Typhi H58 Research Articles

An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58.

Salmonella typhi is notorious for causing enteric fever which is also known as typhoid fever. It emerged as an extreme drug resistant strain that requires urgent attention to prevent its global spread. Statistically, about 11-17 million typhoid illnesses are reported worldwide annually. The only alternative approach for the control of this illness is proper vaccination. However, available typhoid vaccine has certain limitations such as poor long-term efficacy, and non-recommendation for below 6years children, which opens the avenues for designing new vaccines to overcome such limitations. Computational-based reverse vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of vaccine candidates through direct screening of genome sequence assemblies. In the current study, we have successfully designed a peptide-based novel antigen chimeric vaccine candidate against the XDR strain of S. typhi H58. The pipeline revealed four peptides from WP_001176621.1 i.e., peptidoglycan-associated lipoprotein Pal and two peptides from WP_000747548.1 i.e., OmpA family lipoprotein as promising target for the induction of immune response against S. typhi. The six epitopes from both proteins were found as immunogenic, antigenic, virulent, highly conserved, nontoxic, and non-allergenic among whole Salmonella H58 proteome. Furthermore, the binding interaction between a chimeric vaccine and human population alleles was unveiled through structure-based studies. So far, these proteins have never been characterized as vaccine targets against S. typhi. The current study proposed that construct V2 could be a significant vaccine candidate against S. typhi H58. However, to ascertain this, future experimental holistic studies are recommended as follow-up.

Erratum Erratum to: Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

Erratum Erratum to: Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control. To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics. A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis. A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, β-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs. This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.

Multiple Introductions of Salmonellaenterica Serovar Typhi H58 with Reduced Fluoroquinolone Susceptibility into Chile

Salmonella enterica serovar Typhi H58, an antimicrobial-resistant lineage, is globally disseminated but has not been reported in Latin America. Genomic analysis revealed 3 independent introductions of Salmonella Typhi H58 with reduced fluoroquinolone susceptibility into Chile. Our findings highlight the utility of enhanced genomic surveillance for typhoid fever in this region.

A Review on Recent Developments for the Cure of Salmonella Enterica Serovar Typhi, the Causative Agent for Typhoid Fever

Salmonella enterica typhi is typhoid or enteric fever agent which is a serious water-borne disease and is a human host restricted organism. So, an important cause of death in underdeveloped countries, typhoid fever is a public health concern. Worldwide, 15-30 million people suffer from this disease every year, causing more than 200,000 deaths. However, several lines of evidence suggest that the advent of multidrug-resistant non-typhoidal strains of Salmonella has an important impact on the effectiveness of current strategies, including reductions in the effectiveness of early empirical treatment for controlling and managing foodborne diseases. Recent studies show more than 2000 strains of salmonella bacteria with around 100 strains connected to human infection - with myriad common strains from Salmonella Heidelberg to Typhimurium to Salmonella infantis. The multi-medicinal strain S. Typhi H58 has developed into the main circulating strain in many parts of the world, and an extensively drug-resistant (XDR) subclade has been recently found. Most of the people agree that the most effective way to control infection is to vaccinate susceptible populations. The commercially available live attenuated (Ty21a) vaccine, on the other hand, is not recommendable for children under the age of six, whereas the poor long-term efficacy of Vi-polysaccharide-based vaccine against typhoid fever. Furthermore, there are no vaccines available to protect against S. para typhi infection. Subsequently, a new formulation is urgently needed that can provide long-term protection against both pathogens while healthy for all age groups. Pakistan is the first country in the world to incorporate the WHO-recommended conjugate vaccine into its routine typhoid immunization program (2019). As a result, the purpose of this review is to describe the various diagnostic procedures for typhoid fever diagnosis and cure development. This article addressed some of the elements and components required for the implementation of typhoid vaccine.
 With an analysis of past and current enteric fever vaccines in progress as well as the ethical issues relevant to CHIM in typhoid vaccine efficacy research, we have combined the new methods to predict typhoid burden and vaccines impact.

Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures.

Understanding the driving forces of an epidemic is key to inform intervention strategies against it. Correlating measures of the epidemic success of a pathogen with ancillary parameters such as its drug resistance profile provides a flexible tool to identify such driving forces. The recently described time‐scaled haplotypic density (THD) method facilitates the inference of a pathogen's epidemic success from genetic data. Contrary to demogenetic approaches that define success in an aggregated fashion, the THD computes an independent index of success for each isolate in a collection. Modeling this index using multivariate regression, thus, allows us to control for various sources of bias and to identify independent predictors of success. We illustrate the use of THD to address key questions regarding three exemplary epidemics of multidrug‐resistant (MDR) bacterial lineages, namely Mycobacterium tuberculosis Beijing, Salmonella Typhi H58, and Staphylococcus aureus ST8 (including ST8‐USA300 MRSA), based on previously published, international genetic datasets. In each case, THD analysis allowed to identify the impact, or lack thereof, of various factors on the epidemic success, independent of confounding by population structure and geographic distribution. Our results suggest that rifampicin resistance drives the MDR Beijing epidemic and that fluoroquinolone resistance drives the S. aureus ST8/USA300 epidemic, in line with previous evidence of a lack of resistance‐associated fitness cost in these pathogens. Conversely, fluoroquinolone resistance measurably hampered the success of S. Typhi H58 and non‐H58. These findings illustrate how THD can help leverage the massive genomic datasets generated by molecular epidemiology studies to address new questions. THD implementation for the R platform is available at https://github.com/rasigadelab/thd.

Laboratory characterisation of Salmonella enterica serotype Typhi isolates from Zimbabwe, 2009\u20132017

BackgroundTyphoid fever remains a major public health problem in Zimbabwe with recurrent outbreaks reported since 2009. To provide guidance on appropriate treatment choice in order to minimise the morbidity and mortality of typhoid fever and prevent large scale outbreaks, we investigated the antimicrobial susceptibility patterns, prevalence of Salmonella enterica serotype Typhi (S. Typhi) H58 haplotype and molecular subtypes of S. Typhi from outbreak strains isolated from 2009 to 2017 in Zimbabwe and compared these to isolates from neighbouring African countries.MethodsAntimicrobial susceptibility testing was performed on all isolates using the disk diffusion, and E-Test, and results were interpreted using Clinical and Laboratory Standards Institute (CLSI) guidelines (2017). S. Typhi H58 haplotype screening was performed on 161 (58.3%) isolates. Pulsed-field gel electrophoresis (PFGE) was performed on 91 selected isolates across timelines using antibiotic susceptibility results and geographical distribution (2009 to 2016).ResultsBetween 2009 and 2017, 16,398 suspected cases and 550 confirmed cases of typhoid fever were notified in Zimbabwe. A total of 276 (44.6%) of the culture-confirmed S. Typhi isolates were analysed and 243 isolates (88.0%) were resistant to two or more first line drugs (ciprofloxacin, ampicillin and chloramphenicol) for typhoid. The most common resistance was to ampicillin-chloramphenicol (172 isolates; 62.3%). Increasing ciprofloxacin resistance was observed from 2012 to 2017 (4.2 to 22.0%). Out of 161 screened isolates, 150 (93.2%) were haplotype H58. Twelve PFGE patterns were observed among the 91 isolates analysed, suggesting some diversity exists among strains circulating in Zimbabwe. PFGE analysis of 2013, 2014 and 2016 isolates revealed a common strain with an indistinguishable PFGE pattern (100% similarity) and indistinguishable from PFGE patterns previously identified in strains isolated from South Africa, Zambia and Tanzania.ConclusionsResistance to first line antimicrobials used for typhoid fever is emerging in Zimbabwe and the multidrug resistant S. Typhi H58 haplotype is widespread. A predominant PFGE clone circulating in Zimbabwe, South Africa, Zambia and Tanzania, argues for cross-border cooperation in the control of this disease.

Salmonella Typhi outer membrane protein STIV is a potential candidate for vaccine development against typhoid and paratyphoid fever

Enteric fever, caused by Salmonella enterica serovars, Typhi (S. Typhi) and Paratyphi (S. Paratyphi) is a major public health challenge for the developing nations. Globally, the disease affects ˜15-30 million individuals every year, resulting in >200,000 deaths. Multidrug-resistant S. Typhi H58 strain has emerged as the dominant circulating strain in a large part of the world and an extensively drug-resistant (XDR) subclade of the strain was recently reported. Many believe that vaccination of the susceptible populations is urgently needed and the best option to control the infection. However, the commercial live attenuated (Ty21a) vaccine is not recommended for children below six years of age while the Vi-polysaccharide-based vaccine has poor long-term efficacy against typhoid fever. Moreover, no vaccines are available against S. Paratyphi infection. Thus, a new formulation capable of providing long term protection against both the pathogens and safe for all age groups is immediately required. We show that recombinant, S. Typhi outer membrane protein STIV (rSTIV) is immunogenic in mice and elicits high serum titers of different immunoglobulin subtypes. STIV antibodies opsonize S. Typhi and S. Paratyphi A to promote antibody-dependent cellular cytotoxicity and complement-mediated lysis. Immunization with rSTIV also induces robust cell-mediated immunity, including antigen-specific T cell proliferation and cytotoxic T lymphocyte response. Finally, mice immunized with rSTIV are significantly protected against S. Typhi and S. Paratyphi A challenge, with reduced visceral bacterial load. Our results underscore the potential of rSTIV as a novel vaccine candidate for enteric fever.

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

BackgroundChildren are substantially affected by enteric fever in most settings with a high burden of the disease, including Nepal. However pathogen population structure and transmission dynamics are poorly delineated in young children, the proposed target group for immunization programs. Here we present whole genome sequencing and antimicrobial susceptibility data on 198 S. Typhi and 66 S. Paratyphi A isolated from children aged 2 months to 15 years of age during blood culture surveillance at Patan Hospital, Nepal, 2008–2016.Principal findingsS. Typhi was the dominant agent and comprised several distinct genotypes, dominated by 4.3.1 (H58). The heterogeneity of genotypes in children under five was reduced compared to data from 2005–2006, attributable to ongoing clonal expansion of H58. Most isolates (86%) were non-susceptible to fluoroquinolones, associated mainly with S. Typhi H58 lineage II and S. Paratyphi A harbouring mutations in the quinolone resistance-determining region (QRDR); non-susceptible strains from these groups accounted for 50% and 25% of all isolates. Multi-drug resistance (MDR) was rare (3.5% of S. Typhi, 0 S. Paratyphi A) and restricted to chromosomal insertions of resistance genes in H58 lineage I strains. Temporal analyses revealed a shift in dominance from H58 Lineage I to H58 Lineage II, with the latter being significantly more common after 2010. Comparison to global data sets showed the local S. Typhi and S. Paratyphi A strains had close genetic relatives in other South Asian countries, indicating regional strain circulation. Multiple imports from India of ciprofloxacin-resistant H58 lineage II strains were identified, but these were rare and showed no evidence of clonal replacement of local S. Typhi.SignificanceThese data indicate that enteric fever in Nepal continues to be a major public health issue with ongoing inter- and intra-country transmission, and highlights the need for regional coordination of intervention strategies. The absence of a S. Paratyphi A vaccine is cause for concern, given its prevalence as a fluoroquinolone resistant enteric fever agent in this setting.

The impact of migration and antimicrobial resistance on the transmission dynamics of typhoid fever in Kathmandu, Nepal: A mathematical modelling study.

BackgroundA substantial proportion of the global burden of typhoid fever occurs in South Asia. Kathmandu, Nepal experienced a substantial increase in the number of typhoid fever cases (caused by Salmonella Typhi) between 2000 and 2003, which subsequently declined but to a higher endemic level than in 2000. This epidemic of S. Typhi coincided with an increase in organisms with reduced susceptibility against fluoroquinolones, the emergence of S. Typhi H58, and an increase in the migratory population in Kathmandu.MethodsWe devised a mathematical model to investigate the potential epidemic drivers of typhoid in Kathmandu and fit this model to weekly data of S. Typhi cases between April 1997 and June 2011 and the age distribution of S. Typhi cases. We used this model to determine if the typhoid epidemic in Kathmandu was driven by heightened migration, the emergence of organisms with reduced susceptibility against fluoroquinolones or a combination of these factors.ResultsModels allowing for the migration of susceptible individuals into Kathmandu alone or in combination with the emergence of S. Typhi with reduced susceptibility against fluoroquinolones provided a good fit for the data. The emergence of organisms with reduced susceptibility against fluoroquinolones organisms alone, either through an increase in disease duration or increased transmission, did not fully explain the pattern of S. Typhi infections.ConclusionsOur analysis is consistent with the hypothesis that the increase in typhoid fever in Kathmandu was associated with the migration of susceptible individuals into the city and aided by the emergence of reduced susceptibility against fluoroquinolones. These data support identifying and targeting migrant populations with typhoid immunization programmes to prevent transmission and disease.

The emergence and intercontinental spread of a multidrug-resistant clade of typhoid agent Salmonella enterica serovar Typhi

BackgroundMultidrug-resistant typhoid is a global health problem. Previous studies conducted in countries of Asia and Africa have identified a highly clonal, multidrug-resistant lineage of Salmonella enterica serovar Typhi (S Typhi), known as H58. However, little is known about the emergence and geographical spread of the H58 clade. In this study, we have used whole-genome sequencing of a global collection of S Typhi to investigate this highly successful lineage. MethodsWe sequenced the whole-genome sequences of 1832 strains of S Typhi isolated between 1905 and 2013 (HiSeq platform, Illumina, San Diego, CA, USA). The isolates originated from 63 countries in six continents (Asia, Africa, North America, South America, Europe, and Oceania). The genomes of all 1832 S Typhi were mapped to the reference strain CT18 from Vietnam, and all single nucleotide changes were extracted and used to generate a maximum likelihood phylogeny of the whole collection. Transmission routes were also investigated with Bayesian analysis. The genomes were interrogated for the presence of plasmids and antimicrobial resistance genes. Long-read sequencing (PacBio platform, Pacific Biosciences, Menlo Park, CA, USA) was used to confirm the chromosomal location of resistance genes in representative isolates. FindingsPhylogenetic reconstruction showed that the multidrug-resistant lineage H58 emerged approximately 30 years ago and has undergone clonal expansion resulting in a widespread global distribution, involving at least 20 countries across Asia, Africa, and Oceania. The analyses showed numerous transmission pathways by which S Typhi H58 is disseminating to many locations worldwide: our data provide evidence that a multidrug-resistant typhoid epidemic is moving across Eastern and Southern Africa. Comparative genomic analysis revealed that the H58 lineage has a distinct genetic profile. Furthermore, isolates from this lineage frequently carried a composite transposable element encoding multiple antimicrobial resistance determinants, which was found either in IncHI1 plasmids or integrated within the chromosome. InterpretationOur study highlights the urgent need for routine surveillance to detect epidemics and monitor fluctuations in the population structure of S Typhi. These data will facilitate public health measures, such as the effective use of antimicrobial agents and the introduction of vaccine programmes, and in doing so will help to address the significant burden of disease caused by typhoid. FundingVKW, DP, AJP, and GD were funded by the Wellcome Trust (098051). NAF was supported by a Wellcome Trust research fellowship (WT092152MA). NAF and this work were supported by a strategic award from the Wellcome Trust for the Malawi-Liverpool Wellcome Trust Clinical Research Programme (101113/Z/13/Z). KEH was supported by the National Health and Medical Research Council of Australia (fellowship 1061409) and the Victorian Life Sciences Computation Initiative (grant VR0082). SB is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (100087/Z/12/Z). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the abstract.

Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam

BackgroundTyphoid fever remains a public health problem in Vietnam, with a significant burden in the Mekong River delta region. Typhoid fever is caused by the bacterial pathogen Salmonella enterica serovar Typhi (S. Typhi), which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-based drugs, the first choice for the treatment of typhoid fever. We used a GoldenGate (Illumina) assay to type 1,500 single nucleotide polymorphisms (SNPs) and analyse the genetic variation of S. Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005.Principal FindingsThe population of S. Typhi circulating during the study was highly clonal, with 91% of isolates belonging to a single clonal complex of the S. Typhi H58 haplogroup. The patterns of disease were consistent with the presence of an endemic haplotype H58-C and a localised outbreak of S. Typhi haplotype H58-E2 in 2004. H58-E2-associated typhoid fever cases exhibited evidence of significant geo-spatial clustering along the Sông H u branch of the Mekong River. Multidrug resistance was common in the established clone H58-C but not in the outbreak clone H58-E2, however all H58 S. Typhi were nalidixic acid resistant and carried a Ser83Phe amino acid substitution in the gyrA gene.SignificanceThe H58 haplogroup dominates S. Typhi populations in other endemic areas, but the population described here was more homogeneous than previously examined populations, and the dominant clonal complex (H58-C, -E1, -E2) observed in this study has not been detected outside Vietnam. IncHI1 plasmid-bearing S. Typhi H58-C was endemic during the study period whilst H58-E2, which rarely carried the plasmid, was only transient, suggesting a selective advantage for the plasmid. These data add insight into the outbreak dynamics and local molecular epidemiology of S. Typhi in southern Vietnam.