data quality, adapters and low-quality sequences were removed through Trimmomatic-v0.36. High quality reads were then assembled de novo using A5-miseq pipeline. For further refinement, reference-guided contig ordering and orienting were performed on the scaffold assemblies using ABACAS (http://abacas.sourceforge.net/). The assembled genome was annotated using Prokka v1.12 to identify and annotate the gene content. Plasmid replicons in bacterial isolates were identified by PlasmidFinder, whereas mobile genetic elements were predicted using Mobile Element Finder. Referenced-based SNP tree with maximum likelihood method was built with CSI phylogeny v1.4.

RESULTS

All three isolates exhibited resistance to ceftriaxone, cefixime, ciprofloxacin, ampicillin, and co-trimoxazole, while demonstrating sensitivity to azithromycin and chloramphenicol. The whole-genome sequencing of these strains revealed the presence of blaCTX-M-15 gene for cephalosporin resistance in addition to gyrA, qnr and IncY plasmid replicon. A 5 ​kb IS91 Sbo1 gene cassette (IncY plasmid) was identified which carried extended spectrum β-lactamase blaCTX-M-15, blaTEM-1D (resistance to ampicillin and cephalosporin), sul2, dfrA14 (resistant to trimethoprim-sulfamethoxazole) and qnrS (resistant to ciprofloxacin). These isolates belong to H58 lineage and grouped as sequence type 1 (ST1) on multilocus sequence typing (MLST) analysis.

CONCLUSION

In the present study we report the isolation of blaCTX-M-15 positive S. Typhi from two paediatric patients presenting with fever and one from stool culture of their contact from North India and highlight the need for further investigations to understand the different factors contributing to ceftriaxone resistance in Salmonella Typhi.

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Background

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).

Methods

This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.

Results

Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.

Conclusions

The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.

Funding

No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).

Safety of Procalcitonin Guided Early Discontinuation of Antibiotic Therapy among Children Receiving Cancer Chemotherapy and Having Low-Risk Febrile Neutropenia: A Randomized Feasibility Trial (ProFenC Study)

In low-risk febrile neutropenia (LR-FN), the safety of early discontinuation of empiric antibiotics without marrow recovery is not well established. This study aimed to evaluate the safety of procalcitonin (PCT) guided early discontinuation of antibiotics in LR-FN. In this trial, children with LR-FN with an afebrile period of at least 24 h, sterile blood culture, and negative/normalized PCT were randomized at 72 h of starting antibiotics into two groups: intervention arm and standard arm. The antibiotics were stopped in the intervention arm regardless of absolute neutrophil count (ANC), while in the standard arm, antibiotics were continued for at least 7 days or until recovery of ANC (>500/mm3). The primary objective was to determine the treatment failure rates, and the secondary objective was to compare the duration of antibiotics and all-cause mortality between the two arms. A total of 46 children with LR-FN were randomized to either the intervention arm (n = 23) or the standard arm (n = 23). Treatment failure was observed in 2/23 (8.7%) of patients in the intervention arm compared to 1/23 (4.3%) in the standard arm [RR: 2 (95% CI: 0.19-20.6); p = 0.55]. The median duration of antibiotics in the intervention arm and standard arm were 3 days vs 7 days (P= <0.001). There was no mortality in this study. PCT-guided early discontinuation of empirical antibiotics in LR-FN is feasible. There was no significant difference observed in treatment failure between the early discontinuation of antibiotics vs standard therapy. The total duration of antibiotic exposure was significantly lesser in the discontinuation arm. Further, larger multicenter studies are needed to confirm the finding of this study.

Procalcitonin for Detecting Culture-Positive Sepsis in Neonates: A Prospective, Multicenter Study

INTRODUCTION

It is unclear if serum procalcitonin (PCT) estimated at sepsis suspicion can help detect culture-positive sepsis in neonates. We evaluated the diagnostic performance of PCT in culture-positive sepsis in neonates.

METHODS

This was a prospective study (February 2016 to September 2020) conducted in four level-3 units in India. We enrolled neonates suspected of sepsis in the first 28 days of life. Neonates with birth weight <750 g, asphyxia, shock, and major malformations were excluded. Blood for PCT assay was drawn along with the blood culture at the time of suspicion of sepsis and before antibiotic initiation. The investigators labeled the neonates as having culture-positive sepsis or "no sepsis" based on the culture reports and clinical course. PCT assay was performed by electrochemiluminescence immunoassay, and the clinicians were masked to the PCT levels while assigning the label of sepsis. Primary outcomes were the sensitivity, specificity, and likelihood ratios to identify culture-positive sepsis.

RESULTS

The mean birth weight (SD) and median gestation (IQR) were 2,113 (727) g and 36 (32-38) weeks, respectively. Of the 1,204 neonates with eligible cultures, 155 (12.9%) had culture-positive sepsis. Most (79.4%) were culture-positive within 72 h of birth. The sensitivity, specificity, and positive and negative likelihood ratios at 2 ng/mL PCT threshold were 52.3% (95% confidence interval: 44.1-60.3), 64.5% (60.7-68.1), 1.47 (1.23-1.76), and 0.74 (0.62-0.88), respectively. Adding PCT to assessing neonates with 12.9% pretest probability of sepsis generated posttest probabilities of 18% and 10% for positive and negative test results, respectively.

CONCLUSION

Serum PCT did not reliably identify culture-positive sepsis in neonates.

Tick-tock, beat the clock: comparative analysis of disc diffusion testing with 6-, 10-, and 24-h growth for accelerated antimicrobial susceptibility testing and antimicrobial stewardship

Disc diffusion testing by Kirby-Bauer technique is the most used method for determining antimicrobial susceptibility in microbiological laboratories. The current guidelines by The Clinical and Laboratory Standards Institute (CLSI) 2022 specify using an 18- to 24-h growth for testing by disc diffusion. We aim to determine if using an early growth (6 h and 10 h) would produce comparable results, thus ultimately leading to reduced turnaround time. Six-hour, 10-h, and 24-h growths of 20 quality control strains and 6-h and 24-h growths of 48 clinical samples were used to perform disc diffusion testing using a panel of appropriate antimicrobial agents. Disc diffusion zone sizes were interpreted for all and comparative analyses were performed to determine categorical agreement, minor errors (mE), major errors (ME), and very major errors (VME) according to CLSI guidelines. On comparing with the standard 24 h of incubation, disc diffusion from 6-h and 10-h growths of quality control strains showed 94.38% categorical agreement, 5.10% mE, 0.69% MEs, and no VMEs. Disc diffusion testing for the additional 40 clinical samples yielded a similarly high level of categorical agreement (98.15%) and mE, ME, and VME of 1.29%, 1.22%, and 0% respectively. Disc diffusion testing using early growth is a simple and accurate method for susceptibility testing that can reduce turnaround time and may prove to be critical for timely patient management.

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.

Genome profiling of uropathogenic E. coli from strictly defined community-acquired UTI in paediatric patients: a multicentric study

BACKGROUND

Urinary tract infection (UTI) in children is a common bacterial infection. The emergence of extended-spectrum beta-lactamases (ESBLs) poses a major challenge against the treatment of uropathogens. We aimed to characterize the E. coli isolates recovered from children with UTI for their resistance profile and circulating sequence types (ST).

METHODS

Children (> 1.5-18 years of age) from different community health centres of India with symptoms of UTI were enrolled. Isolates causing significant bacteriuria were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility by the automated system, VITEK-2 (Biomeriux, Durhum, US). Nineteen E. coli isolates (15 ESBL positive and 4 ESBL negative) were sequenced in Oxford Nanopore platform followed by core-genome phylogeny, accessory genome cluster analysis, identification of sequence types, mobile genetic elements, genetic antimicrobial resistance markers. The correlation between detection of antimicrobial resistance genes with phenotypic resistance profiles was also investigated.

RESULTS

Eleven percent of children had significant bacteriuria [male:female-1:1, > 50% were 11-18 years of age group]. E. coli was predominant (86%) followed by K. pneumoniae (11%). Susceptibility of E. coli was highest against fosfomycin (100%) followed by carbapenems (90.7%) and nitrofurantoin (88.8%). ST131 (15.8%) and ST167 (10.5%) found as high-risk clones with the presence of plasmid [IncFIB (63.1%), IncFIA (52.6%)], and composite transposon [Tn2680 (46.6%)] in many isolates. Few isolates coharboured multiple beta-lactamases including blaNDM-5 (33.3%), blaOXA-1 (53.3%), blaCTX-M-15 (60%) and blaTEM-4 (60%).

CONCLUSIONS

This study highlights horizontal transmission of resistance genes and plasmids in paediatric patients at community centers across the nation harbouring multidrug-resistant genes such as blaNDM-5 and blaCTX-M-15 associated with high-risk clones ST131 and ST167. The data is alarming and emphasizes the need for rapid identification of resistance markers to reduce the spread in community. To our knowledge, this is the first multicentric study targeting paediatric UTI patients from the community setting of India.

Central Line-Associated Bloodstream Infections: Effect of Patient and Pathogen Factors on Outcome

Introduction

Patients on central lines are often having multiple morbidities, and invasive devices provide a niche for biofilm formation, which makes central line-associated bloodstream infections (CLABSIs), a serious concern in health-care settings, as the infections difficult to treat. In this study, we evaluated the common bacteria causing CLABSI, and various patient and pathogen factors affecting the clinical outcome.

Methods

In the prospective observational study, patients diagnosed with CLABSI were recruited. Extensive clinical, microbiological, and other laboratory workup was done, and observations were recorded. Congo red agar method, tube test, and microtiter plate assay were used for eliciting the biofilm-forming attributes of the bacterial pathogens.

Results

Klebsiella pneumoniae was responsible for 48% of CLABSI, followed by Coagulase-negative Staphylococci (16%) and Staphylococcus aureus and Acinetobacter baumannii (12% each). Fifty-six percent of the isolates produced biofilms. The median (interquartile range) duration of hospital stay till death or discharge was 30 (20, 43) days. The all-cause mortality was 44%. Patients having a deranged liver function on the day of diagnosis (P value for total bilirubin 0.001 and for aspartate transaminase 0.02), and those infected with multidrug-resistant organisms (P value = 0.04) had significantly poor prognosis. The difference in the demographic, clinical, laboratory profile, and outcome of patients infected with biofilm producers and nonproducers was not found to be statistically significant.

Conclusion

The study throws light on various host and pathogen factors determining the cause and outcome of CLABSI patients. To the best of our knowledge, this is the first study trying to decipher the role of biofilm formation in the virulence of pathogens and the prognosis of CLABSI.

Small molecule bio-signature in childhood intra-thoracic tuberculosis identified by metabolomics

The diagnosis of pediatric tuberculosis (TB) remains a major challenge, hence the evaluation of new tools for improved diagnostics is urgently required. We investigated the serum metabolic profile of children with culture-confirmed intra-thoracic TB (ITTB) (n = 23) and compared it with those of non-TB controls (NTCs) (n = 13) using proton NMR spectroscopy-based targeted and untargeted metabolomics approaches. In targeted metabolic profiling, five metabolites (histidine, glycerophosphocholine, creatine/phosphocreatine, acetate, and choline) differentiated TB children from NTCs. Additionally, seven discriminatory metabolites (N-α-acetyl-lysine, polyunsaturated fatty acids, phenylalanine, lysine, lipids, glutamate + glutamine, and dimethylglycine) were identified in untargeted metabolic profiling. The pathway analysis revealed alterations in six metabolic pathways. The altered metabolites were associated with impaired protein synthesis, hindered anti-inflammatory and cytoprotective mechanisms, abnormalities in energy generation processes and membrane metabolism, and deregulated fatty acid and lipid metabolisms in children with ITTB. The diagnostic significance of the classification models obtained from significantly distinguishing metabolites showed sensitivity, specificity, and area under the curve of 78.2%, 84.6%, and 0.86, respectively, in the targeted profiling and 92.3%, 100%, and 0.99, respectively, in the untargeted profiling. Our findings highlight detectable metabolic changes in childhood ITTB; however, further validation is warranted in a large cohort of the pediatric population.

Computational biology: Role and scope in taming antimicrobial resistance

BACKGROUND

Infectious diseases pose many challenges due to increasing threat of antimicrobial resistance, which necessitates continuous research to develop novel strategies for development of new molecules with antibacterial activity. In the era of computational biology there are tools and techniques available to address and solve the disease management issues in the field of clinical microbiology. The sequencing techniques, structural biology and machine learning can be implemented collectively to tackle infectious diseases e.g. for the diagnosis, epidemiological typing, pathotyping, antimicrobial resistance detection as well as the discovery of novel drugs and vaccine biomarkers.

OBJECTIVES

The present review is a narrative review representing a comprehensive literature-based assessment regarding the use of whole genome sequencing, structural biology and machine learning for the diagnosis, molecular typing and antibacterial drug discovery.

CONTENT

Here, we seek to present an overview of molecular and structural basis of resistance to antibiotics, while focusing on the recent bioinformatics approaches in whole genome sequencing and structural biology. The application of next generation sequencing in management of bacterial infections focusing on investigation of microbial population diversity, genotypic resistance testing and scope for the identification of targets for novel drug and vaccine candidates, has been addressed along with the use of structural biophysics and artificial intelligence.

Identification of novel natural MurD ligase inhibitors as potential antimicrobial agents targeting Acinetobacter baumannii: In silico screening and biological evaluation

The increased multidrug resistance in Acinetobacter baumannii (A. baumannii) to the present-day known antibiotics has stimulated academic and industrial efforts globally for the development of novel antibacterial agents. Natural compounds as potential drug leads are gaining significant attention due to their less toxic and more tolerant nature. In the current study, the natural product-based compounds were explored as probable inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate (MurD) ligase from A.baumannii (AbMurD) to provide a new class of drug leads. The prepared natural library of 3,16,714 compounds from ZINC database was screened into the active site of AbMurD using in silico high-throughput virtual screening which resulted in 100 compounds having high binding affinities. Further screening through flexible molecular docking yielded four potential compounds selected on the basis of estimated binding affinity (ΔG) and favorable protein-ligand interactions. MD simulation of these four compounds under physiological conditions and free binding energy calculations using MM/PBSA (molecular mechanics with Poisson- Boltzmann and surface area solvation) approach revealed three compounds ZINC08879777, ZINC30726863, and ZINC95486217 as potential binders of AbMurD. The calculated physicochemical and ADME properties of these compounds revealed that they can be exploited and modified to improve their binding affinity with the enzyme. Two compounds were purchased and tested against bacterial cell cultures of A. baumannii, Salmonella Typhi, and Staphylococcus aureus to determine their broad-spectrum antibacterial activity. The results suggest that the identified compounds can be exploited as potential herbal leads to target both Gram-positive and Gram-negative pathogens. Communicated by Ramaswamy H. Sarma.

Antibiotic resistance of uropathogens among the community-dwelling pregnant and nonpregnant female: a step towards antibiotic stewardship

BACKGROUND

Indiscriminate and widespread use of antibiotics has resulted in emergence of many antibiotic-resistant organisms. Antibiotic administration during pregnancy is mostly avoided, unless there is compelling medical condition. We hypothesized that the uropathogens isolated from pregnant women would be more susceptible to antibiotics compared to those isolated from nonpregnant women, thus will be helpful in formulating separate empiric guideline for pregnant women based on the resistance pattern.

METHODS

This was a prospective cross-sectional study conducted over a period of 2 years in which females with the clinical diagnosis of either cystitis or asymptomatic bacteriuria during pregnancy were included from the community settings. Uropathogen species and their antimicrobial resistance pattern were compared between the pregnant and nonpregnant groups. After accounting for centre-to-centre variation and adjusting for age and socio-economic status, the adjusted odds ratio for antibiotic resistance was calculated and compared between pregnant and nonpregnant women using logistic regression analysis.

RESULTS

A total of 1758 women (pregnant: 43.3%; nonpregnant: 56.6%) were screened in the study over a period of 2 years, out of which 9.3% (163/1758) were having significant bacteriuria. Escherichia coli and Klebsiella pneumoniae were the two commonest uropathogen in both the groups; their prevalence being 83.6% in pregnant women and 85.2% in nonpregnant women, respectively. Resistance against ampicillin, cefixime, cefoxitin, ceftazidime, ceftriaxone and amoxicillin-clavulanic acid were found significantly lower in the pregnant women compared to nonpregnant. After adjusting the age and socio-economic status accounting for centre-to-centre variation, the odds of resistance for cefixime, amoxicillin-clavulanic acid and co-trimoxazole were found lower and statistically significant among the pregnant women group.

CONCLUSIONS

The antimicrobial resistance was significantly higher among the community-dwelling nonpregnant women compared to pregnant women in case of few antibiotics. The study highlighted the need of building local antibiogram that could help to initiate the empirical treatment and thus prevent emergence of antimicrobial resistance.

Comparative Analysis of Clinical and Genomic Characteristics of Hypervirulent Klebsiella pneumoniae from Hospital and Community Settings: Experience from a Tertiary Healthcare Center in India

Hypervirulent Klebsiella pneumoniae (hvKp) is a hypermucoviscous phenotype of classical Klebsiella pneumoniae (cKp) that causes serious infections in the community. The recent emergence of multidrug-resistant hvKp isolates (producing extended-spectrum beta-lactamases and carbapenemases) along with other virulence factors in health care settings has become a clinical crisis. Here, we aimed to compare the distribution of virulence determinants and antimicrobial resistance (AMR) genes in relation to various sequence types (STs) among the clinical hvKp isolates from both settings, to reinforce our understanding of their epidemiology and pathogenic potential. A total of 120 K. pneumoniae isolates confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry were selected. hvKp was phenotypically identified by string test and genotypically confirmed by the presence of the iucA gene using PCR. Molecular characterization of hvKp isolates was done by whole-genome sequencing (WGS). Of the K. pneumoniae isolates, 11.6% (14/120) isolates were confirmed as hvKp by PCR (9.1% [11/120] string positive and 3.3% [4/120] positive by both methods); these were predominantly isolated from bloodstream infection (50%, 7/14), urinary tract infection (29%, 4/14), and respiratory tract infection (21%, 3/14). For all 14 hvKp infections, for 14.2% the source was in the community and for 85.7% the source was a health care setting. Two virulent plasmids were identified by WGS among the hvKp isolates from both settings. K64 was found to be the commonest capsular serotype (28.5%, 4/14), and ST2096 was the most common ST (28.5%, 4/14) by WGS. Two new STs were revealed: ST231 (reported to cause outbreaks) and ST43. The genome of one isolate was determined to be carrying AMR genes (blaCTX-M-15, blaNDM-1, blaNDM-5, blaOXA-181, blaOXA-232, etc.) in addition to virulence genes, highlighting the clonal spread of hvKp in both community and health care settings. IMPORTANCE To date, studies comparing the genomic characteristics of hospital- and community-acquired hvKp were very few in India. In this study, we analyzed the clinical and genomic characteristics of hvKp isolates from hospital and community settings. ST2096 was found as the most common ST along with novel STs ST231 and ST43. Our study also revealed the genome is simultaneously carrying AMR as well as virulence genes in isolates from both settings, highlighting the emergence of MDR hvKp STs integrated with virulence genes in both community and health care settings. Thus, hvKp may present a serious global threat, and essential steps are needed to prevent its further dissemination.

Genomic analysis of Fosfomycin resistance in multi-drug resistant uropathogens and comparison of in-vitro susceptibility methods uropathogens

BACKGROUND AND OBJECTIVES

Urinary tract infection is one of the most common bacterial infections causing high morbidity and mortality. The alarming rise of multidrug-resistant uropathogens worldwide forced the clinician to rethink the old drugs like Fosfomycin for its therapeutic management. Our objective was to compare agar dilution, disc diffusion and E-test method for antimicrobial susceptibility testing of Fosfomycin against different drug-resistant uropathogens.

MATERIALS AND METHODS

Consecutive 181 uropathogens were tested for Fosfomycin susceptibility using agar dilution, disc diffusion and E-test. Results were interpreted using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Whole genome sequencing analysis was done on the 4 XDR/PDR Fosfomycin resistant Klebsiella pneumoniae isolates.

RESULTS

Escherichia coli was found as the most common (62.4%) uropathogen followed by Klebsiella pneumoniae (21%). Considering agar dilution as the gold standard, 6.1% of isolates were resistant to Fosfomycin. Following CLSI breakpoints, the susceptibility of Escherichia coli, Klebsiella pneumoniae, other Enterobacterales and Pseudomonas aeruginosa were 92.9%, 92.1%, 100%, 100%; whereas using EUCAST breakpoints the susceptibility rates were 85.7%, 86.9%, 92.9%, and 100%, respectively. The essential agreement, categorical agreement, major error, and very major error for E-test/disc diffusion for all the organisms were 91.2%/Not Applicable, 95%/93.9%, 1.8%/4.7%, 9.1%/9.1%, respectively. Whole-genome sequencing showed mutation UhpT gene as well as the presence of plasmid-mediated fosA5 or fosA6 genes conferring Fosfomycin resistance.

CONCLUSION

This result supports very low resistance of Enterobacterales against Fosfomycin; hence should be considered a valuable option to treat multidrug-resistant uropathogens. Disc diffusion was observed to be a convenient method for Fosfomycin susceptibility testing compared to agar dilution.

Azithromycin resistance and its molecular characteristics in Neisseria gonorrhoeae isolates from a tertiary care centre in North India

Treatment guidelines for management of uncomplicated gonorrhoeae have been recently modified owing to alarming upsurge in azithromycin resistance. This study investigated the prevalence and genetic determinants of gonococcal azithromycin resistance in India. Four (5.7%) of 70 gonococcal isolates were resistant to azithromycin. Of 16 isolates investigated for molecular mechanisms of resistance, 13 (81.3%) and 6 (37.5%) isolates exhibited mutations in coding and promoter regions of mtrR gene, respectively. However, ermA, ermB and ermC genes or mutations in rrl gene were absent in all isolates. Azithromycin resistance is low in India posing no immediate threat to use of dual-therapy for syndromic management.

Frailty and Neutrophil Lymphocyte Ratio as Predictors of Mortality in Patients with Catheter-Associated Urinary Tract Infections or Central Line-Associated Bloodstream Infections in the Neurosurgical Intensive Care Unit: Insights from a Retrospective Study in a Developing Country

OBJECTIVE

We aim to evaluate the role of frailty and inflammatory markers in predicting the short-term outcomes after catheter-associated urinary tract infections (CAUTI) and central line-associated bloodstream infections (CLABSI).

METHODS

Data regarding the patients' characteristics, isolates on CAUTI and CLABSI, antibiotic susceptibility, frailty (11-point Modified Frailty Index), and inflammatory markers were retrospectively collected. Their impact on the short-term outcomes was assessed using regression modeling response.

RESULTS

One hundred and one patients with CAUTI (n = 71) and CLABSI (n = 30) between January 2018 and December 2019 were included in this study. The pooled incidence rates for CAUTI were 5.50 and for CLABSI 3.58 episodes/1000 catheter-days. We observed 74.7% drug resistance in our CAUTI isolates and 93.3% in CLABSI. In the multivariate analysis, frailty (P = 0.006), neutrophil/lymphocyte ratio (NLR) (P = 0.007) and the presence of sepsis (P = 0.029) were found to be significant predictors of in-hospital mortality in CAUTI. In patients with CLABSI, frailty (P = 0.029) and NLR (P = 0.029) were found significant and along with sepsis (P = 0.069) resulted in a regression model with good accuracy in predicting mortality. The receiver operating characteristic curve showed that 11-point Modified Frailty Index and NLR as well as the regression model significantly predicted mortality with an area under the curve of 86.1%, 81.4%, and 95.4%, respectively, in CAUTI, and 70.9%, 77.8%, and 95.2%, respectively, in CLABSI.

A Century With Craniopagus Twin Separation Surgeries: Nihilism to Optimism

Craniopagus conjoined twins are extremely rare, reported 1 in 2.5 million live births. To date, 62 separation attempts in 69 well-documented cases of craniopagus twins have been made. Of these, 34 were performed in a single-stage approach, and 28 were attempted in a multistage approach. One or both twins died of massive intraoperative blood loss and cardiac arrest in 14 cases. We report our surgical experience with conjoined craniopagus twins (JB) with type III total vertical joining and shared circumferential/circular sinus with left-sided dominance. A brief review of the literature is also provided. In our twins, the meticulous preoperative study and planning by the multidisciplinary team consisting of 125-member, first-staged surgical separation consisted of creation of venous conduit to bypass part of shared circumferential sinus and partial hemispheric disconnection. Six weeks later, twin J manifested acute cardiac overload because of one-way fistula development from blocked venous bypass graft necessitating emergency final separation surgery. Unique perioperative issues were abnormal anatomy, hemodynamic sequelae from one-way fistula development after venous bypass graft thrombosis, cardiac arrest after massive venous air embolism requiring prolonged cardiopulmonary resuscitation, and return of spontaneous circulation at 15 minutes immediately after separation. This is the first Indian craniopagus separation surgery in a complex total vertical craniopagus twin reported by a single-center multidisciplinary team. Both twins could be sent home, but one remained severely handicapped. Adequate perioperative planning and multidisciplinary team approach are vital in craniopagus twin separation surgeries.

Ceftriaxone treatment failure in two cases of Enteric Fever caused by CTX-M15 positive Salmonella Typhi and its gastrointestinal carriage

We report two cases of culture positive typhoid fever caused by ceftriaxone resistant Salmonella Typhi. Bacterial isolates from both the cases were positive for ESBL by phenotypic methods. Both patients didn't respond to ceftriaxone and were finally treated with meropenem. Screening of family members of one patient isolated a similar strain from a healthy carrier with the same antibiogram pattern. All isolates were subjected to PCR, which confirmed the presence of blaCTX-M15 ESBL gene. These two cases confirm emergence of ESBL-producing Salmonella Typhi causing Enteric Fever in India and also their presence in the gut flora of healthy carriers.

Virulence gene mutations as a differentiator of clinical phenotypes: insights from community-acquired uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) remains an important cause of urinary tract infection during pregnancy. Multiple molecular virulence determinants and antibiotic resistant genes facilitate its pathogenesis and virulence phenotype. Hence it is hypothesized that there will be considerable variation in genes among the isolates from symptomatic as well as asymptomatic bacteriuria (ABU) during pregnancy. The aim of this study was to decipher the genetic variation among the two phenotypes. Six different UPEC isolates collected from urine specimens of consecutive pregnant females (five, symptomatic bacteriuria and one, ABU) were tested for their growth kinetics, and biofilm formation. A total of 87 virulence determinants and 56 antibiotic resistance genes were investigated using whole-genome sequencing, to identify putative drives of virulence phenotype. In this analysis, we identified eight different types of fully functional toxin antitoxin (TA) systems [HipAB, YefM-YoeB, YeeU-YeeV (CbtA), YhaV-PrlF, ChpBS, HigAB, YgiUT and HicAB] in the isolates from symptomatic bacteriuria; whereas partially functional TA system with mutations were observed in the asymptomatic one. Isolates of both the groups showed equivalent growth characteristics and biofilm-formation ability. Genes for an iron transport system (Efe UOB system, Fhu system except FhuA) were observed functional among all symptomatic and asymptomatic isolates, however functional mutations were observed in the latter group. Gene YidE was observed predominantly associated with the biofilm formation along with few other genes (BssR, BssS, YjgK, etc.). This study outlines putative critical relevance of specific variations in the genes for the TA system, biofilm formation, cell adhesion and colonization among UPEC isolates from symptomatic and asymptomatic bacteriuria among pregnant women. Further functional genomic study in the same cohort is warranted to establish the pathogenic role of these genes.

Analysis of colistin resistance in carbapenem-resistant Enterobacterales and XDR Klebsiella pneumoniae

Introduction:

Increasing occurrence of infections caused by multidrug-resistant Gram-negative bacteria resulted in colistin being the last agent for treatment. Apart from plasmid-mediated mcr genes, mutations involving several genes like mgrB, phoP/phoQ, pmrA, pmrB, pmrC, and crrABC genes, are leading causes of colistin resistance. Four colistin susceptibility testing methods were compared against broth microdilution (BMD) and determined the presence of the mcr1-5 gene.

Methodology:

A total of 100 carbapenem-resistant Enterobacterales isolates were tested for colistin susceptibility by commercial broth microdilution (cBMD), E-test, VITEK-2, and rapid polymyxin NP assay (RPNP) and compared with BMD. The presence of the mcr1-5 gene was determined by modified RPNP and PCR. Two non-mcr colistin-resistant XDR isolates were subjected to whole-genome sequencing using Illumina MiSeq sequencing platform.

Results:

Among 100 carbapenem-resistant Enterobacterales isolates, 15% were resistant to colistin. Essential agreement, categorical agreement, major error, and very major error for cBMD/E-test/VITEK-2/RPNP were 96%/73%/82%/NA; 99%/86%/88%/91%, 1.2%/9.4%/11.8%/8.2% and 0%/40%/13.3%/13.3%, respectively. Only one Klebsiella pneumoniae isolate harbored the mcr-1 gene, observed by both methods. Whole-genome sequencing of two non-mcr XDR Klebsiella pneumoniae showed multiple mutations in 10 genes responsible for lipopolysaccharide biosynthesis.

Conclusions:

The performance of cBMD was excellent, whereas the E-test was unacceptable. VITEK-2 and RPNP performed better but remained unreliable due to high error rates. Multiple mutations in the target proteins involving lipopolysaccharide formation, modification, and regulation were seen, resulting in colistin resistance.

Prevalence and resistance pattern of uropathogens from community settings of different regions: an experience from India

Introduction

Urinary tract infection (UTI) is one of the most common infections in clinical practice worldwide in both healthcare and community settings causing significant morbidity and mortality. It is one of the major conditions at the community level treated empirically and regarded as a potential cause of emergence of antimicrobial resistance (AMR). Limited information is available regarding community-acquired UTI (CA-UTI) from India.

Methodology

This is a first of its kind, multicentric-cross-sectional study at the community level targeting patients attending the out-patient department (OPD) of the community health centre (CHC) from four geographical regions (North, South, West and East) of India. The study had been designed to determine the epidemiology, antibiogram profile and identification of extended-spectrum beta-lactamase (ESBL) producer and carbapenem resistant (CR) uropathogens. Samples were collected prospectively from UTI suspected patients coming at CHC and processed at the tertiary healthcare centres using a common standard operating procedure. Clinical history of all the patients exhibiting significant bacteriuria was collected and data was analysed.

Result

Overall, 250 out of a total of 2459 (10.1 %) urine samples were positive for bacteria with significant bacteriuria (adult: paediatrics, 6.7 : 1). Females were predominantly affected (male: female, 1 : 2.9). History of recent episode of UTI was observed as the commonest risk factor followed by diabetes mellitus. Altogether, 86 % of total cases were caused by Escherichia coli (68 %) and Klebsiella pneumoniae (17.6 %) together. Among the commonly used oral antibiotics for the Gram-negative bacilli (GNB), the highest resistance was observed against beta-lactams, first- and second-generation cephalosporins, fluoroquinolones and co-trimoxazole. Overall, the prevalence of ESBL producer and CR isolates were 44.8, and 4.3 %, respectively. However, the ESBL production, CR and nitrofurantoin resistance among the uropathogenic E. coli (UPEC) isolates was 52.8, 5.1 and 14 %, respectively. No resistance was found against fosfomycin among the UPEC isolates.

Conclusion

The current study highlights the increasing incidence of AMR among uropathogens at the community-settings of India. A significant percentage of ESBL producers among the isolated UPEC and K. pneumoniae were observed. The currently available evidence supports the clinical recommendation of fosfomycin and nitrofurantoin for empiric therapy in CA-UTI in India.

Polymicrobial growth in standard urine culture: Time to Act or Ignore?

Diagnosing Urinary Tract Infections (UTI) remains a clinical challenge. A monobacterial growth in standard urine culture is diagnostic while polymicrobial growth is usually considered as contaminants. However, in certain cases, true mixed infections may exist making it important to correctly identify the pathogens and streamline the therapy. Communication between the clinician and microbiologist is essential to establish the right diagnosis at right time. Here, we would like to share our experience about a polymicrobial UTI in a paediatric patient in which coordinated discussion between the clinical team and microbiologist was helpful for favourable outcome.

Clinical use of multiplex-PCR for the diagnosis of acute bacterial meningitis

Background and Objectives:

Methods:

Results:

Conclusion:

Intestinal Colonization Due to Carbapenem-Resistant Enterobacteriaceae Among Hematological Malignancy Patients in India: Prevalence and Molecular Charecterisation

Faecal carriage of Carbapenem-resistant Enterobacteriaceae (CRE) is being observed as an important risk factor for bacteremia among patients with hematological malignancies. A prospective surveillance study was conducted among these patients to determine the gut colonization of CRE. Rectal/perianal swabs were collected to isolate CRE. Carbapenem resistance was detected by disk diffusion, modified-Hodge, Carba-NP test, and PCR for ^bla NDM-1, ^bla KPC, ^bla OXA-48, ^bla VIM, ^bla IMP genes. A total of 209 CRE isolates were identified from 151 patients. E. coli was the most common (83.2%) CRE identified, followed by Klebsiella spp. (9.6%). The majority of CRE were observed resistant to ertapenem (86%). ^bla NDM-1 was the most common gene (57.3%), followed by ^bla OXA-48 (37.8%). 26.8% isolates found to carry both ^bla NDM-1 and ^bla OXA-48 genes. CRE is increasingly observed to cause bacteremia among hematological malignancy patients due to increased colonization. Screening for gut CRE colonization is necessary to guide empirical therapy and apply infection control measures among these patients.

Ileal Perforation and Enteric Fever: Implications for Burden of Disease Estimation

Background

Ileal perforation occurs in about 1% of enteric fevers as a complication, with a case fatality risk (CFR) of 20%–30% in the early 1990s that decreased to 15.4% in 2011 in South East Asia. We report nontraumatic ileal perforations and its associated CFR from a 2-year prospective enteric fever surveillance across India.

Methods

The Surveillance for Enteric Fever in India (SEFI) project established a multitiered surveillance system for enteric fever between December 2017 and March 2020. Nontraumatic ileal perforations were surveilled at 8 tertiary care and 6 secondary care hospitals and classified according to etiology.

Results

Of the 158 nontraumatic ileal perforation cases identified,126 were consented and enrolled. Enteric fever (34.7%), tuberculosis (19.0%), malignancy (5.8%), and perforation of Meckel diverticulum (4.9%) were the common etiology. In those with enteric fever ileal perforation, the CFR was 7.1%.

Conclusions

Enteric fever remains the most common cause of nontraumatic ileal perforation in India, followed by tuberculosis. Better modalities of establishing etiology are required to classify the illness, and frame management guidelines and preventive measures. CFR data are critical for comprehensive disease burden estimation and policymaking.

Evaluation of Antimicrobial Susceptibility Profile in Salmonella Typhi and Salmonella Paratyphi A: Presenting the Current Scenario in India and Strategy for Future Management

Background

Systematic studies to estimate the disease burden of typhoid and paratyphoid in India are limited. Therefore, a multicenter study on the Surveillance of Enteric Fever in India was carried out to estimate the incidence, clinical presentation, and antimicrobial resistance (AMR) trend. The data presented here represent the national burden of AMR in Salmonella Typhi and Salmonella Paratyphi A.

Methods

Antimicrobial susceptibility testing was performed for S. Typhi and S. Paratyphi A (n = 2373) isolates collected prospectively during a 2-year period from November 2017 to January 2020.

Results

Of 2373 Salmonella isolates, 2032 (85.6%) were identified as S. Typhi and 341 (14.4%) were S. Paratyphi A. Approximately 2% of S. Typhi were multidrug-resistant (MDR), whereas all 341 (100%) of S. Paratyphi A isolates were sensitive to the first-line antimicrobials. Among 98% of ciprofloxacin nonsusceptible isolates, resistance (minimum inhibitory concentration [MIC] &gt;0.5 µg/mL) was higher in S. Typhi (37%) compared with S. Paratyphi A (20%). Azithromycin susceptibility was 99.9% and 100% with a mean MIC of 4.98 μg/mL for S. Typhi and 7.39 μg/mL for S. Paratyphi A respectively. Ceftriaxone was the only agent that retained 100% susceptibility. Moreover, beta-lactam/beta-lactamase inhibitors showed potent in vitro activity against the study isolates.

Conclusions

Data obtained from this systematic surveillance study confirms the declining trend of MDR Salmonella isolates from India. The higher prevalence of ciprofloxacin nonsusceptibility enforces to limit its use and adhere to the judicious usage of azithromycin and ceftriaxone for enteric fever management.

Cost of Illness Due to Severe Enteric Fever in India

Background

Lack of robust data on economic burden due to enteric fever in India has made decision making on typhoid vaccination a challenge. Surveillance for Enteric Fever network was established to address gaps in typhoid disease and economic burden.

Methods

Patients hospitalized with blood culture-confirmed enteric fever and nontraumatic ileal perforation were identified at 14 hospitals. These sites represent urban referral hospitals (tier 3) and smaller hospitals in urban slums, remote rural, and tribal settings (tier 2). Cost of illness and productivity loss data from onset to 28 days after discharge from hospital were collected using a structured questionnaire. The direct and indirect costs of an illness episode were analyzed by type of setting.

Results

In total, 274 patients from tier 2 surveillance, 891 patients from tier 3 surveillance, and 110 ileal perforation patients provided the cost of illness data. The mean direct cost of severe enteric fever was US$119.1 (95% confidence interval [CI], US$85.8–152.4) in tier 2 and US$405.7 (95% CI, 366.9–444.4) in tier 3; 16.9% of patients in tier 3 experienced catastrophic expenditure.

Conclusions

The cost of treating enteric fever is considerable and likely to increase with emerging antimicrobial resistance. Equitable preventive strategies are urgently needed.

Corynebacterium striatum: An emerging nosocomial skin and soft-tissue pathogen

The genus Corynebacterium is composed of Gram-positive, aerobic, non-motile, non-spore-forming bacilli that are widely distributed throughout the environment. They are usually found as commensals on the skin and are often considered as mere contaminants when isolated from clinical samples. We describe a patient with skin and soft-tissue infections due to Corynebacterium striatum following exploratory laparotomy identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The clinical importance and pathogenic potential of Corynebacterium species, especially C. striatum, cannot be underestimated. This report is a reminder to physicians of the possible pathogenicity of non-diphtherial Corynebacteria.

Molecular Characterization of Resistance-Nodulation-cell Division Efflux Pump Genes in Multidrug-Resistant Acinetobacter baumannii

Introduction:

Multidrug-resistant Acinetobacter baumannii is galloping, posing threat to tackle, and leaving us with limited options of treatment.

Methods:

The purpose of this study is to find the genotypic association in drug-resistant A. baumannii isolated from different sterile body fluids. Matrix-assisted laser desorption/ionization–time of flight confirmed A. baumannii isolates were taken and minimum inhibitory concentration (MIC) was determined by VITEK-2 AST system. The presence of resistance nodulation–division (RND)-efflux pump genes AdeABC-RS was detected by multiplex polymerase chain reaction.

Results:

Of the total 40 A. baumannii, 32 (80%) were multidrug resistant though all isolates were susceptible to Tigecycline. Similarly, 26 (81.25%) isolates were positive for RND-efflux pump genes AdeABC-RS.

Discussion:

RND efflux pump AdeABC-RS system plays a significant role in emerging multi drug resistant A. baumannii. Mutation in AdeS gene deciphers the role of regulatory gene. Hence, antimicrobial stewardship should be strictly followed and efflux pump inhibiting substances should be vigorously searched to bring back the era of existing antibiotics.

Molecular characterization of decreased susceptibility to ceftriaxone and genotyping of Neisseria gonorrheae isolates in New Delhi, India

Data on genetic characteristics of Neisseria gonorrhoeae isolates exhibiting decreased susceptibility to extended-spectrum cephalosporins in India is deficient. In this study, we have sequenced penA, porB, mtrR and ponA and bla_TEM genes in 70 clinical isolates of NG with varying ceftriaxone MICs. Amongst these, 22 (31.4%) were PPNG. Additionally, N. gonorrheae Multiantigen Sequence Typing was performed. Fisher exact and χ² were used to evaluate significance of mutations with MICs. A total of six non-mosaic penA (Penicillin binding protein 2 [PBP2]) amino acid patterns were seen (II, IV, IX, XII, XIX, XXII) of which, pattern IX was significantly associated with decreased susceptibility to ceftriaxone. Other significant associations were noted in porB & mtrR genes. There were no mutations in bla_TEM gene. ST6069 was significantly associated with decreased susceptibility to ceftriaxone. To conclude, development of decreased susceptibility to ceftriaxone in gonococci involves cumulation of different mutations in the four chromosomal genes investigated.

Risk factors of multidrug-resistant bacterial infections among patients admitted in a tertiary care hospital of north India

INTRODUCTION

Infections with drug-resistant organisms (DRO) have been associated with poor patient outcomes. To tackle this global problem, it is necessary to understand the risk factors that predispose to infections with DRO.

METHODOLOGY

This was a prospective observational study conducted over a three-year period at a tertiary-care hospital. Bacterial culture isolates from patients admitted in medicine wards with community or hospital-acquired infections were included. Logistic regression analysis was used to determine risk factors for drug-resistant infections.

RESULTS

Of the 295 patients with 323 isolates included, 40 (12.3%) had non-MDR (N-MDR) infections, 86 (26.6 %) had MDR infections and 197 (61%) had possible extensively drug-resistant (P-XDR) infections. History of previous admission in the preceding three months (Odds Ratio, OR = 4.53, 95% Confidence interval, CI = 1.8 - 11.42, p = -0.01), high SOFA score at admission (OR = 1.14, 95% CI = 1.0 - 1.290, p = -0.039) and prolonged duration of ventilation (OR = 1.25, 95% CI = 1.05 - 1.41, p = -0.012) were independently associated P-XDR infections when compared to patients with N-MDR.

CONCLUSIONS

High rate of multidrug-resistant infections in the studied area is alarming. In this single-centre study, we elicited various risk factors for drug-resistant bacterial infections ranging from patient characteristics to iatrogenic risk factors during the hospital stay. Infections with P-XDR and MDR isolates independently increased hospital and ICU stay duration and were associated with increased mortality.

Evaluating the efficacy of a multistrain probiotic supplementation for prevention of neonatal sepsis in 0-2-month-old low birth weight infants in India-the "ProSPoNS" Study protocol for a phase III, multicentric, randomized, double-blind, placebo-controlled trial

Background

Progress has been made in the reduction of under-five mortality in India; however, neonatal mortality is reducing at a slower rate. Efforts are required to bring down neonatal mortality in order to attain the Sustainable Development Goal-3. Prevention of sepsis among the high-risk, vulnerable low birth weight neonates by a newer intervention with probiotic supplementation is promising.

Methods

A phase III, multicenter, randomized, double-blind, placebo-controlled study is being conducted at six sites in India. A total of 6144 healthy low birth weight (LBW) infants fulfilling the eligibility criteria would be enrolled within the first week of life, after obtaining written informed consent from the parents of the infant. Randomization in 1:1 ratio, stratified by site, sex, and birth weight, would be done through an interactive web response system (IWRS) using a standard web browser and email service. Vivomixx®, a probiotic containing a mix of 8 strains of bacteria, in a suspension form standardized to deliver 10 billion CFU/ml, or an organoleptically similar placebo would be fed to enrolled infants in a 1-ml/day dose for 30 days. The follow-up of enrolled infants for 60 days would take place as per a pre-specified schedule for recording morbidities and outcome assessments at the six participating sites. Screening for morbidities would be conducted by trained field workers in the community, and sick infants would be referred to designated clinics/hospitals. A physician would examine the referred infants presenting with complaints and clinical signs, and blood samples would be collected from sick infants for diagnosis of neonatal sepsis by performing sepsis screen and blood culture. Appropriate treatment would be provided as per hospital protocol. The study would be implemented as per the MRC guideline for the management of Global Health Trials in accordance with ICH-GCP and Indian Regulatory guidelines. A contract research organization would be engaged for comprehensive monitoring and quality assurance. The final analysis would be conducted in a blinded manner as per the statistical analysis plan (SAP) to estimate the primary outcomes of sepsis, possible serious bacterial infection (PSBI), and secondary outcomes. The codes will be broken after DMC permission. The protocol has been reviewed by the Research Ethics Committee of the Liverpool School of Tropical Medicine (REC-LSTM), from Research Ethics Committees of the six subject recruitment participating sites.

Discussion

This adequately powered and well-designed trial would conclusively answer the question whether probiotics can prevent neonatal sepsis in the high-risk group of low birth weight infants as indicated by a pilot study in 1340 LBW infants, evidence from systematic reviews of hospital-based studies, and a primary study on healthy newborns in Orissa. Results of the study would be generalizable to India and other low–middle-income countries.

Trial registration

Clinical Trial Registry of India (CTRI) CTRI/2019/05/019197. Registered on 16 May 2019

AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae

Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours.

In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network.

Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1–8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.

A pilot study to determine Neisseria gonorrhoeae-Chlamydia trachomatis coinfection rates in symptomatic patients attending STI Clinics, New Delhi, India

BACKGROUND

Neisseria gonorrhoeae and Chlamydia trachomatis are the two most prevalent bacterial sexually transmitted infections. For over two decades, treatment guidelines have recommended empirical co-treatment for N.gonorrhoeae and C.trachomatis as symptoms overlap and co-infection is common. Studies from India estimating the same are limited and mostly based on conventional techniques.

AIM AND OBJECTIVE

The aim of this study was to determine the frequency of N.gonorrhoeae and C.trachomatis coinfection using nucleic acid amplification tests. Further, we assessed the utility of pus cell estimation in Gram stained smears as a screening tool for inclusion of samples for molecular diagnosis.

METHODS

This was a prospective study conducted at two tertiary care hospitals; 100 patients (55 females and 45 males) with genitourinary discharge attending STI clinics were recruited, and endocervical or urethral swabs were collected. PCRs for N.gonorrhoeae and C.trachomatis were put up. In addition, microscopy and culture for gonococcus was performed followed by antimicrobial susceptibility testing. Statistical analysis was performed using the SPSS 16 software.

RESULTS

N.gonorrhoeae infection was more common than C.trachomatis. A total of 14 patients were positive by PCR (9 males and 5 females) for gonococcus. However, culture was positive only in 8 male patients. PCR for C.trachomatis was positive in 9 (4 males and 5 females) and the co-infection rate was 5%. The sensitivity and negative predictive value of pus cell estimation was 100% for males and 64% and 94.6% respectively for females. All isolates were susceptible to extended spectrum cephalosporins and azithromycin.

LIMITATION

The sample size of the study was small.

CONCLUSION

Frequency of N.gonorrhoeae/C.trachomatis coinfection in symptomatic STI patients is low. Coinfection is considerably overestimated and necessary confirmation of etiological diagnosis could reduce widespread empirical administration of broad-spectrum antibiotics.

Twenty-Four-Hour Esophageal pH Measurement in Mechanically Ventilated Children: A Prospective Cohort Study

OBJECTIVES

To assess the prevalence of gastroesophageal reflux in mechanically ventilated children using 24-hour esophageal pH-metry and its role as a risk factor for ventilator-associated pneumonia.

DESIGN

Prospective cohort study.

SETTING

PICU of a tertiary care hospital from North India.

PATIENTS

Mechanically ventilated children 1-15 years old in PICU from July 2015 to June 2017, excluding those receiving acid suppressants, known cases of gastroesophageal reflux disease, having upper gastrointestinal bleed.

INTERVENTION

Demographic details, baseline investigations, diagnosis, treatment details, and Pediatric Risk of Mortality III score were recorded at enrollment. Gastroesophageal reflux was evaluated using 24-hour esophageal pH-metry. Children were followed up for 7 days or 48 hours after extubation for development of ventilator-associated pneumonia using Centers for Disease Control and Prevention criteria. Pathologic acidic gastroesophageal reflux was defined as fall in esophageal pH less than 4 for more than 4% of total time, whereas pathologic alkaline gastroesophageal reflux as rise in esophageal pH greater than 7 for more than 17% of total time.

MEASUREMENTS AND MAIN RESULTS

Sixty-one children (median [interquartile range], age 73 mo [30-132 mo]; 44 boys [72%]) were enrolled. Median Pediatric Risk of Mortality III score was 10.0 (3-16). Median duration of ventilation was 6 days (3-9 d). Pathologic gastroesophageal reflux (acidic or alkaline) was present in 47 children (77%). Twelve children (19.7%) met criteria for pathologic acidic gastroesophageal reflux, whereas 44 children (72.1%) had pathologic alkaline gastroesophageal reflux; nine children (14.7%) had both pathologic acidic and alkaline gastroesophageal reflux. Of the enrolled children, 17 (27.9 %) developed ventilator-associated pneumonia. No patient had both pathologic acidic gastroesophageal reflux and ventilator-associated pneumonia. Of 17 children who developed ventilator-associated pneumonia, 12 (70.5%) had pathologic alkaline gastroesophageal reflux as compared to 32 children (72.7%) among the 44 children who did not develop ventilator-associated pneumonia (p = 0.87).

CONCLUSIONS

The current study shows high incidence of gastroesophageal reflux on 24-hour esophageal pH-metry in mechanically ventilated children with medical diagnoses. The significance of this finding and its impact on ventilator-associated pneumonia and other ventilator-associated events need to be examined in larger studies.

Clinical correlation and antimicrobial susceptibility pattern of Chryseobacterium spp.: A three year prospective study

Chryseobacterium species are widely distributed in the environment. They are rarely found in hospital settings causing nosocomial infections. Limited data is available regarding their epidemiology, clinical significance and antimicrobial susceptibility patterns. This study was aimed to identify different species of Chryseobacterium using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and to correlate clinically with antimicrobial susceptibility patterns in a tertiary care hospital in north India. We also performed phenotypic tests, which may be useful to differentiate this bacterium from other non-fermenters. A total of 20 isolates of Chryseobacterium spp. were identified over a period of 3 years. Chryseobacterium indologenes (18/20) was the most common species isolated followed by Chryseobacterium gleum (2/20) from various clinical samples. Antimicrobial susceptibility testing (AST) was performed. Susceptibility to rifampicin was observed at a maximum (75%) followed by piperacillin-tazobactum (45%). Susceptibility against imipenem, meropenem, cotrimoxazole and cefoperazone-sulbactum were observed approximately 33%. Amikacin, cefotaxime and ceftazidime showed least susceptibility results. Further clinical correlation was established.