The scope of the antimicrobial resistance challenge

The Lancet, Год журнала: 2024, Номер 403(10442), С. 2426 - 2438

Опубликована: Май 23, 2024

Язык: Английский

---

Understanding bacterial pathogenicity: a closer look at the journey of harmful microbes

Frontiers in Microbiology, Год журнала: 2024, Номер 15

Опубликована: Фев. 20, 2024

Bacteria are the most prevalent form of microorganisms and classified into two categories based on their mode existence: intracellular extracellular. While bacteria beneficial to human health, others pathogenic can cause mild severe infections. These use various mechanisms evade host immunity diseases in humans. The susceptibility a bacterial infection depends effectiveness immune system, overall genetic factors. Malnutrition, chronic illnesses, age-related vulnerabilities additional confounders disease severity phenotypes. impact pathogens public health includes transmission these from healthcare facilities, which contributes increased morbidity mortality. To identify significant threats it is crucial understand global burden common pathogenicity. This knowledge required improve immunization rates, vaccines, consider antimicrobial resistance when assessing situation. Many have developed resistance, has implications for infectious favors survival resilient microorganisms. review emphasizes significance understanding that this threat scale.

Язык: Английский

---

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

Microbial Genomics, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 15, 2025

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

Язык: Английский

---

Typhoid fever

Nature Reviews Disease Primers, Год журнала: 2023, Номер 9(1)

Опубликована: Дек. 14, 2023

Язык: Английский

---

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

The Lancet Global Health, Год журнала: 2024, Номер 12(3), С. e406 - e418

Опубликована: Фев. 15, 2024

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

Язык: Английский

---

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

Nature, Год журнала: 2024, Номер 625(7994), С. 237 - 240

Опубликована: Янв. 8, 2024

Язык: Английский

---

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

Communications Biology, Год журнала: 2024, Номер 7(1)

Опубликована: Июнь 28, 2024

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

Язык: Английский

---

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

Microbiology Spectrum, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

ABSTRACT 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 strains isolated from India. Comparative genome analysis revealed the new clone ceftriaxone-resistant harboring three plasmids incompatibility groups IncFIB(K), IncX1, IncFIB(pHCM2). Among these, IncFIB(K) plasmid confers resistance through bla CTX-M-15 gene, along with other determinants such as aph(3") , aph(6') sul2 dfrA14 qnrS tet(A) Phylogenetic showed that isolates Gujarat n = 140/142) belong distinct subclade (genotype 4.3.1.2.2) within genotype 4.3.1.2 (H58 lineage II). Single nucleotide polymorphism-based phylogenetic core genes in suggested close relatedness backbone Enterobacteriales, indicating H58 II possesses capability acquire MDR these organisms. This could indicate potential onset wave implementation control measures—such vaccination improved water, sanitation, hygiene systems—is crucial areas where or extensively drug-resistant are prevalent curb impact strains. IMPORTANCE Typhoid fever remains concern, especially lacking sanitation clean water. rise complicates treatment, increasing illness, death, healthcare expenses. Travel facilitates worldwide. Multidrug-resistant (XDR) strains, including those first-line antibiotics fluoroquinolones, pose significant challenges. Azithromycin now preferred treatments. Recently, XDR typhoid emerged Pakistan, even cephalosporins. India also faces challenges, sporadic cases initially declining but re-emerging. New show due acquisition bacteria, particularly CTX-M -carrying IncFIB(K). Due ongoing nature outbreak, data study deserve further consideration order its

Язык: Английский

---

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

eLife, Год журнала: 2023, Номер 12

Опубликована: Апрель 12, 2023

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

Язык: Английский

---

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

PLoS neglected tropical diseases, Год журнала: 2024, Номер 18(4), С. e0012132 - e0012132

Опубликована: Апрель 17, 2024

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 mainly affected Asia. Methods Consecutively, 1038 blood cultures were obtained from patients all age groups with and/or suspicion serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar 2015–2016. analyzed antimicrobial susceptibility testing short read (61 strains) long (9 whole genome sequencing, including three strains isolated pilot study 2012–2013. Results Sixty-three isolates (98%) MDR carrying bla TEM-1B , sul1 sul2 dfrA7 catA1 genes. Low-level ciprofloxacin was detected 69% (43/62), single gyrase mutation gyrA -D87G 41 strains, gyrA- S83F the non-MDR strain. All susceptible to ceftriaxone azithromycin. belonged genotype 4.3.1 lineage I (4.3.1.1), determinants located on composite transposon integrated into chromosome. Phylogenetically, subgroup clusters together two external isolates. Conclusions We report high rate low-level resistant circulating Zanzibar, belonging 4.3.1.1, which widespread Southeast Asia African countries associated resistance. Few therapeutic options are available for treatment typhoid setting. Surveillance prevalence, can guide control efforts.

Язык: Английский

---