Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

Companion animals as sources of hazardous critically important antimicrobial-resistant Escherichia coli: Genomic surveillance in Shanghai

This study provides the first comprehensive genomic surveillance of critically important antimicrobial (CIA)-resistant Escherichia coli in companion animals, addressing gaps in the understanding of antimicrobial resistance (AMR) transmission dynamics and the environmental dissemination of hazardous resistance genes within urban ecosystems. A total of 244 CIA-resistant Escherichia coli (CIA-EC) isolates were obtained from 730 anal swabs collected across 11 pet hospitals in Shanghai. High-risk zoonotic clones, such as ST410 and ST405, were identified across multiple districts, with blaNDM-5-positive IncX3 plasmids demonstrating exceptional stability, efficient conjugation, and broad host adaptability. These plasmids significantly amplify the global risk of cross-species blaNDM-5 dissemination. Mobile genetic elements (ISKox3, IS5, ISAba125) further facilitated blaNDM-5 transfer, enhancing the persistence and adaptability of these zoonotic pathogens. Additionally, novel sequence types (ST87, ST12624) exhibited resistance to last-resort antimicrobials, including tigecycline (tet(X4)), exacerbating the public health risks. The findings demonstrate that companion animals serve as critical reservoirs at the human-animal-environment interface, facilitating the environmental spread of hazardous resistance elements such as blaNDM-5-positive IncX3 plasmids. Integrating companion animals into One Health AMR surveillance and implementing antimicrobial stewardship are crucial to mitigating the spread of CIA-resistance determinants and preserving the efficacy of last-resort antimicrobials.

Whole-genome sequencing-based characterization of Listeria monocytogenes isolated from cattle and pig slaughterhouses

Listeria monocytogenes is a foodborne pathogen that causes human listeriosis and may be transmitted to humans via the food chain, beginning at slaughter and extending through food production and consumption. In this study, we performed whole-genome sequencing (WGS) analysis to determine the genetic characteristics of L. monocytogenes from the carcasses and environments of cattle and pig slaughterhouses in Korea. In total, 50 L. monocytogenes isolates were collected from 46 cattle and 47 pig slaughterhouses nationwide from 2014 to 2022. They were classified into two lineages, 12 sublineages, 12 sequence types, 11 clonal complexes (CCs), and 15 core-genome multilocus sequence types. L. monocytogenes isolates were divided into two lineages: lineage I (serotypes 1/2b and 4b) and lineage II (serotypes 1/2a and 1/2c). The most frequent CCs were CC9 (46.0 %), followed by CC224 (16.0 %) and CC155 (14.0 %). Although all isolates exhibited highly conserved LIPI-1, 20.0 % and 2.0 % contained LIPI-3 or LIPI-4, respectively. Moreover, 96.0 % of the isolates had full-length inlA. Interestingly, 21 of the 23 CC9 isolates contained mutations in inlA resulting from premature stop codon (PMSC). The mdrL and Listeria genomic island-2 (LGI-2) were identified in all L. monocytogenes isolates, whereas LGI-3 was identified in 32.0 % of the isolates. The L. monocytogenes isolates contained various antimicrobial resistance genes, moreover, the plasmid-borne resistance genes tetM and mprF were also identified in 34.0 % and 100 % of the isolates, respectively. Twenty-four isolates (48.0 %) harbored one or two plasmids (pLM33, DOp1, pLGUG1, and pLM5578), and 29 isolates (58.0 %) harbored at least one insertion sequence, composite transposon, and integrative conjugative element. Four isolates showed two CRISPR-Cas types IB and II-A. In addition, phage sequences associated with the spacer constituting the CRISPR array were identified in 26 Listeria phages from 14 L. monocytogenes isolates. The genetic composition of L. monocytogenes was conserved in a collinearity relationship between each of the five L. monocytogenes isolates from the cattle and pig slaughterhouses. These findings suggest that L. monocytogenes isolated from cattle and pig slaughterhouses have the ability to cause human disease and exhibit virulent characteristics.

Epidemiological and genomic insights of mcr-1-positive colistin-resistant Klebsiella pneumoniae species complex strains from wastewater treatment plants in Shanghai

The emergence of mcr-1-positive Klebsiella pneumoniae species complex (MP-KpSC) poses a significant threat to public health due to its resistance to last-resort antibiotics like colistin. This study aimed to investigate the prevalence, genomic characteristics, and transmission features of MP-KpSC in wastewater treatment plants (WWTPs) in Shanghai, China. A total of 13 (0.36 %) MP-KpSC isolates were identified, including 12 K. pneumoniae and 1 K. quasipneumoniae subsp. similipneumoniae (Kqps). Nine multidrug-resistant (MDR) MP-KpSC and 3 extensively drug-resistant (XDR) MP-KpSC strains were identified. Twenty-two resistance determinants were present in over 30 % of the strains, with the most prevalent being mcr-1 (100 %), floR (84.62 %), mphA (69.23 %), and tet(A) (69.23 %). MP-KpSC exhibited 11 sequence types, 4 plasmid types, 6 mcr-1-flanked regions, 4 clonal groups, and diverse serotypes. In 53.85 % of strains, transposons were identified within the mcr-1-flanked regions. One strain contained both mcr-8.2 and mcr-1 gene. Notably, the mcr-1 gene was identified for the first time in Kqps and was located on the conjugative IncP1 plasmid, with ISApl1 elements upstream of it. Worryingly, two carbapenem- and colistin-resistant XDR MP-KpSC stains, and three possible hypervirulence (hv) were found in MDR MP-KpSC strains. Moreover, multiple virulence genes and mcr-1, on the same contig with IS679 insert element. The evolutionary trajectories of these strains among WWTPs-human-animals were unveiled in Shanghai. The study reveals that WWTPs serve as critical environmental reservoirs for MP-KpSC, highlighting the potential transmission risks posed by XDR and hv strains to both humans and aquatic ecosystems. These findings advocate for the implementation of active surveillance targeting WWTPs to curb the spread of MP-KpSC.

Whole-genome sequencing of soil- and foodborne Bacillus cereus sensu lato indicates no clear association between their virulence repertoire, genomic diversity and food matrix

Bacillus cereus sensu lato is frequently involved in foodborne toxico-infections and is found in various foodstuff. It is unclear whether certain strains have a higher affinity for specific food matrices, which can be of interest for risk assessment. This study reports the characterization by whole-genome sequencing of 169 B. cereus isolates, isolated from 12 food types and soil over two decades. Any potential links between the food matrix of isolation, the isolate's genetic lineage and/or their (putative) virulence gene reservoir were investigated. More than 20 % of the strains contained the genes for the main potential enterotoxins (nheABC, hblCDA and cytK_2). Cereulide biosynthesis genes and genes encoding hemolysins and phospholipases, were detected in multiple isolates. Strain typing revealed a high diversity, as illustrated by 84 distinct sequence types, including 26 not previously described. This diversity was also reflected in the detection of all seven panC types and 71 unique virulence gene profiles. Core-genome MLST was used for phylogenomic investigation of the entire collection and SNP-based clustering was performed on the four most abundant sequence types, which did not reveal a clear affinity for specific B. cereus lineages or (putative) virulence genes for certain food matrices. Additionally, minimal genetic overlap was observed between soil and foodborne isolates. Clusters of closely-related isolates with common epidemiological metadata were detected. However, some isolates from different food matrices or collected several years apart were found to be genetically identical. This study provides elements that can be used for risk assessment of B. cereus in food.

Defining a genomic threshold for investigating Pseudomonas aeruginosa hospital outbreak

BACKGROUND

When investigating Pseudomonas aeruginosa (PA) outbreak, the clonality of isolates should be demonstrated using molecular typing method. Whole-genome sequencing (WGS) is the new Gold Standard for bacterial genotyping, but results interpretation must be careful about considering isolates as part of the same chain of transmission.

AIM

To determine genomic threshold to identify recent transmission events considering the spatiotemporal scale of the outbreak.

METHODS

PA outbreaks occurring in our hospital during the past 15 years were retrospectively analysed by both core-genome MLST and single-nucleotide polymorphism (SNP) in regards of epidemiological data. Our results were discussed in the light of previous published literature employing WGS to investigate hospital outbreaks of PA.

FINDINGS

14 investigations of PA outbreaks in our hospital were included, lasting a few days to 9 years. Isolates belonging to a same chain of transmission presented up to 13 loci differences and 25 SNPs. These results were in accordance with the 19 published outbreaks that mostly reported a similarity among epidemiologically related isolates below 15-25 SNPs. The impact of time and space on the threshold of eligible SNPs or loci differences was possibly masked by other factors including the genotype, the number of isolates included in the WGS analysis, the path of transmission and the presence of environmental reservoir.

CONCLUSIONS

Our study emphasizes the need to integrate genomic thresholds with epidemiological data, especially when environmental reservoirs or hypermutators are involved, to accurately assess transmission dynamics and outbreak origins.

Genomic and phenotypic insights into ST164 blaNDM-1-positive Acinetobacter baumannii from intestinal colonization in China

BACKGROUND

Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a critical global threat, especially in ICUs. Yet, reports on ST164 CRAB harboring blaNDM-1 remain scarce. This study investigates two clinical CRAB isolates, L4773hy and L4796hy, derived from intestinal colonization in Hangzhou, China, focusing on their phenotypic and genomic characteristics as well as the broader transmission of ST164 A. baumannii.

METHODS

Bacterial identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) mass spectrometry. Antimicrobial susceptibility was assessed via agar and broth microdilution. Whole-genome sequencing employed Illumina NovaSeq 6000 and Oxford Nanopore platforms. Resistance genes, insertion elements, transposons, and integrons were detected using ResFinder, PlasmidFinder, VFDB, ISFinder, pdifFinder, and IntegronFinder. Strains were typed by MLST, and a phylogenetic tree was constructed with kSNP3.0. Genetic environment diagrams were generated using Easyfig 2.2.5.

RESULTS

Two blaNDM-1-carrying A. baumannii isolates exhibiting extensive resistance to carbapenems, cephalosporins, and fluoroquinolones. Whole-genome sequencing and genetic environment analysis revealed the presence of a conserved structural sequence (ISAba14-ISAba14-aphA-ISAba125-blaNDM-1-bleMBL) on their chromosomes. Phylogenetic and clonal dissemination analysis showed that ST164 CRAB is primarily distributed in China and exhibits clonal spread. Pathogenicity studies indicated that blaNDM-1-positive ST164 strains have enhanced survival under immune pressure but do not display increased virulence in infection models.

CONCLUSION

This study provides the genomic and phenotypic characterization of intestinally colonized ST164 blaNDM-1 positive CRAB in Hangzhou, China. The elucidation of the genetic environment of blaNDM-1 further confirms the clonal dissemination of ST164 isolates, highlighting the importance of enhanced surveillance and infection control measures to mitigate the spread of these multidrug-resistant pathogens.

Drivers of the emergence and dissemination of high-risk resistance genes in cattle farm

Extended spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE) are recognized by WHO as critical concerns. The high cephalosporin resistance rate in a cattle farm in 2018 prompted us to conduct long-term (2019-2023) and extensive monitoring to explore risk factors for the import and transmission of ESBLs and CPE in this farm. Among 1288 samples from cattle, the environment, milk, and biological vectors, 48.8 % carried blaCTX-M-positive Enterobacterales with blaCTX-M-55 being dominant (76.4 %), and blaNDM-5-positive strains emerged in 2022 with a 1.9 % detection rate. blaCTX-M-55 and blaNDM-5 were likely introduced through various routes, especially wild birds, and have persisted due to overuse of cephalosporins in the farm. The spread of these genes was driven by the horizontal transmission of IncHI2 and IncX3 plasmids and clonal dissemination of certain clones. Cross-regional and cross-border transmission of blaCTX-M-55- and/or blaNDM-5-bearing bacteria and plasmids possibly occurred via wild birds, animal trade, and other means. Our findings suggest that the import, persistence, and dissemination of these genes within and beyond this farm, were fueled by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to prevent the spread of resistance genes as part of a holistic One Health strategy. ENVIRONMENTAL IMPLICATION: The high prevalence and long-term persistence of extended-spectrum β-lactamases and the emergence of carbapenemases in cattle and the environment signify a critical risk of transmitting high-risk resistance genes, posing a significant threat to human health. Consequently, bacteria carrying these genes in animal farms should be regarded as "hazardous materials". Import, persistence, and dissemination of these genes within and beyond this farm were exacerbated by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to mitigate the environmental risks associated with gene transmission as part of a comprehensive One Health strategy.

Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.

Genomic diversity and tracing of Paenibacillus larvae in Australia: implications for American foulbrood outbreak surveillance in low-diversity populations

Paenibacillus larvae is the causative agent of American foulbrood (AFB) in honeybees (Apis mellifera) and a devastating pathogen for honey and pollination industries worldwide. Despite this threat, a genomic survey of P. larvae has not been attempted within Australia. To examine the diversity of Australian populations, we sequenced 368 P. larvae genomes sourced primarily from south-eastern Australia. Multilocus sequencing typing analysis identified only 4 sequence types across all 368 samples, with 2 sequence types (ST18 and ST5) representing 96% of all isolates. In comparison to European-sourced P. larvae, sequences revealed much less genetic diversity in Australian isolates. However, Australian genotypes were very similar to those found in New Zealand populations. All Australian isolates were identified as enterobacterial repetitive intergenic consensus (ERIC) type I. To determine the feasibility of a genomic tracing system in a low-diversity genetic background, we investigated core-genome SNP (cgSNP) genotyping of isolates from a single beekeeper and from isolates across multiple apiaries and sample sites. We identified highly related cgSNP clusters, one with known epidemiological links, but another highly related cluster spanned several decades. Results strongly suggest that cgSNP analysis does have the discriminatory power to assist in the trace-forward and trace-back of AFB outbreaks, but importantly, the inclusion of background sequences and careful consideration of multiple analysis methods are required to avoid erroneous conclusions.

One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings

BACKGROUND

WGS can potentially be routinely used in clinical microbiology settings, especially with the increase in sequencing accuracy and decrease in cost. Escherichia coli is the most common bacterial species analysed in those settings, thus fast and accurate diagnostics can lead to reductions in morbidity, mortality and healthcare costs.

OBJECTIVES

To evaluate WGS for diagnostics and surveillance in a collection of clinical E. coli; to examine the pool of antimicrobial resistance (AMR) determinants circulating in Denmark and the most frequent STs; and to evaluate core-genome MLST (cgMLST) and SNP-based clustering approaches for detecting genetically related isolates.

METHODS

We analysed the genomes of 699 E. coli isolates collected throughout all Danish Clinical Microbiology Laboratories. We used rMLST and KmerFinder for species identification, ResFinder for prediction of AMR, and PlasmidFinder for plasmid identification. We used Center for Genomic Epidemiology MLST, cgMLSTFinder and CSI Phylogeny to perform typing and clustering analysis.

RESULTS

Genetic AMR determinants were detected in 56.2% of isolates. We identified 182 MLSTs, most frequently ST-69, ST-73, ST-95 and ST-131. Using a maximum 15-allele difference as the threshold for genetic relatedness, we identified 23 clusters. SNP-based phylogenetic analysis within clusters revealed from 0 to 13 SNPs, except two cases with 111 and 461 SNPs.

CONCLUSIONS

WGS data are useful to characterize clinical E. coli isolates, including predicting AMR profiles and subtyping in concordance with surveillance data. We have shown that it is possible to adequately cluster isolates through a cgMLST approach, but it remains necessary to define proper interpretative criteria.

Extensive dissemination of ESBL-producing Clonal Complex 14 Escherichia coli is likely spread through sexual transmission among men who have sex with men at risk of sexually transmitted infections

OBJECTIVES

We characterized the genetic proximity of Sequence Type (ST) 131, 1193 and 14 Extended-Spectrum Beta-Lactamase-producing E. coli (ESBL-Ec) to assess human determinants of carriage in community settings.

METHODS

In this cross-sectional study, we included individuals seeking care at a sexually transmitted infection (STI) or HIV outpatient clinic. ESBL-Ec were compared using phylogeny, core-genome Multi-Locus Sequence Typing and Single-Nucleotide Polymorphism (SNP) determination. Determinants were compared between STs and correlated to genetic distances.

RESULTS

103 individuals carried 112 strains of ST131 (n=63), ST14 (n=26) and ST1193 (n=23). Compared to ST131, ST14 isolates were more commonly found in individuals with any STI (p=0.031), men who have sex with men (p<0.001) and recent antibiotic use (p=0.021); whereas ST1193 isolates were more commonly found in individuals who engaged in insertive anal sex in <6 months (p=0.017). ST131 isolates showed high genomic diversity, while other STs evidenced a high level of proximity. SNPs data indicated the likely spread of a single ST14 (range=1;32) and some ST1193 clusters (range=2;111), which were linked to ST-specific sexual behaviors.

CONCLUSIONS

In populations of those at risk of acquiring STI, ST14 and ST1193 ESBL-Ec are emerging. Specific sexual transmissions routes are likely to play a role in their spread.

A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens

Antimicrobial resistance continues to be a growing threat globally, specifically in health-care settings in which antimicrobial-resistant pathogens cause a substantial proportion of health-care-associated infections (HAIs). Next-generation sequencing (NGS) and the analysis of the data produced therein (ie, bioinformatics) represent an opportunity to enhance our capacity to address these threats. The 3rd Geneva Infection Prevention and Control Think Tank brought together experts to identify gaps, propose solutions, and set priorities for the use of NGS for HAIs and antimicrobial-resistant pathogens. The major deliverable recommendation from this meeting was a proposed framework for implementing the sequencing of HAI pathogens, specifically those harbouring antimicrobial-resistance mechanisms. The key components of the proposed framework relate to wet laboratory quality, sequence data quality, database and tool selection, bioinformatic analyses, data sharing, and NGS data integration, to support public health and actions for infection prevention and control. In this Personal View we detail and discuss the framework in the context of global implementation, specifically in low-income and middle-income countries.

Comprehensive genomic epidemiology and antimicrobial resistance profiles of clinical Klebsiella pneumoniae species complex isolates from a tertiary hospital in Wenzhou, China (2019-2021)

BACKGROUND

The main issue of the Klebsiella pneumoniae species complex (KpSC) research in clinical settings is the accurate identification and differentiation of the closely related species within this complex. Moreover, the emergence and spread of carbapenem-resistant K. pneumoniae (CRKP) represent a significant public health threat due to limited treatment options and high mortality rates. Understanding the genetic basis of resistance and virulence is crucial for developing effective infection control strategies. In this work, the genomic epidemiology and antimicrobial resistance profile of KpSC isolates from Wenzhou, China, was investigated to fully understand the implications of the KpSC in clinical settings.

METHODS

We conducted a comprehensive analysis of 156 clinical KpSC isolates collected from a tertiary hospital in China over a three-year period (2019-2021). Antimicrobial susceptibility testing was performed according to CLSI standards. Whole-genome sequencing (WGS) and subsequent bioinformatic analyses were conducted to identify resistance genes, plasmid types, and virulence factors. Phylogenetic relationships were determined using maximum-likelihood analysis.

RESULTS

All CRKP isolates exhibited high levels of resistance to carbapenems, cephalosporins, and aminoglycosides. The most prevalent carbapenemase genes were blaKPC-2 (100%), with significant associations between blaKPC-2 and ST11. Phylogenetic analysis revealed considerable genetic diversity, with over 50 sequence types (STs) present. A subset of isolates harbored both resistance and hypervirulence genes, including rmpA, rmpA2, and siderophore systems, which were associated with potential higher pathogenesis.

CONCLUSION

This study provides novel insights into the molecular epidemiology of KpSC in Wenzhou, China, highlighting the coexistence of antimicrobial resistance and virulence factors in clinical isolates. The findings underscore the importance of continuous genomic surveillance and targeted therapeutic strategies to combat KpSC infections. Our research fills critical gaps in the current understanding of KpSC epidemiology in China and offers valuable data for global comparative studies, contributing to the development of effective infection control measures. Genomic surveillance in China thus provides crucial insights for local risk mapping and informs necessary adaptions for implementation of control strategies.

Genetic characterization and transmission of the multidrug resistance gene cfr in fecal and environmental pathways on a chicken farm in China

The emergence and spread of the multidrug-resistant gene cfr have raised significant public health concerns worldwide. To investigate its prevalence and dissemination dynamics, 18 cfr-positive strains were isolated in 2021 from fecal and environmental samples. Antimicrobial susceptibility testing showed that all strains were 100 % multidrug-resistant. Conjugation experiments demonstrated that a cfr- carrying IncFII(K)-IncR-IncFIB multi-replicon plasmid could transfer to E. coli J53. S1-nuclease digestion and Southern blotting identified cfr on plasmids of varying sizes, while whole-genome sequencing confirmed its presence on multiple plasmid types: IncX4, IncN, IncFII(K)-IncR-IncFIB, IncFIB-IncFII-IncR-IncHI2-IncHI2A multi-replicon plasmids, and two plasmids of unknown types. Genetic environment analysis revealed that cfr is categorized into five distinct structures (Types I-V). Reverse PCR results showed that Types I, II, and IV can form three circular intermediates of varying lengths (cfr-IS26). Network analysis further indicated strong association between cfr, tet(M), and dfrA14 mediated by IS26. Phylogenetic analysis revealed that the four ST1140 E. coli strains and all nine K. pneumoniae strains showed minimal genetic divergence. These findings suggest both clonal and horizontal transmission of cfr within the poultry farm. Continuous monitoring of cfr in animal-related environments is essential to mitigate its potential transfer to humans.

RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for clinical microbiology

Background. Whole-genome sequencing of bacterial isolates is increasingly becoming routine in clinical microbiology; however, subsequent analysis often needs to be started by a bioinformatician even for comprehensive pipelines. To increase the robustness of our workflow and free up bioinformatician work hours for development and advanced analysis, we aimed to produce a robust, customizable bioinformatic pipeline for bacterial genome assembly and routine analysis results that could be initiated by non-bioinformaticians. Results. We introduce the RSYD-BASIC pipeline for bacterial isolate sequence analysis and provide a demonstration of its functionality with two datasets composed of publicly available sequences, in which comparable results are obtained in most cases. In some instances, the pipeline provided additional information, corresponding to in vitro results where these could be obtained. In routine use at our department, the pipeline has already yielded clinically relevant results, allowing us to type a variety of bacterial pathogens isolated in our clinical laboratory. We also demonstrate how RSYD-BASIC results aided in disproving a potential outbreak. Conclusion. With the RSYD-BASIC pipeline, we present a configurable reads-to-results analysis pipeline operated by non-expert users that greatly eases the investigation of potential outbreaks by expert end users. Results obtained with publicly available sequences show comparable performance to the original methods, while underlining the importance of standardized methods.

Prevalence and molecular characterization of Campylobacter spp. isolated from chicken, beef, pork and sheep livers at Irish abattoirs

Thermotolerant Campylobacter spp. are the leading causes of food-borne diarrhoea in humans with most cases attributed to C. jejuni, and C. coli. Although chicken meat is considered the main source of infection in humans, the significance of other sources for campylobacteriosis in humans is less understood. The objective of this study was to determine the prevalence of thermotolerant Campylobacter spp. in chicken, beef, pork, and sheep liver in Ireland and to carry out whole genome sequencing (WGS) on the resulting isolates to characterize them molecularly. In addition, genome sequences of Irish clinical isolates were downloaded from the National Center for Biotechnology Information (NCBI) and compared with sequences from this study. The prevalence of Campylobacter spp. in chicken, beef, pork and sheep liver was 70 %, 4.4 %, 16 % and 80.0 %, respectively. Chi-Squared analysis indicated that the statistical differences in positivity rates between the four species were significant (P < 0.001). Amongst the 81 (43 %) positive liver samples, speciation revealed an overall predominance of C. jejuni (62 %), followed by C. coli (48 %) and C. lari (1 %) in all meat types except pork. Nine (11 %) samples were confirmed positive for more than one Campylobacter species with five of these nine samples recovered from sheep livers. Following analysis of WGS data, a wide range of diversity was observed and where clusters were identified, all were confined to the same animal species. No AMR genes were identified in the C. lari isolate, while C. jejuni and C. coli isolates were found to harbour resistance genes for tetracyclines, beta-lactams, aminoglycosides, and quinolones. Two clusters were identified between isolates from this study and human clinical data and the most prevalent clonal complex was CC-21, identified in this study and in clinical isolates. These results highlight the role of liver as a potential source of human Campylobacter infection. The significance of liver as a vehicle of human campylobacteriosis needs to be examined further particularly in respect to ovine sources.

Epidemic trend of Salmonella from swines and broilers in China from 2014 to 2023 and genetic evolution analysis of ESBLs-producing strains

Introduction

In recent years, the epidemic trend and antimicrobial resistance of Salmonella from swines and broilers, especially the extended-spectrum β-lactamase (ESBLs)-producing Salmonella, pose a serious threat to human and animal health.

Methods

In this study, we employed serotype identification, drug sensitivity testing, detection of ESBL-producing strains, and whole genome sequencing to analyze the epidemiological trends and drug resistance of Salmonella isolates from swines and broilers, as well as the genetic evolutionary relationships of ESBL-producing strains in China from 2014 to 2023.

Results

The results showed that the most prevalent serotypes of Salmonella from swines and broilers in China in recent 10 years were S. Typhimurium (133/381, 34.91%) and S. Enteritidis (156/416, 37.50%), respectively. Overall, 80.58% strains from swines and 70.67% strains from broilers were multidrug resistant. The multidrug resistance rate (MDR) showed a downward trend. The types of drugs exhibiting an increasing trend in resistance rates among Salmonella from broilers (7) were significantly greater than those from swines (2). The detection rates of ESBLs-producing Salmonella from swines and broilers were 9.45 and 29.58%, respectively, with the former showing a downward trend and the latter showing an upward trend. The drug resistance phenotype of Salmonella produced in ESBLs from swines and broilers is consistent with the results of the resistance genes carried. Whole genome sequencing analysis revealed that 36 swine-derived ESBL-producing Salmonella strains contained 6 ST-types and 13 cgST-types, among which ST34 and ST17 were dominant ST-types; a total of 35 resistance genes across 11 classes, blaCTX-M-14, blaTEM-1B, and blaCTX-M-65 were the predominant subtypes of β-lactam resistance genes. 126 broiler-derived ESBL-producing Salmonella strains included 19 ST-types and 37 cgST-types, with ST17 and ST198 as the dominant ST-types; a total of 52 resistance genes belonging to 12 classes, blaCTX-M-55, blaCTX-M-65, blaTEM-1B, and blaOXA-1 identified as the major subtypes of β-lactam resistance genes.

Discussion

This suggests that we should thoroughly implement management policies aimed at reducing the use of veterinary antimicrobials. Additionally, we should enhance research on traceability technology and the abatement of resistance genes, thereby providing support for the effective prevention and control of the spread of Salmonella and its drug resistance.

Co-occurrence of triple carbapenemase genes, blaVIM-2, blaNDM-1, and blaOXA-48 in Enterobacter hormaechei clinical isolates -first report from Croatia

Two Enterobacter hormaechei isolates harbouring three carbapenemase genes each, were isolated from two patients from different ICUs at University Hospital Centre Zagreb, Croatia, which is to our knowledge, the first report of triple carbapenemase (blaVIM-2, blaNDM-1, and blaOXA-48) co-existence in E. hormachei strains and also among Enterobacterales members in Croatia. Antimicrobial susceptibility testing showed susceptibility only to colistin and amikacin. The production of carbapenemases was phenotypically tested by immunochromatographic assay and confirmed by PCR. Detailed analysis by Whole Genome Sequencing (WGS) of short reads by Illumina and long reads by Oxford Nanopore Technologies (ONT) was additionally performed and showed that both isolates belonged to ST200. They were separated by 98 Single Nucleotide Polymorphisms (SNPs) having variations in the number of blaVIM-2 genes on the chromosome, the number of blaNDM-1 genes on the plasmid, non-identical blaNDM-1 plasmids, different plasmid content in general, and only one isolate carried a 94 kb prophage.

Multicenter evaluation of Fourier transform infrared (FTIR) spectroscopy as a first-line typing tool for carbapenemase-producing Klebsiella pneumoniae in clinical settings

Early use of infection control methods is critical for preventing the spread of antimicrobial resistance. Whole-genome sequencing (WGS) is considered the gold standard for investigating outbreaks; however, the turnaround time is usually too long for clinical decision-making and the method is also costly. The aim of this study was to evaluate the performance of Fourier transform infrared (FTIR) and artificial intelligence tools as a first-line typing tool for typing carbapenemase-producing Klebsiella pneumoniae (CPK) in the hospital setting. For this purpose, we analyzed 365 CPK isolates from two tertiary hospitals in Spain in parallel by applying unsupervised principal component analysis (PCA) and supervised algorithms (artificial neural network [ANN], support vector machine [SVM] linear, SVM radial basis function in the IR Biotyper software, and random forest in the Clover MSDAS software). Concordance with FTIR clustering considering the sequence type (ST) and the clonal cluster, obtained by cgMLST for reference purposes, was measured using the adjusted Wallace index (AWI), yielding values of 0.611 and 0.652, respectively. Different regions of the spectra were studied in relation to repeatability and reproducibility, and the polysaccharides region proved the best for FTIR differential analysis. The best results for accuracy were obtained using the ANN algorithm in the IR Biotyper software, with 80.5% of correct prediction. Regarding accuracy, the poorest results were obtained for isolates belonging to ST392 (55.5%) and the best results for ST307 (94.4%). The findings demonstrate the utility of the FTIR method as a rapid, inexpensive, first-line typing tool for detecting CPK, preserving WGS for confirmation and further characterization.

Utilizing whole genome sequencing to characterize central line-associated bloodstream infections due to Staphylococcus epidermidis

Whole genome sequencing (WGS) and clinical review were used to characterize 14 cases of central line-associated bloodstream infection (CLABSI) due to Staphylococcus epidermidis. WGS, which demonstrated disparate strains, suggested that 42.9% of S. epidermidis CLABSI cases were due to contamination, while clinical review suggested that 57.1% were contamination events.

Adaptation for Staphylococcus aureus to hosts via insertion mutation in the accessory gene regulator agrC gene: decreased virulence and enhanced persistence capacity

Staphylococcus aureus is an important human pathogen due to its vast array of virulence factors regulated by multiple regulatory mechanisms, including the accessory gene regulator. In this study, two S. aureus strains were simultaneously isolated from the blood of a febrile patient, belonging to the same clone, designated as 23H with a complete hemolytic phenotype, and 23B, exhibiting an incomplete hemolytic phenotype. The genomic comparison between strains 23B and 23H revealed that 23B had a single adenine base insertion at position 923 in the agrC gene, leading to a functional loss of the encoded AgrC. Experimental findings showed that strain 23B had decreased hemolytic activity, lower cytotoxicity against human alveolar epithelial A549 cells and in the Galleria mellonella model, and a reduced ability to survive intracellularly after infecting macrophages, in comparison to 23H. Conversely, 23B exhibited enhanced biofilm formation, greater adherence to A549 cells, and increased persistence in the face of vancomycin and daptomycin treatment. Transcriptomic analysis revealed that 23B upregulated surface protein-encoding genes while simultaneously reducing the expression levels of virulence factors, highlighting the intricate regulatory adjustments facilitating its persistence and reducing pathogenic potential. ATP assay results indicated that 23B maintained elevated ATP levels during the exponential phase yet exhibited reduced levels in the stationary phase when compared with 23H. Our findings suggested that the mutation in the agrC gene of S. aureus results in diminished virulence but markedly enhances persistence. This mutated strain warrants clinical attention because it may lead to treatment failures and persist in patients.

IMPORTANCE

In clinical antimicrobial therapy, bacterial strains often develop resistance to antimicrobial agents. Additionally, mutations in their gene regulatory networks can increase their persistence, especially in immunocompromised patients. This study identified an insertion mutation in the accessory gene regulator, agrC gene, carried by a Staphylococcus aureus strain isolated from the blood of a febrile patient, leading to the functional loss of AgrC. Further research revealed that despite the reduced virulence of the mutated strain, it significantly bolstered the capacity to adapt and endure within the host during prolonged infections. This was evidenced by increased adhesion and biofilm formation capabilities, development of antimicrobial tolerance, and decreased ATP levels linked to persistence. Therefore, monitoring these mutations in S. aureus is crucial clinically, as they can complicate treatment strategies.

Genomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Klebsiella pneumoniae

BACKGROUND

The infections of bacterial origin represent a significant problem to the public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the 'global clones of high risk'. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is more and more often used for these purposes, including the epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations.

DESCRIPTION

In this database, we provide the results of a thorough genomic analysis of 61,857 genomes of a highly dangerous bacterial pathogen Klebsiella pneumoniae. Important isolate typing information including multilocus sequence typing (MLST) types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, the presence of CRISPR-Cas systems, and cgMLST profiles are given, and the information regarding the presence of AMR, virulence genes and plasmid replicons within the genomes is provided.

CONCLUSION

This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.11069018 . The database will facilitate selection of the proper reference isolate sets for any types of genome-based investigations. It will be helpful for investigations in the field of K. pneumoniae genomic epidemiology, as well as antimicrobial resistance analysis and the development of prevention measures against this important pathogen.

Potential use of Fourier-transform infrared spectroscopy as a rapid screening tool for investigating nosocomial outbreaks of ST-80 vancomycin-resistant Enterococcus faecium

BACKGROUND

Fourier-transform infrared (FT-IR) spectroscopy is a non-genomic, spectrum-based typing technology useful for characterizing outbreaks of multidrug-resistant organisms.

AIM

To assess the performance of FT-IR spectroscopy in characterizing ST-80 vancomycin-resistant Enterococcus faecium (VREf) isolates from a nosocomial outbreak.

METHODS

Core-genome single-nucleotide polymorphism phylogeny was used as a reference method to characterize a nosocomial outbreak caused by ST-80 VREf. It identified 22 of 25 epidemiologically related isolates as belonging to an outbreak cluster.

FINDINGS

The use of FT-IR spectroscopy with a cluster-defining cut-off of 0.071 resulted in the correct classification of 21 out of 22 phylogenetically related isolates in a single cluster. It successfully distinguished three phylogenetically unrelated isolates from the outbreak cluster, along with five ST-80-unrelated control isolates, and five isolates from a previous outbreak in May 2023, yielding only one mischaracterized environmental isolate.

CONCLUSION

These findings support the potential use of FT-IR spectroscopy as a rapid screening tool to assist outbreak investigations. Notably, this study is the first to focus on the performance of FT-IR spectroscopy in the epidemiological analysis of VREf isolates with the same sequence type.

Tracing carriage, acquisition, and transmission of ESBL-producing Escherichia coli over two years in a tertiary care hospital

BACKGROUND

The impact of community carriage on the influx of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) into hospitals remains understudied. In this prospective 2-year single-centre study, we investigate the community ESBL-E influx and trace the colonisation, nosocomial acquisition, transmission, and infection dynamics of ESBL-producing Escherichia coli (ESBL-Ec) in non-ICU wards at a tertiary care hospital.

METHODS

This study reports primary and post hoc outcomes of the clinical trial NCT01208519 in which hospitalised patients were screened for rectal carriage of ESBL-E. ESBL-Ec isolates from ≈50% of carriers, including all patients who developed infections, were sequenced and genotyped. Endogenous infection was defined as infection by the same strain (< 10 SNPs distance) as colonizing strain.

RESULTS

Of 3703 screened patients, 456 (12.3%) were ESBL-positive-at-admission (PA-ESBL). Of the 2268 ESBL-negative-at-admission (NA-ESBL) patients with follow-up samples, 240 (10.6%) acquired ESBL-E (HA-ESBL), with an incidence density rate of 7.96 cases/1000 patient-day, notably higher in patients receiving antibiotics (P < 0.001). PA- and HA-ESBL patients developed significantly more ESBL-E infections than ESBL-free patients (P < 0.001). Sequenced ESBL-Ec showed high clonal diversity dominated by the multidrug-resistant and highly virulent ST131 clade, C2/H30-Rx. Among ESBL-Ec infections, 60% (18/30) were endogenous. Direct between-patients transmission clusters (n = 21) involved 23.9% (48/201) of patients and 23.0% (84/366) of ESBL-Ec isolates.

CONCLUSIONS

Our data show a high prevalence of nosocomial acquisition of ESBL-E in a non-ICU setting. The study provides genomic evidence that the endogenous reservoir is the main driver of ESBL-Ec infections underscoring the need for wide implementation of antibiotic stewardship programmes to reduce antibiotic pressure.

Steady existence of Escherichia coli co-resistant to carbapenem and colistin in an animal breeding area even after the colistin forbidden

Carbapenem- and colistin-resistant Escherichia coli (CCREC) cause high mortality rates and health costs, and have become serious health concerns. Total 1764 samples were collected from 60 animal farms in 2019 and 2021, including worker and animal faeces, wastewater, well water, air, vegetables, human hands, object surfaces, throat swabs, soil, and flies to investigate the prevalence and potential transmission pathways of CCREC. Eleven CCREC were detected: 9 (5 in 2019 and 4 in 2021) from 5 worker faeces, 3 animal faeces, 1 wastewater, and 2 from 1 flies sample. Chicken farms had the highest number of CCREC (n = 9). The detection rate was low (<1.1%) overall, and there was no significant difference in both years, indicating that CCREC existed stably after 4 years of colistin ban. The combinations of chromosomes and plasmids harbouring blaNDM and mcr-1.1 were divided into 4 patterns: IncX3 plasmid-blaNDM & chromosome-mcr.1.1 (n = 5); IncX3 plasmid-blaNDM & IncHI2 plasmid-mcr.1.1 (n = 3); IncFII plasmid-blaNDM & IncI2 plasmid-mcr.1.1 (n = 2); both chromosome (n = 1). The blaNDM located on plasmids was surrounded by similar genetic structures: Tn3-IS-blaNDM-bleMBL-TrpF-DsbD-IS. The genetic contexts of mcr-1.1 were highly similar, with 'ISApl1-mcr-1.1-PAP2' and 'mcr-1.1-PAP2'. All plasmids can be successfully transferred into E. coli J53, except for the IncHI2 plasmids with the transfer rate of 33.3%. The IncFII and IncI2 plasmids from same strain of flies could be co-transferred. The clonal spread of CCREC from humans to humans occurred on the same pig farm (P4) or different chicken farms (BC9 and LH7). This study suggested that flies, chromosomes, and plasmids jointly contribute to the steady existence of CCREC.

NanoCore: core-genome-based bacterial genomic surveillance and outbreak detection in healthcare facilities from Nanopore and Illumina data

Genomic surveillance enables the early detection of pathogen transmission in healthcare facilities and contributes to the reduction of substantial patient harm. Fast turnaround times, flexible multiplexing, and low capital requirements make Nanopore sequencing well suited for genomic surveillance purposes; the analysis of Nanopore data, however, can be challenging. We present NanoCore, a user-friendly method for Nanopore-based genomic surveillance in healthcare facilities, enabling the calculation and visualization of cgMLST-like (core-genome multilocus sequence typing) sample distances directly from unassembled Nanopore reads. NanoCore implements a mapping, variant calling, and multilevel filtering strategy and also supports the analysis of Illumina data. We validated NanoCore on two 24-isolate data sets of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). In the Nanopore-only mode, NanoCore-based pairwise distances between closely related isolates were near-identical to Illumina-based SeqSphere+ distances, a gold standard commercial method (average differences of 0.75 and 0.81 alleles for MRSA and VRE; sd = 0.98 and 1.00), and gave an identical clustering into closely related and non-closely related isolates. In the "hybrid" mode, in which only Nanopore data are used for some isolates and only Illumina data for others, increased average pairwise isolate distance differences were observed (average differences of 3.44 and 1.95 for MRSA and VRE, respectively; sd = 2.76 and 1.34), while clustering results remained identical. NanoCore is computationally efficient (<15 hours of wall time for the analysis of a 24-isolate data set on a workstation), available as free software, and supports installation via conda. In conclusion, NanoCore enables the effective use of the Nanopore technology for bacterial pathogen surveillance in healthcare facilities.

IMPORTANCE

Genomic surveillance involves sequencing the genomes and measuring the relatedness of bacteria from different patients or locations in the same healthcare facility, enabling an improved understanding of pathogen transmission pathways and the detection of "silent" outbreaks that would otherwise go undetected. It has become an indispensable tool for the detection and prevention of healthcare-associated infections and is routinely applied by many healthcare institutions. The earlier an outbreak or transmission chain is detected, the better; in this context, the Oxford Nanopore sequencing technology has important potential advantages over traditionally used short-read sequencing technologies, because it supports "real-time" data generation and the cost-effective "on demand" sequencing of small numbers of bacterial isolates. The analysis of Nanopore sequencing data, however, can be challenging. We present NanoCore, a user-friendly software for genomic surveillance that works directly based on Nanopore sequencing reads in FASTQ format, and demonstrate that its accuracy is equivalent to traditional gold standard short read-based analyses.

Characterization of Pseudomonas aeruginosa Isolated from Bovine Mastitis in Northern Jiangsu Province and Correlation to Drug Resistance and Biofilm Formability

This study aimed to provide experimental support for the prevention and treatment of Pseudomonas aeruginosa infections and to elucidate the epidemiological distribution of resistance and virulence genes of Pseudomonas aeruginosa from mastitis in dairy cows in the northern part of Jiangsu Province and their relationship with the biofilm-forming ability of the strains. Mastitis presents a significant challenge within dairy farming, adversely impacting the health of dairy cows and precipitating substantial economic losses in milk production. In this study, Pseudomonas aeruginosa (PA) was isolated and identified from mastitis milk samples in Jiangsu Province, China. In order to characterize the isolates, multilocus sequence typing (MLST), drug resistance phenotypes, virulence genes, and biofilm formations were detected. The isolation and identification of pathogenic bacteria from 168 clinical mastitis milk samples using 16S rRNA and PCR revealed 63 strains of Pseudomonas aeruginosa, which were determined to be highly homologous according to phylogenetic tree analysis. In addition, the MLST indicated five major ST types, namely ST277, ST450, ST571, ST641, and ST463. The susceptibility to 10 antimicrobials was determined, and it was found that 63 strains of Pseudomonas aeruginosa did not have a strong resistance to the antimicrobials in general. However, there were differences in the phenotypes' resistance to antimicrobials among the different ST types. It was also found that the more resistant the strains were to antimicrobials, the lower the carriage of virulence genes detected. The biofilm content was measured using the semi-quantitative crystal violet method. It was found that there were a few strains with medium or strong biofilm-forming abilities. However, the number of virulence genes carried by the 63 strains of Pseudomonas aeruginosa was inversely proportional to the biofilm-forming ability. It was also found that there were significantly more Pseudomonas aeruginosa in the biofilm state than in the planktonic state and that strains with strong biofilm-forming abilities were more resistant to antimicrobials.

Extended-spectrum beta-lactamase-producing Enterobacterales in human health: Experience from the tricycle project, Ghana

BACKGROUND

Vulnerable groups, such as pregnant women, are at increased risk of potentially life-threatening infections with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) for both mother and newborn. However, data regarding ESBL-E carriage and associated risk factors in Ghanaian pregnant women remain scarce.

OBJECTIVE

This study aimed to determine the prevalence of ESBL-E carriage and its associated risk factors among pregnant women attending the antenatal clinic at the Korle Bu Teaching Hospital.

METHODS

A systematic sample of 700 pregnant women with gestational age ≥ 34 weeks attending the antenatal clinic at Korle Bu Teaching Hospital was included in the study. After administering a structured questionnaire to assess potential risk factors associated with ESBL-E carriage, patients were given a sterile stool container to submit at least 1 g of stool specimen. Recovered isolates from faecal specimens were identified using MALDI-TOF-MS technology. These isolates were then subjected to susceptibility testing and ESBL identification. A random subset of 24 ESBL-producing Escherichia coli isolates was whole-genome sequenced on the MiSeq Illumina platform. Risk factors associated with ESBL-E carriage were determined using multivariable logistic regression analysis.

RESULTS

Among the 700 pregnant women, 42% (294) carried ESBL-E. The predominant ESBL-producing Enterobacterales were Escherichia coli (95%). Fifty percent (50%) of ESBL-E were multidrug resistant isolates (MDRs). Whole-genome sequencing of 24 ESBL-producing E. coli isolates revealed that blaCTX-M-15 (96%) was the most prevalent ESBL gene type. Notably, most isolates belonged to commensal phylogenetic groups (A, B1, and C; 88%). Having a primary level of education (aOR 1.45, 95% CI 1.05-1.96) and consuming legumes as the main source of protein (aOR 0.17, 0.40-0.83) were significantly associated with intestinal carriage of ESBL-E.

CONCLUSION

This study identified a high prevalence of ESBL-E and MDR-ESBL-E carriage among pregnant women. Our findings underscore the urgent need for public health interventions to control the spread of AMR.

Unraveling the impact of genome assembly on bacterial typing: a one health perspective

BACKGROUND

In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool).

METHODS

Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa.

RESULTS

The results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied.

CONCLUSION

This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.

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.

The circulation of methicillin-resistant Staphylococcus aureus between humans, horses and the environment at the equine clinic

OBJECTIVES

We performed a retrospective analysis of MRSA isolates collected at the university equine clinic including clinical isolates from 2008 to 2021 and screening environmental, equine and personnel isolates from 2016.

METHODS

Screening and clinical samples were cultured on Brilliance MRSA 2 and Columbia agar (Oxoid), respectively, with enrichment for environmental samples. Antimicrobial susceptibility was assessed by disc diffusion. All the isolates were characterized by spa typing. Eighteen selected isolates were subjected to WGS with subsequent wgMLST clonal analysis.

RESULTS

Among 75 MRSA isolates, five spa types were identified, the majority (n = 67; 89.33%) was t011. All isolates were resistant to cefoxitin and ampicillin and carried the mecA gene. In addition, the isolates were resistant to tetracycline (n = 74; 98.67%), gentamicin (n = 70; 93.33%), enrofloxacin (n = 54; 72.00%), sulfamethoxazole-trimethoprim (n = 5; 6.67%) and lincomycin (n = 3; 4.00%) with corresponding genetic markers for the resistance detected in the sequenced isolates. All 18 sequenced isolates belonged to ST398, 16 carried SCCmec type IVa and two carried SCCmec type Vc (5C2&5). Further, isolates carried aur, hlgA, hlgB and hlgC virulence genes, and five isolates carried sak and scn genes, which are part of the immune evasion cluster. Close genetic relatedness was found between isolates from the staff of the clinic and clinical samples of horses.

CONCLUSIONS

Repeated introduction and long-term persistence of the equine LA-MRSA subclone (ST398-MRSA-IVa/Vc(5C2&5), t011) among the infected horses at the equine clinic with the colonization of personnel, and the environment contamination that might contribute to transmission were observed.

Emergence of Escherichia coli ST131 carrying carbapenemase genes, European Union/European Economic Area, August 2012 to May 2024

Analysis of 594 isolates of Escherichia coli sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were bla OXA-244 (n = 230) and bla OXA-48 (n = 224), detected in 14 and 12 countries, respectively. Isolates carrying bla OXA-244 have increased rapidly since 2021. The increasing detection of carbapenemase genes in the E. coli high-risk lineage ST131 is a public health concern.

Investigation of failure of flexible GI endoscope disinfection because of Burkholderia cepacia contamination in irrigation tubing

BACKGROUND AND AIMS

This study aims to identify the cause of disinfection failure for multiple flexible GI endoscopes and to enhance the cleaning and disinfection procedures.

METHODS

Samples from the endoscopy devices, surrounding objects, cleaning water, automatic sterilizer, and integrated endoscopic washing workstation in a Digestive Endoscopy Center were collected and analyzed for microbial contamination and DNA/gene contents between May and July 2021.

RESULTS

The sample analysis revealed that the sink irrigation tubing of the washing workstation was contaminated with Burkholderia cepacia. After effective disinfection measures, the B cepacia detection in the disinfected endoscope dropped from 13.23% to 0% (P = .041). The presence of B cepacia was confirmed through homology search and gene sequencing.

CONCLUSIONS

The primary reason for endoscope disinfection failure is the contamination of the sink irrigation tubing by the B cepacia bacteria. These findings emphasize the need for thorough cleaning of irrigation tubing in integrated endoscopic washing workstations, which is generally neglected in routine maintenance.

Identification of a new Clostridium perfringens variant with a chromosomally encoded enterotoxin gene in a suspected persistent food poisoning outbreak in Eritrea

Clostridium perfringens is a causative agent of various human and animal enteric diseases including food poisoning. In this study, we describe an interesting case of a persistent food poisoning outbreak among Finnish peacekeepers in Eritrea, possibly caused by Clostridium perfringens carrying a new variant of the chromosomally encoded enterotoxin gene. C. perfringens strains causing food poisoning carry the enterotoxin gene, cpe, in its chromosome (c-cpe) or on a plasmid (p-cpe). PCR assays are widely used for toxinotype C. perfringens strains. The integration sites for the cpe gene are highly conserved, and PCR assays targeting the cpe gene and the adjacent IS elements (the IS1470 in c-cpe and the IS1470-like or IS1151 in p-cpe strains) are used to further determine the genetic location of the cpe gene. We sequenced nine enteropathogenic C. perfringens strains related to a persistent food poisoning outbreak among Finnish peacekeepers in Eritrea. Six of these strains produced non-typeable cpe results in the standard PCR assay due to divergence in the enterotoxin integration site. The gene order of the new variant of the chromosomal cpe insertion site with an additional IS1470 element impairing genotyping PCR assay for the location of cpe is described. In addition, variant c-cpe strains carried 58-81 copies of IS1470 in their genomes, compared to 9-23 copies found in previously described c-cpe strains. Thus, the present study represents an untraditional type of C. perfringens food poisoning caused by variant c-cpe strains, and the sequenced strains bring geographic variation to the existing strain collection of sequenced C. perfringens.

Whole-genome sequencing of non-typeable Haemophilus influenzae isolated from a tertiary care hospital in Surabaya, Indonesia

BACKGROUND

Haemophilus influenzae causes life-threatening invasive diseases such as septicaemia and meningitis. Reports on circulating H. influenzae causing invasive disease in lower-middle income settings, including Indonesia, are lacking. This study describes the serotype distributions and whole-genome sequence (WGS) data of H. influenzae isolated from hospitalized patients at Soetomo Hospital, Surabaya, Indonesia.

METHODS

H. influenzae isolates were isolated from blood and pleural fluid specimens and identified using culture-based and molecular methods, followed by serotyping and WGS using RT‒PCR and Illumina MiSeq, respectively. Sequencing reads were assembled, and further analyses were undertaken to determine the genomic content and reconstruct the phylogeny. A second dataset consisting of publicly available H. influenzae genomes was curated to conduct phylogenetic analyses of isolates in this study in the context of globally circulating isolates.

RESULTS

Ten H. influenzae isolates from hospitalized patients were collected, and septicaemia was the most common diagnosis (n=8). RT‒PCR and WGS were performed to determine whether all the isolates were nontypeable H. influenzae (NTHi). There were four newly identified STs distributed across the two main clusters. A total of 91 out of 126 virulence factor (VF)-related genes in Haemophilus sp. were detected in at least one isolate. Further evaluation incorporating a global collection of H. influenzae genomes confirmed the diverse population structure of NTHi in this study.

CONCLUSION

This study showed that all H. influenzae recovered from invasive disease patients were nonvaccine-preventable NTHi isolates. The inclusion of WGS revealed four novel STs and the possession of key VF-associated genes.

Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance

The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid.

IMPORTANCE

Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.

Towards quantifying plasmid similarity

Plasmids are extrachromosomal replicons which can quickly spread resistance and virulence genes between clinical pathogens. From the tens of thousands of currently available plasmid sequences we know that overall plasmid diversity is structured, with related plasmids sharing a largely conserved 'backbone' of genes while being able to carry very different genetic cargo. Moreover, plasmid genomes can be structurally plastic and undergo frequent rearrangements. So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.

Corynebacterium pseudotuberculosis: Whole genome sequencing reveals unforeseen and relevant genetic diversity in this pathogen

Corynebacterium pseudotuberculosis (CPS) is an important bacterial animal pathogen. CPS causes chronic, debilitating and currently incurable infectious diseases affecting a wide range of livestock and wild herbivores including camelids worldwide. Belonging to the Corynebacterium diphtheriae complex, this pathogen can also infect humans. The classical characterization of CPS is typically based on the testing of nitrate reductase activity, separating the two biovars Equi and Ovis. However, more refined resolutions are required to unravel routes of infection. This was realized in our study by generating and analyzing whole genome sequencing (WGS) data. Using newly created core genome multilocus sequence typing (cgMLST) profiles we were the first to discover isolates grouping in a cluster adjacent to clusters formed by CPS biovar Equi isolates. This novel cluster includes CPS isolates from alpacas, llamas, camels and dromedaries, which are characterized by a lack of nitrate reductase activity as encountered in biovar Ovis. This is of special interest for molecular epidemiology. Nevertheless, these isolates bear the genes of the nitrate locus, which are characteristic of biovar Equi isolates. However, sequence analysis of the genes narG and narH of the nitrate locus revealed indels leading to frameshifts and inactivity of the enzymes involved in nitrate reduction. Interestingly, one CPS isolate originating from another lama with an insertion in the MFS transporter (narT) is adjacent to a cluster formed by ovine CPS isolates biovar Equi. Based on this knowledge, the combination of biochemical and PCR based molecular biological nitrate reductase detection can be used for a fast and uncomplicated classification of isolates in routine diagnostics in order to check the origin of camelid CPS isolates. Further analysis revealed that partial sequencing of the ABC transporter substrate binding protein (CP258_RS07935) is a powerful tool to assign the biovars and the novel genomovar.

Development and implementation of a core genome multilocus sequence typing scheme for Yersinia enterocolitica: a tool for surveillance and outbreak detection

Yersinia enterocolitica (Y. enterocolitica) is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and international levels. In this study, we developed and implemented a cgMLST scheme for Y. enterocolitica. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different Y. enterocolitica biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested Y. enterocolitica: 563 Norwegian genomes collected between 2012 and 2022 and 327 genomes from public data sets. We applied the scheme to known outbreaks to establish a threshold for identifying major complex types (CTs) based on the number of allelic differences. The final cgMLST scheme included 2,582 genes with a median of 97.9% (interquartile range 97.6%-98.8%) targets found across all tested genomes. Analysis of outbreaks identified all outbreak strains using single linkage clustering at four allelic differences. This threshold identified 311 unique CTs in Norway, of which CT18, CT12, and CT5 were identified as the most frequently associated with outbreaks. The cgMLST scheme showed a very good performance in typing Y. enterocolitica using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate Y. enterocolitica surveillance and improve outbreak response in national and cross-border outbreaks.

Bacterial strain sharing between humans, animals, and the environment among urban households

Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low- and middle-income countries. In this study, we assessed bacterial strain-sharing and dissemination of antibiotic resistance across humans, domesticated poultry, canines, household soil, and drinking water in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households and performed Pooling Isolated Colonies-seq (PIC-seq) by sequencing pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and overlap of antibiotic-resistant genes (ARGs). Bacterial strains isolated from the household environment carried clinically relevant ARGs, reinforcing the role of the environment in antibiotic resistance dissemination. Strain-sharing rates and resistome similarities across sample types were strongly correlated within households, suggesting clonal spread of bacteria is a main driver of dissemination of ARGs in the domestic urban environment. Within households, E. coli strain-sharing was rare between humans and animals but more frequent between humans and drinking water. E. coli contamination in stored drinking water was also associated with higher strain-sharing between humans in the same household. Our study demonstrates that contaminated drinking water facilitates human to human strain sharing and water treatment can disrupt transmission.

Implementation of the WHO Tricycle protocol for surveillance of extended-spectrum β-lactamase producing Escherichia coli in humans, chickens, and the environment in Madagascar: a prospective genomic epidemiology study

BACKGROUND

Antimicrobial resistance (AMR) is a major public health threat, affecting not only people but also animals and the environment. The One Health dimension of AMR is well known; however, data are lacking on the circulation of resistance-conferring genes, particularly in low-income countries. In 2017, WHO proposed a protocol called Tricycle, focusing on extended-spectrum β-lactamase (ESBL)-Escherichia coli surveillance in the three sectors (humans, animals, and the environment). We implemented Tricycle in Madagascar to assess ESBL-E coli prevalence and describe intrasector and intersector circulation of ESBL-E coli and plasmids.

METHODS

In this prospective study, we collected blood culture data from hospitalised patients with a suspected bloodstream infection processed from May 1, 2018, to April 30, 2019, and rectal swabs from healthy pregnant women from July 30, 2018, to April 27, 2019, both from three hospitals in Antananarivo, Madagascar; and caeca from farm chickens and surface waters from the Ikopa river, wastewater, and slaughterhouse effluents in the Antananarivo area, Madagascar, from April 9, 2018, to April 30, 2019. All samples were tested for ESBL-E coli. The genomes of all isolates were sequenced using a short-read method on NextSeq 500 and NovaSeq 6000 platforms (Illumina, San Diego, CA, USA) and those carrying plasmid replicons using an additional long-read method on a MinION platform (Oxford Nanopore Technologies, Oxford, UK). We characterised genomes of isolated strains (sequence type, resistance and virulence gene content, and plasmid replicons). We then compared isolates using the variant calling method (single-nucleotide polymorphism).

FINDINGS

Data from 1056 blood cultures were collected and 289 pregnant women, 246 chickens, and 28 surface waters were sampled. Of the blood cultures, 18 contained E coli, of which seven (39%) were ESBL. ESBL-E coli was present in samples from 86 (30%) of 289 pregnant women, 140 (57%) of 246 chickens, and 28 (100%) of 28 surface water samples. The wet season (November to April) was associated with higher rates of carriage in humans (odds ratio 3·08 [1·81-5·27]) and chickens (2·79 [1·65-4·81]). Sequencing of 277 non-duplicated isolates (82 from pregnant women, 118 from chickens, and 77 from environmental samples) showed high genetic diversity (90 sequence types identified) with sector-specific genomic features. Single nucleotide polymorphism (SNP) analysis revealed that 169 (61%) of 277 isolates grouped into 44 clusters (two or more isolates) of closely related isolates (<40 SNPs), of which 24 clusters contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M variants (215 [78%] of 277 being blaCTX-M-15) and were located on a plasmid in 113 (41%) of 277 isolates. These ESBL-carrying plasmids were mainly IncF (63 [55%] of 114; one strain carried two plasmids) and IncY (42 [37%] of 114). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) pMLST subtypes, and the IncY plasmids, which were all highly conserved, were observed in isolates of differing genetic backgrounds from all sectors and were transferable in vitro by conjugation.

INTERPRETATION

Despite sector-specific population structures, both ESBL-E coli strains and plasmids are circulating among humans, chickens, and the environment in Antananarivo, Madagascar. The Tricycle protocol can be implemented in a low-income country and represents a powerful tool for investigating dissemination of AMR from a One Health perspective.

FUNDING

Fondation Mérieux and INSERM, Université Paris Cité.

Electroosmotic Sensing of Uncharged Peptides and Differentiating Their Phosphorylated States Using Nanopores

The correct characterization and identification of different kinds of proteins is crucial for the survival and development of living organisms, and proteomics research promotes the analysis and understanding of future genome functions. Nanopore technique has been proved to accurately identify individual nucleotides. However, accurate and rapid protein sequencing is difficult due to the variability of protein structures that contains more than 20 amino acids, and it remains very challenging especially for uncharged peptides as they can not be electrophoretically driven through the nanopore. Graphene nanopores have the advantages of high accuracy, sensitivity and low cost in identifying protein phosphorylation modifications. Here, by using all-atom molecular dynamics simulations, charged graphene nanopores are employed to electroosmotically capture and sense uncharged peptides. By further mimicking AFM manipulation of single molecules, it is also found that the uncharged peptides and their phosphorylated states could also be differentiated by both the ionic current and pulling force signals during their pulling processes through the nanopore with a slow and constant velocity. The results shows ability of using nanopores to detect and discriminate single amino acid and its phosphorylation, which is essential for the future low-cost and high-throughput sequencing of protein residues and their post-translational modifications.

Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae

Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.

Unearthing New ccr Genes and Staphylococcal Cassette Chromosome Elements in Staphylococci Through Genome Mining

Staphylococcal cassette chromosome mec (SCCmec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.

Epidemiological characteristics of human- and chicken-derived CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli from China

Bacterial resistance to β-lactams is mainly attributed to CTX-M-type extended-spectrum β-lactamases (ESBLs). However, the predominant sequence type (ST) of blaCTX-M-carrying Escherichia coli (blaCTX-M-Ec) in chickens, an important food animal, in China and its contribution to human β-lactam resistance are not investigated. In this study, approximately 1808 chicken-derived strains collected from 10 provinces from 2012 to 2020 were screened for blaCTX-M-Ec, and 222 blaCTX-M-Ec were identified. Antimicrobial susceptibility tests, whole genome sequencing and conjugation experiment were performed. All quality-controlled 136 chicken-derived blaCTX-M-Ec and 1193 human-derived blaCTX-M-Ec genomes were downloaded from NCBI and EnteroBase to comprehensively analyze the prevalence of blaCTX-M-Ec in China. blaCTX-M-55 (153/358, 42.7% in chicken isolates; 312/1193, 26.2% in human isolates) and blaCTX-M-14 (92/358, 25.7% in chicken isolates; 450/1193, 37.7% in human isolates) were dominant in blaCTX-M-Ec. The STs of blaCTX-M-Ec were diverse and scattered, with ST155 (n = 21) and ST152 (n = 120) being the most abundant in chicken- and human-derived isolates, respectively. Few examples indicated that chicken- and human-derived blaCTX-M-Ec have 10 or less core genome single nucleotide polymorphisms (cgSNPs). Genetic environment analysis indicated that ISEcp1, IS26 and IS903B were closely associated with blaCTX-M transfer. The almost identical pc61-55 and pM-64-1161 indicated the possibility of plasmid-mediated transmission of blaCTX-M between humans and chickens. Although the genomes of most blaCTX-M-Ec isolated from chickens and humans were quite different, the prevalence and genetic environment of blaCTX-M variants in both hosts were convergent. CTX-M-mediated resistance is more likely to spread through horizontal gene transmission than bacterial clones.

Genomic characterisation of Escherichia coli isolated from poultry at retail through Sink Surveillance in Dhaka, Bangladesh reveals high levels of multi-drug resistance

The surveillance of antimicrobial resistance (AMR) in commensal Escherichia coli from livestock at slaughter is widely employed to assess the potential for risk to humans. There is currently a limited understanding of AMR in Bangladesh poultry at retail in live bird markets, with studies focussing solely on phenotypic characterisation of resistance. To address this evidence gap we performed antimicrobial susceptibility testing and whole genome sequencing on E. coli obtained from chickens from live bird markets in Dhaka in 2018 (n = 38) and 2020 (n = 45). E. coli were isolated from caeca samples following ISO guidelines and sequenced using short and long read methods. Multidrug resistance was extremely common (n = 77) and there was excellent concordance between AMR phenotype and the presence of corresponding AMR genes or mutations. There was considerable genomic diversity, with 43 different sequence types detected. Public health considerations included the high occurrence of resistance to ciprofloxacin (n = 75) associated with plasmid-residing qnrS or mutations in the gyrA and parC chromosomal genes; and the detection of a tigecycline resistant isolate harbouring tet(X4) on an IncHI1A/B-IncFIA mosaic plasmid. Thirty-nine isolates were resistant to azithromycin and harboured mphA, with a significant increase in the incidence of resistance between 2018 and 2020. Although azithromycin is banned for veterinary use in Bangladesh it remains an important treatment option for humans. Interestingly, mphA confers high-level resistance to azithromycin and erythromycin, and the latter is commonly used on poultry farms in Bangladesh. Seven isolates were colistin resistant and carried mcr1. For two isolates hybrid assemblies revealed that mcr1 resided on a highly conserved IncHI2 plasmid that had 93% nucleotide identity to a plasmid from the published genome of an E. coli isolate of Bangladeshi human origin. Six isolates had resistance to third generation cephalosporins, associated with plasmid-residing bla CTX-M-55, bla CTX-M-65, or bla DHA-1. By employing phenotypic and genomic approaches for AMR surveillance we have provided new insights into the potential for One Health AMR linkages in Bangladesh. Employing similar approaches in human and environmental sectors will help inform the One Health approach to addressing AMR, and generate evidence to support mitigation measures such as improved antimicrobial stewardship.

Antimicrobial resistance spectrum and virulence characterization of Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis isolated from asymptomatic and diarrheal rhesus monkeys

This study aims to deepen our understanding of the drug resistance and virulence characterization among gut bacteria in asymptomatic and diarrheal captive rhesus macaques (RMs). A total of 31 samples, including 8 asymptomatic RMs, 10 diarrheal RMs, and 1 dead RM, were collected from a breeding base in Sichuan, China, for bacterial isolation. As a result, Escherichia coli (n = 23), Klebsiella (n = 22), Proteus mirabilis (n = 10), Enterococcus (n = 10), Salmonella (n = 2), and Staphylococcus (n = 2) were isolated. All isolates were subjected to antimicrobial susceptibility testing and whole-genome sequencing, among which some E. coli, K. pneumoniae, and P. mirabilis were subjected to the Galleria mellonella and mice infection testing. The antimicrobial resistance rates of levofloxacin, enrofloxacin, and cefotaxime in diarrhea-associated isolates were higher than those of asymptomatic isolates. Consistent with the antimicrobial resistance phenotype, diarrheal isolates had a higher prevalence rate to qnrS1, blaTEM-1B and blaCTX-M-27 than asymptomatic isolates. Furthermore, compared with asymptomatic isolates, diarrheal isolates demonstrated a higher pathogenic potential against larvae and mice. Additionally, sequence types (STs) 14179-14181 in E. coli and ST 625 and ST 630-631 in Klebsiella aerogenes were firstly characterized. Our evidence underscores the considerable challenge posed by high rates of bacterial drug resistance in the effective treatment of diarrheal RMs.

The Genome of Bifidobacterium longum subsp. infantis YLGB-1496 Provides Insights into Its Carbohydrate Utilization and Genetic Stability

Bifidobacterium longum subsp. infantis YLGB-1496 (YLGB-1496) is a probiotic strain isolated from human breast milk. The application of YLGB-1496 is influenced by carbohydrate utilization and genetic stability. This study used genome sequencing and morphology during continuous subculture to determine the carbohydrate utilization characteristics and genetic stability of YLGB-1496. The complete genome sequence of YLGB-1496 consists of 2,758,242 base pairs, 2442 coding sequences, and a GC content of 59.87%. A comparison of carbohydrate transport and metabolism genes of Bifidobacterium longum subsp. infantis (B. infantis) showed that YLGB-1496 was rich in glycosyl hydrolase 13, 20, 25, and 109 gene families. During continuous subculture, the growth characteristics and fermentation activity of the strain were highly stable. The bacterial cell surface and edges of the 1000th-generation strains were progressively smoother and well-defined, with no perforations or breaks in the cell wall. There were 20 SNP loci at the 1000th generation, fulfilling the requirement of belonging to the same strain. The presence of genes associated with cell adhesion and the absence of resistance genes supported the probiotic characteristics of the strain. The data obtained in this study provide insights into broad-spectrum carbohydrate utilization, genomic stability, and probiotic properties of YLGB-1496, which provide theoretical support to promote the use of YLGB-1496.

Comparative analysis of IR-Biotyper, MLST, cgMLST, and WGS for clustering of vancomycin-resistant Enterococcus faecium in a neonatal intensive care unit

Healthcare-associated infections caused by vancomycin-resistant Enterococcus faecium (VREFM) pose a significant threat to healthcare. Confirming the relatedness of the bacterial isolates from different patients is challenging. We aimed to assess the efficacy of IR-Biotyper, multilocus sequencing typing (MLST), and core-genome MLST (cgMLST) in comparison with whole-genome sequencing (WGS) for outbreak confirmation in the neonatal intensive care unit (NICU). Twenty VREFM isolates from four neonates and ten control isolates from unrelated patients were analyzed. Genomic DNA extraction, MLST, cgMLST, and WGS were performed. An IR-Biotyper was used with colonies obtained after 24 h of incubation on tryptic soy agar supplemented with 5% sheep blood. The optimal clustering cutoff for the IR-Biotyper was determined by comparing the results with WGS. Clustering concordance was assessed using the adjusted Rand and Wallace indices. MLST and cgMLST identified sequence types (ST) and complex types (CT), revealing suspected outbreak isolates with a predominance of ST17 and CT6553, were confirmed by WGS. For the IR-Biotyper, the proposed optimal clustering cut-off range was 0.106-0.111. Despite lower within-run precision, of the IR-Biotyper, the clustering concordance with WGS was favorable, meeting the criteria for real-time screening. This study confirmed a nosocomial outbreak of VREFM in the NICU using an IR-Biotyper, showing promising results compared to MLST. Although within-run precision requires improvement, the IR-Biotyper demonstrated high discriminatory power and clustering concordance with WGS. These findings suggest its potential as a real-time screening tool for the detection of VREFM-related nosocomial outbreaks.

IMPORTANCE

In this study, we evaluated the performance of the IR-Biotyper in detecting nosocomial outbreaks caused by vancomycin-resistant Enterococcus faecium, comparing it with MLST, cgMLST, and WGS. We proposed a cutoff that showed the highest concordance compared to WGS and assessed the within-run precision of the IR-Biotyper by evaluating the consistency in genetically identical strain when repeated in the same run.

Genomic epidemiology and molecular characteristics of blaNDM-1-positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa

PURPOSE

The emergence of carbapenem-resistant P. aeruginosa (CRPA) harbouring acquired carbapenemase genes (blaVIM, blaIMP and blaNDM) has become a global public health threat. Three CRPA isolates included in the study had an extensively drug-resistant phenotype with susceptibility to colistin only and were positive for the blaNDM-1 gene. The current study aimed to investigate the genomic epidemiology and molecular characteristics of the blaNDM-1-positive CRPA isolates collected from the Gauteng region, South Africa.

METHODS

Short read whole genome sequencing (WGS) was performed to determine sequence types (STs), genetic relatedness, resistome, virulome and the genetic environment of the blaNDM-1 gene.

RESULTS

The WGS and phylogenetic analyses revealed that the study isolates belonged to an international high-risk clone ST773 and belonged to the same clade with eight blaNDM-1-positive ST773 isolates from Hungary, India, Nigeria, South Korea and USA. The study isolates harboured a wide repertoire of intrinsic and acquired antibiotic resistance genes (ARGs) related with mobile genetic elements, porins and efflux pumps, as well as virulence factor genes. The clade-specific ARGs (blaNDM-1, floR2/cmlA9, rmtB4, tetG) were found in a putative integrative and conjugative element (ICE) region similar to ICE6660-like.

CONCLUSION

As ICE carrying the blaNDM-1 gene can easily spread to other P. aeruginosa isolates and other Gram-negative bacteria, the findings in this study highlight the need for appropriate management strategies and active surveillance of CRPA isolates in the Gauteng region, South Africa.