Purpose. Ceftriaxone is the drug of choice for typhoid fever and the emergence of resistant Salmonella Typhi raises major concerns for treatment. There are an increasing number of sporadic reports of ceftriaxone-resistant S. Typhi and limiting the risk of treatment failure in the patient and outbreaks in the community must be prioritized. This study describes the use of whole genome sequencing to guide outbreak identification and case management. Methodology. An isolate of ceftriaxone-resistant S. Typhi from the blood of a child taken in 2000 at the Popular Diagnostic Center, Dhaka, Bangladesh was subjected to whole genome sequencing, using an Illumina NextSeq 500 and analysis using Geneious software. Results/Key findings. Comparison with other ceftriaxone-resistant S. Typhi revealed an isolate from the Democratic Republic of the Congo in 2015 as the closest relative but no evidence of an outbreak. A plasmid belonging to incompatibility group I1 (IncI1-ST31) which included bla CTX-M-15 (ceftriaxone resistance) associated with ISEcp-1 was identified. High similarity (90 %) was seen with pS115, an IncI1 plasmid from S. Enteritidis, and with pESBL-EA11, an incI1 plasmid from E. coli (99 %) showing that S. Typhi has access to ceftriaxone resistance through the acquisition of common plasmids. Conclusions. The transmission of ceftriaxone resistance from E. coli to S. Typhi is of concern because of clinical resistance to ceftriaxone, the main stay of typhoid treatment. Whole genome sequencing, albeit several years after the isolation, demonstrated the success of containment but clinical trials with alternative agents are urgently required.

Non-typhoidal Salmonella (NTS) represents a leading cause of food-borne disease worldwide. It is a global public health concern: more than 94 million cases and 115,000 deaths are reported every year, with a disproportionate impact in developing countries. The prevalence of multi-drug-resistant (MDR) Salmonella strains is another major health concern which affects antimicrobial treatment, as many studies report that infections caused by MDR strains are more severe than those caused by susceptible strains. In Algeria, NTS represent one of the primary causes of salmonellosis in both humans and food animal production, especially poultry. Epidemiological surveillance systems and monitoring programs for Salmonella infections are essential requirements to provide data useful for the effective detection and control of Salmonella outbreaks. The present review will supply a perspective on NTS infection, pathogenesis and antimicrobial resistance with a focus on the epidemiology of salmonellosis in Algeria.

Campylobacter is the leading bacterial cause of infectious intestinal disease, but the pathogen typically accounts for a very small proportion of the overall stool microbiome in each patient. Diagnosis is even more difficult due to the fastidious nature of Campylobacter in the laboratory setting. This has, in part, driven a change in recent years, from culture-based to rapid PCR-based diagnostic assays which have improved diagnostic detection, whilst creating a knowledge gap in our clinical and epidemiological understanding of Campylobacter genotypes – no isolates to sequence. In this study, direct metagenomic sequencing approaches were used to assess the possibility of replacing genome sequences with metagenome sequences; metagenomic sequencing outputs were used to describe clinically relevant attributes of Campylobacter genotypes. A total of 37 diarrhoeal stool samples with Campylobacter and five samples with an unknown pathogen result were collected and processed with and without filtration, DNA was extracted, and metagenomes were sequenced by short-read sequencing. Culture-based methods were used to validate Campylobacter metagenome-derived genome (MDG) results. Sequence output metrics were assessed for Campylobacter genome quality and accuracy of characterization. Of the 42 samples passing quality checks for analysis, identification of Campylobacter to the genus and species level was dependent on Campylobacter genome read count, coverage and genome completeness. A total of 65% (24/37) of samples were reliably identified to the genus level through Campylobacter MDG, 73% (27/37) by culture and 97% (36/37) by qPCR. The Campylobacter genomes with a genome completeness of over 60% (n=21) were all accurately identified at the species level (100%). Of those, 72% (15/21) were identified to sequence types (STs), and 95% (20/21) accurately identified antimicrobial resistance (AMR) gene determinants. Filtration of stool samples enhanced Campylobacter MDG recovery and genome quality metrics compared to the corresponding unfiltered samples, which improved the identification of STs and AMR profiles. The phylogenetic analysis in this study demonstrated the clustering of the metagenome-derived with culture-derived genomes and revealed the reliability of genomes from direct stool sequencing. Furthermore, Campylobacter genome spiking percentages ranging from 0 to 2% total metagenome abundance in the ONT MinION sequencer, configured to adaptive sequencing, exhibited better assembly quality and accurate identification of STs, particularly in the analysis of metagenomes containing 2 and 1% of Campylobacter jejuni genomes. Direct sequencing of Campylobacter from stool samples provides clinically relevant and epidemiologically important genomic information without the reliance on cultured genomes.

Introduction: The frequency of Enterobacteriaceae involved in urinary tract infections (UTI) has increased significantly since the early 1990s, particularly in at-risk facilities such as resuscitation, surgery, urology and nephrology. The objective of this study was to evaluate the antimicrobial susceptibility of Enterobacteriaceae causing urinary tract infections (UTIs)at the University Hospital Centre of Benimessous in Algiers. Methodology: The study was designed as a retrospective study (between January 1st 2010 and December 31st 2012) and a prospective study (between January 1standApril 30th 2013) on 13,611 urine samples. Antimicrobial resistance phenotyping was conducted on the bacterial isolates using disk-diffusion method. Results: On 13,611 urine samples analysed, 1,790 (13.15%) fulfilled the criteria for urinary tract infection. Enterobacteriaceae were identified in 1,561 analysed samples (87%). Escherichia coli was the dominant uropathogen (66,15%) in both hospitalized and non-hospitalized patients. The other main detected Enterobacteriaceae members were Klebsiella pneumoniae (11,96%) and Proteus mirabilis (5,42%). Analysis of results showed also that women were more prone to UTI than men with sex ratio of 3.76(W/M). The susceptibilities of isolated Enterobacteriaceae to antibiotics revealed that they had acquired resistance to several classes, particularly toward β-lactams. Resistance frequencies were relatively high to ampicillin and sulfomethoxasole, while being very low to aminoglycosides and furans. Results obtained revealed also that 7% of isolates where resistant to third generation cephalosporins by production of extended spectrum β-lactamases (ESBL). Conclusions: The continuous monitoring of antibiotic resistance of uropathogenic Escherichia coli is crucial to guide the clinician to choose the best empiric treatment.

Salmonella is a significant public health pathogen responsible for a wide spectrum of diseases, ranging from gastroenteritis to invasive non-typhoidal salmonellosis and enteric fever. Although advancements in whole-genome sequencing have improved surveillance and outbreak investigations, traditional single-colony sequencing methods overlook within-host diversity, potentially underestimating the complexity of infections. This study explores the genome-wide diversity of Salmonella strains recovered from stool samples of eight patients, with up to 20 isolates analysed per sample. A total of 156 Salmonella enterica isolates were recovered. All isolates from individual patients displayed consistent serovars and sequence types. Despite the serotype consistency, microevolution was observed in S. Java ST149 and S. Java ST43, with SNP analyses revealing higher diversity (13 and 5 SNP differences, respectively) compared to the clonal populations of other serovars. Phylogenetic analysis of S. Java ST149 isolates from Patient 2 revealed distinct branching, driven by mutations in genes such as secY and cnoX, while S. Java ST43 isolates from Patient 1 displayed multiple clades with notable SNPs affecting transcriptional regulators. Genome structure (GS) analyses using hybrid assemblies identified uniform GS1.0 across all isolates. Antimicrobial resistance (AMR) profiling revealed the presence of multidrug efflux pump genes (mdsA and mdsB) in all isolates. However, S. Typhimurium isolates from Patient 4 exhibited additional AMR genes, including sul2, aph(3'')-Ib and blaTEM-1, associated with an 8.7 kb resistance region. A single isolate from Patient 4 lacked these additional genes due to the deletion of a ~19 kb genomic region, highlighting structural variation as a driver of phenotypic differences. These findings emphasize the genetic diversity of Salmonella within hosts, particularly in serovars such as S. Java, and underscore the limitations of single-colony sequencing in capturing this complexity. The study highlights the utility of hybrid sequencing strategies for comprehensive analysis of genome variation, offering valuable insights into transmission dynamics, AMR and evolutionary processes in Salmonella.

Salmonella is a significant public health pathogen responsible for a wide spectrum of diseases, ranging from gastroenteritis to invasive non-typhoidal salmonellosis (iNTS) and enteric fever. Although advancements in whole genome sequencing (WGS) have improved surveillance and outbreak investigations, traditional single-colony sequencing methods overlook within-host diversity, potentially underestimating the complexity of infections. This study explores the genome-wide diversity of Salmonella strains recovered from stool samples of eight patients, with up to 20 isolates analysed per sample. A total of 156 Salmonella enterica isolates were recovered. All isolates from individual patients displayed consistent serovars and sequence types. Despite the serotype consistency, microevolution was observed in S. Java ST149 and S. Java ST43, with SNP analyses revealing higher diversity (13 and 5 SNP differences, respectively) compared to the clonal populations of other serovars. Phylogenetic analysis of S. Java ST149 isolates from Patient 2 revealed distinct branching, driven by mutations in genes such as secY and cnoX , while S. Java ST43 isolates from Patient 1 displayed multiple clades with notable SNPs affecting transcriptional regulators. Genome structure (GS) analyses using hybrid assemblies identified uniform GS1.0 across all isolates. Antimicrobial resistance (AMR) profiling revealed the presence of multidrug efflux pump genes ( mdsA and mdsB ) in all isolates. However, S. Typhimurium isolates from Patient 4 exhibited additional AMR genes, including sul2 , aph(3’’)-Ib , and blaTEM-1 , associated with an 8.7 kb resistance region. A single isolate from Patient 4 lacked these additional genes due to the deletion of a ∼19 kb genomic region, highlighting structural variation as a driver of phenotypic differences. These findings emphasise the genetic diversity of Salmonella within hosts, particularly in serovars such as S. Java, and underscore the limitations of single-colony sequencing in capturing this complexity. The study highlights the utility of hybrid sequencing strategies for comprehensive analysis of genome variation, offering valuable insights into transmission dynamics, antimicrobial resistance, and evolutionary processes in Salmonella . Impact statement: This study provides a transformative perspective on Salmonella genomics, uncovering the significant within-host diversity of Salmonella populations through the analysis of multiple single-colony isolates. By leveraging hybrid sequencing technologies, we reveal critical insights into the microevolution of Salmonella during infection, capturing genome-wide variation at both single nucleotide and chromosomal scales. Our findings highlight the inherent limitations of traditional single-colony sequencing in detecting within-host diversity, particularly in genetically diverse serovars such as S. Java ST149. The identification of antimicrobial resistance (AMR) determinants and structural genomic variation demonstrates the dynamic nature of Salmonella genomes, offering crucial implications for clinical management and public health surveillance. Importantly, we show that within-host diversity may influence epidemiological interpretations, particularly in outbreak investigations and source attribution, where genetic differences between isolates can mask deeper transmission links. Data Summary: All relevant supporting data are available in the accompanying supplementary data files. The online version of this article contains four supplementary table. All Salmonella isolate genome sequences are available in the National Centre for Biotechnology Information (NCBI), Sequence Read Archive (SRA) under the Bioproject accession numbers PRJNA1230128. SRA accession numbers and associated metadata for isolate genomes are included in the supplementary table S2-S4.