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

Genomic characterization and antimicrobial resistance profile of Salmonella spp. clinical isolates: A single-centre hospital-based exploratory study from Uttarakhand, India

OBJECTIVES

This single-centre, hospital-based study from Uttarakhand, India, aimed to describe the genomic characterization data of Salmonella spp. isolated from clinical samples.

METHODS

This study was performed between January 2019 and January 2023 and included eighteen clinical Gram-negative bacterial isolates which were identified as Salmonella species as per standard microbiological guidelines. The test isolates were sent to the Central Research Laboratory (CRL), Bengaluru, India, for characterization and whole-genome sequencing (WGS). At CRL, the test isolates were revived and subjected to preliminary identification and antibiotic susceptibility testing (AST) using the VITEK 2 Compact system, the results of which were interpreted according to the Clinical Laboratory Standards Institute (CLSI) guidelines 2023.

RESULTS

Of the 18 Salmonella spp. test isolates, twelve belonged to serovar Typhi, five to serovar Paratyphi A, and one isolate to serovar Typhimurium. The serotyping results were further confirmed by WGS in which no disparity was observed. Genotyping results were determined for twelve S. Typhi isolates, of which 41.7 % (5/12) belonged to genotype 4.3.1.2 (H58 LII) and one isolate belonged to genotype 4.3.1.1 (H58 LI), respectively. All isolates were susceptible to ampicillin, chloramphenicol, co-trimoxazole, ceftriaxone and azithromycin. Ciprofloxacin resistance and intermediate susceptibility were observed in 14 and four isolates, respectively. Genes conferring resistance to fluoroquinolones were detected in all test isolates and were mainly associated with mutations on the gyrA and parC genes. Triple mutants bearing gyrA-S83F, gyrA-D87N, and parC-S80I genes were observed in three isolates belonging to genotype 4.3.1.2.1. Genes encoding resistance to other antimicrobial drug classes were not observed in the dataset. The major Pathogenicity islands, SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9, were detected in all test isolates.

DISCUSSION

This study indicates that Salmonella strains are susceptible to most antibiotics for enteric fever, except fluoroquinolones. However, gathering data from diverse Indian regions is essential to understanding regional variations in Salmonella antimicrobial resistance emergence.

Genomic insights into the role of Salmonella Typhi carriers in antimicrobial resistance and typhoid transmission in Urban Kenya

Typhoid fever cases and carriers can transmit Salmonella enterica serovar Typhi (S. Typhi) through fecal shedding. It remains unclear whether the S. Typhi shedding by carriers exhibits similar phenotypic and genotypic characteristics to those from acute cases. We investigated multidrug resistance in S. Typhi from individuals residing in urban informal settlements in Nairobi, Kenya. We recruited participants ≤ 65 years from six health facilities and tested for typhoid infection through blood and stool cultures. The S. Typhi culture-positive cases were treated and followed up after treatment, where index cases and their household contacts provided stool samples for culture. The susceptibility of all S. Typhi isolates was tested against 14 antibiotics using Kirby Bauer disc diffusion. Total deoxyribonucleic acid (DNA) was extracted from selected multi-drug resistant (MDR) S. Typhi for whole genome sequencing using Illumina Nextseq2000, and their genomes were analyzed on Pathogen-watch. Of the 115 S. Typhi isolates, 81/115 (70%) were from cases, while 34/115 (30%) were from carriers. S. Typhi resistance against ampicillin was observed in 32/81 (40%) and 11/34 (32%) of isolates from cases and carriers, respectively, while resistance against co-trimoxazole was observed in 34/81 (42%) and 10/34 (29%) of isolates from cases and carriers, respectively. In addition, resistance against chloramphenicol was observed in 30/81(37%) and 10/34 (29%) in isolates from cases and carriers, respectively. Multidrug resistance was observed in 33% (38/115) of the S. Typhi isolates, with majority, 28/38 (74%) recovered from cases. A subset (22/38, 15 from cases and 7 from carriers) of the MDR isolates was randomly selected for sequencing. All the 22 S. Typhi belonged to genotype 4.3.1, with the majority 15/22 (68%) from genotype 4.3.1.2EA3. All these isolates carried the blaTEM-1D, catA1, dfrA7; sul1, and sul2 AMR genes. GyrA point mutations conferring reduced susceptibility to quinolones and fluoroquinolones were detected in 19/22 (86%) isolates, with the majority 15/22 (79%) occurring on codon 83. This study's findings highlight the plausibility of typhoid transmission within communities in disease endemic settings. Consequently, the study demonstrates the need for surveillance of antimicrobial resistance, antimicrobial stewardship, deployment of typhoid vaccine and improvement of water, hygiene and sanitation infrastructure in disease endemic settings.

A global atlas and drivers of antimicrobial resistance in Salmonella during 1900-2023

Although previous studies using phenotypic or/and genomic approaches monitoring have revealed the spatiotemporal distribution of antimicrobial resistance (AMR) in Salmonella in local areas, their geographical patterns and driving factors remain largely unknown at a global scale. Here, we performed an analysis of publicly available data of 208,233 Salmonella genomes in 148 countries/regions between 1900 and 2023 and explored driving indicators of AMR. Overall, we found that the geographic distribution of AMR varied depending on the location, source, and serovar. The proportion of AMR levels increased across six continents, especially in serovars Agona, Dublin, I 1,4,[5],12:i:-, Muenchen, Senftenberg, Mbandaka mainly from chickens, food, wild animals, and the environment, while decreased in Schwarzengrund and Saintpaul mainly from cattle, pigs, and turkeys. We also found that S. Typhimurium exhibiting macro, red, dry, and rough was detected as early as 1992 in the USA, earlier than in China. Moreover, we identified that antibiotic consumption, agriculture, climate, urban, health, and socioeconomic factors contribute to the development of AMR in Salmonella. We present a globally high-resolution genetic atlas of Salmonella and also identify some factors driving the rise of AMR, which can provide valuable information for understanding the transmission dynamics and evolutionary trajectories of Salmonella.

Genomics for antimicrobial resistance-progress and future directions

Antimicrobial resistance (AMR) is a critical global public health threat, with bacterial pathogens of primary concern. Pathogen genomics has revolutionized the study of bacterial pathogens and provided deep insights into the mechanisms and dissemination of AMR, with the precision of whole-genome sequencing informing better control strategies. However, generating actionable data from genomic surveillance and diagnostic efforts requires integration at the public health and clinical interface that goes beyond academic efforts to identify resistance mechanisms, undertake post hoc analyses of outbreaks, and share data after research publications. In addition to timely genomics data, consideration also needs to be given to epidemiological sampling frames, analysis, and reporting mechanisms that meet International Organization for Standardization (ISO) standards and generation of reports that are interpretable and actionable for public health and clinical "end-users." Importantly, ensuring all countries have equitable access to data and technology is critical, through timely data sharing following the FAIR principles (findable, accessible, interoperable, and re-usable). In this review, we describe (i) advances in genomic approaches for AMR research and surveillance to understand emergence, evolution, and transmission of AMR and the key requirements to enable this work and (ii) discuss emerging and future applications of genomics at the clinical and public health interface, including barriers to implementation. Harnessing advances in genomics-enhanced AMR research and embedding robust and reproducible workflows within clinical and public health practice promises to maximize the impact of pathogen genomics for AMR globally in the coming decade.

Assessing Salmonella Typhi Pathogenicity and Prevention: The Crucial Role of Vaccination in Combating Typhoid Fever

Enteric fever is caused by Salmonella enterica serovar Typhi (S. Typhi) and Salmonella enterica serovar Paratyphi (S. Paratyphi) A, B, and C. Globally, an estimated 11 to 21 million cases of typhoid and paratyphoid fever occur annually, with approximately 130,000-160,000 deaths, most of which are reported in South/Southeast Asia and sub-Saharan Africa. The antibiotic susceptibility of S. Typhi strains varies between countries within broad limits, from 3% to 97% for ampicillin, 9% to 95% for ciprofloxacin, 4% to 94% for chloramphenicol (India vs. Pakistan), and 0% to 99% for ceftriaxone (India vs. Iraq). With S. Typhi increasingly exhibiting resistance to antibiotics, vaccination becomes an essential preventive measure. Currently, three vaccines are licensed for typhoid fever: the typhoid conjugate vaccine (TCV), live-attenuated oral vaccine Ty21a (Ty21a), and Vi capsular polysaccharide vaccine (Vi-CPS). While no specific vaccine exists for paratyphoid fever, the genetic and antigenic similarities between S. Paratyphi and S. Typhi offer potential for the development of such a vaccine. Early studies show promising results, demonstrating both safety and immunogenicity in preclinical trials. Whole genome sequencing (WGS) provides a powerful tool for assigning genotypes, identifying plasmids, comparing genetic elements, and investigating molecular factors that contribute to antibiotic resistance and virulence.

Recent emergence of cephalosporin-resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene

The emergence and spread of Salmonella Typhi (S. Typhi) resistant to third-generation cephalosporins is a serious global health concern. In this study, we genomically characterized 142 cephalosporin-resistant S. Typhi strains isolated from India. Comparative genome analysis revealed the emergence of a new clone of ceftriaxone-resistant S. Typhi harboring three plasmids of the incompatibility groups IncFIB(K), IncX1, and IncFIB(pHCM2). Among these, the IncFIB(K) plasmid confers resistance to third-generation cephalosporins through the blaCTX-M-15 gene, along with other resistance determinants such as aph(3"), aph(6'), sul2, dfrA14, qnrS, and tet(A). Phylogenetic analysis showed that the isolates from Gujarat (n = 140/142) belong to a distinct subclade (genotype 4.3.1.2.2) within genotype 4.3.1.2 (H58 lineage II). Single nucleotide polymorphism-based phylogenetic analysis of the core genes in IncFIB(K) suggested a close relatedness of the plasmid backbone to that of IncFIB(K) from other Enterobacteriales, indicating that H58 lineage II possesses the capability to acquire MDR plasmids from these organisms. This could indicate the potential onset of a new wave of ceftriaxone-resistant S. Typhi in India. The implementation of control measures-such as vaccination and improved water, sanitation, and hygiene systems-is crucial in areas where MDR or extensively drug-resistant S. Typhi strains are prevalent to curb the spread and impact of these resistant strains.

IMPORTANCE

Typhoid fever remains a global health concern, especially in areas lacking sanitation and clean water. The rise of drug-resistant strains complicates treatment, increasing illness, death, and healthcare expenses. Travel facilitates the spread of these strains worldwide. Multidrug-resistant and extensively drug-resistant (XDR) strains, including those resistant to first-line antibiotics and fluoroquinolones, pose significant challenges. Azithromycin and third-generation cephalosporins are now preferred treatments. Recently, XDR typhoid emerged in Pakistan, resistant even to third-generation cephalosporins. India also faces challenges, with sporadic cases initially declining but now re-emerging. New strains in India show resistance to third-generation cephalosporins due to plasmid acquisition from other bacteria, particularly blaCTX-M-carrying IncFIB(K). Due to the ongoing nature of this outbreak, the data from this study deserve further consideration in order to control its spread in India.

Changes in enteric fever trends during the COVID-19 pandemic from the Surveillance for Enteric Fever in Asia Project: a cross-sectional study

Background

The Surveillance for Enteric Fever in Asia Project (SEAP) conducted blood culture surveillance for Salmonella enterica serotype Typhi (S. Typhi) and Paratyphi (S. Paratyphi) to provide an evidence base for prevention and control measures in Bangladesh, Nepal, and Pakistan.

Methods

From October 2020 to September 2022, we conducted prospective clinical surveillance and retrospective laboratory surveillance at health facilities in Dhaka, Bangladesh; Kathmandu and Kavrepalanchok, Nepal; and Karachi, Pakistan. Patients were eligible if they were outpatients with three or more days of fever in the last week. In Nepal and Pakistan, inpatients were eligible if they had suspected or confirmed enteric fever; in Bangladesh, only inpatients with confirmed enteric fever were enrolled. Patients with blood culture-confirmed enteric fever identified by hospital laboratories and laboratory network sites were also enrolled. Patients completed interviews and medical records were reviewed and abstracted. All enrolled patients had blood cultures performed. Antibiograms were performed to characterize drug sensitivity. We summarized the data descriptively.

Findings

A total of 17,593 patients were enrolled from 19 facilities. Of these, 8410 patients had culture-confirmed enteric fever. Case counts in all countries decreased in the early stages of the COVID-19 pandemic, but increased over time in Bangladesh and Pakistan. Case counts remained low throughout the study period in Nepal. In all countries, typhoid was more common than paratyphoid; the proportion of paratyphoid cases ranged from 8.4% in Pakistan to 16% in Nepal. Extensively drug-resistant typhoid was common in Pakistan (69%), but was not detected in Bangladesh or Nepal.

Interpretation

Cases of enteric fever decreased during the COVID-19 pandemic, though it is not clear how much of this decrease relates to true changes in transmission versus health-seeking behavior.

Funding

This project was funded by the Gates Foundation through INV-008335.

Epidemiological characteristics and trends of notified enteric fevers in Germany, 2001 to 2023

BackgroundEnteric fevers (EF) are caused by infections with Salmonella Typhi (STY) or Salmonella Paratyphi (SP) A-C (except the SPB enteric pathovar) and exhibit increasing antimicrobial resistance (AMR). Notification is mandatory in Germany.AimTo describe characteristics and trends of notified EF cases in Germany.MethodsWe analysed German EF notifications 2001-2023 fulfilling the case definition. We calculated numbers of imported EF cases per 100,000 air travellers by country of exposure 2012-2023.ResultsIn 2001-2023, 2,670 confirmed EF cases were notified: 56% (1,498/2,670) STY, 44% (1,172/2,670) SP, with seasonal peaks in April-May and August-September. Aside from years with COVID-19-related travel restrictions, STY notifications were stable, while SP notifications decreased. Median age of EF cases was 26 years (range: 0-93) and 55% (1,458/2,663) were male. Of cases with information, 93% (2,491/2,670) had fever, 71% (1,906/2,670) diarrhoea, 78% (2,033/2,607) were hospitalised (STY: 85% (1,234/1,459) vs SP: 70% (799/1,148), p < 0.001) and four died (two STY, one SPA, one SPB). Of STY cases, 7% (88/1,221) reported vaccination. Overall, 86% (2,251/2,613) of cases acquired EF abroad, most commonly in India, Pakistan and Türkiye. Ciprofloxacin resistance was reported for 50/59 STY and 16/18 SPA cases and cefotaxime resistance for 10/57 STY cases (exposure: Pakistan (9/10), India (1/10)) with information since 2017. We also report outbreaks and incidence among travellers.ConclusionsMost cases were imported and had high hospitalisation rates and AMR. Typhoid vaccination was underutilised, highlighting that additional ways to reach at-risk travellers with information and vaccination offers are needed.

Plasma concentration of azithromycin and correlation with clinical outcomes in patients with enteric fever

Background

Azithromycin is the only oral option available for XDR enteric fever. Studies correlating azithromycin levels with treatment success are rare.

Methods

Serum azithromycin levels after administration of a once-daily 20 mg/kg dose for 7 days were measured in a single-centre prospective cohort of 25 consecutive adults with blood culture-positive enteric fever. Five blood samples were collected on Day 2 after starting azithromycin, i.e. 30 min before dosing (trough), and 2, 5, 12 and 24 h after dosing. The MIC was determined for all isolates and azithromycin plasma concentration was determined using LC-MS. Clinical and microbiological outcomes were documented.

Results

Salmonella enterica serovar Typhi accounted for 92% (n = 23) and Salmonella enterica serovar Paratyphi 8% (n = 2). Ten (40%) patients received IV azithromycin, and the rest received oral therapy. The median (IQR, range) MIC for azithromycin was 4 (4-6, 3-12) mg/L. Mean azithromycin plasma concentration ranges were: trough, 0.24 ± 0.19 mg/L; 2 h, 1.24 ± 0.98 mg/L; 5 h, 0.64 ± 0.51 mg/L; 12 h, 0.31 ± 0.16 mg/L; and 24 h, 0.37 ± 0.30 mg/L. The C max/MIC and AUC/MIC for azithromycin were 0.29 ± 0.22 and 2.64 ± 1.64, respectively. The median (IQR, range) fever clearance time was 3 (2-3, 2-5) days and the length of hospital stay was 7 (5.5-12, 4-16) days. There was no clinical or microbiological failure, relapse or mortality.

Conclusions

Azithromycin was effective in treatment of enteric fever, despite low extracellular azithromycin plasma levels.

Typhoid fever in Jakarta, Indonesia 2017-2023: spatial clustering and seasonality of hospitalization data to inform better intervention

Typhoid fever is one of the common enteric fevers in developing countries, especially in emerging metropolitan areas in Indonesia. Yet, studies on spatial and temporal distribution of tyhoid fever are lacking. This study was conducted to analyze retrospective hospital-based data at the village level over the period 2017-2023 to understand the spatial and temporal variation of typhoid fever in Jakarta. Spatial analyses were performed by Moran's I and Local Indicators of Spatial Association (LISA) to examine spatial clustering of typhoid incidence and to identify high-risk villages for typhoid fever, respectively. Seasonal decomposition analysis was performed to investigate the seasonality of this infection. A total of 57,468 typhoid cases, resulting in a cumulative incidence of 533.99 per 100,000 people, were reported during the study period. The incidence was significantly clustered (I=0.548; p=0.001) at the village level across Jakarta. Statistically significant high-risk clusters were detected in the South and East of Jakarta that were heterogeneous over time. We identified seven persistent high-risk clusters in the eastern part of the city and two in the southern part. Moreover, the typhoid incidence showed a strong seasonality trend, significantly associated with monthly total rainfall (p=0.018). The study revealed a significant spatial variation with strong seasonality in typhoid incidence across the city suggesting a variation in transmission intensity and needs for effective public health interventions, especially in the high-risk areas. Improvement in water and sanitation facilities, hygiene awareness and surveillance are essential to help reduce typhoid transmission in Jakarta.

Exploring SNP filtering strategies: the influence of strict vs soft core

Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample. However, as sample size and genome diversity increase, a strict core can shrink markedly, discarding potentially informative data. Here, we propose and provide evidence to support the use of a 'soft core' that tolerates some missing data, preserving more information for phylogenetic analysis. Using large datasets of Neisseria gonorrhoeae and Salmonella enterica serovar Typhi, we assess different core thresholds. Our results show that strict cores can drastically reduce informative sites compared to soft cores. In a 10 000-genome alignment of Salmonella enterica serovar Typhi, a 95% soft core yielded ten times more informative sites than a 100% strict core. Similar patterns were observed in N. gonorrhoeae. We further evaluated the accuracy of phylogenies built from strict- and soft-core alignments using datasets with strong temporal signals. Soft-core alignments generally outperformed strict cores in producing trees displaying clock-like behaviour; for instance, the N. gonorrhoeae 95% soft-core phylogeny had a root-to-tip regression R 2 of 0.50 compared to 0.21 for the strict-core phylogeny. This study suggests that soft-core strategies are preferable for large, diverse microbial datasets. To facilitate this, we developed Core-SNP-filter (https://github.com/rrwick/Core-SNP-filter), an open-source software tool for generating soft-core alignments from whole-genome alignments based on user-defined thresholds.

Clostridioides difficile recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences

Genomic data on Clostridioides difficile from the African continent are currently lacking, resulting in the region being under-represented in global analyses of C. difficile infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare C. difficile isolates from diarrhoeic human patients (n=142), livestock (n=38), poultry manure (n=5) and dogs (n=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global C. difficile population. In addition, selected isolates were tested for antimicrobial susceptibility (n=33) and characterized by PCR ribotyping (n=53). Hierarchical clustering of core-genome multilocus sequence typing (cgMLST) allelic profiles revealed large diversity at the level HC150 (i.e. clusters of related genomes with maximally 150 pairwise allelic differences), which was previously shown to correlate with PCR ribotypes (RT). While several globally disseminated strains were detected, including HC150_1 (associated with RT078), HC150_3 (RT001) and HC150_3622 (RT014), 42 HC150 clusters (79%) represented unique genotypes that were new to the public genomic record, and 16 (30%) of these were novel PCR ribotypes. Considerable proportions of the C. difficile isolates displayed resistance to fluoroquinolones, macrolides and linezolid, potentially reflecting human and animal antibiotic consumption patterns in the region. Notably, our comparative phylogenomic analyses revealed human-human, human-livestock and farm-farm sharing of near-identical C. difficile genomes (≤2 core-genome allelic differences), suggesting the continued spread of multiple strains across human and animal (pig, poultry, cattle and dog) host populations. Our findings highlight the interconnectivity between livestock production and the epidemiology of human CDI and inform the need for increased CDI awareness among clinicians in this region. A large proportion of C. difficile strains appeared to be unique to the region, reflecting both the significant geographic patterning present in the C. difficile population and a general need for additional pathogen sequencing data from Africa.

Carbapenems: The Final Line of Defense in Typhoid Fever Treatment at Hayatabad Medical Complex, Peshawar

INTRODUCTION

Typhoid fever, caused by Salmonella enterica serovar Typhi, remains a significant public health issue, particularly in low-income countries with inadequate sanitation. The rise of extensively drug-resistant (XDR) strains of Salmonella Typhi has led to a growing reliance on carbapenems as the final line of defense. This study aims to evaluate the effectiveness of carbapenems in treating multidrug-resistant (MDR) and XDR typhoid at Hayatabad Medical Complex, Peshawar.

OBJECTIVE

This study aims to assess the efficacy of carbapenems in treating MDR and XDR typhoid fever and identify alternative therapeutic strategies.

METHODOLOGY

A retrospective cohort study was conducted at Hayatabad Medical Complex from January to June 2024. A total of 501 patients with confirmed typhoid fever were included. Data on demographics, drug sensitivity, and resistance patterns were extracted from the hospital's Health Management Information System (HMIS) and analyzed using IBM SPSS Statistics for Windows, Version 25 (Released 2017; IBM Corp., Armonk, New York). Statistical significance was set at p < 0.05.

RESULTS

Among 501 patients, 299 (59.7%) were male, with a mean age of 23.84 ± 0.24 years. MDR was observed in 106 (36%) patients, while XDR and carbapenem resistance were present in only three (0.6%) cases. Imipenem demonstrated a high sensitivity of 466 (93%), while meropenem had 380 (75.8%) sensitivity with no resistance. Non-carbapenem antibiotics, such as polymyxin 468 (93.4%) sensitivity and colistin 446 (89%) sensitivity, exhibited higher efficacy than carbapenems. Alarmingly, cephalosporins such as cefepime exhibited 454 (91%) resistance. Resistance to carbapenems was rare, affecting only three (0.6%) patients.

CONCLUSION

Carbapenems remain highly effective against MDR and XDR typhoid, but non-carbapenem options such as polymyxin and colistin offer viable alternatives in reducing carbapenem dependence. Enhanced antimicrobial stewardship is critical to preserving these last-resort treatments.

An exploration of unusual antimicrobial resistance phenotypes in Salmonella Typhi from Blantyre, Malawi reveals the ongoing role of IncHI1 plasmids

Typhoid fever is a significant public health problem endemic in Southeast Asia and Sub-Saharan Africa. Antimicrobial treatment of typhoid is however threatened by the increasing prevalence of antimicrobial resistant (AMR) S. Typhi, especially in the globally successful lineage (4.3.1) which has rapidly spread in East and Southern Africa. AMR elements can be found either on plasmids or in one of the three chromosomal integration sites, and there is variability of this across the lineage. Several previous studies with Malawian isolates indicated a clonal, locally spreading lineage with chromosomally integrated resistance genes. In a recent study however we noted three isolates with predicted resistance genes unusual for the region, and we here present the resolved genomes of these isolates using long- and short-read sequencing. Our work shows that these isolates are potentially imported cases, most closely related to the recently described sub-lineage 4.3.1.EA1, although they encode IncHI1 plasmids with reduced resistance gene repertoire compared to the main IncHI1 plasmids spreading in East Africa. Similar reduced plasmids were reported in a recent large-scale study in five isolates from Tanzania, highlighting the urgency for better coverage of the African continent in genome studies to better understand the dynamics of these potentially co-circulating plasmids.

Genomic perspective on the bacillus causing paratyphoid B fever

Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB.

IAPSM's Position Paper on Typhoid Vaccines for Adult Immunization in India

Typhoid is a major public health concern in India, particularly among those dwelling in urban slums with poor sanitation. The disease caused by Salmonella enterica serovar Typhi spread majorly through contaminated food and water. The economic burden of the disease is catastrophic and affects both families and the government making a strong case for including typhoid vaccines in the national immunization schedule. The World Health Organization has prequalified several vaccines and has recommended their use in endemic areas. While there is robust evidence for vaccination of children from India and other LMICs, the case for adult vaccination remains less clear. The Indian Association of Preventive and Social Medicine acknowledges the necessity to adopt a widespread typhoid immunization program, along with other preventive strategies, especially in the vulnerable pockets. IAPSM recommends focusing on newer-generation Typhoid Conjugate Vaccines (TCVs), which provide long-lasting and superior immunological benefits, and are effective across all ages including adults. IAPSM suggests routine use of Typbar-TCV™ for adults up to 45 years old in India. The organization also highlights the necessity for post-marketing surveillance of these vaccines, to monitor the long-term safety and effectiveness of various vaccines in different communities. IAPSM encourages members to take front-line efforts in their community health service areas, and finally appeals for the development of vaccines to cover a more extensive range of Salmonella infections so that control over typhoid can be strengthened.

Azithromycin-resistant mph(A)-positive Salmonella enterica serovar Typhi in the United States

OBJECTIVES

The United States Centers for Disease Control and Prevention (CDC) conducts active surveillance for typhoid fever cases caused by Salmonella enterica serovar Typhi (Typhi). Here we describe the characteristics of the first two cases of mph(A)-positive azithromycin-resistant Typhi identified through US surveillance.

METHODS

Isolates were submitted to public health laboratories, sequenced, and screened for antimicrobial resistance determinants and plasmids, as part of CDC PulseNet's routine genomic surveillance. Antimicrobial susceptibility testing and long-read sequencing were also performed. Basic case information (age, sex, travel, outcome) was collected through routine questionnaires; additional epidemiological data was requested through follow-up patient interviews.

RESULTS

The patients are related and both reported travel to India (overlapping travel dates) before illness onset. Both Typhi genomes belong to the GenoTyphi lineage 4.3.1.1 and carry the azithromycin-resistance gene mph(A) on a PTU-FE (IncFIA/FIB/FII) plasmid. These strains differ genetically from mph(A)-positive Typhi genomes recently reported from Pakistan, suggesting independent emergence of azithromycin resistance in India.

CONCLUSIONS

Cases of typhoid fever caused by Typhi strains resistant to all available oral treatment options are cause for concern and support the need for vaccination of travellers to Typhi endemic regions. US genomic surveillance serves as an important global sentinel for detection of strains with known and emerging antimicrobial resistance profiles, including strains from areas where routine surveillance is not conducted.

Trends in antimicrobial resistance amongst Salmonella Typhi in Bangladesh: A 24-year retrospective observational study (1999-2022)

BACKGROUND

Rising antimicrobial resistance (AMR) in Salmonella Typhi restricts typhoid treatment options, heightening concerns for pan-oral drug-resistant outbreaks. However, lack of long-term temporal surveillance data on AMR in countries with high burden like Bangladesh is scarce. Our study explores the AMR trends of Salmonella Typhi isolates from Bangladesh, drawing comparisons with antibiotic consumption to optimize antibiotic stewardship strategies for the country.

METHODOLOGY/PRINCIPAL FINDINGS

The typhoid fever surveillance from 1999 to 2022 included two pediatric hospitals and three private clinics in Dhaka, Bangladesh. Blood cultures were performed at treating physicians' discretion; cases were confirmed by microbiological, serological, and biochemical tests. Antibiotic susceptibility was determined following CLSI guidelines. National antibiotic consumption data for cotrimoxazole, ciprofloxacin, and azithromycin was obtained from IQVIA-MIDAS database for comparison. Over the 24 years of surveillance, we recorded 12,435 culture-confirmed typhoid cases and observed declining resistance to first-line drugs (amoxicillin, chloramphenicol, and cotrimoxazole); multidrug resistance (MDR) decreased from 38% in 1999 to 17% in 2022. Cotrimoxazole consumption dropped from 0.8 to 0.1 Daily defined doses (DDD)/1000/day (1999-2020). Ciprofloxacin non-susceptibility persisted at >90% with unchanged consumption (1.1-1.3 DDD/1000/day, 2002-2020). Low ceftriaxone resistance (<1%) was observed, with slightly rising MIC (0.03 to 0.12 mg/L, 1999-2019). Azithromycin consumption increased (0.1 to 3.8 DDD/1000/day, 1999-2020), but resistance remained ≤4%.

CONCLUSION

Our study highlights declining MDR amongst Salmonella Typhi in Bangladesh; first-line antimicrobials could be reintroduced as empirical treatment options for typhoid fever if MDR rates further drops below 5%. The analysis also provides baseline data for monitoring the impact of future interventions like typhoid conjugate vaccines on typhoid burden and associated AMR.

Phylogenetic Analysis Based on Whole Genome Sequences, Antibiotic Resistance, and Virulence of Salmonella enterica Clinical Isolates from South Korea

Salmonella is a major cause of foodborne disease and frequently causes human salmonellosis in South Korea. In this study, we investigated the genome diversity, antimicrobial resistance, and virulence of clinical isolates of Salmonella enterica from South Korea. We collected 42 S. enterica subsp. enterica isolates from two hospitals in South Korea. Whole genome sequences were determined. Serovars and sequence types (STs) based on multilocus sequence typing (MLST) were identified from whole genome sequences. Phylogenetic trees based on whole genome sequences and a minimum spanning tree based on MLST were constructed. Human serum resistance assays and gentamicin protection assays were performed to assess in vitro virulence. Nineteen serovars were identified among 42 clinical isolates, including nine Salmonella Typhi isolates. There were inconsistencies between serogroups and phylogenetic clusters in the phylogenetic tree and minimum spanning tree, but high clonality of S. Typhi was observed. Salmonella Typhi isolates were divided into two clusters, corresponding to ST1 and ST2. Isolates of serovars Typhimurium and I4,[5],12:i:- clustered into a group, and a hybrid isolate between the two serovars was identified. Four ciprofloxacin-resistant isolates were identified among nine S. Typhi isolates, and all isolates of S. Enteritidis and S. Panama were resistant to colistin. The gentamicin protection assay revealed that serogroup D1 was significantly less virulent than the other serogroups. Our study suggests high diversity of S. enterica clinical isolates from South Korea and non-monophyly of serogroups. In addition, subgroups of S. Typhi isolates and a hybrid isolate between serovars Typhimurium and I4,[5],12:i:- were identified.

Clinical Characteristics, Serotypes and Antimicrobial Resistance of Invasive Salmonella Infections in HIV-Infected Patients in Hangzhou, China, 2012-2023

Purpose

Developing countries, invasive Salmonella infections can cause considerable morbidity and mortality. There is a relative lack of data on coinfection with Salmonella in HIV-infected patients in Hangzhou, China.

Patients and Methods

In this study, we manually collected case data of patients aged >18 years with HIV combined with invasive Salmonella infections admitted to Xixi Hospital in Hangzhou from January 2012 to August 2023 by logging into the Hospital Information System, and identified 26 strains of invasive Salmonella using a fully automated microbiological identification system and mass spectrometer. Serotypes were determined using Salmonella diagnostic sera based on the White-Kauffmann-Le Minor scheme. Drug sensitivity tests were performed using the automated instrumental method of the MIC method.

Results

A total of 26 HIV-infected patients with invasive Salmonella coinfections were identified over 11 years; Twenty-five of the 26 patients (96.2%) were males, with a mean age of 33.5 years (26.75, 46.75). The most common type of infection was bloodstream infection (92.3%). One patient also had concomitant meningitis and osteoarthritis, followed by pneumonia (7.7%). The presence of multiple bacterial infections or even multiple opportunistic pathogens was clearly established in 7 (26.9%) patients. Three (11.6%) patients were automatically discharged from the hospital with deterioration of their condition, and one (3.8%) patient died. Salmonella enteritidis was the most common serotype in 6 patients (23.2%), and Salmonella Dublin was the most common serotype in 6 patients (23.2%). Drug sensitivity results revealed multidrug resistance in a total of 8 (30.8%) patients.

Conclusion

The clinical presentation of invasive Salmonella infection in HIV patients is nonspecific and easily masked by other mixed infections. A CD4+ count <100 cells/µL and comorbid intestinal lesions may be important susceptibility factors. Salmonella has a high rate of resistance to common antibiotics, and the risk of multidrug resistance should not be ignored.

Genetic heterogeneity in the Salmonella Typhi Vi capsule locus: a population genomic study from Fiji

Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji implemented a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology of Salmonella Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (n=419) of the total cases from the Northern and Central Divisions of Fiji that occurred in the period 2017-2019. We found elevated rates of nucleotide polymorphisms in the tviD and tviE genes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemic S. Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12 382 S. Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the same tviE mutations across the S. Typhi population, indicating that tvi selection has occurred both independently and globally. The functional impact of tvi mutations on the Vi-capsular structure and other phenotypic characteristics are not fully elucidated, yet commonly occurring tviE polymorphisms localize adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide in S. Typhi biology and vaccination, further integrated epidemiological, genomic and phenotypic surveillance is required to determine the spread and functional implications of these mutations.

Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome

Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.

Linking epidemiological and genomic data in cases of enteric fever in England to inform clinical management and public health action

OBJECTIVES

To explore the feasibility of linking data from enhanced surveillance patient questionnaires from each enteric fever case in England with genome sequencing data, including antimicrobial resistance (AMR) profiles, from the corresponding isolate of typhoidal salmonellae.

METHODS

After linking data we interrogated the merged dataset and assessed the utility of passive surveillance data to match and monitor antimicrobial treatment regimens in enteric fever patients with the AMR profiles of the infectious agent.

RESULTS

A high proportion of cases were given antibiotics (n = 1230/1415; 86.9%); half of the cases stated the class of antibiotic they were given (n = 630/1239) and half were prescribed cephalosporins (n = 316/630). Reported treatment with a combination of antibiotics increased with symptom severity. Nearly half of isolates (n = 644/1415; 45.5%) had mutations conferring resistance to ciprofloxacin. Based on genome-derived AMR profiles, typhoidal salmonellae isolates inferred to be susceptible to the recommended first-line antimicrobials were twice as likely to be isolated from individuals residing in the least deprived areas compared with the most deprived (n = 26/169; 15.4% versus n = 32/442; 7.2%).

CONCLUSIONS

Due to the high proportion of missing data obtained from patient interviews, we recommend a more transparent and systematic approach to recording the antibiotic prescription details by healthcare professionals in primary and secondary care. A more robust approach to data capture at this point in the care pathway would enable us to audit inconsistencies in the prescribing algorithms across England and ensure equitable treatment across all sections of society. Integrating prescribing data with the genome-derived AMR profiles of the causative agent at the individual patient level provides an opportunity to monitor the impact of treatment on clinical outcomes, and to promote best practice in real time.

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.

The cost of typhoid illness in low- and middle-income countries, a scoping review of the literature

Typhoid fever is responsible for a substantial health burden in low- and middle-income countries (LMICs). New means of prevention became available with the prequalification of typhoid conjugate vaccines (TCV) by the World Health Organization (WHO) in 2018. Policymakers require evidence to inform decisions about TCV. The economic burden related to typhoid fever can be considerable, both for healthcare providers and households, and should be accounted for in the decision-making process. We aimed to understand the breadth of the evidence on the cost of typhoid fever by undertaking a scoping review of the published literature. We searched scientific databases with terms referring to typhoid fever cost of illness to identify published studies for the period January 1st 2000 to May 24th 2024. We also conferred with stakeholders engaged in typhoid research to identify studies pending completion or publication. We identified 13 published studies reporting empirical data for 11 countries, most of them located in Asia. The total cost of a typhoid episode ranged from $23 in India to $884 in Indonesia (current 2022 United States Dollar [USD]). Household expenditures related to typhoid fever were characterized as catastrophic in 9 studies. We identified 5 studies pending completion or publication, which will provide evidence for 9 countries, most of them located in Africa. Alignment in study characteristics and methods would increase the usefulness of the evidence generated and facilitate cross-country and regional comparison. The gap in evidence across regions should be mitigated when studies undertaken in African countries are published. There remains a lack of evidence on the cost to treat typhoid in the context of increasing antimicrobial resistance. Decision-makers should consider the available evidence on the economic burden of typhoid, particularly as risk factors related to antimicrobial resistance and climate change increase typhoid risk. Additional studies should address typhoid illness costs, using standardized methods and accounting for the costs of antimicrobial resistance.

The scope of the antimicrobial resistance challenge

Each year, an estimated 7·7 million deaths are attributed to bacterial infections, of which 4.95 million are associated with drug-resistant pathogens, and 1·27 million are caused by bacterial pathogens resistant to the antibiotics available. Access to effective antibiotics when indicated prolongs life, reduces disability, reduces health-care expenses, and enables access to other life-saving medical innovations. Antimicrobial resistance undoes these benefits and is a major barrier to attainment of the Sustainable Development Goals, including targets for newborn survival, progress on healthy ageing, and alleviation of poverty. Adverse consequences from antimicrobial resistance are seen across the human life course in both health-care-associated and community-associated infections, as well as in animals and the food chain. The small set of effective antibiotics has narrowed, especially in resource-poor settings, and people who are very young, very old, and severely ill are particularly susceptible to resistant infections. This paper, the first in a Series on the challenge of antimicrobial resistance, considers the global scope of the problem and how it should be measured. Robust and actionable data are needed to drive changes and inform effective interventions to contain resistance. Surveillance must cover all geographical regions, minimise biases towards hospital-derived data, and include non-human niches.

Antimicrobial Resistance Genes in Respiratory Bacteria from Weaned Dairy Heifers

Bovine respiratory disease (BRD) is the leading cause of mortality and antimicrobial drug (AMD) use in weaned dairy heifers. Limited information is available regarding antimicrobial resistance (AMR) in respiratory bacteria in this population. This study determined AMR gene presence in 326 respiratory isolates (Pasteurella multocida, Mannheimia haemolytica, and Histophilus somni) from weaned dairy heifers using whole genome sequencing. Concordance between AMR genotype and phenotype was determined. Twenty-six AMR genes for 8 broad classes of AMD were identified. The most prevalent, medically important AMD classes used in calf rearing, to which these genes predict AMR among study isolates were tetracycline (95%), aminoglycoside (94%), sulfonamide (94%), beta-lactam (77%), phenicol (50%), and macrolide (44%). The co-occurrence of AMR genes within an isolate was common; the largest cluster of gene co-occurrence encodes AMR to phenicol, macrolide, elfamycin, β-lactam (cephalosporin, penam cephamycin), aminoglycoside, tetracycline, and sulfonamide class AMD. Concordance between genotype and phenotype varied (Matthew's Correlation Coefficient ranged from -0.57 to 1) by bacterial species, gene, and AMD tested, and was particularly poor for fluoroquinolones (no AMR genes detected) and ceftiofur (no phenotypic AMR classified while AMR genes present). These findings suggest a high genetic potential for AMR in weaned dairy heifers; preventing BRD and decreasing AMD reliance may be important in this population.

Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar

BACKGROUND

Typhoid fever is a common cause of febrile illness in low- and middle-income countries. While multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) has spread globally, fluoroquinolone resistance has mainly affected Asia.

METHODS

Consecutively, 1038 blood cultures were obtained from patients of all age groups with fever and/or suspicion of serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar in 2015-2016. S. Typhi were analyzed with antimicrobial susceptibility testing and with short read (61 strains) and long read (9 strains) whole genome sequencing, including three S. Typhi strains isolated in a pilot study 2012-2013.

RESULTS

Sixty-three S. Typhi isolates (98%) were MDR carrying blaTEM-1B, sul1 and sul2, dfrA7 and catA1 genes. Low-level ciprofloxacin resistance was detected in 69% (43/62), with a single gyrase mutation gyrA-D87G in 41 strains, and a single gyrA-S83F mutation in the non-MDR strain. All isolates were susceptible to ceftriaxone and azithromycin. All MDR isolates belonged to genotype 4.3.1 lineage I (4.3.1.1), with the antimicrobial resistance determinants located on a composite transposon integrated into the chromosome. Phylogenetically, the MDR subgroup with ciprofloxacin resistance clusters together with two external isolates.

CONCLUSIONS

We report a high rate of MDR and low-level ciprofloxacin resistant S. Typhi circulating in Zanzibar, belonging to genotype 4.3.1.1, which is widespread in Southeast Asia and African countries and associated with low-level ciprofloxacin resistance. Few therapeutic options are available for treatment of typhoid fever in the study setting. Surveillance of the prevalence, spread and antimicrobial susceptibility of S. Typhi can guide treatment and control efforts.

Estimating the subnational prevalence of antimicrobial resistant Salmonella enterica serovars Typhi and Paratyphi A infections in 75 endemic countries, 1990-2019: a modelling study

BACKGROUND

Enteric fever, a systemic infection caused by Salmonella enterica serovars Typhi and Paratyphi A, remains a major cause of morbidity and mortality in low-income and middle-income countries. Enteric fever is preventable through the provision of clean water and adequate sanitation and can be successfully treated with antibiotics. However, high levels of antimicrobial resistance (AMR) compromise the effectiveness of treatment. We provide estimates of the prevalence of AMR S Typhi and S Paratyphi A in 75 endemic countries, including 30 locations without data.

METHODS

We used a Bayesian spatiotemporal modelling framework to estimate the percentage of multidrug resistance (MDR), fluoroquinolone non-susceptibility (FQNS), and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections for 1403 administrative level one districts in 75 endemic countries from 1990 to 2019. We incorporated data from a comprehensive systematic review, public health surveillance networks, and large multicountry studies on enteric fever. Estimates of the prevalence of AMR and the number of AMR infections (based on enteric fever incidence estimates by the Global Burden of Diseases study) were produced at the country, super-region, and total endemic area level for each year of the study.

FINDINGS

We collated data from 601 sources, comprising 184 225 isolates of S Typhi and S Paratyphi A, covering 45 countries over 30 years. We identified a decline of MDR S Typhi in south Asia and southeast Asia, whereas in sub-Saharan Africa, the overall prevalence increased from 6·0% (95% uncertainty interval 4·3-8·0) in 1990 to 72·7% (67·7-77·3) in 2019. Starting from low levels in 1990, the prevalence of FQNS S Typhi increased rapidly, reaching 95·2% (91·4-97·7) in south Asia in 2019. This corresponded to 2·5 million (1·5-3·8) MDR S Typhi infections and 7·4 million (4·7-11·3) FQNS S Typhi infections in endemic countries in 2019. The prevalence of third-generation cephalosporin-resistant S Typhi remained low across the whole endemic area over the study period, except for Pakistan where prevalence of third-generation cephalosporin resistance in S Typhi reached 61·0% (58·0-63·8) in 2019. For S Paratyphi A, we estimated low prevalence of MDR and third-generation cephalosporin resistance in all endemic countries, but a drastic increase of FQNS, which reached 95·0% (93·7-96·1; 3·5 million [2·2-5·6] infections) in 2019.

INTERPRETATION

This study provides a comprehensive and detailed analysis of the prevalence of MDR, FQNS, and third-generation cephalosporin resistance in S Typhi and S Paratyphi A infections in endemic countries, spanning the last 30 years. Our analysis highlights the increasing levels of AMR in this preventable infection and serves as a resource to guide urgently needed public health interventions, such as improvements in water, sanitation, and hygiene and typhoid fever vaccination campaigns.

FUNDING

Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill and Melinda Gates Foundation.

Typhoid Fever and Non-typhoidal Salmonella Outbreaks: A Portrait of Regional Socioeconomic Inequalities in Brazil

Typhoid fever occurs in an endemic form in Brazil and is a serious public health problem in some regions. In this scenario, further research is urgently needed to identify the associations between socioeconomic factors and typhoid fever, contributing to guiding policy decisions in the country. We aimed to investigate the influence of socioeconomic disparities on the prevalence of typhoid fever and non-typhoidal Salmonella (NTS) in Brazil. A search for data from 2010 to 2019 was carried out with the national health and human development agencies. As milk and derivatives are the fourth food incriminated in food outbreaks in Brazil, analyses for detecting Salmonella spp. in commercial dairy products allowed us to assess whether the outbreaks associated with these foods are due to inadequacies in sanitary control in dairy establishments or whether they are mainly home-based outbreaks. Predictive models validated by the bootstrapping method demonstrate an association of NTS prevalence reduction with improvements in the Sanitation Service Index (Rv ≥  -8 0.686; p ≤ 0.01) and Municipal Human Development Index - MHDI - (Rv =  -0.789; p ≤ 0.02). In the North, typhoid fever prevalence had seasonal variability with the rainfall, while sanitation services (Rv ≥-0.684; p ≤ 0.04) and MHDI (Rv ≥-0.949; p ≤ 0.003) directly influenced Northeast and South Brazil. Thus, the unequal distribution of investments in the sanitation sector contributed to disparities in typhoid fever prevalence among Brazilian regions. The absence of Salmonella spp. in commercial samples ratified the collected data that the outbreaks of Salmonella spp. in the Brazilian population occur mainly at residences. These findings show that implementing public health education and increasing investments in sanitation in regions with poor service can control outbreaks of Salmonella spp. in Brazilian endemic areas.

Boosting microbiome science worldwide could save millions of children's lives

Studies of the microbes living on and in our bodies are conducted mainly in a few rich countries, squandering opportunities to improve the health of people globally.

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.

Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient

In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of β-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2″)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.

Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning

Salmonella enterica serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by the consumption of imported food products or contracted during foreign travel, therefore, making the rapid identification of the geographical source of new infections a requirement for robust public health outbreak investigations. Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of S. Enteritidis infections from whole genome sequencing data. 2313 S. Enteritidis genomes, collected by the UKHSA between 2014-2019, were used to train a 'local classifier per node' hierarchical classifier to attribute isolates to four continents, 11 sub-regions, and 38 countries (53 classes). The highest classification accuracy was achieved at the continental level followed by the sub-regional and country levels (macro F1: 0.954, 0.718, 0.661, respectively). A number of countries commonly visited by UK travelers were predicted with high accuracy (hF1: >0.9). Longitudinal analysis and validation with publicly accessible international samples indicated that predictions were robust to prospective external datasets. The hierarchical machine learning framework provided granular geographical source prediction directly from sequencing reads in <4 min per sample, facilitating rapid outbreak resolution and real-time genomic epidemiology. The results suggest additional application to a broader range of pathogens and other geographically structured problems, such as antimicrobial resistance prediction, is warranted.