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]).

Is it time to move on to gene-based Salmonella typing: Evidence and implications

Non-typhoidal Salmonella (NTS) is the major cause of foodborne infections globally, with considerable morbidity and mortality. The accurate identification of Salmonella serovars is important in disease management and public health surveillance. However, traditional serotyping methods are laborious, time-consuming and may produce ambiguous results. In this study, we evaluated traditional serotyping and seven gene-based multilocus sequence typing (MLST) methods to determine the serogroups of Salmonella strains. This study analysis suggests that MLST based serotyping is accurate in serogroup identification and discrimination of Salmonella serovars compared to the traditional serotyping method and can be implemented in routine clinical practice.

Genomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence

PURPOSE

Brucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform.

METHODS

The two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out.

RESULTS

Phylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes.

CONCLUSION

Here we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.

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.

A secular trend in invasive non-typhoidal Salmonella in South India, 2000-2020: Identification challenges and antibiogram

PURPOSE

Invasive non-typhoidal Salmonella (iNTS) disease is an important cause of morbidity and mortality in African countries. However, the incidence in Indian subcontinent remains poorly documented. This study has assessed the incidence of iNTS in India with a perspective on its AMR profiles and serovar distribution for a period of 21 years from 2000 to 2020 from a tertiary care centre in South India.

METHODS

A total of 461 iNTS isolates were subjected to serotyping and antimicrobial susceptibility testing (AST). A subset of isolates was genotyped by multi locus sequence typing (MLST) and results were compared to serotyping to predict the accuracy.

RESULTS

Overall, 461 iNTS isolates were characterised mostly comprising of S. Typhimurium (49.2%) and S. Enteritidis (28.8%). Proportion of isolates resistant to first line antibiotics such as ampicillin, chloramphenicol and trimethoprim/sulphamethoxazole were 6.7%, 1.7% and 3.6% respectively. Isolates resistant to third generation cephalosporin are at a gradual rise while decreased susceptibility to quinolones was most common. The incidence of iNTS infection was maximum in the age group of >15 years. MLST analysis showed discrepancies in assigning the serovars by serotyping as three S. Saintpaul were identified as S. Typhimurium.

CONCLUSION

The clinical epidemiology, serovar distribution and antimicrobial susceptibility patterns of invasive Salmonella isolates from India suggest that there is only a small burden of iNTS disease. However the gradual emergence of AMR in iNTS isolates indicates serious risk for public health warranting the importance enhanced molecular surveillance.

Genomic Characterization of Mobile Genetic Elements Associated With Carbapenem Resistance of Acinetobacter baumannii From India

With the excessive genome plasticity, Acinetobacter baumannii can acquire and disseminate antimicrobial resistance (AMR) genes often associated with mobile genetic elements (MGEs). Analyzing the genetic environment of resistance genes often provides valuable information on the origin, emergence, evolution, and spread of resistance. Thus, we characterized the genomic features of some clinical isolates of carbapenem-resistant A. baumannii (CRAb) to understand the role of diverse MGEs and their genetic context responsible for disseminating carbapenem resistance genes. For this, 17 clinical isolates of A. baumannii obtained from multiple hospitals in India between 2018 and 2019 were analyzed. AMR determinants, the genetic context of resistance genes, and molecular epidemiology were studied using whole-genome sequencing. This study observed an increased prevalence of bla_OXA–23 followed by dual carbapenemases, bla_OXA–23, and bla_NDM. This study identified three novel Oxford MLST sequence types. The majority of the isolates belonged to the dominant clone, IC2, followed by less prevalent clones such as IC7 and IC8. This study identified variations of AbaR4 and AbGRI belonging to the IC2 lineage. To the best of our knowledge, this is the first study that provides comprehensive profiling of resistance islands, their related MGEs, acquired AMR genes, and the distribution of clonal lineages of CRAb from India.

Hybrid Plasmids Encoding Antimicrobial Resistance and Virulence Traits Among Hypervirulent Klebsiella pneumoniae ST2096 in India

Background

Hypervirulent variants of Klebsiella pneumoniae (HvKp) were typically associated with a broadly antimicrobial susceptible clone of sequence type (ST) 23 at the time of its emergence. Concerningly, HvKp is now also emerging within multidrug-resistant (MDR) clones, including ST11, ST15, and ST147. MDR-HvKp either carry both the virulence and resistance plasmids or carry a large hybrid plasmid coding for both virulence and resistance determinants. Here, we aimed to genetically characterize a collection of MDR-HvKp ST2096 isolates haboring hybrid plasmids carrying both antimicrobial resistance (AMR) and virulence genes.

Methods

Nine K. pneumoniae ST2096 isolated over 1 year from the blood sample of hospitalized patients in southern India that were MDR and suspected to be HvKp were selected. All nine isolates were subjected to short-read whole-genome sequencing; a subset (n = 4) was additionally subjected to long-read sequencing to obtain complete genomes for characterization. Mucoviscosity assay was also performed for phenotypic assessment.

Results

Among the nine isolates, seven were carbapenem-resistant, two of which carried bla_NDM-5 on an IncFII plasmid and five carried bla_OXA-232 on a ColKP3 plasmid. The organisms were confirmed as HvKp, with characteristic virulence genes (rmpA2, iutA, and iucABCD) carried on a large (~320 kbp) IncFIB–IncHI1B co-integrate. This hybrid plasmid also carried the aadA2, armA, bla_OXA-1, msrE, mphE, sul1, and dfrA14 AMR genes in addition to the heavy-metal resistance genes. The hybrid plasmid showed about 60% similarity to the IncHI1B virulence plasmid of K. pneumoniae SGH10 and ~70% sequence identity with the first identified IncHI1B pNDM-MAR plasmid. Notably, the hybrid plasmid carried its type IV-A3 CRISPR-Cas system which harbored spacer regions against traL of IncF plasmids, thereby preventing their acquisition.

Conclusion

The convergence of virulence and AMR is clinically concerning in K. pneumoniae. Our data highlight the role of hybrid plasmids carrying both AMR and virulence genes in K. pneumoniae ST2096, suggesting that MDR-HvKp is not confined to selected clones; we highlight the continued emergence of such genotypes across the species. The convergence is occurring globally amidst several clones and is of great concern to public health.

Relevance of immune response and vaccination strategies of SARS-CoV-2 in the phase of viral red queen dynamics

BACKGROUND

Following a relatively mild first wave of coronavirus disease 2019 (COVID-19) in India, a deadly second wave of the pandemic overwhelmed the healthcare system due to the emergence of fast-transmitting SARS-CoV-2 genetic variants. The emergence and spread of the B.1.617.2/Delta variant considered to be driving the devastating second wave of COVID-19 in India. Currently, the Delta variant has rapidly overtaken the previously circulating variants to become the dominant strain. Critical mutations in the spike/RBD region of these variants have raised serious concerns about the virus's increased transmissibility and decreased vaccine effectiveness. As a result, significant scientific and public concern has been expressed about the impact of virus variants on COVID-19 vaccines.

OBJECTIVES

The purpose of this article is to provide an additional explanation in the context of the evolutionary trajectory of SARS-CoV-2 variants in India, the vaccine-induced immune response to the variants of concern (VOC), and various vaccine deployment strategies to rapidly increase population immunity.

CONTENT

Phylogenetic analysis of SARS-CoV-2 isolates circulating in India suggests the emergence and spread of B.1.617 variant. The immunogenicity of currently approved vaccines indicates that the majority of vaccines elicit an antibody response and some level of protection. According to current data, vaccines in the pre-fusion configuration (2p substitution) have an advantage in terms of nAb titer, but the duration of vaccine-induced immunity, as well as the role of T cells and memory B cells in protection, remain unknown. Since vaccine efficacy on virus variants is one of the major factors to be considered for achieving herd immunity, existing vaccines need to be improved or effective next-generation vaccines should be developed to cover the new variants of the virus.

Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance

Background

Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination.

Methods

Five ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae.

Results

Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with bla_CTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term persistence of resistance plasmids such as IncX3 (bla_SHV-12) or IncN (bla_TEM-1B + bla_DHA-1).

Conclusion

Considering the selection pressure exerted by the extensive use of ceftriaxone in India, there are potential risks for the occurrence of plasmid transmission events in the predominant H58 lineages. Therefore, continuous monitoring of S. Typhi lineages carrying plasmid-mediated cephalosporin resistant genes is vital not just for India but also globally.

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S. Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae.

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Independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58 lineage II of S. Typhi.

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A short-term persistence of drug-resistant plasmids in H58 lineage II can be the reason for the sporadic cases cephalosporin resistant S. Typhi in India.

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Plasmid acquisition and maintenance of cephalosporin resistant S. Typhi appears to be specific to the phylogenetic lineage.

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Critical strategies in monitoring and control of cephalosporin resistant S. Typhi is needed to tackle further public health crisis.

Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India

Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spectrum of nosocomial infections with high rates of morbidity and mortality. The emergence of pan drug-resistant international high-risk clones such as ST258, ST14, ST15, ST147, and ST101 is a global concern. This study was performed to investigate the carbapenemases, the plasmid profile, and the clonal relationship among Indian K. pneumoniae. Materials and Methods: A total of 290 K. pneumoniae isolates from seven centers in India were characterized to determine sequence types (STs) and carbapenemases. A subset of isolates was subjected to whole genome sequencing and hybrid genome assembly to obtain the complete genome. Plasmids carrying carbapenemases were characterized to determine the dissemination of carbapenem-resistant (CR) K. pneumoniae. Results: From this study, 75 different STs were observed with ST231 being predominant. About 79% of the analyzed isolates were CR with 59% (n = 136) producing OXA48-like carbapenemases. While ST231 was the predominant clone among the OXA48-like producers; NDM producers and NDM+OXA48-like producers were mostly associated with ST14. Interestingly, 61% (n = 138) of the total CR K. pneumoniae were colistin resistant, belonging to 22 different STs. Plasmid profiling shows that bla_OXA48-like was exclusively carried by ColKP3, whereas bla_NDM was associated with IncFII-like plasmids. Conclusion: The highly mosaic genome of K. pneumoniae coupled with the diverse ecological niches in India makes it a hotspot for antimicrobial resistance, leading to increased morbidity and mortality. Extensive molecular surveillance of the clonal spread of K. pneumoniae could help in understanding AMR dynamics and thus rework therapeutic management.

Hybrid genome assembly of Shigella sonnei reveals the novel finding of chromosomal integration of an IncFII plasmid carrying a mphA gene

Azithromycin is increasingly being used for the treatment of shigellosis despite a lack of interpretative guidelines and with limited clinical evidence. The present study determined azithromycin susceptibility and correlated this with macrolide-resistance genes in Shigella spp. isolated from stool specimens in Vellore, India. The susceptibility of 332 Shigella isolates to azithromycin was determined using the disc diffusion method. Of these, 31 isolates were found to be azithromycin resistant. The azithromycin minimum inhibitory concentration (MIC) was determined using the broth microdilution method. In addition, isolates were screened for mphA and ermB genes using conventional PCR. Furthermore, an isolate that was positive for resistance genes was subjected to complete genome analysis, and was analysed for mobile genetic elements. The azithromycin MIC for the 31 resistant Shigella isolates ranged between 2 and 16 mg l^-1. PCR results showed that a single isolate of Shigella sonnei carried a mphA gene. Complete genome analysis revealed integration of an IncFII plasmid into the chromosome of S. sonnei , which was also found to carry the following resistance genes: sul1, bla _DHA1, qnrB4, mphA, tetR. Mutations in the quinolone-resistance-determining region (QRDR) were also observed. Additionally, prophages, insertion sequences and integrons were identified. The novel finding of IncFII plasmid integration into the chromosome of S. sonnei highlights the potential risk of Shigella spp. becoming resistance to azithromycin in the future. These suggests that it is imperative to monitor Shigella susceptibility and to study the resistance mechanism of Shigella to azithromycin considering the limited treatment choices for shigellosis.

Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution

Background

In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity.

Methods

Two hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains.

Results

The study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C₂, IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp’s hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions.

Conclusion

To the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.

A nineteen-year report of serotype and antimicrobial susceptibility of enteric non-typhoidal Salmonella from humans in Southern India: changing facades of taxonomy and resistance trend

BACKGROUND

The steady increase in the proportion of Non-typhoidal Salmonella (NTS) infections in humans represents a major health problem worldwide. The current study investigated the serovar distribution and antimicrobial susceptibility trends of NTS isolated from faecal samples during the period 2000-2018.

METHODS

Faecal specimens of patients were cultured according to standard lab protocol. The isolates were serotyped and antimicrobial susceptibility testing (AST) were performed according to CLSI guidelines.

RESULTS

A total of 1436 NTS isolates were obtained from faeces samples mostly comprising of S. Typhimurium (27.3%), S. Weltevreden (13%), S. Bareilly (11%), S. Newport (4.2%), S. Cholerasuis (4%), S. Infantis (3.4%), and S. Enteritidis (2.4%). Resistance to nalidixic acid (26%) was most common among the tested NTS, followed by ampicillin (18.5%), cotrimoxazole (13.5%), ciprofloxacin (12%), ceftriaxone (6.3%) and chloramphenicol (3.6%). Multidrug resistance was observed in 5% of NTS isolates with the highest rate (10.52%) in 2014. The incidence of NTS infection was maximum in children < 5 years of age with an average 19.3% of the total affected patients during the time period.

CONCLUSIONS

Based on this study, the faecal NTS isolates have high resistance rates against first line antimicrobial agents except chloramphenicol. The gradual but consistent increase in resistance to fluoroquinolones, third generation cephalosporins and macrolide may restrict future treatment options. Hence periodic monitoring of NTS infections, serotype distribution and antimicrobial resistance trend is recommended.

MLST based serotype prediction for the accurate identification of non typhoidal Salmonella serovars

Traditional serotyping based on the phenotypic variation of O- and H-antigen remains as the gold-standard for the identification and classification of Salmonella isolates for last 70 years. Although this classification is a globally recognized nomenclature, huge diversity of Salmonella serotypes have made the serovar identification to be very complex. Seven gene multilocus sequence typing (MLST) on the other hand can provide serovar prediction as well as the evolutionary origin between the serovars. In this study non typhoidal Salmonella (NTS) strains (n = 45) isolated from clinical samples (blood, faeces and pus) were identified by traditional phenotypic serotyping and biochemical testing. All the tested Salmonella isolates were designated as serovar Typhimurium based on phenotyping. However, by MLST 60% (27/45) of the isolates were S. Typhimurium, 35.5% (16/45) were S. Agona (ST13), 2.2% (1/45) were S. Kentucky (ST198) and 2.2% (1/45) were S. Saintpaul (ST27). MLST analysis assigned S. Typhimurium isolates as ST36 (18/127), ST19 (7/27) and ST313 (2/27). Mismatches in serovar designation between MLST database and phenotypic serotyping can be due to the misinterpretation of phenotypic serotyping as the antigenic structures of S. Typhimurium, S. Agona differs by a surface antigen. MLST based phylogeny of study isolates showed clustering according to sequence types. Concordance between MLST based sequence type and phenotypic serotype is important to provide insights into genetic population structure of Salmonella.

Draft genome sequence of carbapenem-resistant Elizabethkingia anophelis strain BP8467 clinical isolate from India

OBJECTIVES

Elizabethkingia spp. are Gram-negative, glucose-non-fermenting bacilli that are ubiquitous in natural environments such as soil, plant and water sources. Besides environmental sources, the bacterium can be found in hospital environments, particularly medical equipment and reagents. Here we report the draft genome sequence of an Elizabethkingia anophelis isolate from a blood culture.

METHODS

Genomic DNA of E. anophelis strain BP8467 was sequenced on an Ion Torrent PGM platform and the reads were assembled de novo using SPAdes v.5.0.0. The draft genome was annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) v.4.9. Genetic determinants of antimicrobial resistance as well as virulence factors were identified using computational tools.

RESULTS

The assembled draft genome is 3859105bp in length with a G+C content of 35.62% distributed in 30 contigs. Presence of the bla_BlaB and bla_GOB-4 genes associated with resistance to carbapenems was identified. In addition, genes conferring resistance to other β-lactams (bla_CME-1), aminoglycosides [ant(6)-I] and chloramphenicol (catB) were also detected. Antimicrobial susceptibility testing showed that the isolate was susceptible to levofloxacin, trimethoprim/sulfamethoxazole, tetracycline and rifampicin.

CONCLUSION

The presence of a multidrug-resistant isolate harbouring diverse antimicrobial resistance genes along with numerous virulence factors suggests the risk associated with Elizabethkingia spp. infections. This genome analysis provides insights into the antimicrobial resistance and pathogenicity mechanisms of multidrug-resistant E. anophelis that can help in the management of Elizabethkingia spp. infections in the future.

Genomic evolution of severe acute respiratory syndrome Coronavirus 2 in India and vaccine impact

Recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and subsequent containment procedures have impacted the world as never seen before. Therefore, there is considerable curiosity about the genome evolution related to the origin, transmission and vaccine impact of this virus. We have analysed genome sequences of SARS-CoV-2 isolated from Indian patients to gain an in-depth understanding of genomic evolution and transmission in India. Phylogenetic analysis and mutation profiling revealed major lineages being evolved by characteristic mutations. As the mutation frequency in spike protein is comparatively lesser, the candidate vaccines expected to have wide coverage worldwide including India.

Immobilisation of lipase enzyme onto bacterial magnetosomes for stain removal

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Lipase was immobilized on magnetosome via glutaraldehyde, confirmed in FTIR and SEM.

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Release of p-nitro phenol confirmed the enzyme activity of immobilize lipase (88 %).

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The optimal pH (7) and temperature (40 °C) was standardised for activity.

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The immobilized lipase stored at 4 °C retained higher activity (87 %) than free lipase after 30 days.

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Immobilized lipase removed vegetable oil stain, better cleaning efficiency than free lipase.

Lipase was immobilized onto bacterial magnetosomes using glutaraldehyde cross-linking and confirmed by Fourier transform infrared spectrometry (FT-IR) and Scanning electron microscopy (SEM). Enzyme activity of immobilised lipase as well as free lipase was estimated by the release of p-nitro phenol due to the hydrolysis of p-nitro phenyl acetate (pNPA). The immobilisation yield of lipase onto magnetosome was found to be 88 %. The optimal pH (7) and temperature (40 °C) for activity was standardised and found to be similar to free lipase. The stored immobilized lipase maintained higher activity even after 30 days at a temperature of 4 °C whereas compared to free lipase. Immobilized lipase found to have removed vegetable oil stain and showed higher cleaning efficiency when compared to free lipase. The results suggest that bacterial magnetosome displays great potential as a support material for the immobilization of industrial enzymes such as lipase.

Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.

Extensive drug resistant Salmonella enterica serovar Senftenberg carrying blaNDM encoding plasmid p5558 (IncA/C) from India

Non-typhoidal Salmonella (NTS) are foodborne pathogens that are responsible for self-limiting gastroenteritis in humans. The present study aims at the molecular characterisation and comparative genomics of Salmonella enterica serovar Senftenberg strain P5558 isolated from the pus samples of a patient suffering from stump infection. The isolate was subjected to serotyping and antimicrobial susceptibility test to understand the phenotypical characteristics. Whole genome sequencing (WGS) was carried out and comparative genomics using computational tools showed the antimicrobial resistance and virulence gene profile of the isolates from the genome sequence data. Typing experiments confirmed that the isolate belong to S. Senftenberg with sequence type ST14. Resistance against β-lactams is associated with the presence of bla_TEM-1, bla_OXA-9, bla_CMY-2 and bla_NDM-1 genes. Similarly resistance to aminoglycoside was associated with five aminoglycoside modifying enzymes aac(6')-Ia, aac(6')-Ib, aph(3')-Ib, aph(6')-Ib and ant(3'')-Ia, sulfonamide with sul-1 and sul-2 and chloramphenicol with florR gene. Substitutions in gyrA (S83Y, D87G) and parC (S80I) genes found to be the reason for fluoroquinolone resistance. The plasmid profiling showed the isolate has four resistance plasmids in which plasmid p5558-NDM (IncA/C) harbours major resistance genes including bla_NDM-1 and bla_CMY-2. Determination of virulence gene profile revealed that the genome carries all major Salmonella pathogenicity islands and virulence factors. From our findings it is clear that the isolate possess characteristic pathogenicity islands (SPI 1-6, 13, 14), major virulence factors and acquired resistance genes. Comparative analysis suggests the evolution and distribution of the MDR gene encoding plasmids in NTS.

Magnetotactic bacteria and magnetosomes - Scope and challenges

Geomagnetism aided navigation has been demonstrated by certain organisms which allows them to identify a particular location using magnetic field. This attractive technique to recognize the course was earlier exhibited in numerous animals, for example, birds, insects, reptiles, fishes and mammals. Magnetotactic bacteria (MTB) are one of the best examples for magnetoreception among microorganisms as the magnetic mineral functions as an internal magnet and aid the microbe to move towards the water columns in an oxic-anoxic interface (OAI). The ability of MTB to biomineralize the magnetic particles (magnetosomes) into uniform nano-sized, highly crystalline structure with uniform magnetic properties has made the bacteria an important topic of research. The superior properties of magnetosomes over chemically synthesized magnetic nanoparticles made it an attractive candidate for potential applications in microbiology, biophysics, biochemistry, nanotechnology and biomedicine. In this review article, the scope of MTB, magnetosomes and its challenges in research and industrial application have been discussed in brief. This article mainly focuses on the application based on the magnetotactic behaviour of MTB and magnetosomes in different areas of modern science.

Isolation and characterization of Magnetospirillum from saline lagoon

Magnetotactic bacteria (MTB) are aquatic prokaryotes that orient themselves to earth's magnetic field with the help of intracellular organelle magnetosomes. Although many species of MTB have been identified, the isolation of MTB is a challenging task due to the lack of systematic isolation procedure and/or commercial media. In this study, we are reporting the isolation of magnetotactic spirillum from the Pulicat lagoon, India using a systematic and selective procedure. Sampling site was chosen on the basis of physicochemical properties of the ecosystem and the catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) analysis of sediment samples. In the current study, a combination of techniques including 'capillary racetrack' Purification and gradient cultivation resulted in the isolation of magnetotactic spirilla from aquatic sediments. Based on the 16S rRNA gene sequence analysis, the strain was identified as Magnetospirillum and was designated as Magnetospirillum sp. VITRJS1. The genes responsible for magnetosome formation (mamA, B, E, F, K, M, O, P, Q, T) were successfully detected using PCR amplification. The presence of cbbM gene confirmed that the isolate is chemolithoautotroph and utilises reduced sulphur as an electron source. Furthermore, magnetosomes extracted from VITRJS1 found to be cubo-octahedral in shape and 45 nm in size. Our results indicate that the systematic procedure using sediment analysis, CARD-FISH, and a combination of isolation methods enables the selective and rapid isolation of MTB from aquatic sediment sample.

Klinefelter's syndrome with renal tubular acidosis: impact on height

A 19-year-old Indian man presented with a history of proximal muscle weakness, knock knees and gynaecomastia. On examination he had features of rickets and bilateral small testes. Karyotyping revealed a chromosomal pattern of 47,XXX, confirming the diagnosis of Klinefelter's syndrome. He was also found to have hyperchloraemic metabolic acidosis with hypokalaemia, hypophosphataemia, phosphaturia and glycosuria, which favoured a diagnosis of proximal renal tubular acidosis. Patients with Klinefelter's syndrome typically have a tall stature due to androgen deficiency, resulting in unfused epiphyses and an additional X chromosome. However, this patient had a short stature due to associated proximal renal tubular acidosis. To the best of our knowledge, this is the second case of Klinefelter's syndrome with short stature due to associated renal tubular acidosis reported in the literature. This report highlights the need to consider other causes when patients with Klinefelter's syndrome present with a short stature.

Foreign body aspiration in a boy with Prader-Willi Syndrome

A five-year-old boy presented with progressive weight gain with effort intolerance and nocturnal symptoms suggesting obstructive sleep apnoea. A clinical diagnosis of Prader-Willi Syndrome was made. As the initial radiography and computed tomography suggested a foreign body, bronchoscopy was done under general anaesthesia and impacted peanuts were removed from the left main bronchus. His symptoms resolved instantly and the patient was asymptomatic at six months follow-up. This report highlights the need to consider foreign body aspiration as a cause for dyspnoea in children with Prader-Willi Syndrome. The report also focuses on the need to adopt strategies that prevent foreign body aspiration and choking in patients with Prader- Willi Syndrome.

Intracardiac blood-filled cysts of the heart: a rare cause of embolic stroke

Intracardiac blood cysts are thin-walled congenital cysts located in the endocardium and are seen predominantly in infants. They are rare in adults and are typically asymptomatic. However, complications such as valve dysfunction and left ventricular outflow tract obstruction have been reported in adults. We report a 42-year-old woman who developed an embolic stroke in association with intracardiac blood cysts. To the best of our knowledge, this is the first case report of intracardiac blood cysts manifesting as an embolic stroke.

Oncogenic osteomalacia

A 59-year-old gentleman presented with symptoms of progressively worsening low back pain associated with difficulty in rising from a squat over a period of two years. Biochemical tests confirmed the initial clinical diagnosis of osteomalacia. Blood pool scanning revealed a focal hot spot on the site of the clinically visible swelling close to the metacarpo-phalangeal joint of the left index finger. The biopsy of the specimen obtained by excision was reported to be consistent with a phosphaturic mesenchymal tumour. The patient had complete resolution of symptoms six months following excision of the lesion.

Ionizing radiation dosimetry in the absorbed dose range 0.01-50 MGy based on resistance and ESR linewidth measurements of organic conducting crystals

The materials studied in the present work as high-dose dosimeters are members of a large class of molecular crystals which are organic conductors of electricity. Very different from each other in the details of their molecular and crystal structures, they all behave in the same way when subjected to increasing high doses of radiation, at least from the point of view of their electronic transport properties, because of the quasi-one-dimensional character of the conduction process. Their resistivities increase exponentially with the absorbed dose while their electron spin resonance (ESR) linewidths decrease exponentially. Very small single crystals less than 10 micron thick can be used as dosimeters in the dose range 0.01-50 MGy for gamma rays as well as for electron irradiations, by applying four probe resistance measurements. Only a few compounds over a large number of candidates have been irradiated in the present work with gamma-rays, low energy x-rays and electrons. In some favourable cases the energy and temperature dependences of the dosimeters have been checked experimentally. Their mass energy absorption coefficients and electron stopping powers have been also calculated. It is hoped to extend this kind of dosimetry to lower and higher doses by trying new compounds from the large family of organic conductors or by improving the resistivity and ESR measurement techniques.

Local inhibition of inflammatory pain by naloxone and its N-methyl quaternary analogue

Inflammation was induced in rats by intraplantar administration of carrageenan (500 micrograms in 0.1 ml). Nociceptive thresholds were measured on both inflamed and contralateral hindpaws with the pressure test of Randal and Sellito. Low doses (0.03-10 micrograms/kg) of naloxone hydrochloride (Nx) or of methylnaloxone methylsulfonate (MeNx) were injected 4 h after carrageenan in the inflamed paw: Nx (3 micrograms) and MeNx (1-10 micrograms) diminished inflammatory pain; a slight, nonspecific hyperalgesia was observed in the contralateral paw after Nx, MeNx or NaCl. Neither drug was effective when injected s.c. at the same doses and time; however activities were shown to be influenced by the experimental schedule. Low s.c. doses of Nx antagonized the analgesia produced by s.c. morphine whereas MeNx did not. This work demonstrates the local site of the analgesic action of the doses of Nx and MeNx used here, bringing new evidence in favour of the existence of cutaneous opioid receptors. Opiate antagonists might inhibit inflammatory pain by interacting with a particular population of cutaneous receptors and (or) by being dealkylated locally into agonists.

Effects of various serotoninergic agonists and an antagonist on a nociceptive reaction in mice

Low doses of 5-methoxy-N,N-dimethyltryptamine (5-MeODMT), quipazine and cyproheptadine produced facilitation of jumping in mice using the hot plate method. Higher doses produced severe motor disturbances which precluded the assessment of effects on nociception. The observed hyperalgesia might be a consequence of diminution of serotoninergic tone resulting either from triggering of presynaptic serotoninergic receptors in the case of 5-MeODMT and quipazine or from the blockade of postsynaptic serotoninergic receptors in the case of cyproheptadine. The 5-MeODMT-induced hyperalgesia was not attenuated by buprenorphine, which under similar conditions antagonized completely the hyperalgesic effects of naloxone; thus, the hyperalgesic effects of 5-MeODMT do not seemingly involve opioidergic receptors.

Inhibition of inflammatory pain by naloxone and its N methyl quaternary analogue

Naloxone hydrochloride (Nx) and methylnaloxone methylsulfate (MeNx) antagonized the inflammatory pain, but not oedema, produced by intraplantar carrageenan in rats. The liminar effective dose (3 microgram/kg) was the same for the two drugs after intraplantar or subcutaneous injection. The s.c. dose effects curves were, as a whole, similar for the two drugs. The effect was long lasting and stereospecific. The low "analgesic" s.c. doses of Nx were able to antagonize morphine analgesia, those of MeNx were not. The interpretation is difficult; a peripheral action or better the local production of morphinomimetic metabolite(s) might account for most facts.

Stress hyperalgesia in rats: an experimental animal model of anxiogenic hyperalgesia in human

Emotional, non-noxious stress consisting of inescapable holding or exposure to novelty were found to produce clearcut and reproducible hyperalgesia in the rat. The mechanisms of the two stress hyperalgesia appeared to be different: 1) hypophysectomy enhanced holding hyperalgesia but reduced novelty hyperalgesia, indicating that pituitary factors respectively compensate (through opioids ?) and participate (through ACTH ?) in stress hyperalgesia; 2) diazepam did not alter holding hyperalgesia but abolished novelty hyperalgesia. The two types of stress hyperalgesia might represent animal models of anxiogenic hyperalgesia observed in human: as for clinical anxieties, they are alleviated or not by diazepam.

A comparison of some pharmacological effects of naloxone and N-methylnaloxone in mice

The effects of N-methylnaloxone following subcutaneous and intracerebroventricular administrations on nociception were investigated using the hot plate technique. Unlike naloxone, subcutaneous administration of N-methylnaloxone did not enhance the nociceptive reactions. In contrast, intracerebroventricular injection of N-methylnaloxone produced antinociception and tremor. Compared with naloxone, N-methylnaloxone was very weak in precipitating the signs of abstinence in mice rendered acutely dependent on morphine. Two factors, poor penetration into the central nervous system and steric hindrance, might render N-methylnaloxone very weak and hence both these factors must be taken into consideration while analyzing the effects following quaternary derivatives of opioid antagonists.

A pharmacological analysis of levonantradol antinociception in mice

Using the hot plate test, the potency and mechanism of the analgesic activity of levonantradol was studied in mice. Levonantradol is 10 to 30 times more potent than morphine; the antinociception can be only partially blocked by naloxone. Similar limited antagonism by cholinergics indicates possible opiodergic mechanism. The role of serotoninergic pathways is unclear; antinociception is partially blocked by 5,7-dihydroxytryptamine, unaffected by p-chlorophenylalanine, and potentiated by cyproheptadine. Levonantradol blocks naloxone-induced signs of abstinence in morphine-dependent mice, being 3000 times more potent than morphine and 300 times more potent than delta 9-tetrahydrocannabinol (THC).

Mixed agonist-antagonist opiates and physical dependence

1 General methods (chronic, subacute and acute) for assessing physical dependence potential, abstinence precipitating capacity and abstinence preventing activity are briefly presented. 2 Direct dependence experiments indicate that, in general, mixed agonist-antagonist analgesics have relatively lower physical dependence potentials than pure agonist analgesics. That of buprenorphine seems to be particularly low in various animal species. 3 When substitution techniques are used, the dependence potential of buprenorphine seems to be somewhat more developed than with direct dependence techniques. 4 Among various agonists (morphine, methadone and etorphine), antagonists (naloxone, naltrexone and diprenorphine) and mixed agonist-antagonists (pentazocine, butorphanol and buprenorphine), buprenorphine is the most potent and the longest acting drug in preventing precipitated abstinence in mice, rats and dogs. 5 The low physical dependence potential of buprenorphine may result in part from the very slow dissociation of the complex it forms with opiate receptors. This potential might be underestimated when precipitated abstinence methods are used, as naloxone would displace buprenorphine from its receptors only to a very limited extent. New means of evaluating dependence by more direct means need to be developed. 6 Overall, the properties of mixed agonists in general justify their use as analgesics with lower physical dependence potential than the pure opiates and further, those of buprenorphine seem to indicate its possible utility for the treatment of opiate addiction.

Serotonin antagonists and central hyperthermia produced by biogenic amines in conscious rabbits

Previous studies have shown that the hyperthermia produced by intracerebroventricular injection of 5-hydroxytryptamine (5-HT) to conscious rabbits was antagonized by cyproheptadine and increased by LSD. Other putative antagonists, i.e. cinanserin, methiothepin, 2-bromo LSD, methysergide and dimetiotazine are investigated in the present report. Cinanserin and methiothepin resembeld cyproheptadine, 2-bromo LSD had almost the same effects as LSD and methysergide exhibited a mixed pattern of action, being depressant or potentiating as a function of dose. Dimetiotazine had no specific action. Cinanserin, however, differed from cyproheptadine in selectively antagonizing and early component of the 5-HT rise, unmasking an important fall and leaving a late hyperthermic component unaffected, thus disclosing three distinct effects of 5-HT action. The cinanserin, methiothepin and methysergide antagonism of the 5-HT-induced temperature rise was greater than the antagonism of the noradrenaline (NA)-induced rise. Methiothepin and methysergide inhibited both the 5-HT and DA hyperthermia; cinanserin--like cyproheptadine--was more effective on the 5-HT rise. The potentiation of the 5-HT temperature rise by 2-bromo LSD and methysergide was more developed than was the potentiation of the NA and DA rises. The effects of the drugs studied on 5-HT action argue in favour of the existence of several types of central 5-HT receptors. The dissociation observed between the antagonism to 5-HT and that to DA does not favour a mediation of DA hyperthermia by 5-HT; antiserotonin drug antagonism of DA hyperthermia is more simply accounted for by interactions at the level fo specific DA receptors. The potentiation of the 5-HT-induced temperature rise by 2-bromo LSD and methysergide might result from an antagonism of the hypothermic component. As with LSD, 2-bromo LSD and methysergide alone also produced hyperthermia, the origin of which is briefly discussed.

Facilitatory effect of naloxone and involvement of specific ligand-opiate receptor system in the antinociceptive effects of non-opioid drugs

The facilitatory effects exerted by naloxone on a nociceptive reaction (jumping) in the hot plate test was not modified by three phosphodiesterase inhibitors, theophylline, Ro-20-1724 and I.C.I. 63197 which had on themselves different effects on the latency of jumping. The facilitatory effects of naloxone were not diminished by neuroleptics, cholinergic agonists or miscellaneous drugs (baclofen, indomethacin, ketoprofen, n-dipropylacetate, diazepam and potassium chlorazepate). Naloxone antagonized the antinocieceptive effects of neuroleptics in different patterns. No competitive component could be observed with haloperidol, whereas such a phenomenon was apparent with benperidol. Pimozide was an intermediary case. The antinociceptive effects of two cholinergic agonists, arecoline and eserine were antagonized by naloxone and stereospecifically by the (-) isomer, Mr 2266. The (+) isomer, Mr 2267 was inactive. The antagonism by the opioid antagonists of the antinociceptive effects of cholinergic agonists appeared to be of a competitive type. Thus the facilitatory effects of naloxone did not apparently involve activation of adenyl cyclase or the mediation of dopaminergic or cholinergic (neural) structures. The antinociceptive effects of benperidol and pimozide but not of haloperidol might result from the triggering of specific opiate receptors and those of cholinergic agonists from such a triggering and/or from release of endogenous ligands.

Enhancement of a nociceptive reaction by opioid antagonists in mice

1. The opioid antagonists, naloxone, GPA 2163, levallorphan and Mr-2266 reduced the latency of the jumping reaction of mice in the hot plate test. The (+)-isomers of levallorphan and Mr-2266 which are devoid of antagonistic activity did not increase this latency. 2. In the same nociceptive reaction test, the enhancing effect of naloxone progressed in a dose-range similar to that required for the antagonism by naloxone of the depressive action of morphine. 3. The facilitatory effect of naloxone was not blocked by the previous administration of morphine or etorphine but it was prevented by pretreatment with a high dose of buprenorphine. 4. The antagonism by naloxone of morphine and of buprenorphine did not follow the same pattern. 5. The factors which are or may be involved in the efficacy of naloxone in enhancing nociceptive reactions are discussed. 6. The enhancing effect of naloxone may be due to an antagonism of endogenous ligands for the opiate receptor. If so, these ligands would be involved in reaction to but not in perception of nociceptive stimuli which need not be harmful ones.