Salmonella chronic carriage: epidemiology, diagnosis, and gallbladder persistence

Treatment failure and the threshold of disease extinction

Antibiotic treatment failure related to carriers poses a serious problem to physicians and epidemiologists. Due to the sparsity of data, assessing the role in infection dynamics is difficult. In this study, we examined the possibility that a particular therapeutic effectiveness will be regarded as the disease extinction threshold through the mathematical modelling approach. Including the treatment state in the generic epidemic model with carrier allows us to describe the role of carriers in the treatment failure. The parameterized extinction thresholds were derived via the basic reproduction number for deterministic model, and via the Jury stability criterion for the stochastic model. Existence conditions for the stochastic threshold were derived without the exact formula of the spectral radius of the expectation matrix. The results show that the transmissibility of carrier is necessary for the extinction threshold via treatment failure. The expected extinction threshold may occur subject to the certain range of the transmission potential of the symptomatic infection. This existence conditions are independent of the rate at which the carriers undergo treatment and can be used to support a control strategy.

Biofilm-forming Abilities of Salmonella Serovars Isolated From Clinically Ill Livestock at 48 and 168 h

Little is known regarding the biofilm-forming capabilities of a somewhat distinct population of Salmonellae present on-farm and responsible for illnesses in livestock and humans. Evaluation of cleaning and disinfection in preharvest environments has found little success in eradicating Salmonella biofilms to date. Disrupting the environmental survival of Salmonella via biofilm removal will be critical to reducing carriage in livestock reservoirs and the risk of foodborne illness. Therefore, the objective of this study was to characterize the biofilm-forming abilities of Salmonellae relevant to livestock and human health. Eighty-one isolates from 8 serovars (S. Typhimurium, Heidelberg, Montevideo, Agona, Newport, Dublin, 4,[5],12:i:-, Enteritidis) were sourced from poultry and clinically ill cattle, swine, and equine. We hypothesized that biofilm production rate would vary significantly between serovars, and biofilm density would increase from 48 to 168 hrs. Isolates were grown in 24-well microplates in tryptone soy broth at ambient temperature, with media refreshed every 48 h. Biofilm density was quantified using crystal violet assays. Strong biofilm formers comprised 84% (68/81) of isolates tested, while 5.9% (4/81) were considered weak. Biofilm density was significantly greater at 168 h versus 48 h for all serovars except Dublin. Additionally, biofilm growth rate varied by serovar. Differences in biofilm-associated genes were evaluated, and only the detection of csrB was significantly associated with the categorization of biofilm producers. Results suggest inconsistent cleaning likely allows for the establishment of biofilms in on-farm environments. Further, some serovars may pose a greater risk for rapid biofilm establishment. This study provides data necessary to inform the development of evidence-based cleaning and disinfection protocols effective against the most prolific biofilm-forming strains of virulent Salmonella.

A genome-wide screen in ex vivo gallbladders identifies Listeria monocytogenes factors required for virulence in vivo

Listeria monocytogenes is a Gram-positive pathogen that causes the severe foodborne disease listeriosis. Following oral infection of the host, L. monocytogenes disseminates from the gastrointestinal tract to peripheral organs, including the gallbladder, where it replicates to high densities, establishing the gallbladder as the primary bacterial reservoir. Despite its importance in pathogenesis, little is known about how L. monocytogenes survives and replicates in the gallbladder. In this study, we assessed the L. monocytogenes genes required for growth and survival in ex vivo non-human primate gallbladders using a transposon sequencing approach. The screen identified 43 genes required for replication in the gallbladder, some of which were known to be important for virulence, and others had not been previously studied in the context of infection. We evaluated the roles of 19 genes identified in our screen both in vitro and in vivo, and demonstrate that most were required for replication in bile in vitro, for intracellular infection of murine cells in tissue culture, and for virulence in an oral murine model of listeriosis. Interestingly, strains lacking the mannose and glucose phosphoenolpyruvate-dependent phosphotransferase system (PTS) permeases Mpt and Mpo exhibited no defects in intracellular growth or intercellular spread, but were significantly attenuated during murine infection. While the roles of PTS systems in vivo were not previously appreciated, these results suggest that PTS permeases are necessary for extracellular replication during infection. Overall, this study demonstrates that L. monocytogenes genes required for replication in the gallbladder also play broader roles in disease.

Gallbladder cholangiocyte organoids

Organoids are miniature three-dimensional (3D) organ-like structures developed from primary cells that closely mimic the key histological, functional, and molecular characteristics of their parent organs. These structures self-organize through cell-cell and cell-matrix interaction in culture. In the last decade, organoids and allied 3D culture technologies have catalyzed studies involving developmental biology, disease biology, high-throughput drug screening, personalized medicine, biomarker discovery, tissue engineering, and regenerative medicine. Many organoid systems have been generated from the gastrointestinal system, for example, intestine, stomach, liver, pancreas, or colon. Gallbladder cancer (GBC) is the most common and highly aggressive form of biliary tract cancer. GBC is rare in the west but has a high incidence in South America and India. Prolonged chronic inflammation is implicated in the pathogenesis of GBC but the driving molecular pathways leading to neoplasia are not well understood. Gallbladder cholangiocyte organoids (GCO) will facilitate the understanding of the evolution of the disease and novel therapeutic strategies. In this review, we have discussed alternative methodologies and culture conditions developed to generate GCO models, applications that these models have been subjected to and the current limitations for the use of GCOs in addressing the challenges in GBC research.

MtlD as a therapeutic target for intestinal and systemic bacterial infections

The ability to treat infections is threatened by the rapid emergence of antibiotic resistance among pathogenic microbes. Therefore, new antimicrobials are needed. Here we evaluate mannitol-1-phosphate 5-dehydrogenase (MtlD) as a potential new drug target. In many bacteria, mannitol is transported into the cell and phosphorylated by MtlA, the EIICBA component of a phosphoenolpyruvate-dependent sugar phosphotransferase system. MtlD catalyzes the conversion of mannitol-1-phosphate (Mtl-1P) to fructose-6-phosphate, which enters the glycolytic pathway. Mutants lacking mtlD are sensitive to mannitol due to accumulation of Mtl-1P. Here, we constructed mtlD mutants in four different bacterial species (Cronobacter sakazakii, Pseudomonas aeruginosa, five serovars of Salmonella enterica, and three strains of Escherichia coli), confirming and quantifying their mannitol sensitivity. The quantification of mannitol sensitivity in vitro was complicated by an inoculum effect and a resumption of growth following mannitol intoxication. The rate of resumption at different mannitol concentrations and cell population densities is fairly constant and reveals what is likely an intoxication processing rate. Provision of mannitol in drinking water, or by intraperitoneal injection, dramatically attenuates infection of a Salmonella enterica serovar Typhimurium mtlD mutant in mouse models of both gastroenteritis and systemic infection. Using CC003/Unc mice, we find that a mtlD mutant of Salmonella enterica serovar Typhi is also attenuated by provision of mannitol in drinking water. Therefore, we postulate that MtlD could be a valuable new therapeutic target.

IMPORTANCE

The ability to treat infections is threatened by the rapid emergence of antibiotic resistance. Mannitol is a polyol used in human medicine and the food industry. During catabolism of mannitol, many bacteria transport mannitol across the inner membrane forming the toxic intermediate mannitol-1-phosphate (Mtl-1P). Mtl-1P must be processed by mannitol dehydrogenase (MtlD) or it accumulates intracellularly, causing growth attenuation. We test and confirm here that mtlD mutants of Escherichia coli (including UPEC, and EHEC), Salmonella (including serovars Typhi, and Paratyphi A, B, and C), Cronobacter, and Pseudomonas experience mannitol sensitivity in vitro. Furthermore, providing mannitol in drinking water can alleviate both gastrointestinal and systemic Salmonella infections in mice. This suggests that inhibition of MtlD could be a viable antimicrobial strategy.

A temporary cholesterol-rich diet and bacterial extracellular matrix factors favor Salmonella spp. biofilm formation in the cecum

Asymptomatic chronic carriers occur in approximately 5% of humans infected with Salmonella enterica serovar Typhi (S. Typhi) and represent a critical reservoir for bacterial dissemination. While chronic carriage primarily occurs in the gallbladder (GB) through biofilms on gallstones, additional anatomic sites have been suggested that could also harbor Salmonella. S. Typhimurium, orally infected 129 × 1/SvJ mice were pre-treated with a cholesterol-rich diet as a gallstone model for chronic carriage. We observed S. Typhimurium in feces and the cecum during early and persistent infection. Furthermore, bacterial biofilm-like aggregates were associated with the cecum epithelium at 7 and 21 days post-infection (DPI) in mice on a lithogenic diet (Ld) and correlated with an increase in cecal cholesterol at 21 DPI. Salmonella's extracellular matrix (ECM) was demonstrated as important in colonizing the cecum, as survival and aggregate formation significantly decreased when mice were infected with a quadruple ECM mutant strain. Gallbladder Salmonella counts were low at 36 DPI while cecal Salmonella were high, suggesting that gallbladder colonization was likely not responsible for the high cecal burden. All cecum phenotypes were significantly diminished in mice fed a normal diet (Nd). Finally, we examined the capability of S. Typhi to colonize the cecum and showed S. Typhi in feces and in aggregates in the cecum up to 7 DPI, with slightly higher counts in mice fed a Ld compared to Nd. Our findings suggest that the cecum, particularly under cholesterol-rich conditions, serves as an adaptative niche for Salmonella spp. aggregates/biofilms and is a putative site for long-term infection.IMPORTANCETyphoid fever is a systemic infectious disease triggered by the gastrointestinal dissemination of Salmonella Typhi and Paratyphi in humans. Three to five percent of infected individuals become chronic carriers, a state in which gallstone biofilm formation facilitates spread of the bacteria in feces. Notably, surgical removal of the gallbladder (GB) in some chronic carriers (22%) does not guarantee the elimination of the bacteria, and the rationale for this remains poorly understood. This study is significant as it explores other tissues associated with the chronic carrier state. It highlights not only a cholesterol-rich diet as an important etiological factor for Salmonella colonization but also identifies the cecum as a crucial tissue promoting fecal shedding. Additionally, we determined that biofilm matrix components of Salmonella are key factors contributing to these effects. A greater understanding of these mechanisms will allow the formulation of new therapeutic strategies specifically targeted at preventing typhoid fever dissemination from chronic carriers.

Phenotypic variation in the lipopolysaccharide O-antigen of Salmonella Paratyphi A and implications for vaccine development

Enteric fever remains a major public health problem in South and Southeast Asia. The recent roll-out of the typhoid conjugate vaccine protecting against S. Typhi exhibits great promise for disease reduction in high burden areas. However, some endemic regions remain vulnerable to S. Paratyphi A due to a lack of licensed vaccines and inadequate WASH. Several developmental S. Paratyphi A vaccines exploit O-antigen as the target antigen. It has been hypothesised that O-antigen is under selective and environmental pressure, with mutations in O-antigen biosynthesis genes being reported, but their phenotypic effects are unknown. Here, we aimed to evaluate O-antigen variation in S. Paratyphi A originating from Nepal, and the potential effect of this variation on antibody binding. O-antigen variation was determined by measuring LPS laddering shift following electrophoresis; this analysis was complemented with genomic characterisation of the O-antigen region. We found structural O-antigen variation in <10 % of S. Paratyphi A organisms, but a direct underlying genetic cause could not be identified. High-content imaging was performed to determine antibody binding by commercial O2 monoclonal (mAb) and polyclonal antibodies, as well as polyclonal sera from convalescent patients naturally infected with S. Paratyphi A. Commercial mAbs detected only a fraction of an apparently "clonal" bacterial population, suggesting phase variation and nonuniform O-antigen composition. Notably, and despite visible subpopulation clusters, O-antigen structural changes did not appear to affect the binding ability of polyclonal human antibody considerably, which led to no obvious differences in the functionality of antibodies targeting organisms with different O-antigen conformations. Although these results need to be confirmed in organisms from alternative endemic areas, they are encouraging the use of O-antigen as the target antigen in S. Paratyphi A vaccines.

Salmonella Typhi Haplotype 58 biofilm formation and genetic variation in isolates from typhoid fever patients with gallstones in an endemic setting in Kenya

Although typhoid fever has largely been eliminated in high-income countries, it remains a major global public health concern especially among low- and middle-income countries. The causative agent, Salmonella enterica serovar Typhi (S. Typhi), is a human restricted pathogen with a limited capacity to replicate outside the human host. Human carriers, 90% of whom have gallstones in their gallbladder, continue to shed the pathogen for an ill-defined period of time after treatment. The genetic mechanisms involved in establishing the carrier state are poorly understood, but S. Typhi is thought to undergo specific genetic changes within the gallbladder as an adaptive mechanism. In the current study, we aimed to identify the genetic differences in longitudinal clinical S. Typhi isolates from asymptomatic carriers with gallstones in a typhoid endemic setting in Nairobi, Kenya. Whole-genome sequences were analyzed from 22 S. Typhi isolates, 20 from stool samples, and 2 from blood samples, all genotype 4.3.1 (H58). Out of this, 19 strains were from four patients also diagnosed with gallstones, of whom three had typhoid symptoms and continued to shed S. Typhi after treatment. All isolates had point mutations in the quinolone resistance-determining region (QRDR), and only sub-lineage 4.3.1.2.EA3 encoded multidrug resistance genes. There was no variation in antimicrobial resistance patterns among strains from the same patient/household. Non-multidrug resistant (MDR) isolates formed significantly stronger biofilms in vitro than the MDR isolates, p<0.001. A point mutation within the treB gene (treB A383T) was observed in strains isolated after clinical resolution from patients living in 75% of the households. For missense mutations in Vi capsular polysaccharide genes, tviE P263S was also observed in 18% of the isolates. This study provides insights into the role of typhoid carriage, biofilm formation, AMR genes, and genetic variations in S. Typhi during asymptomatic carriage.

Bridging Classical Methodologies in Salmonella Investigation with Modern Technologies: A Comprehensive Review

Advancements in genomics and machine learning have significantly enhanced the study of Salmonella epidemiology. Whole-genome sequencing has revolutionized bacterial genomics, allowing for detailed analysis of genetic variation and aiding in outbreak investigations and source tracking. Short-read sequencing technologies, such as those provided by Illumina, have been instrumental in generating draft genomes that facilitate serotyping and the detection of antimicrobial resistance. Long-read sequencing technologies, including those from Pacific Biosciences and Oxford Nanopore Technologies, offer the potential for more complete genome assemblies and better insights into genetic diversity. In addition to these sequencing approaches, machine learning techniques like decision trees and random forests provide powerful tools for pattern recognition and predictive modeling. Importantly, the study of bacteriophages, which interact with Salmonella, offers additional layers of understanding. Phages can impact Salmonella population dynamics and evolution, and their integration into Salmonella genomics research holds promise for novel insights into pathogen control and epidemiology. This review revisits the history of Salmonella and its pathogenesis and highlights the integration of these modern methodologies in advancing our understanding of Salmonella.

Locally acquired typhoid fever outbreak linked to chronic carriage in Ottawa, Canada, 2018-2022

Background

In Canada, Salmonella enterica serovar Typhi infections are uncommon and typically travel-related. In November 2021, Ottawa Public Health identified a link between two typhoid fever cases, with no recent history of international travel, to the same grocery store ready-to-eat counter.

Objective

This report describes the outbreak response to a rare occurrence of chronic S. Typhi carriage in Ottawa, Ontario, Canada and provides recommendations for investigations of small-scale protracted outbreaks.

Methods

We administered exposure questionnaires using a single interviewer approach, tested stool samples of contacts and food handlers, inspected food premises, collected food samples and reviewed takeout receipts. Social network, spatial and whole genome sequencing analyses were used to investigate additional possible links between cases.

Results

Seven people with typhoid fever and onset from October 2018 to May 2022 were linked to an asymptomatic chronic S. Typhi carrier. Whole-genome sequencing confirmed that all eight isolates matched the outbreak cluster. All cases and carrier resided within an eight km radius in Ottawa. The chronic carrier worked as a food handler at various locations of a grocery store chain, including the implicated ready-to-eat counter. Transmission occurred via food handling, shared workspaces and social and household networks.

Conclusion

The chronic carrier was excluded from food handling until successful completion of treatment and clearance testing. We overcame the challenges of a small but prolonged outbreak by identifying an asymptomatic carrier using a multi-method approach including whole genome sequencing and social network analysis.

Multidrug-resistant Salmonella Typhi among symptomatic and asymptomatic children in informal settlements in Nairobi, Kenya

BACKGROUND

The emergence and persistence of multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) infections is a significant global health problem. The carrier state of typhoid makes it prudent to conduct routine surveillance for both acute cases and carriers especially those caused by MDR S. Typhi. We report on the prevalence of MDR S. Typhi, resistance phenotypes and antimicrobial resistance genes detected in symptomatic and asymptomatic children living in informal settlements in Nairobi, Kenya.

METHODS

215 archived presumed S. Typhi isolates from stool samples provided by children ≤ 16 years collected from 2013 to 2018 were revived in May, 2022 and confirmed using culture and antisera serotyping. The Kirby Bauer disc diffusion technique was used to test the S. Typhi against 14 antibiotics. The MDR S. Typhi (resistant to ampicillin, chloramphenicol and sulfamethoxazole trimethoprim) which in addition were also resistant to either a cephalosporin or a fluoroquinolone were analyzed for Beta lactams and quinolone resistance genes using polymerase chain reaction.

RESULTS

A total of 215 isolates were confirmed to be positively S. Typhi; of these, 105 (49%) and 110 (51%) were from symptomatic and asymptomatic children respectively. On average, S. Typhi resistance from asymptomatic and symptomatic children against 1st line drugs was observed at; 77% &70%, ampicillin; 60% & 64%, sulfamethoxazole-trimethoprim, and 45% & 54%, chloramphenicol respectively. Multi drug resistance was observed in 90 (42%) of the isolates, of these, 44 (49%) were isolated from symptomatic and 46 (51%) from asymptomatic children. Fifteen resistance phenotypes (p) were observed with, ampicillin/chloramphenicol/sulfamethoxazole-trimethoprim/nalidixic acid (amp/chl/sxt/na) as the most common among the symptomatic 43/90 (48%) and asymptomatic 55/90 (61%) children. The blaTEM-D, AMR genes were detected in 37/44 (84%) S. Typhi isolates, out of this 18 (49%) were from symptomatic while 19 (51%) were from asymptomatic children respectively.

CONCLUSION

The carriage of MDR S. Typhi among the asymptomatic children is concerning as they can act as potential transmitters of the typhoid disease to unsuspecting children. These study findings highlight the need for continued surveillance of antimicrobial resistance and mass immunization of children living in these urban informal areas.

Only time will tell: lipopolysaccharide glycoform and biofilm-formation kinetics in Salmonella species and Escherichia coli

In Gram-negative bacteria, LPS (lipopolysaccharide) has been thoroughly characterized and has been shown to play a major role in pathogenesis and bacterial defense. In Salmonella and Escherichia coli, LPS also influences biofilm development. However, the overall role of LPS glycoform in biofilm formation has not been conclusively settled, as there is a lack of consensus on the topic. Some studies show that LPS mutants produce less biofilm biomass than the wild-type strains, while others show that they produce more. This review summarizes current knowledge of LPS biosynthesis and explores the impact of defective steps on biofilm-related characteristics, such as motility, adhesion, auto-aggregation, and biomass production in Salmonella and E. coli. Overall, motility tends to decrease, while adhesion and auto-aggregation phenotypes tend to increase in most LPS-mutant strains. Interestingly, biofilm biomass of various LPS mutants revealed a clear pattern dependent on biofilm maturation time. Incubation times of less than 24 h resulted in a biofilm-defective phenotype compared to the wild-type, while incubation exceeding 24 h led to significantly higher levels of biofilm production. This explains conflicting results found in reports describing the same LPS mutations. It is therefore critical to consider the effect of biofilm maturation time to ascertain the effects of LPS glycoform on biofilm phenotype. Underlying reasons for such changes in biofilm kinetics may include changes in signalling systems affecting biofilm maturation and composition, and dynamic LPS modifications. A better understanding of the role of LPS in the evolution and modification of biofilms is crucial for developing strategies to disperse biofilms.

RpoS activates formation of Salmonella Typhi biofilms and drives persistence in the gall bladder

The development of strategies for targeting the asymptomatic carriage of Salmonella Typhi in chronic typhoid patients has suffered owing to our basic lack of understanding of the molecular mechanisms that enable the formation of S. Typhi biofilms. Traditionally, studies have relied on cholesterol-attached biofilms formed by a closely related serovar, Typhimurium, to mimic multicellular Typhi communities formed on human gallstones. In long-term infections, S. Typhi adopts the biofilm lifestyle to persist in vivo and survive in the carrier state, ultimately leading to the spread of infections via the fecal-oral route of transmission. In the present work, we studied S. Typhi biofilms directly, applied targeted as well as genome-wide genetic approaches to uncover unique biofilm components that do not conform to the CsgD-dependent pathway established in S. Typhimurium. We undertook a genome-wide Tn5 mutation screen in H58, a clinically relevant multidrug resistance strain of S. Typhi, in gallstone-mimicking conditions. We generated New Generation Sequencing libraries based on the ClickSeq technology to identify the key regulators, IraP and RpoS, and the matrix components Sth fimbriae, Vi capsule and lipopolysaccharide. We discovered that the starvation sigma factor, RpoS, was required for the transcriptional activation of matrix-encoding genes in vitro, and for S. Typhi colonization in persistent infections in vivo, using a heterologous fish larval model. An rpoS null mutant failed to colonize the gall bladder in chronic zebrafish infections. Overall, our work uncovered a novel RpoS-driven, CsgD-independent paradigm for the formation of cholesterol-attached Typhi biofilms, and emphasized the role(s) of stress signaling pathways for adaptation in chronic infections. Our identification of the biofilm regulators in S. Typhi paves the way for the development of drugs against typhoid carriage, which will ultimately control the increased incidence of gall bladder cancer in typhoid carriers.

The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0-24 months of age in resource-limited settings

Background

Campylobacter is the leading cause of bacterial gastroenteritis worldwide. It is generally associated with an acute gastrointestinal infection causing a self-limiting diarrheal episode. However, there is evidence that persistent/recurrent carriage of Campylobacter also occurs. In hyperendemic settings the epidemiology and consequences of persistent Campylobacter enteric infections is poorly studied.

Methods

Risk factors for and growth consequences of persistent Campylobacter infections detected by polymerase chain reaction (qPCR) were evaluated with data from the MAL-ED birth cohort study in children 0-24 months of age between November 2009 and February 2012. A persistent Campylobacter infection was defined as three or more consecutive Campylobacter positive monthly stools.

Findings

Across all study sites, 45.5% (781/1715) of children experienced at least one persistent Campylobacter episode. The average cumulative duration of days in which children with persistent Campylobacter were positive for Campylobacter spp. was 150 days (inter-quartile range: 28-236 days). Children who experienced a persistent Campylobacter episode had an attained 24-month length-for-age (LAZ) score that was 0.23 (95% (CI): -0.31, -0.15) less than children without a persistent Campylobacter episode. Among children who had at least one episode of Campylobacter over a 3-month or 9-month window, persistent episodes were not significantly associated with poorer 3-month weight gain (-28.7 g, 95% CI: -63.4 g, 6.0 g) but were associated with poorer 9-month linear growth (-0.134 cm 95% CI: -0.246, -0.022) compared to children with an episode that resolved within 31 days.

Interpretation

Persistent/recurrent Campylobacter infection is common among children and has a measurable negative impact on linear growth in early childhood.

Funding

Funding for this study was provided by the Bill and Melinda Gates Foundation (OPP1066146 and OPP1152146), the National Institutes of Health United States (R01AI158576 and R21AI163801 to MNK and CTP; K43TW012298 to FS; K01AI168493 to JMC; GOL was supported by K01AI145080. This research was also supported in part by USDA-ARS CRIS project 2030-42000-055-00D. The funders had no role in study design, study implementation, data analysis, or interpretation of the results.

From acute to persistent infection: revealing phylogenomic variations in Salmonella Agona

Salmonella enterica serovar Agona (S. Agona) has been increasingly recognised as a prominent cause of gastroenteritis. This serovar is a strong biofilm former that can undergo genome rearrangement and enter a viable but non-culturable state whilst remaining metabolically active. Similar strategies are employed by S. Typhi, the cause of typhoid fever, during human infection, which are believed to assist with the transition from acute infection to chronic carriage. Here we report S. Agona's ability to persist in people and examine factors that might be contributing to chronic carriage. A review of 2233 S. Agona isolates from UK infections (2004-2020) and associated carriage was undertaken, in which 1155 had short-read sequencing data available. A subset of 207 isolates was selected from different stages of acute and persistent infections within individual patients. The subset underwent long-read sequencing and genome structure (GS) analysis, as well as phenotyping assays including carbon source utilisation and biofilm formation. Associations between genotypes and phenotypes were investigated to compare acute infections to those which progress to chronic. GS analysis revealed the conserved arrangement GS1.0 in 195 isolates, and 8 additional GSs in 12 isolates. These rearranged isolates were typically associated with early, convalescent carriage (3 weeks- 3 months). We also identified an increase in SNP variation during this period of infection. We believe this increase in genome-scale and SNP variation reflects a population expansion after acute S. Agona infection, potentially reflecting an immune evasion mechanism which enables persistent infection to become established.

Genotypic Diversity among Salmonella Typhi Isolated from Children Living in Informal Settlements in Nairobi, Kenya

The persistence of multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) is a challenge especially in regions where typhoid is endemic. Surveillance of circulating genotypes of MDR S. Typhi is crucial in typhoid acute cases and carriers. This study aimed to investigate genotypic diversity of S. Typhi from symptomatic and asymptomatic children in endemic settings in Nairobi, Kenya. Symptomatic and asymptomatic individuals' ≤ 16 years were recruited at four health facilities and tested for typhoid through stool cultures. The S. Typhi isolates were subjected to antibiotic susceptibility testing to investigate multidrug resistance. The MDR S. Typhi isolates' DNA was extracted and illumina sequenced. Raw reads were de novo assembled and analyzed by pathogen-watch. From the 90 sequenced isolates, 60 (67%) were confirmed to be S. Typhi (sequence Type 1 and genotype 4.3.1). Out of the 60 S. Typhi strains; 39 (65%) had plasmids, from these 38 (97%) had IncHI1 plasmids alone. Out of the 60, 59 (98%) S. Typhi isolates had bla TEM-1D . Point mutations conferring reduced susceptibility to quinolones were detected in 42 (70%) of S. Typhi isolates, from these; 14 (33%) had gyrA S83Y, and 28 (67%) gyrB S464F genes, respectively. This study reports 4.3.1 (H58) as the most dominant S. Typhi genotype responsible for spread of MDR phenotypes carried on IncHI1 plasmids. Presence of MDR S. Typhi with resistance genes such as bla TEM-1D and reduced susceptibility to ciprofloxacin especially among asymptomatic individuals, reiterates the need for use of typhoid conjugate vaccine among vulnerable children as a control and prevention measure against typhoid.

Bacterial persisters: molecular mechanisms and therapeutic development

Persisters refer to genetically drug susceptible quiescent (non-growing or slow growing) bacteria that survive in stress environments such as antibiotic exposure, acidic and starvation conditions. These cells can regrow after stress removal and remain susceptible to the same stress. Persisters are underlying the problems of treating chronic and persistent infections and relapse infections after treatment, drug resistance development, and biofilm infections, and pose significant challenges for effective treatments. Understanding the characteristics and the exact mechanisms of persister formation, especially the key molecules that affect the formation and survival of the persisters is critical to more effective treatment of chronic and persistent infections. Currently, genes related to persister formation and survival are being discovered and confirmed, but the mechanisms by which bacteria form persisters are very complex, and there are still many unanswered questions. This article comprehensively summarizes the historical background of bacterial persisters, details their complex characteristics and their relationship with antibiotic tolerant and resistant bacteria, systematically elucidates the interplay between various bacterial biological processes and the formation of persister cells, as well as consolidates the diverse anti-persister compounds and treatments. We hope to provide theoretical background for in-depth research on mechanisms of persisters and suggest new ideas for choosing strategies for more effective treatment of persistent infections.

The origins of haplotype 58 (H58) Salmonella enterica serovar Typhi

Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.

Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi

Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S. Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control Vi polymerization or acetylation is enough to result in different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper Vi capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo Vi capsule variants have primarily been identified in Africa, whereas the hyper Vi capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.

Salmonella Typhi Haplotype 58 (H58) Biofilm Formation and Genetic Variation in Typhoid Fever Patients with Gallstones in an Endemic Setting in Kenya

The causative agent of typhoid fever, Salmonella enterica serovar Typhi, is a human restricted pathogen. Human carriers, 90% of whom have gallstones in their gallbladder, continue to shed the pathogen after treatment. The genetic mechanisms involved in establishing the carrier state are poorly understood, but S. Typhi is thought to undergo specific genetic changes within the gallbladder as an adaptive mechanism. In the current study, we aimed to identify biofilm forming ability and the genetic differences in longitudinal clinical S. Typhi isolates from asymptomatic carriers with gallstones in Nairobi, Kenya. Whole genome sequences were analyzed from 22 S. Typhi isolates, 20 from stool and 2 from blood samples, all genotype 4.3.1 (H58). Nineteen strains were from four patients also diagnosed with gallstones, of whom, three had typhoid symptoms and continued to shed S. Typhi after treatment. All isolates had point mutations in the quinolone resistance determining region (QRDR) and only sub-lineage 4.3.1.2EA3 encoded multidrug resistance genes. There was no variation in antimicrobial resistance patterns among strains from the same patient/household. Non-multidrug resistant (MDR), isolates formed significantly stronger biofilms in vitro than the MDR isolates, p<0.001. A point mutation within the treB gene (treB A383T) was observed in strains isolated after clinical resolution from patients living in 75% of the households. Missense mutations in Vi capsular polysaccharide genes, tviE P263S was also observed in 18% of the isolates. This study provides insights into the role of typhoid carriage, biofilm formation, AMR genes and genetic variations in S. Typhi from asymptomatic carriers.

Tackling salmonellosis: A comprehensive exploration of risks factors, impacts, and solutions

Salmonellosis, caused by Salmonella species, is one of the most common foodborne illnesses worldwide with an estimated 93.8 million cases and about 155,00 fatalities. In both industrialized and developing nations, Salmonellosis has been reported to be one of the most prevalent foodborne zoonoses and is linked with arrays of illness syndromes such as acute and chronic enteritis, and septicaemia. The two major and most common Salmonella species implicated in both warm-blooded and cold-blooded animals are Salmonella bongori and Salmonella enterica. To date, more than 2400 S. enterica serovars which affect both humans and animals have been identified. Salmonella is further classified into serotypes based on three primary antigenic determinants: somatic (O), flagella (H), and capsular (K). The capacity of nearly all Salmonella species to infect, multiply, and survive in human host cells with the aid of their pathogenic and virulence arsenals makes them deadly and important public health pathogens. Primarily, food-producing animals such as poultry, swine, cattle, and their products have been identified as important sources of salmonellosis. Additionally, raw fruits and vegetables are among other food types that have been linked to the spread of Salmonella spp. Based on the clinical manifestation of human salmonellosis, Salmonella strains can be categorized as either non-typhoidal Salmonella (NTS) and typhoidal Salmonella. The detection of aseptically collected Salmonella in necropsies, environmental samples, feedstuffs, rectal swabs, and food products serves as the basis for diagnosis. In developing nations, typhoid fever due to Salmonella Typhi typically results in the death of 5%-30% of those affected. The World Health Organization (WHO) calculated that there are between 16 and 17 million typhoid cases worldwide each year, with scaring 600,000 deaths as a result. The contagiousness of a Salmonella outbreak depends on the bacterial strain, serovar, growth environment, and host susceptibility. Risk factors for Salmonella infection include a variety of foods; for example, contaminated chicken, beef, and pork. Globally, there is a growing incidence and emergence of life-threatening clinical cases, especially due to multidrug-resistant (MDR) Salmonella spp, including strains exhibiting resistance to important antimicrobials such as beta-lactams, fluoroquinolones, and third-generation cephalosporins. In extreme cases, especially in situations involving very difficult-to-treat strains, death usually results. The severity of the infections resulting from Salmonella pathogens is dependent on the serovar type, host susceptibility, the type of bacterial strains, and growth environment. This review therefore aims to detail the nomenclature, etiology, history, pathogenesis, reservoir, clinical manifestations, diagnosis, epidemiology, transmission, risk factors, antimicrobial resistance, public health importance, economic impact, treatment, and control of salmonellosis.

A retrospective investigation of the population structure and geospatial distribution of Salmonella Paratyphi A in Kathmandu, Nepal

Salmonella Paratyphi A, one of the major etiologic agents of enteric fever, has increased in prevalence in recent decades in certain endemic regions in comparison to S. Typhi, the most prevalent cause of enteric fever. Despite this increase, data on the prevalence and molecular epidemiology of S. Paratyphi A remain generally scarce. Here, we analysed the whole genome sequences of 216 S. Paratyphi A isolates originating from Kathmandu, Nepal between 2005 and 2014, of which 200 were from patients with acute enteric fever and 16 from the gallbladder of people with suspected chronic carriage. By exploiting the recently developed genotyping framework for S. Paratyphi A (Paratype), we identified several genotypes circulating in Kathmandu. Notably, we observed an unusual clonal expansion of genotype 2.4.3 over a four-year period that spread geographically and systematically replaced other genotypes. This rapid genotype replacement is hypothesised to have been driven by both reduced susceptibility to fluoroquinolones and genetic changes to virulence factors, such as functional and structural genes encoding the type 3 secretion systems. Finally, we show that person-to-person is likely the most common mode of transmission and chronic carriers seem to play a limited role in maintaining disease circulation.

The frequency and associated factors of typhoid carriage in patients undergoing cholecystectomy for gallbladder disease in Pakistan: A cross-sectional study

BACKGROUND

Enteric fever is caused by Salmonella enterica serovars Typhi (S. Typhi) and Paratyphi A, B, and C. It continues to be a significant cause of morbidity and mortality worldwide. In highly endemic areas, children are disproportionately affected, and antimicrobial resistance reduces therapeutic options. It is estimated that 2-5% of enteric fever patients develop chronic asymptomatic infection. These carriers may act as reservoirs of infection; therefore, the prospective identification and treatment of carriers are critical for long-term disease control. We aimed to find the frequency of Salmonella Typhi carriers in patients undergoing cholecystectomy. We also compared the detection limit of culturing versus qPCR in detecting S. Typhi, performed a geospatial analysis of the carriers identified using this study, and evaluated the accuracy of anti-Vi and anti-YncE in identifying chronic typhoid carriage.

METHODS

We performed a cross-sectional study in two centers in Pakistan. Gallbladder specimens were subjected to quantitative PCR (qPCR) and serum samples were analyzed for IgG against YncE and Vi by ELISA. We also mapped the residential location of those with a positive qPCR result.

FINDINGS

Out of 988 participants, 3.4% had qPCR-positive gallbladder samples (23 S. Typhi and 11 S. Paratyphi). Gallstones were more likely to be qPCR positive than bile and gallbladder tissue. Anti-Vi and YncE were significantly correlated (r = 0.78 p<0.0001) and elevated among carriers as compared to qPCR negative controls, except for anti-Vi response in Paratyphi A. But the discriminatory values of these antigens in identifying carriers from qPCR negative controls were low.

CONCLUSION

The high prevalence of typhoid carriers observed in this study suggests that further studies are required to gain information that will help in controlling future typhoid outbreaks in a superior manner than they are currently being managed.

Antimicrobial resistance and genetic relatedness of Salmonella serotypes isolated from food, asymptomatic carriers, and clinical cases in Shiyan, China

Salmonella is a primary cause of foodborne diseases globally. Despite food contamination and clinical infections garnering substantial attention and research, asymptomatic Salmonella carriers, potential sources of infection, have been comparatively overlooked. In this study, we conducted a comparative analysis of serotype distribution, antimicrobial resistance phenotypes, and genetic profiles of archived Salmonella strains isolated from food (26), asymptomatic carriers (41), and clinical cases (47) in Shiyan City, China. Among the 114 Salmonella strains identified, representing 31 serotypes and 34 Sequence Types (STs), the most prevalent serovars included Typhimurium, Derby, Enteritidis, Thompson, and London, with the most predominant STs being ST11, ST40, ST26, ST34, and ST155. Antimicrobial resistance testing revealed that all strains were only sensitive to meropenem, with 74.6% showing antimicrobial resistance (AMR) and 53.5% demonstrating multidrug resistance (MDR). Strains resistant to five and six classes of antibiotics were the most common. Pearson's chi-square test showed no statistically significant difference in the occurrence of AMR (p = 0.105) or MDR (p = 0.326) among Salmonella isolates from the three sources. Our findings underscore associations and diversities among Salmonella strains isolated from food, asymptomatic carriers, and clinical patients, emphasizing the need for increased vigilance towards asymptomatic Salmonella carriers by authorities.

Prevalence of multidrug resistance Salmonella species isolated from clinical specimens at University of Gondar comprehensive specialized hospital Northwest Ethiopia: A retrospective study

BACKGROUND

Multidrug resistance Salmonellosis remains an important public health problem globally. The disease is among the leading causes of morbidity and mortality in developing countries, but there have been limited recent studies about the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from various clinical specimens.

OBJECTIVE

Aimed to assess the prevalence, antimicrobial resistance, and multidrug resistance patterns of Salmonella isolates from clinical specimens at the University of Gondar Comprehensive Specialised Hospital, northwestern Ethiopia.

METHOD

A retrospective hospital-based cross-sectional study was conducted to determine the prevalence, antimicrobial resistance, and multidrug resistance patterns of isolated from all clinical specimens at the University of Gondar Salmonella Comprehensive Specialised Hospital from June 1st, 2017 to June 3rd, 2022. A total of 26,154 data points were collected using a checklist of records of laboratory registration. Clinical specimens were collected, inoculated, and incubated for about a week with visual inspection for growth and gram staining. The isolates were grown on MacConkey agar and Xylose Lysine Deoxycholate agar. Pure colonies were identified with a conventional biochemical test, and those unidentified at the species level were further identified by the analytical profile index-20E. Then, antimicrobial susceptibility was determined by the Kirby-Bauer disc diffusion technique. The multidrug resistance Salmonella isolates was identified using the criteria set by Magiorakos. Finally, the data was cleaned and checked for completeness and then entered into SPSS version 26 for analysis. Then the results were displayed using tables and figures.

RESULTS

Of the total 26,154 Salmonella suspected clinical samples, 41 (0.16%) Salmonella species were isolated. Most of the Salmonella isolates, 19 (46.3%), were in the age group of less than 18 years, followed by the age group of 19-44 years, 11 (26.8%). In this study, S. enterica subsp. arizonae accounts for the highest 21 (51%), followed by S. paratyphi A 9 (22%). Of the Salmonella isolates, S. typhi were highly resistant to ampicillin (100%), followed by tetracycline and trimethoprim-sulfamethoxazole, each accounting for 83.3%. Furthermore, S. paratyphi A was resistant to ampicillin (100%), tetracycline (88.9%), and chloramphenicol (88.9%). The overall multi-drug resistance prevalence was 22 (53.7%; 95% CI: 39.7-61). Accordingly, S. paratyphi A was 100% multidrug-resistant, followed by S. typhi (66.6%).

CONCLUSION

A low prevalence of Salmonella species was observed in the past six years. Moreover, most S. typhi and S. paratyphi strains in the study area were found to be resistant to routinely recommended antibiotics like ciprofloxacin and ceftriaxone, compared to what was reported earlier. In addition, all isolates of S. paratyphi A and the majority of S. typhi were multidrug resistant. Therefore, health professionals should consider antimicrobial susceptibility tests and use antibiotics with caution for Salmonellosis management.

Fecal Shedding, Antimicrobial Resistance and In Vitro Biofilm formation on Simulated Gallstones by Salmonella Typhi Isolated from Typhoid Cases and Asymptomatic Carriers in Nairobi, Kenya

Typhoid fever, caused by the human restricted pathogen Salmonella Typhi, remains a major global public health concern. Even after successful treatment, approximately 3-5% of patients with typhoid fail to clear the bacteria within one year and become chronic carriers. Most typhoid carriers have gallstones in their gallbladder, and biofilm formation on gallstones is highly correlated with chronic carriage. This study's goal was to identify asymptomatic typhoid carriers in an endemic setting in Kenya, and to compare acute versus chronic isolates. A cohort of typhoid fever patients identified through blood and/or stool culture, and their household contacts, were followed up after treatment to detect longitudinal S. Typhi stool shedding. An abdominal ultrasound scan was used to identify individuals with gallstones. A total of 32 index patients and 32 household contacts were successfully followed-up. Gallstones were detected in 4 cases and 1 household contact. The duration of S. Typhi shedding was significantly longer in individuals with gallstones compared to those without, P<0.001. Eighty-three (83) S. Typhi strains were tested for susceptibility to commonly used antimicrobials and examined by in vitro biofilm formation assays. Out of 37 infected individuals, 32.4% had infections caused by multidrug resistant (MDR) S. Typhi strains and only 18.9% were infected by susceptible strains. Non-MDR strains formed significantly better biofilms in vitro than the MDR strains (P<0.001). This study provides data on S. Typhi chronic carriage that will influence public health approaches aimed at reducing typhoid transmission and the burden of infection.

Cost-effectiveness and public health impact of typhoid conjugate vaccine introduction strategies in Bangladesh

PURPOSE

Typhoid fever causes substantial morbidity and mortality in Bangladesh. The government of Bangladesh plans to introduce typhoid conjugate vaccines (TCV) in its expanded program on immunization (EPI) schedule. However, the optimal introduction strategy in addition to the costs and benefits of such a program are unclear.

METHODS

We extended an existing mathematical model of typhoid transmission to integrate cost data, clinical incidence data, and recently conducted serosurveys in urban, semi-urban, and rural areas. In our primary analysis, we evaluated the status quo (i.e., no vaccination) and eight vaccine introduction strategies including routine and 1-time campaign strategies, which differed by age groups targeted and geographic focus. Model outcomes included clinical incidence, seroincidence, deaths, costs, disability-adjusted life years (DALYs), and incremental cost-effectiveness ratios (ICERs) for each strategy. We adopted a societal perspective, 10-year model time horizon, and 3 % annual discount rate. We performed probabilistic, one-way, and scenario sensitivity analyses including adopting a healthcare perspective and alternate model time horizons.

RESULTS

We projected that all TCV strategies would be cost saving compared to the status quo. The preferred strategy was a nationwide introduction of TCV at 9-12 months of age with a single catch-up campaign for children ages 1-15, which was cost saving compared to all other strategies and the status quo. In the 10 years following implementation, we projected this strategy would avert 3.77 million cases (95 % CrI: 2.60 - 5.18), 11.31 thousand deaths (95 % CrI: 3.77 - 23.60), and save $172.35 million (95 % CrI: -14.29 - 460.59) compared to the status quo. Our findings were broadly robust to changes in parameter values and willingness-to-pay thresholds.

CONCLUSIONS

We projected that nationwide TCV introduction with a catch-up campaign would substantially reduce typhoid incidence and very likely be cost saving in Bangladesh.

β-lactam-induced OMV release promotes polymyxin tolerance in Salmonella enterica sv. Typhi

The rise of multidrug-resistant bacteria is a global concern, leading to a renewed reliance on older antibiotics like polymyxins as a last resort. Polymyxins, cationic cyclic peptides synthesized nonribosomally, feature a hydrophobic acyl tail and positively charged residues. Their antimicrobial mechanism involves initial interaction with Gram-negative bacterial outer-membrane components through polar and hydrophobic interactions. Outer membrane vesicles (OMVs), nano-sized proteoliposomes secreted from the outer membrane of Gram-negative bacteria, play a crucial role in tolerating harmful molecules, including cationic peptides such as polymyxins. Existing literature has documented environmental changes' impact on modulating OMV properties in Salmonella Typhimurium. However, less information exists regarding OMV production and characteristics in Salmonella Typhi. A previous study in our laboratory showed that S. Typhi ΔmrcB, a mutant associated with penicillin-binding protein (PBP, a β-lactam antibiotic target), exhibited hypervesiculation. Consequently, this study investigated the potential impact of β-lactam antibiotics on promoting polymyxin tolerance via OMVs in S. Typhi. Our results demonstrated that sub-lethal doses of β-lactams increased bacterial survival against polymyxin B in S. Typhi. This phenomenon stems from β-lactam antibiotics inducing hypervesiculation of OMVs with higher affinity for polymyxin B, capturing and diminishing its biologically effective concentration. These findings suggest that β-lactam antibiotic use may inadvertently contribute to decreased polymyxin effectivity against S. Typhi or other Gram-negative bacteria, complicating the effective treatment of infections caused by these pathogens. This study emphasizes the importance of evaluating the influence of β-lactam antibiotics on the interaction between OMVs and other antimicrobial agents.

Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study

BACKGROUND

Ciprofloxacin is the first-line drug for treating typhoid fever in many countries in Africa with a high disease burden, but the emergence of non-susceptibility poses a challenge to public health programmes. Through enhanced surveillance as part of vaccine evaluation, we investigated the occurrence and potential determinants of ciprofloxacin non-susceptibility in Blantyre, Malawi.

METHODS

We conducted systematic surveillance of typhoid fever cases and antibiotic prescription in two health centres in Blantyre, Malawi, between Oct 1, 2016, and Oct 31, 2019, as part of the STRATAA and TyVAC studies. In addition, blood cultures were taken from eligible patients presenting at Queen Elizabeth Central Hospital, Blantyre, as part of routine diagnosis. Inclusion criteria were measured or reported fever, or clinical suspicion of sepsis. Microbiologically, we identified Salmonella enterica serotype Typhi (S Typhi) isolates with a ciprofloxacin non-susceptible phenotype from blood cultures, and used whole-genome sequencing to identify drug-resistance mutations and phylogenetic relationships. We constructed generalised linear regression models to investigate associations between the number of ciprofloxacin prescriptions given per month to study participants and the proportion of S Typhi isolates with quinolone resistance-determining region (QRDR) mutations in the following month.

FINDINGS

From 46 989 blood cultures from Queen Elizabeth Central Hospital, 502 S Typhi isolates were obtained, 30 (6%) of which had either decreased ciprofloxacin susceptibility, or ciprofloxacin resistance. From 11 295 blood cultures from STRATAA and TyVAC studies, 241 microbiologically confirmed cases of typhoid fever were identified, and 198 isolates from 195 participants sequenced (mean age 12·8 years [SD 10·2], 53% female, 47% male). Between Oct 1, 2016, and Aug 31, 2019, of 177 typhoid fever cases confirmed by whole-genome sequencing, four (2%) were caused by S Typhi with QRDR mutations, compared with six (33%) of 18 cases between Sept 1 and Oct 31, 2019. This increase was associated with a preceding spike in ciprofloxacin prescriptions. Every additional prescription of ciprofloxacin given to study participants in the preceding month was associated with a 4·2% increase (95% CI 1·8-7·0) in the relative risk of isolating S Typhi with a QRDR mutation (p=0·0008). Phylogenetic analysis showed that S Typhi isolates with QRDR mutations from September and October, 2019, belonged to two distinct subclades encoding two different QRDR mutations, and were closely related (4-10 single-nucleotide polymorphisms) to susceptible S Typhi endemic to Blantyre.

INTERPRETATION

We postulate a causal relationship between increased ciprofloxacin prescriptions and an increase in fluoroquinolone non-susceptibility in S Typhi. Decreasing ciprofloxacin use by improving typhoid diagnostics, and reducing typhoid fever cases through the use of an efficacious vaccine, could help to limit the emergence of resistance.

FUNDING

Wellcome Trust, Bill & Melinda Gates Foundation, and National Institute for Health and Care Research (UK).

The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel

BACKGROUND

The transition to PCR-based diagnosis of bacterial gastroenteritis (BGE) can increase the sensitivity but might reduce the clinical specificity. The aims of this study were (1) to compare the effect of the change from culture to PCR-based diagnostics on the reported incidence and positivity rates of BGE due to Salmonella, Shigella and Campylobacter species and (2) to compare the demographics, medical background, clinical characteristics and pre-analytic variables between cases with PCR-positive, culture-negative samples to cases with PCR-positive, culture-positive samples.

METHODS

The study was performed at the Emek Medical Centre that serves a population of 0.5 million people in Northern Israel. The study included two parts: (1) a retrospective cohort study, comparing the incidence and positivity rates of laboratory-diagnosed BGE from January 2016 until December 22nd, 2019 when culture was the sole method to January 2020 until April 2023 when PCR was used; (2) a prospective cohort study, conducted between November 2020 until April 2023 that compared the demographics and clinical characteristics of BGE cases that were diagnosed by PCR alone versus cases that were diagnosed by both PCR and culture.

RESULTS

The incidence rate between-periods comparability ratio was only 113% since the incidence rate did not increase during 2020, the first year of the COVID-19 pandemic. The sample positivity rate increased since 2020, with between-periods comparability ratio of 159%. In the second period, the sample positivity rates of culture vs. PCR alone differed between the pathogens and were 90.2%, 63.8% and 54.2% for Salmonella, Campylobacter and Shigella species, respectively (p < 0.001). The following variables were identified as independent predictors of culture positivity: (1) Salmonella infection (O.R. = 10.6, 95% C.I. 3.6-31.1, p < 0.001); (2) Shigella infection (O.R. = 0.46, 95% C.I.0.23-0.93, p = 0.032); (3) time from sample submission to culture (O.R.=0.73, 95% C.I. 0.58-0.92, p = 0.008); (4) the presence of abdominal pain (O.R. = 1.98, 95% C.I. 1.04-3.79, p = 0.038) and the PCR mean Ct value (O.R. = 0.89, 95% C.I.0.85-0.94, p < 0.001).

CONCLUSIONS

The use of PCR had led to improved sensitivity, without noticeable decrease in the clinical specificity. This was especially important in the case of the more fastidious organisms.

Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi

Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S . Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control the length or acetylation of Vi is enough to create different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper-capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo-capsule variants have primarily been identified in Africa, whereas the hyper-capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.

Typhoid fever

Typhoid fever is an invasive bacterial disease associated with bloodstream infection that causes a high burden of disease in Africa and Asia. Typhoid primarily affects individuals ranging from infants through to young adults. The causative organism, Salmonella enterica subsp. enterica serovar Typhi is transmitted via the faecal-oral route, crossing the intestinal epithelium and disseminating to systemic and intracellular sites, causing an undifferentiated febrile illness. Blood culture remains the practical reference standard for diagnosis of typhoid fever, where culture testing is available, but novel diagnostic modalities are an important priority under investigation. Since 2017, remarkable progress has been made in defining the global burden of both typhoid fever and antimicrobial resistance; in understanding disease pathogenesis and immunological protection through the use of controlled human infection; and in advancing effective vaccination programmes through strategic multipartner collaboration and targeted clinical trials in multiple high-incidence priority settings. This Primer thus offers a timely update of progress and perspective on future priorities for the global scientific community.

Nanoparticles and nanofiltration for wastewater treatment: From polluted to fresh water

Water pollution poses significant threats to both ecosystems and human health. Mitigating this issue requires effective treatment of domestic wastewater to convert waste into bio-fertilizers and gas. Neglecting liquid waste treatment carries severe consequences for health and the environment. This review focuses on intelligent technologies for water and wastewater treatment, targeting waterborne diseases. It covers pollution prevention and purification methods, including hydrotherapy, membrane filtration, mechanical filters, reverse osmosis, ion exchange, and copper-zinc cleaning. The article also highlights domestic purification, field techniques, heavy metal removal, and emerging technologies like nanochips, graphene, nanofiltration, atmospheric water generation, and wastewater treatment plants (WWTPs)-based cleaning. Emphasizing water cleaning's significance for ecosystem protection and human health, the review discusses pollution challenges and explores the integration of wastewater treatment, coagulant processes, and nanoparticle utilization in management. It advocates collaborative efforts and innovative research for freshwater preservation and pollution mitigation. Innovative biological systems, combined with filtration, disinfection, and membranes, can elevate recovery rates by up to 90%, surpassing individual primary (<10%) or biological methods (≤50%). Advanced treatment methods can achieve up to 95% water recovery, exceeding UN goals for clean water and sanitation (Goal 6). This progress aligns with climate action objectives and safeguards vital water-rich habitats (Goal 13). The future holds promise with advanced purification techniques enhancing water quality and availability, underscoring the need for responsible water conservation and management for a sustainable future.

A novel rspA gene regulates biofilm formation and virulence of Salmonella Typhimurium

Salmonella spp. are facultative anaerobic, Gram-negative, rod-shaped bacteria and belongs to the Enterobacteriaceae family. Although much has been known about Salmonella pathogenesis, the functional characterizations of certain genes are yet to be explored. The rspA (STM14_1818) is one such gene with putative dehydratase function, and its role in pathogenesis is unknown. The background information showed that rspA gene is upregulated in Salmonella when it resides inside macrophages, which led us to investigate its role in Salmonella pathogenesis. We generated the rspA knockout strain and complement strain in S. Typhimurium 14028. Ex-vivo and in-vivo infectivity was looked at macrophage and epithelial cell lines and Caenorhabditis elegans (C. elegans). The mutant strain differentially formed the biofilm at different temperatures by altering the expression of genes involved in the synthesis of cellulose and curli. Besides, the mutant strain is hyperproliferative intracellularly and showed increased bacterial burden in C. elegans. The mutant strain became more infectious and lethal, causing faster death of the worms than the wild type, and also modulates the worm's innate immunity. Thus, we found that the rspA deletion mutant was more pathogenic. In this study, we concluded that the rspA gene differentially regulates the biofilm formation in a temperature dependent manner by modulating the genes involved in the synthesis of cellulose and curli and negatively regulates the Salmonella virulence for longer persistence inside the host.

Salmonella Bloodstream Infections

Salmonella is a major foodborne pathogen of both animals and humans. This bacterium is responsible for considerable morbidity and mortality world-wide. Different serovars of this genus cause diseases ranging from self-limiting gastroenteritis to a potentially fatal systemic disease known as enteric fever. Gastrointestinal infections with Salmonella are usually self-limiting and rarely require medical intervention. Bloodstream infections, on the other hand, are often fatal even with hospitalization. This review describes the routes and underlying mechanisms of the extraintestinal dissemination of Salmonella and the chronic infections that sometimes result. It includes information on the pathogenicity islands and individual virulence factors involved in systemic dissemination as well as a discussion of the host factors that mediate susceptibility. Also, the major outbreaks of invasive Salmonella disease in the tropics are described.

Differential regulatory control of curli (csg) gene expression in Salmonella enterica serovar Typhi requires more than a functional CsgD regulator

The human-specific Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever, a systemic disease with no known reservoir. Curli fimbriae are major components of biofilm produced by Salmonella and are encoded by the csg gene cluster (csgBAC and csgDEFG). The role of curli in S. Typhi is unknown, although detection of anti-curli antibodies suggests they are produced during host infection. In this study, we investigated curli gene expression in S. Typhi. We demonstrated that the CsgD regulatory protein binds weakly to the csgB promoter. Yet, replacing S. Typhi csgD with the csgD allele from S. Typhimurium did not modify the curli negative phenotype on Congo Red medium suggesting that differential regulation of curli gene expression in S. Typhi is not dependent on modification of the CsgD regulator. The entire csg gene cluster from S. Typhimurium was also cloned into S. Typhi, but again, despite introduction of a fully functional csg gene cluster from S. Typhimurium, curli were still not detected in S. Typhi. Thus, in addition to intrinsic genomic differences in the csg gene cluster that have resulted in production of a modified CsgD protein, S. Typhi has likely undergone other changes independent of the csg gene cluster that have led to distinctive regulation of csg genes compared to other Salmonella serovars.

Pyroptosis modulation by bacterial effector proteins

Pyroptosis is a proinflammatory form of programmed cell death featured with membrane pore formation that causes cellular swelling and allows the release of intracellular inflammatory mediators. This cell death process is elicited by the activation of the pore-forming proteins named gasdermins, and is intricately orchestrated by diverse regulatory factors in mammalian hosts to exert a prompt immune response against infections. However, growing evidence suggests that bacterial pathogens have evolved to regulate host pyroptosis for evading immune clearance and establishing progressive infection. In this review, we highlight current understandings of the functional role and regulatory network of pyroptosis in host antibacterial immunity. Thereafter, we further discuss the latest advances elucidating the mechanisms by which bacterial pathogens modulate pyroptosis through adopting their effector proteins to drive infections. A better understanding of regulatory mechanisms underlying pyroptosis at the interface of host-bacterial interactions will shed new light on the pathogenesis of infectious diseases and contribute to the development of promising therapeutic strategies against bacterial pathogens.

An immuno-epidemiological model for transient immune protection: A case study for viral respiratory infections

The dynamics of infectious disease in a population critically involves both within-host pathogen replication and between host pathogen transmission. While modeling efforts have recently explored how within-host dynamics contribute to shaping population transmission, fewer have explored how ongoing circulation of an epidemic infectious disease can impact within-host immunological dynamics. We present a simple, influenza-inspired model that explores the potential for re-exposure during a single, ongoing outbreak to shape individual immune response and epidemiological potential in non-trivial ways. We show how even a simplified system can exhibit complex ongoing dynamics and sensitive thresholds in behavior. We also find epidemiological stochasticity likely plays a critical role in reinfection or in the maintenance of individual immunological protection over time.

Vertebral discitis caused by Salmonella enterica serovar Montevideo infection

Salmonellosis is a common cause of foodborne illness worldwide, manifesting as non-invasive non-typhoidal salmonellosis, invasive non-typhoidal salmonellosis, and typhoid fever. It also rarely presents as Salmonella osteomyelitis in children with hemoglobinopathies and immunocompromised adults and even rarer osteomyelitis in an immunocompetent host without significant risk factors. Our case is of a 38-year-old immunocompetent male without significant risk factors presented with biopsy proven Salmonella vertebral discitis due to exposure to contaminated and undercooked poultry. It illustrates the importance of thorough and complete history taking even in immunocompetent patients and early recognition with prompt targeted treatment of Salmonella osteomyelitis/discitis to prevent unfavorable outcomes.

Murine Models of Salmonella Infection

The pathogen Salmonella enterica encompasses a range of bacterial serovars that cause intestinal inflammation and systemic infections in humans. Mice are a widely used infection model due to their relative simplicity and versatility. Here, we provide standardized protocols for culturing the prolific zoonotic pathogen S. enterica serovar Typhimurium for intragastric inoculation of mice to model colitis or systemic dissemination, along with techniques for direct extraintestinal infection. Furthermore, we present procedures for quantifying pathogen burden and for characterizing the immune response by analyzing tissue pathology, inflammatory markers, and immune cells from intestinal tissues. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Murine colitis model utilizing oral streptomycin pretreatment and oral S. Typhimurium administration Basic Protocol 2: Intraperitoneal injection of S. Typhimurium for modeling extraintestinal infection Support Protocol 1: Preparation of S. Typhimurium inoculum Support Protocol 2: Preparation of mixed S. Typhimurium inoculum for competitive infection Basic Protocol 3: Assessment of S. Typhimurium burden Support Protocol 3: Preservation and pathological assessment of S. Typhimurium-infected tissues Support Protocol 4: Measurement of inflammatory marker expression in intestinal tissues by qPCR Support Protocol 5: Preparation of intestinal content for inflammatory marker quantification by ELISA Support Protocol 6: Immune cell isolation from Salmonella-infected intestinal tissues.

Bacterial shedding and serologic responses following an outbreak of Salmonella Typhi in an endemic cohort

BACKGROUND

Salmonella enterica serovar Typhi (Salmonella Typhi) is the cause of typhoid fever. Salmonella Typhi may be transmitted through shedding in the stool, which can continue after recovery from acute illness. Shedding is detected by culturing stool, which is challenging to co-ordinate at scale. We hypothesised that sero-surveillance would direct us to those shedding Salmonella Typhi in stool following a typhoid outbreak.

METHODS

In 2016 a typhoid outbreak affected one in four residents of a Nursing School in Malosa, Malawi. The Department of Health asked for assistance to identify nursing students that might spread the outbreak to other health facilities. We measured IgG antibody titres against Vi capsular polysaccharide (anti-Vi IgG) and IgM / IgG antibodies against H:d flagellin (anti-H:d) three and six months after the outbreak. We selected participants in the highest and lowest deciles for anti-Vi IgG titre (measured at visit one) and obtained stool for Salmonella culture and PCR. All participants reported whether they had experienced fever persisting for three days or more during the outbreak (in keeping with the WHO definitions of 'suspected typhoid'). We tested for salmonellae in the Nursing School environment.

RESULTS

We obtained 320 paired serum samples from 407 residents. We cultured stool from 25 residents with high anti-Vi IgG titres and 24 residents with low titres. We did not recover Salmonella Typhi from stool; four stool samples yielded non-typhoidal salmonellae; one sample produced a positive PCR amplification for a Salmonella Typhi target. Median anti-Vi and anti-H:d IgG titres fell among participants who reported persistent fever. There was a smaller fall in anti-H:d IgG titres among participants who did not report persistent fever. Non-typhoidal salmonellae were identified in water sampled at source and from a kitchen tap.

CONCLUSION

High titres of anti-Vi IgG did not identify culture-confirmed shedding of Salmonella Typhi. There was a clear serologic signal of recent typhoid exposure in the cohort, represented by waning IgG antibody titres over time. The presence of non-typhoidal salmonellae in drinking water indicates sub-optimal sanitation. Developing methods to detect and treat shedding remains an important priority to complement typhoid conjugate vaccination in efforts to achieve typhoid elimination.

Milan's forgotten epidemic of summer 1629, a few months before the last great plague: An investigation into the possible cause

An epidemic not attributable to plague caused thousands of deaths in Milan in the summer of 1629, a time of war and famine that immediately preceded the even more fatal Great Plague of 1630 that killed an estimated ten of thousands of people. The 5,993 deaths of 1629 recorded in the Liber Mortuorum of Milan (a city with an estimated population of 130,000 inhabitants at the time) were 45.7% more than the average number recorded between 1601 and 1628. Registered deaths peaked in July, and 3,363 of the deaths (56,1%) were attributed to a febrile illness which, in most cases (2,964, 88%), was not associated with a rash or organ involvement. These deaths involved 1,627 males and 1,334 females and occurred at a median age of 40 years (range 0-95). In this paper, we discuss the possible cause of the epidemic, which may have been an outbreak of typhoid fever.

Salmonella antimicrobials inherited and the non-inherited resistance: mechanisms and alternative therapeutic strategies

Salmonella spp. is one of the most important foodborne pathogens. Typhoid fever and enteritis caused by Salmonella enterica are associated with 16-33 million infections and 500,000 to 600,000 deaths annually worldwide. The eradication of Salmonella is becoming increasingly difficult because of its remarkable capacity to counter antimicrobial agents. In addition to the intrinsic and acquired resistance of Salmonella, increasing studies indicated that its non-inherited resistance, which commonly mentioned as biofilms and persister cells, plays a critical role in refractory infections and resistance evolution. These remind the urgent demand for new therapeutic strategies against Salmonella. This review starts with escape mechanisms of Salmonella against antimicrobial agents, with particular emphasis on the roles of the non-inherited resistance in antibiotic failure and resistance evolution. Then, drug design or therapeutic strategies that show impressive effects in overcoming Salmonella resistance and tolerance are summarized completely, such as overcoming the barrier of outer membrane by targeting MlaABC system, reducing persister cells by limiting hydrogen sulfide, and applying probiotics or predatory bacteria. Meanwhile, according to the clinical practice, the advantages and disadvantages of above strategies are discussed. Finally, we further analyze how to deal with this tricky problems, thus can promote above novel strategies to be applied in the clinic as soon as possible. We believed that this review will be helpful in understanding the relationships between tolerance phenotype and resistance of Salmonella as well as the efficient control of antibiotic resistance.

Invasive Non-Typhoidal Salmonella Lineage Biofilm Formation and Gallbladder Colonization Vary But Do Not Correlate Directly with Known Biofilm-Related Mutations

Non-typhoidal Salmonella (NTS) serovars have a broad host range and cause gastroenteritis in humans. However, invasive NTS (iNTS) bloodstream infections have increased in the last decade, causing 60,000 deaths annually. Human-specific typhoidal Salmonella colonizes and forms biofilms on gallstones, resulting in chronic, asymptomatic infection. iNTS lineages are undergoing genomic reduction and may have adapted to person-to-person transmission via mutations in virulence, bile resistance, and biofilm formation. As such, we sought to determine the capacity of iNTS lineages for biofilm formation and the development of chronic infections in the gallbladder in our mouse model. Of the lineages tested (L1, L2, L3 and UK), only L2 and UK were defective for the rough, dry and red (RDAR) morphotype, correlating with the known bcsG (cellulose) mutation but not with csgD (curli) gene mutations. Biofilm-forming ability was assessed in vitro, which revealed a biofilm formation hierarchy of L3 > ST19 > UK > L1 = L2, which did not correlate directly with either the bcsG or the csgD mutation. By confocal microscopy, biofilms of L2 and UK had significantly less curli and cellulose, while L1 biofilms had significantly lower cellulose. All iNTS strains were able to colonize the mouse gallbladder, liver, and spleen in a similar manner, while L3 had a significantly higher bacterial load in the gallbladder and increased lethality. While there was iNTS lineage variability in biofilm formation, gallbladder colonization, and virulence in a chronic mouse model, all tested lineages were capable of colonization despite possessing biofilm-related mutations. Thus, iNTS strains may be unrecognized chronic pathogens in endemic settings.

Typhoid Control in an Era of Antimicrobial Resistance: Challenges and Opportunities

Historically, typhoid control has been achieved with water and sanitation interventions. Today, in an era of rising antimicrobial resistance (AMR), two World Health Organization-prequalified vaccines are available to accelerate control in the shorter term. Meanwhile, water and sanitation interventions could be implemented in the longer term to sustainably prevent typhoid in low- and middle-income countries. This article first approaches typhoid control from a historical perspective, subsequently presents how vaccination could complement water and sanitation activities, and finally discusses the challenges and opportunities for impactful control of typhoid infection. It also addresses data blind spots and knowledge gaps to focus on for typhoid control and to ultimately progress towards elimination. This article presents a synthesis of discussions held in December 2021 during a roundtable session at the "12th International Conference on Typhoid and Other Invasive Salmonelloses".

The Prevalence of Undiagnosed Salmonella enterica Serovar Typhi in Healthy School-Aged Children in Osun State, Nigeria

Typhoid fever remains a significant public health concern due to cases of mis-/overdiagnosis. Asymptomatic carriers play a role in the transmission and persistence of typhoid fever, especially among children, where limited data exist in Nigeria and other endemic countries. We aim to elucidate the burden of typhoid fever among healthy school-aged children using the best surveillance tool(s). In a semi-urban/urban state (Osun), 120 healthy school-aged children under 15 years were enrolled. Whole blood and fecal samples were obtained from consenting children. ELISA targeting the antigen lipopolysaccharide (LPS) and anti-LPS antibodies of Salmonella Typhi, culture, polymerase chain reaction (PCR), and next-generation sequencing (NGS) were used to analyze the samples. At least one of the immunological markers was detected in 65.8% of children, with 40.8%, 37.5%, and 39% of children testing positive for IgM, IgG, and antigen, respectively. Culture, PCR, and NGS assays did not detect the presence of Salmonella Typhi in the isolates. This study demonstrates a high seroprevalence of Salmonella Typhi in these healthy children but no carriage, indicating the inability to sustain transmission. We also demonstrate that using a single technique is insufficient for typhoid fever surveillance in healthy children living in endemic areas.

Profiling of Humoral Immune Response in Typhoid Patients against Differentially Extracted Whole Cell Bacterial Protein Derived from S. typhi and S. spp

Typhoid fever is a multiorgan infectious disease caused by Salmonella typhi. It is transmitted through fecal oral route and can be fatal without proper treatment. Therefore, early diagnosis of typhoid fever is crucial. In the previous study, we have developed TYPHOIDYNE EIA, which showed excellent synergy between the genus conserved and species-specific antigens in the serodiagnosis of typhoid fever. TYPHOIDYNE EIA can effectively detect and differentiate typhoid patients, typhoid vaccinated subjects, healthy subjects, and subjects with other febrile illnesses. Following the successful development of TYPHOIDYNE EIA, in this report, we further characterize the antigenic components of differentially extracted S. typhi and S. spp recognized by IgM, IgG, and IgA antibody isotypes in typhoid patients and possible typhoid carrier by the western blot (WB) assay. The WB characterization revealed a dynamic pattern of recognition, with significant variations in the number of antigenic bands observed between the differentially extracted arrays of antigens. The reactivity of patient's sera was divided into 3 regions, with region 1 (≥55 kDa) showing the strongest reactivity followed by region 2 (54 kDa-34 kDa) and region 3 (<34 kDa). Overall, the good synergy expressed in these bands suggests the potential role of these proteins in differentiating typhoid patients with possible typhoid carrier. The antigenic bands highlighted in this study are also identified as prospective biomarkers for diagnostic use and vaccine development.

Recent advances in the diagnosis and management of typhoid fever in Africa: A review

Typhoid fever, a classical disease of enteric origin caused by Salmonella species of bacteria, is among the most important diseases threatening public health in Africa. The African continent is a marker for both low resources within the healthcare system and poor disease control policy formulations in managing endemic infectious diseases. Since the colonial era, the Widal serological test has been used to confirm typhoid fever in Africa, however recent studies recommend blood culture, and when blood culture cannot be obtained, clinical findings, laboratory Widal test confirmation, and ruling out other febrile illnesses as confirmatory pathway to diagnose typhoid fever in Africa. Managing typhoid fever relies on antimicrobials. In 1980s chloramphenicol was the medication of choice. Years later, amoxicillin and co-trimoxazole were adopted. However, the instantaneous rise of resistant strains of Salmonella enterica confers an important challenge to treat the burdensome enteric fever. The current treatment algorithm of typhoid fever in Africa relies significantly on the use of fluoroquinolones, macrolides, and cephalosporins. Developed nations have successfully addressed and controlled typhoid fever via improvement in accessing safe water and food, better sanitary and hygienic behaviours, and vaccines development. Nevertheless, there is significant evidence to infer improvement in the diagnosis management of typhoid fever over the last few decades, and efforts are underway to control the disease spread in Africa. This review aims to provide an overview of the latest developments in typhoid fever diagnosis and management in Africa and provide key recommendations for a coordinated approach to mitigate typhoid in the continent.

Chronic Salmonella Typhi carriage at sites other than the gallbladder

Typhoid fever caused by infection with Salmonella enterica subspecies enterica serotype Typhi (S. Typhi), an important public health problem in many low- and middle-income countries, is transmitted by ingestion of water or food contaminated by feces or urine from individuals with acute or chronic S. Typhi infection. Most chronic S. Typhi carriers (shedding for ≥12 months) harbor infection in their gallbladder wherein preexisting pathologies, particularly cholelithiasis, provide an environment that fosters persistence. Much less appreciated is the existence of non-gallbladder hepatobiliary chronic S. Typhi carriers and urinary carriers. The former includes parasitic liver flukes as a chronic carriage risk factor. Chronic urinary carriers typically have pathology of their urinary tract, with or without renal or bladder stones. Even as the prevalence of multidrug-resistant and extensively drug-resistant S. Typhi strains is rising, global implementation of highly effective typhoid vaccines is increasing. There is also renewed interest in identifying, monitoring, and (where possible) treating chronic carriers who comprise the long-term reservoir of S. Typhi.