The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Isolation and molecular characterization of Shiga toxin-producing Escherichia coli (STEC) from bovine and porcine carcasses in Poland during 2019-2023 and comparison with strains from years 2014-2018

The presence of Shiga toxin-producing Escherichia coli (STEC) on bovine and porcine carcasses during 2019-2023 was investigated. A total of 368 bovine and 87 porcine carcasses were tested using the ISO/TS 13136 standard and the STEC isolates were further characterized with whole genomic sequencing (WGS). It was found that 119 (32.3 %) of bovine and 14 (16.1 %) of porcine carcasses were positive for the stx Shiga toxin gene. Further analysis of the stx-positive samples allowed to isolate 32 (26.9 %) bovine and two (14.3 %) porcine STEC, respectively. Bovine isolates were classified into 21 different serotypes with the most prevalent O168:H8 (3 isolates), whereas two porcine STEC belonged to two serotypes that were not identified in bovine strains. Isolates of bovine carcass origin were mainly positive for the stx2 Shiga toxin gene, either alone or in combination with stx1 type (26 of 32; 81.2 % isolates). Two STEC from porcine carcasses were positive for the stx2e variant only. All STEC, irrespective of the origin, were negative for the eae intimin gene. MLST and cgMLST analyses of all strains tested revealed that they were diverse. However, a close molecular relationship between some bovine isolates based on cgMLST schemes was observed. Comparison of the current bovine STEC with those isolated between 2014 and 2018 showed that some of them consisted of the same MLST sequence types. However, based on cgMLST analysis only two cases of three genomes of STEC isolates each (two from period 2019-2023 and one isolated between 2014 and 2018) revealed up to 50 allelic differences.

Emergence of polymyxin-resistant Yersinia enterocolitica strains in natural aquatic environments

Aquatic environments serve as ideal reservoirs for antibiotic-resistant bacteria and resistance genes. However, the presence of polymyxin-resistant Yersinia enterocolitica, the pathogen responsible for human yersiniosis, in aquatic environments remains poorly understood. Herein, we isolated polymyxin-resistant Y. enterocolitica strains from natural water for the first time. In addition to intrinsic resistance to ampicillin and cefazolin, the strains demonstrated high resistance to polymyxin B and polymyxin E. All isolates were capable of biofilm production and exerted high virulent effects in Galleria mellonella, with 90% mortality occurring within 48 h post-infection. Furthermore, whole genome sequencing identified 26 antibiotic resistance genes, including polymyxin resistance determinants (arnA and PmrF), beta-lactam resistance determinants (vatF and blaA), and 60 virulence genes such as yaxA and yaxB in Y. enterocolitica isolates. Notably, phylogenetic analysis revealed that Y. enterocolitica involved multilocus sequence types ST937 and ST631, which were clustered with strains isolated from a human in the United States or swine in China. The close relatedness to clinical isolates suggests that polymyxin-resistant Y. enterocolitica may pose considerable health risk to humans. Our findings provide evidence of the presence of polymyxin-resistant Y. enterocolitica in aquatic environments and raise concerns about health risks due to their potential high virulence.

Genomic Comparison of Reoccurring, Emerging, and Persistent (REP) Shiga Toxin-Producing Escherichia coli O157:H7

Escherichia coli O157:H7 strains associated with several recent (2017-2020) multi-state outbreaks linked to leafy green vegetables have been characterized as "reoccurring, emerging, and persistent" (REP). Our recent unpublished work demonstrated that the REP strains had significantly enhanced potential for biofilm formation. In this study, comparative genomic analyses were conducted for a better understanding of the mechanisms behind the enhanced biofilm formation, and thereby potentially increased environmental fitness, by the REP strains. Phylogenetically, the recent outbreak strains formed two distinct clusters represented by REPEXH01 and REPEXH02. Compared with EDL933 and other previous outbreak reference strains, the REP strains (clustering with REPEXH02) exhibiting strong biofilm formation were found to have acquired two genes encoding proteins of unknown functions (hypothetical proteins) and lost certain prophage-related genes. In addition, several single nucleotide polymorphisms in genes related to biofilm formation were identified.

A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex

Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies. Whole-genome sequencing enables studies to scale up to genomic levels but necessitates extended schemes. We have developed a 639-loci core genome MLST (cgMLST) scheme for Borrelia burgdorferi sensu lato (s.l.) that enables unambiguous genotyping and improves the robustness of phylogenies and lineage resolution within species. Notably, all inner nodes of the cgMLST phylogenies had consistently high statistical support. Analyses of the genetically homogeneous European B. bavariensis population support the notion that cgMLST provides high discriminatory power even for closely related isolates. While isolates differed maximally in one MLST locus, there were up to 179 cgMLST loci differences. Thus, the developed cgMLST scheme for B. burgdorferi s.l. resolves lineages at a finer resolution than MLST and improves insights into the evolutionary history of the species complex.

Salmonella pathogenicity Island 1 undergoes decay in serovars adapted to swine and poultry

Human salmonellosis is a high-priority foodborne disease worldwide. The main reservoir of Salmonella is livestock, mainly swine and poultry that are infected both by generalist serovars and serovars adapted to them. The most widespread livestock-adapted serovars are attenuated in both their primary hosts and humans. We previously identified a lineage of the swine-adapted Salmonella Derby carrying mutations in Salmonella Pathogenicity Island-1(SPI-1) giving attenuation. To evaluate if SPI-1 decay is a general feature of swine-adapted serovars, we analyzed the Enterobase global population of Salmonella serovars most frequently isolated from swine. We found that deleterious mutations in SPI-1 are accumulated more in swine-adapted (S. Derby and Salmonella Rissen) than in generalist (Salmonella Typhimurium, I 1,4,[5],12:i:-, and Salmonella Infantis) serovars. The genomes carrying such mutations are widespread in the population of S. Derby and S. Rissen, indicating that the occurrence and fixation of deleterious mutations in SPI-1 are frequent. Similarly, also poultry-adapted Salmonella Kentucky has accumulated deleterious mutations in SPI-1, leading to over 70% of mutated genomes of this serovar compared with negligible proportions of mutated genomes in the generalist serovars from poultry. Although in vitro attenuation of S. Derby carrying mutated SPI-1 had been previously demonstrated, we showed the same phenotype for mutated S. Rissen. Considering also the known attenuation of S. Kentucky, our population-scale findings provide evidence of progressive evolution toward the attenuation of serovars adapted to the main animal reservoirs of human salmonellosis through the food chain. Intensive farming with a high density of animals could be a possible driver of this evolution.IMPORTANCEThis study shows at the global population level of Salmonella that the main attenuated serovars adapted to food-producing animals are undergoing convergent evolution toward further attenuation through the decay of SPI-1, considered critically important for the intestinal phase of Salmonella infection. The drivers of this evolution are unknown, but they could be attributed, at least in part, to the intensive farming of livestock with its high densities. On one side, our results contribute to the knowledge of the interaction between livestock populations and their host-adapted serovars of Salmonella. On the other side, the study provides scientific background for reconsidering the microbiological criteria adopted by the food safety legislation of many countries that ask for the absence of Salmonella in foods, regardless of any virulence evaluation of the detected strain. In this respect, the study provides molecular bases to investigate the virulence of different lineages within these host-adapted serovars.

Genomic perspective on the bacillus causing paratyphoid B fever

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

Epidemiological and genomic analysis revealed the significant role of flies in dissemination of carbapenem-resistant Enterobacteriaceae (CRE) in China

While the role of flies as potential vectors for bacterial transmission is well recognized, the epidemiological features and genomic characteristics of associated antimicrobial-resistant strains remain underexplored. This study conducted a nationwide surveillance including 3689 flies and 838 isolates from sixteen human communities (HCs) and eight animal farms (AFs) across 21 provinces in China. Our findings revealed high carriage rates of carbapenem-resistant Enterobacteriaceae (CRE) in flies, with 27.0 % in AFs and 15.3 % in HCs. Among the 705 CRE strains identified, Providencia spp. (n = 356) and Escherichia coli (n = 231) were predominant, with 90.6 % attributed to the dissemination of the blaNDM gene. Phylogenetic tree analysis highlighted frequent clonal transmission events, with over 18 and 13 clonal evolutionary clades in Providencia spp. and E. coli, respectively. Notably, spearman analysis linked the increase of CRE prevalence in AFs flies to environmental factors like precipitation (p < 0.028) and temperature (p < 0.037), while in HCs, it positively corelated with the total meat production (p < 0.027) in each province except for Hainan. Despite significant differences in ciprofloxacin resistance (p ≤ 0.001) among E. coli strains from HCs and AFs, core genome cluster analysis and Uniform Manifold Approximation and Projection (UMAP) approach indicated these strains exhibiting close relatedness to clinical strains. This comprehensive study underscores the critical role of flies in the escalation of CRE spread within the ecosystem in China. Flies found in both HCs and AFs contribute to the dissemination of CRE, highlighting the need for urgent interventions to address this pressing issue.

Emergence of Salmonella enterica Serovar Heidelberg Producing OXA 48 Carbapenemase in Eastern Algeria

Salmonella infections have become increasingly resistant to antibiotics, including fluoroquinolones, third-generation cephalosporins (C3G), and even carbapenems. This report describes the emergence of a strain of Salmonella enterica serovar Heidelberg that produces the carbapenemase OXA 48. The strain was isolated from a stool sample taken from a newborn. Antimicrobial susceptibility testing was carried out following the recommendations of the Clinical and Laboratory Standard Institute. Whole genome sequencing was performed on MiSeq Illumina™. The strain was resistant to ertapenem (minimal inhibitory concentration [MIC] = 12 µg/mL), intermediate to imipenem (MIC = 1.5 µg/mL), resistant to nalidixic acid, and intermediate to fluoroquinolones but was susceptible to C3G, cotrimoxazole, chloramphenicol, and colistin (MIC = 0.064 µg/mL). The strain was identified as ST-15. The strain of Salmonella Heidelberg ST-15 was found to have antimicrobial resistance genes, specifically blaOXA-48, aac(6')-Iaa and fosA7, which mediate resistance to carbapenems, aminoglycosides and fosfomycin, respectively. Additionally, mutations were detected in the gyrA, parC. Three plasmid replicon type IncL, IncX1, and Col156 have been identified. The strain has the potential to cause an epidemic. The genomic analysis of the strain allowed us to understand the mechanisms of resistance. Preventing the spread of Salmonella carbapenemase-producing strains is crucial, particularly in hospital settings. Epidemiological measures are necessary to achieve this goal.

Demographic, clinical and molecular epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli bloodstream infections in Central Australia

We describe the demographics, clinical and molecular epidemiology of extended-spectrum β-lactamase (ESBL) Escherichia coli bloodstream infections (BSI) in Central Australia. All ESBL-producing E. coli bloodstream isolates from January 2018 to December 2020 were retrospectively identified. Demographic and clinical information was extracted by chart review. Whole-genome sequencing was performed for multi-locus sequence typing, antibiotic-resistance genes, and phylogenetic relationships. We identified 41 non-duplicate episodes of ESBL E. coli BSI. Median age was 55 years (IQR 47-63), 78% were female, 93% were Aboriginal, and half came from a remote community. Infections were predominantly urinary (68%, 28/41). In the 12 months prior, 70% (26/37) of identified patients had been hospitalised and 81% (30/37) prescribed antibiotics. Meropenem and piperacillin-tazobactam susceptibility was maintained in 100% and 95% of isolates, respectively. Co-resistance to non-β-lactam antibiotics was 32% to gentamicin, 61% to trimethoprim/sulfamethoxazole, and 68% to ciprofloxacin. For sequenced isolates, 41% (16/35) were sequence type 131 (ST131). Mean acquired antibiotic-resistance genes for each isolate was 12.3 (SD 3.1). Four isolates carried an OXA-1 gene. Only non-ST131 isolates carried AmpC and acquired quinolone-resistance genes. There was some evidence of clustering of closely related strains, but no evidence of community or healthcare admission overlap. ESBL rates are rapidly rising in Central Australia, which is a conducive environment for antibiotic resistance development (e.g., overcrowding, socioeconomic disadvantages, high healthcare exposure and high antibiotic use). Future research is required to explore resistance-transmission dynamics in this unique setting.

AmpC β-lactamases detected in Southeast Asian Escherichia coli and Klebsiella pneumoniae

Objectives

AmpC β-lactamases are neglected compared with ESBL as a cause of third-generation cephalosporin (3GC) resistance in Enterobacterales in low- and middle-income countries and the burden is unknown. The aim of this study was to investigate the presence of AmpC β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in clinical specimens from three clinical research laboratories in Southeast Asia.

Methods

Stored clinical isolates of E. coli and K. pneumoniae resistant to ceftriaxone or ceftazidime or cefpodoxime and ESBL confirmation test negative were screened using MASTDISCS AmpC, ESBL and Carbapenemase Detection Set-D72C. Short-read WGS was performed to identify ampC genes.

Results

Of 126 isolates collected between 2010 and 2020, 31 (24.6%) and 16 (12.7%) were phenotypically AmpC and inducible AmpC positive by MASTDISCS testing, respectively. All inducible AmpC isolates were ceftriaxone susceptible and 97.7% of AmpC/inducible AmpC isolates tested against cefoxitin were resistant. Through WGS, 17 and eight different STs were detected for the AmpC/inducible AmpC E. coli and K. pneumoniae isolates, respectively. Twelve different β-lactamase resistance genes were detected, with bla CMY-2 most commonly in AmpC-positive isolates (20/31; 64.5%; 15 chromosomal, five plasmid). All inducible AmpC-positive isolates had the bla DHA-1 gene (seven chromosomal, nine plasmid).

Conclusions

Though uncommon, AmpC and inducible AmpC β-lactamases in E. coli and K. pneumoniae are an important cause of infection in Southeast Asia. With current testing methods, these infections may be going undetected, resulting in patients receiving suboptimal treatment.

Escherichia coli novel sequence type 11873 harbours a new CTX-M-15-carrying multidrug resistance type 1/2 hybrid IncC plasmid

OBJECTIVE

The aim of the current study was to determine the genomic map of the resistance genes of two CTX-M-15-carrying Escherichia coli strains belonging to novel sequence type (ST) 11873. Complete, closed genome sequences of the E. coli strains were obtained by applying a combination of short-read Illumina and long-read Oxford Nanopore-based sequencing.

METHODS

Isolation of E. coli was performed using ECC CHROMagar and antibiotic sensitivity patterns were determined using Sensititre EUVSEC plates. Whole-genome sequencing was performed for two E. coli strains (3-338 and 5-325) using Illumina MiSeq- and Oxford Nanopore MinION-based sequencing.

RESULTS

The complete genome of strain 3-338 (GenBank accession no. CP130007-17) was assembled into a circular chromosome of 4.65 Mb and 10 plasmids (between 2 and 148 kb). Strain 5-325 (CP130018-27) exhibited a circular chromosome of 4.7 Mb and 9 plasmids (between 2 and 148 kb). Both strains carried an identical type 1/2 hybrid IncC plasmid (∼148 kb) harbouring multiple antibiotic resistance genes (ARGs), including blaCTX-M-15, blaOXA-1, blaTEM-1, qnrS1, sul2, aphA1, aacC2, mph(A) and floR. This plasmid also carried heavy metal resistance genes, such as chrA and arsR. Strain 5-325 carried an additional IncFIB plasmid (∼78 kb) harbouring additional ARGs, including blaTEM-1, qnrS1, tet(A), dfrA14, sul2, strA and strB.

CONCLUSIONS

Our study shows the emergence of a CTX-M-15-carrying type 1/2 hybrid IncC plasmid in novel E. coli ST11873. These findings emphasise the need for population-based sewage surveillance for understanding the prevalence of antibiotic resistance in pathogens in order to mitigate the further spread of such resistance factors.

High carriage and possible hidden spread of multidrug-resistant Salmonella among asymptomatic workers in Yulin, China

Food workers have frequent contact with unprocessed foods, but their carriage of Salmonella and potential influence on public health have not been comprehensively assessed. We investigated Salmonella carriage among food workers compared with non-food workers based on occupational health screening of 260,315 asymptomatic workers over an 8-year surveillance period in Yulin, China. We confirmed that healthy carriers serve as natural reservoirs for Salmonella, with higher carriage rates in food workers than non-food workers. The isolates from food workers also exhibited greater serovar diversity and likely higher levels of antimicrobial resistance than those from non-food workers. Factors such as meteorological, social, and hygiene factors potentially influenced the carriage rate. Genomic analysis revealed a consistent increase in antimicrobial resistance genes among Salmonella isolates over the study period, with the majority of these antimicrobial resistance genes located on plasmids. Additionally, we identified numerous closely related bacterial clusters, which might reflect clusters of hidden local foodborne infections. This study underscores the elevated risk posed by food workers in the persistence and dissemination of Salmonella as vectors/fomites. Enhanced monitoring and targeted interventions in this group may reduce the dissemination of pathogens and antimicrobial resistance genes.

Survey in ruminants from Rwanda revealed high diversity and prevalence of extended-spectrum cephalosporin-resistant Enterobacterales

BACKGROUND

Antimicrobial resistance (AMR) in Enterobacterales constitutes a significant threat to the health of both humans and animals and a socioeconomic problem. Enterobacterales, mainly Escherichia coli, carrying β-lactamases has become one of the main indicators to estimate the burden of AMR in animals within "One Health" approach.

OBJECTIVES

To assess the presence of extended-spectrum cephalosporin-resistant Enterobacterales associated with ruminants (cattle, sheep, goats) habituated in all five provinces of Rwanda and to perform in depth characterization of isolates.

METHODS

We screened 454 rectal swabs from 203 cows, 170 goats, and 81 sheep and selective isolation of extended-spectrum cephalosporin-resistant Enterobacterales was conducted. Isolates were identified as a members of the order Enterobacterales by MALDI-TOF MS and further characterized by susceptibility testing and by whole-genome sequencing.

RESULTS

Out of the 454 samples, 64 extended-spectrum cephalosporin-resistant Enterobacterales were isolated from 58 animals. Isolates belonged to seven bacterial species and were identified as Escherichia coli (n = 54), Enterobacter bugandensis (n = 4), Enterobacter mori (n = 2), Klebsiella pneumoniae (n = 2), Enterobacter dykesii (n = 1), and Citrobacter freundii (n = 1). All isolates displayed an Extended-spectrum β-lactamases (ESBL) phenotype, with exception of Citrobacter freundii isolate displayed both an ESBL and AmpC phenotype. In addition, all Enterobacter isolates were identified as stably de-repressed AmpC-producers. ESBLs genes, blaCTX-M-15 was predominant. Resistance to tetracycline and tet(A) was most frequently observed among non-β-lactam resistance. Forty-eight isolates displayed multidrug-resistance phenotypes. A shiga toxin-producing E. coli and an enterotoxigenic E. coli isolate were observed. Genome comparisons revealed thirty-five E. coli sequence types (ST) (ST10, ST307 being predominate).

CONCLUSIONS

Considering the high proximity between ruminants and humans in Rwanda, the dissemination of antimicrobial drug resistance highlights the public health threats and requires the joint and multisectoral action of human and veterinary medicine, at human-animal-environment interfaces. Therefore, it is important to establish national and global "One Health" surveillance programs of AMR to tackle the antibiotic-resistant crisis in human and veterinary medicine.

Comparison of three source attribution methods applied to whole genome sequencing data of monophasic and biphasic Salmonella Typhimurium isolates from the British Isles and Denmark

Methodologies for source attribution (SA) of foodborne illnesses comprise a rapidly expanding suite of techniques for estimating the most important source or sources of human infection. Recently, the increasing availability of whole genome sequencing (WGS) data for a wide range of bacterial strains has led to the development of novel SA methods. These techniques utilize the unique features of bacterial genomes adapted to different host types and hence offer increased resolution of the outputs. Comparative studies of different SA techniques reliant on WGS data are currently lacking. Here, we critically assessed and compared the outputs of three SA methods: a supervised classification random forest machine learning algorithm (RandomForest), an Accessory genes-Based Source Attribution method (AB_SA), and a Bayesian frequency matching method (Bayesian). Each technique was applied to the WGS data of a panel of 902 reservoir host and human monophasic and biphasic Salmonella enterica subsp. enterica serovar Typhimurium isolates sampled in the British Isles (BI) and Denmark from 2012 to 2016. Additionally, for RandomForest and Bayesian, we explored whether utilization of accessory genome features as model inputs improved attribution accuracy of these methods over using the core genome derived features only. Results indicated that this was the case for RandomForest, but for Bayesian the overall attribution estimates varied little regardless of the inclusion or not of the accessory genome features. All three methods attributed the vast majority of human isolates to the Pigs primary source class, which was expected given the known high relative prevalence rates in pigs, and hence routes of infection into the human population, of monophasic and biphasic S. Typhimurium in the BI and Denmark. The accuracy of AB_SA was lower than of RandomForest when attributing the primary source classes to the 120 animal test set isolates with known primary sources. A major advantage of both AB_SA and Bayesian was a much faster execution time as compared to RandomForest. Overall, the SA method comparison presented in this study describes the strengths and weaknesses of each of the three methods applied to attributing potential monophasic and biphasic S. Typhimurium animal sources to human infections that could be valuable when deciding which SA methodology would be the most applicable to foodborne disease outbreak scenarios involving monophasic and biphasic S. Typhimurium.

Molecular characteristics of CTX-M β-lactamase-producing and quinolone-resistant Escherichia coli among deer in a popular tourist spot in Japan

Introduction. Antimicrobial resistance (AMR) is a growing global concern. Clonal lineages of CTX-M β-lactamase-producing Escherichia coli (CTXE) and quinolone-resistant E. coli (QREC) were disseminated among the deer population in a famous tourist destination (Nara Park; NP) in Japan. Hypothesis/gap statement. The molecular characteristics of CTXE or QREC isolates, which could pose a threat to public health, have not been elucidated. Aim. This study aimed to characterize the genetic traits of CTXE and QREC isolates derived from NP deer and compare them with lineages prevalent worldwide. Methodology. Sixteen CTXE and three QREC isolates recovered from NP deer faeces between 2018 and 2020 were analysed using whole-genome sequencing (WGS). For endemic lineages, phylogenetic trees were constructed against the isolates registered in the EnteroBase database using the core genome SNP scheme. Results. The most prevalent lineage in NP deer was ST3580. Several pandemic lineages, such as sequence type (ST) 38, ST58 and ST117, were included. The QREC lineages prevalent among deer were designated as extra-intestinal pathogenic E. coli or uropathogenic E. coli (UPEC). Thirteen of the 24 antimicrobial resistance genes (ARGs) were considered high-risk ARG families. Chromosomal integration of bla CTX-M-15 was observed in all plasmid-negative isolates. Phylogenetic analysis suggested relationships between NP isolates and isolates sourced from the environment or poultry. Conclusion. ST3580 has a high potential for clonal dissemination. Furthermore, multiple clinically relevant lineages of CTXE and QREC are endemic in NP deer; however, they could be less virulent than isolates belonging to the same lineages, which could cause severe infectious diseases. Further studies are required to investigate the relationship between chromosomal integration of plasmid-encoded genes and the stable propagation of AMR bacteria in wildlife and the environment.

KleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide

BACKGROUND

Clinically important lineages in Klebsiella, especially those expressing multi-drug resistance (MDR), pose severe threats to public health worldwide. They arose from the co-evolution of the vertically inherited core genome and horizontal gene transfers by plasmids, which has not been systematically explored.

METHODS

We designed KleTy, which consists of dedicated typing schemes for both the core genome and plasmids in Klebsiella. We compared the performance of KleTy with many state-of-the-art pipelines using both simulated and real data.

RESULTS

Employing KleTy, we genotyped 33,272 Klebsiella genomes, categorizing them into 1773 distinct populations and predicting the presence of 87,410 plasmids from 837 clusters (PCs). Notably, Klebsiella is the center of the plasmid-exchange network within Enterobacteriaceae. Our results associated the international emergence of prevalent Klebsiella populations with only four carbapenem-resistance (CR) PCs, two hypervirulent PCs, and two hvCR-PCs encoding both carbapenemase and hypervirulence. Furthermore, we observed the ongoing international emergence of blaNDM, accompanied by the replacement of the previously dominant population, blaKPC-encoding HC1360_8 (CC258), during 2003-2018, with the emerging blaNDM-encoding HC1360_3 (CC147) thereafter. Additionally, expansions of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hvCRKP) were evidenced in both populations, driven by plasmids of MDR-hypervirulence convergences.

CONCLUSIONS

The study illuminates how the global genetic landscape of Klebsiella has been shaped by the co-evolution of both the core genome and the plasmids, underscoring the importance of surveillance and control of the dissemination of plasmids for curtailing the emergence of hvCRKPs.

Genomic and Transcriptomic Comparison Between Invasive Non-Typhoidal Salmonella and Non-Invasive Isolates

Invasive non-typhoidal Salmonella (iNTS) poses a significant threat to global public health. Salmonella enterica Enteritidis and Typhimurium are the primary serovars responsible for both invasive diseases and gastroenteritis. This study aims to investigate the genomic and transcriptomic differences between isolates associated with these contrasting clinical presentations. We retrieved genomes of Salmonella Enteritidis and Salmonella Typhimurium from Enterobase, utilizing blood and stool isolates as representatives for iNTS and non-iNTS, respectively. An indistinguishable phylogenetic relationship was revealed between the blood and stool isolates for both serovars. Few genes were specifically identified in iNTS. Random forest and principal coordinates analysis permitted moderate discrimination between the two sources of isolates based on overall genome content. Notably, the blood isolates of Salmonella Typhimurium displayed an elevated level of antimicrobial resistance and genome degradation compared to stool isolates. Meanwhile, transcriptome sequencing identified few genes that were differentially expressed between blood and stool isolates. Hierarchical clustering and principal component analysis did not effectively differentiate the expression profile of iNTS from non-iNTS. In summary, few genes could serve as reliable biomarkers to distinguish iNTS and non-iNTS at either the genomic or transcriptomic level. Nevertheless, iNTS has indeed accumulated subtle genomic differences from non-iNTS, which might contribute to invasiveness.

Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most prevalent serovars worldwide. Even though these serovars have been the focus of many studies, their spread has not yet been investigated in French pig herds and slaughterhouses at a regional scale. Here, we characterized the genomic diversity of 188 Salmonella strains belonging to sequence type (ST) 19 and 34. These strains were isolated from pigs in metropolitan France between 2014 and 2019. Samples were collected from 10 regions, three of which together represent 75% of French pig production in 2020. To contextualize the French Salmonella genomes at a worldwide level, 193 ST 34 genomes from three continents and 14 countries were also included. This study revealed little diversity in ST 34 strains circulating in France, suggesting that one or two clones are spreading within pig herds and slaughterhouses. In silico virulence and antimicrobial resistance genes were investigated to understand the prevalence of these strains among farmed pigs and in the slaughterhouse environment. A comparison with ST 34 isolates from other countries highlighted the genomic specificity of the ST 34 monophasic variants in France, with some exceptions concerning isolates from bordering countries. This work provides new insights into the dynamics of S. Typhimurium and its monophasic variant sampled in French pig herds and slaughterhouses.

IMPORTANCE

Salmonellosis is a leading cause of bacterial infection in humans and animals around the world. This study provides a snapshot of the genomic diversity of one of the most prevalent Salmonella serovars (Salmonella Typhimurium and Salmonella 4,[5],12:i:-) circulating on French pig farms between 2013 and 2021. We investigated the link between geographical and genomic diversity. The analyses revealed little diversity of the strains, suggesting that one or two clones are spreading within French pig herds. We also in silico screened genetic elements that could explain the prevalence of these strains among farmed pigs and in the slaughterhouse environment. Finally, the comparison with isolates from other countries highlighted the genomic specificity of these two French sequence type 34 clones. This work provides new insights into the dynamics of S. Typhimurium and S. 4,[5],12:i:- sampled from pig herds and slaughterhouses in France, thus laying the foundations for future analyses.

Evaluation of a microfluidic-based point-of-care prototype with customized chip for detection of bacterial clusters

Bacterial infection clusters cause high mortality rates and healthcare costs due to excessive therapy and hygiene measures. The aim of this study was to develop an automated real-time PCR-based point-of-care (POC) system with a customized microfluidic chip that facilitates fast detection of bacterial cluster isolates by targeting cluster-specific single-nucleotide polymorphisms (SNPs). For cluster detection of Acinetobacter baumannii, Staphylococcus aureus, and Escherichia coli, nine TaqMan real-time PCR assays targeting cluster-specific SNPs were designed. Additionally, for DNA input control, a universal PCR amplifying the 16S rDNA was constructed. All reactions were implemented into a microfluidic chip that was analyzed by a POC prototype enabling automated sample processing, fluid handling, and signal detection. Performance of the prototype was evaluated using 45 chips loaded with defined bacterial solutions, including swab eluates. For seven PCRs, implementation into the microfluidic chip was successful, leading to correct identification of all SNPs specific for A. baumannii and E. coli cluster isolates and delineation of all non-cluster strains within 70 min. The remaining three reactions failed in the chip, which resulted in misidentification of the S. aureus cluster. Sensitivity, specificity, and accuracy of the prototype were 43%, 88%, and 55%, respectively. The detection limit was PCR dependent and ranged between 103 and 105 colony-forming units/mL. Once optimized, the microfluidic POC system for cluster detection could be applied as time-saving and easy-to-use method to complement whole-genome sequencing efforts during screening for bacterial clusters.

IMPORTANCE

Especially in medical facilities, where morbid people are nursed in close distance to each other, pathogenic bacteria can accumulate and spread. To contain such infection clusters, usually time- and labor-intensive large-scale screening assays are conducted, where patients and patient-side surfaces are sampled, and PCR or whole-genome sequencing analyses are conducted to confirm or deny cluster affiliation of cultivated bacteria. Hence, fast solutions with easy application are required to complement the current state-of-the-art technology for cluster surveillance. Here, we developed a fully automated microfluidic point-of-care prototype that identified bacterial cluster isolates within 70 min from bacterial solutions, including swab eluates. The system requires only low hands-on time and can be applied apart from laboratory infrastructures near the patient, which considerably reduces the time from sampling to result. This ensures fast implementation of hygiene measures and quick containment of the infection cluster, which would enhance patients' safety and outcome.

Investigating the adherence factors of Escherichia coli at the bovine recto-anal junction

Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens that result in thousands of hospitalizations each year in the United States. Cattle, the natural reservoir, harbor STEC asymptomatically at the recto-anal junction (RAJ). The molecular mechanisms that allow STEC and non-STEC E. coli to adhere to the RAJ are not fully understood, in part because most adherence studies utilize human cell culture models. To identify a set of bovine-specific E. coli adherence factors, we used the primary RAJ squamous epithelial (RSE) cell-adherence assay to coculture RSE cells from healthy Holstein cattle with diverse E. coli strains from bovine and nonbovine sources. We hypothesized that a comparative genomic analysis of the strains would reveal factors associated with RSE adherence. After performing adherence assays with historical strains from the E. coli Reference Center (n = 62) and strains newly isolated from the RAJ (n = 15), we used the bioinformatic tool Roary to create a pangenome of this collection. We classified strains as either low or high adherence and using the Scoary program compiled a list of accessory genes correlated with the "high adherence" strains. While none of the correlations were statistically significant, several gene clusters were associated with the high-adherence phenotype, including two that encode uncharacterized proteins. We also demonstrated that non-STEC E. coli strains from the RAJ are more adherent than other isolates and can outcompete STEC in coculture with RSEs. Further analysis of adherence-associated gene clusters may lead to an improved understanding of the molecular mechanisms of RSE adherence and may help develop probiotics targeting STEC in cattle.

IMPORTANCE

E. coli strains that produce Shiga toxin cause foodborne illness in humans but colonize cattle asymptomatically. The molecular mechanisms that E. coli uses to adhere to cattle cells are largely unknown. Various strategies are used to control E. coli in livestock and limit the risk of outbreaks. These include vaccinating animals against common E. coli strains and supplementing their feed with probiotics to reduce the carriage of pathogens. No strategy is completely effective, and probiotics often fail to colonize the animals. We sought to clarify the genes required for E. coli adherence in cattle by quantifying the attachment to bovine cells in a diverse set of bacteria. We also isolated nonpathogenic E. coli from healthy cows and showed that a representative isolate could outcompete pathogenic strains in cocultures. We propose that the focused study of these strains and their adherence factors will better inform the design of probiotics and vaccines for livestock.

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.

An ancient ecospecies of Helicobacter pylori

Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a 'Hardy' ecospecies of H. pylori that shares the ancestry of 'Ubiquitous' H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.

Multinational investigation of a Salmonella Umbilo outbreak reveals rocket salad and baby spinach as the likely infection vehicles, Europe, 2024

A food-borne outbreak with about 200 Salmonella Umbilo cases occurred mainly between July and September 2024 in several European countries. Collaborative work between outbreak teams in Germany, Austria and Denmark, including epidemiological and microbiological investigations, allowed to rapidly identify rocket salad as the likely infection vehicle. Salmonella Umbilo was detected in rocket salad, and later in baby spinach. The food isolates and clinical outbreak strain were genetically closely related. Both food items originated from the same company in Italy.

Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan

The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.

Whole-Genome Sequencing Analysis of Antimicrobial Resistance, Virulence Factors, and Genetic Diversity of Salmonella from Wenzhou, China

Salmonella species are important foodborne pathogens worldwide. Salmonella pathogenicity is associated with multiple virulence factors and enhanced antimicrobial resistance. To determine the molecular characteristics and genetic correlations of Salmonella, 24 strains of Salmonella isolated from different sources (raw poultry, human stool, and food) in the Wenzhou area were investigated to determine the distribution of antimicrobial resistance and virulence determinants using whole-genome sequencing (WGS). Aminoglycoside resistance genes were detected in all samples. Over half of the samples found antimicrobial resistance genes (ARGs) and point mutations for several clinically frequently used antibiotic, beta-lactams, tetracyclines, and quinolones. Of these strains, 62.5% were predicted to be multidrug-resistant (MDR). The quinolone-modifying enzyme gene aac(6')-Ib-cr, detected in five samples (S1-S4 and S10), was located on integrons. The analysis of Salmonella pathogenicity island (SPI) profiles suggests that serotypes with close genetic relationships share the same distribution of virulence factors, revealing a link between genotype and SPI profiles. cgMLST analysis indicated that five isolates S14-S18 were closely related to strains originating from the United Kingdom, suggesting that they may share a common origin. Data from this study may enrich the molecular traceability database for Salmonella and provide a basis for effective public health policies.

EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens

This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently >1.1 million bacterial isolates, more recently including Streptococcus spp. and Mycobacterium tuberculosis, in addition to Salmonella,Escherichia/Shigella,Clostridioides,Vibrio,Helicobacter,YersiniaandMoraxella. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualizing bacterial genomic population structures, based on pre-computed hierarchical clusters. Access to data and analysis tools is provided through an enhanced graphical user interface and a new application programming interface (RESTful API). EnteroBase is now being developed and operated by an international consortium, to accelerate the development of the platform and ensure the longevity of the resources built. EnteroBase can be accessed at https://enterobase.warwick.ac.uk as well as https://enterobase.dsmz.de.

Conventionally Reared Wallon Meat Lambs Carry Transiently Multi-Drug-Resistant Escherichia coli with Reduced Sensitivity to Colistin Before Slaughter

Major efforts have been made to reduce the use of colistin in livestock since the discovery of the plasmid-borne mobile colistin resistance (mcr) gene in E. coli a decade ago, to curb the burden of its potential transmission to other bacterial species, spread between animals, humans and the environment. This study explored the longitudinal prevalence and characteristics of colistin-resistant and extended-spectrum beta-lactamase-producing (ESBL) E. coli via in vivo fecal and ex vivo carcass swabs from two batches of conventional indoor and organic outdoor Wallon meat sheep from birth to slaughter in 2020 and 2021. Antimicrobial susceptibility testing via broth microdilution revealed that n = 16/109 (15%) E. coli isolates from conventional meat lamb fecal samples had a reduced colistin sensitivity (MIC = 0.5 μg/mL) and thereof, n = 9/109 (8%) were multi-drug-resistant E. coli, while no resistant isolates were recovered from their carcasses. Sequencing revealed causative pmrB genes, indicating that the reduced sensitivity to colistin was not plasmid-borne. While the sample size was small (n = 32), no colistin-resistant and ESBL-producing E. coli were isolated from the organic meat sheep and their carcasses, potentially due to the different husbandry conditions. Prudent and judicious antimicrobial use and strict slaughter hygiene remain imperative for effective risk management to protect consumers in a sustainable One Health approach.

Klebsiella pneumoniae, a human-dog shuttle organism for the genes of CTX-M ESBL

Antimicrobials reserved for human medicines are permitted for companion animals and it is important to understand multidrug-resistant pathogens recovered from companion animals in terms of epidemiological correlation with human pathogens and possibility of transmission to human-beings. Seventeen of each CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP) canine isolates were assessed. Entire genomes of the 34 isolates were sequenced. Plasmid transfer and relative growth rates were assessed at differed temperature conditions indicating the body temperature of dogs, that of human-beings, and environment. ESBL-ECs were clonally diverse, while ESBL-KPs were not. The ESBL-ECs carried the blaCTX-M-15 gene in plasmids and the blaCTX-M-14-like gene either in chromosomes or in plasmids. The ESBL-KPs possessed the blaCTX-M-15 gene in plasmids (n = 15). One of the isolates carried another blaCTX-M-15 gene in a chromosome simultaneously and the other isolate had an additional blaCTX-M-9 gene-harbouring plasmid, together. Two ESBL-KP isolates carried the blaCTX-M-14 gene in plasmids. Plasmid transfer ESBL-EC to K. pneumoniae was efficient and the differed biological costs by temperature was much more in ESBL-EC than in ESBL-KP. Intersectoral dissemination of ESBL-ECs occurred mainly by horizontal gene transfer, while that of ESBL-KPs occurred by clonal dissemination.

Phenotypic and Genotypic Characterization of Escherichia coli and Salmonella spp. Isolates from Pigs at Slaughterhouse and from Commercial Pork Meat in Portugal

Background: Foodborne diseases are a serious public health concern, and food-producing animals are a major source of contamination. Methods: The present study analysed Escherichia coli and Salmonella spp. isolated from faecal samples of 100 fattening pigs and from 52 samples of pork meat. Results: The results showed that the majority of the analysed meat samples were considered satisfactory in terms of microbiological quality (92.3% for E. coli and 94.2% for Salmonella spp.). Salmonella spp. was identified in 5.8% of the meat samples, whereas E. coli was detected in 89.5% of all samples (69.2% in meat and 100% in faecal samples). Furthermore, 1.9% of the faecal samples contained Shiga-toxin-producing E. coli and 3.9% contained enterotoxigenic E. coli. All sequenced isolates presented virulence genes for extraintestinal pathogenic E. coli. Moreover, 75.0% of E. coli isolates from meat and 71.8% from faeces samples showed antibiotic resistance, with 40.7% and 51.4%, respectively, being multidrug-resistant (MDR). The most prevalent resistances were to tetracycline, ampicillin, and sulfamethoxazole, and one E. coli isolate showed resistance to extended-spectrum β-lactamase. Conclusions: This study highlights the role of pigs as a potential source of human contamination and the importance of a One Health approach to ensure food safety and to promote public health.

First report on whole genome sequencing and comparative genomics of Salmonella enterica serovar Abortusequi isolated from Donkey in India

Salmonella enterica subspecies enterica serovar Abortusequi (S. Abortusequi) is a leading cause of abortion in equines that hinders the rapid growth of equine industry. S. Abortusequi infection in equids has re-emerged over last ten years. In the present study, S. Abortusequi was isolated and characterized from donkeys during an abortion storm in the southern peninsular region of India. Further, whole genome sequencing and phylogenomic analysis revealed that the present isolate was clustered among S. Abortusequi clade. The core genome MLST (cgMLST) analysis based on hierarchical clustering and single nucleotide polymorphism (SNP) core-genome dendrogram of the present isolate against 10 S. Abortusequi isolates revealed that the present isolate established a distinct clade compared to all previously reported isolates. A comparison of cgMLST and SNP analyses revealed the same clustering concordance between isolates. In addition, comparative genomics and phylogenetic analysis was carried out with six S. Abortusequi serovars showed a higher number of core genes than accessory genes. Further, comparative analysis of phenotype and genotype antimicrobial resistance revealed a concordance of 32% and discordance of 68% respectively.

Analyzing Antibiotic Resistance in Bacteria from Wastewater in Pakistan Using Whole-Genome Sequencing

Background: Wastewater is a major source of Antibiotic-Resistant Bacteria (ARB) and a hotspot for the exchange of Antibiotic-Resistant Genes (ARGs). The occurrence of Carbapenem-Resistant Bacteria (CRB) in wastewater samples is a major public health concern. Objectives: This study aimed to analyze Antibiotic resistance in bacteria from wastewater sources in Pakistan. Methods: We analyzed 32 bacterial isolates, including 18 Escherichia coli, 4 Klebsiella pneumoniae, and 10 other bacterial isolates using phenotypic antibiotic susceptibility assay and whole-genome sequencing. This study identified the ARGs, plasmid replicons, and integron genes cassettes in the sequenced isolates. One representative isolate was further sequenced using Illumina and Oxford nanopore sequencing technologies. Results: Our findings revealed high resistance to clinically important antibiotics: 91% of isolates were resistant to cefotaxime, 75% to ciprofloxacin, and 62.5% to imipenem, while 31% showed non-susceptibility to gentamicin. All E. coli isolates were resistant to cephalosporins, with 72% also resistant to carbapenems. Sequence analysis showed a diverse resistome, including carbapenamases (blaNDM-5, blaOXA-181), ESBLs (blaCTX-M-15, blaTEM), and AmpC-type β-lactamases (blaCMY). Key point mutations noticed in the isolates were pmrB_Y358N (colistin) and ftsI_N337NYRIN, ftsI_I336IKYRI (carbapenem). The E. coli isolates had 11 different STs, with ST410 predominating (28%). Notably, the E. coli phylogroup A isolate 45EC1, (ST10886) is reported for the first time from wastewater, carrying blaNDM-5, blaCMY-16, and pmrB_Y358N with class 1 integron gene cassette of dfrA12-aadA2-qacEΔ1 on a plasmid-borne contig. Other carbapenamase, blaNDM-1 and blaOXA-72, were detected in K. pneumoniae 22EB1 and Acinetobacter baumannii 51AC1, respectively. The integrons with the gene cassettes encoding antibiotic resistance, and the transport and bacterial mobilization protein, were identified in the sequenced isolates. Ten plasmid replicons were identified, with IncFIB prevalent in 53% of isolates. Combined Illumina and Oxford nanopore sequencing revealed blaNDM-5 on an IncFIA/IncFIC plasmid and is identical to those reported in the USA, Myanmar, and Tanzania. Conclusions: These findings highlight the environmental prevalence of high-risk and WHO-priority pathogens with clinically important ARGs, underscoring the need for a One Health approach to mitigate ARB isolates.

Expression of the locus of enterocyte effacement genes during the invasion process of the atypical enteropathogenic Escherichia coli 1711-4 strain of serotype O51:H40

Atypical enteropathogenic Escherichia coli (aEPEC) is a significant cause of diarrhea in low- and middle-income countries. Certain aEPEC strains, including the Brazilian representative strain of serotype O51:H40 called aEPEC 1711-4, can use flagella to attach to, invade, and persist in T84 and Caco-2 intestinal cells. It can also translocate from the gut to extraintestinal sites in a rat model. Although various aspects of the virulence of this strain were studied and the requirement of a type III secretion system for the efficiency of the invasion process was demonstrated, the expression of the locus of enterocyte effacement (LEE) genes during the invasion and intracellular persistence remains unclear. To address this question, the expression of flagella and the different LEE operons was evaluated during kinetic experiments of the interaction of aEPEC 1711-4 with enterocytes in vitro. The genome of the strain was also sequenced. The results showed that flagella expression remained unchanged, but the expression of eae and escJ increased during the early interaction and invasion of aEPEC 1711-4 into Caco-2 cells, and there was no change 24 h post-infection during the persistence period. The number of actin accumulation foci formed on HeLa cells also increased during the 6-h analysis. No known gene related to the invasion process was identified in the genome of aEPEC 1711-4, which was shown to belong to the global EPEC lineage 10. These findings suggest that the LEE components and the intimate adherence promoted by intimin are necessary for the invasion and persistence of aEPEC 1711-4, but the detailed mechanism needs further study.IMPORTANCEAtypical enteropathogenic Escherichia coli (aEPEC) is a major cause of diarrhea, especially in low- and middle-income countries, like Brazil. However, due to the genome heterogeneity of each clonal group, it is difficult to comprehend the pathogenicity of this strain fully. Among aEPEC strains, 1711-4 can invade eukaryotic cells in vitro, cross the gut barrier, and reach extraintestinal sites in animal models. By studying how different known aEPEC virulence factors are expressed during the invasion process, we can gain insight into the commonalities of this phenotype among other aEPEC strains. This will help in developing preventive measures to control infections caused by invasive strains. No known virulence-encoding genes linked to the invasion process were found. Nevertheless, additional studies are still necessary to evaluate the role of other factors in this phenotype.

Wastewater and environmental sampling holds potential for antimicrobial resistance surveillance in food-producing animals - a pilot study in South African abattoirs

Antimicrobial resistance (AMR) poses a significant global One Health challenge that causes increased mortality and a high financial burden. Animal production contributes to AMR, as more than half of antimicrobials are used in food-producing animals globally. There is a growing body of literature on AMR in food-producing animals in African countries, but the surveillance practices across countries vary considerably. This pilot study aims to explore the potential of wastewater and environmental surveillance (WES) of AMR and its extension to the veterinary field. Floor drainage swab (n = 18, 3/abattoir) and wastewater (n = 16, 2-3/abattoir) samples were collected from six South African abattoirs that handle various animal species, including cattle, sheep, pig, and poultry. The samples were tested for Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase-producing Enterobacterales, Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin-resistant Enterococci (VRE), and Candida auris by using selective culturing and MALDI-TOF MS identification. The phenotype of all presumptive ESBL-producing Escherichia coli (n = 60) and Klebsiella pneumoniae (n = 24) isolates was confirmed with a disk diffusion test, and a subset (15 and 6 isolates, respectively), were further characterized by whole-genome sequencing. In total, 314 isolates (0-12 isolates/sample) withstood MALDI-TOF MS, from which 37 species were identified, E. coli and K. pneumoniae among the most abundant. Most E. coli (n = 48/60; 80%) and all K. pneumoniae isolates were recovered from the floor drainage samples, while 21 presumptive carbapenem-resistant Acinetobacter spp. isolates were isolated equally from floor drainage and wastewater samples. MRSA, VRE, or C. auris were not found. All characterized E. coli and K. pneumoniae isolates represented ESBL-phenotype. Genomic analyses revealed multiple sequence types (ST) of E. coli (n = 10) and K. pneumoniae (n = 5), including STs associated with food-producing animals globally, such as E. coli ST48 and ST10 and K. pneumoniae ST101. Common beta-lactamases linked to food-producing animals, such as bla CTX-M-55 and bla CTX-M-15, were detected. The presence of food-production-animal-associated ESBL-gene-carrying E. coli and K. pneumoniae in an abattoir environment and wastewater indicates the potential of WES in the surveillance of AMR in food-producing animals. Furthermore, the results of this pilot study encourage studying the topic further with refined methodologies.

PmrB Y358N, E123D amino acid substitutions are not associated with colistin resistance but with phylogeny in Escherichia coli

Colistin resistance in Escherichia coli is of public health significance for its use to treat multidrug-resistant Gram-negative infections. Amino acid variations in PmrB have been implicated in colistin resistance in E. coli. In this cross-sectional study, 288 generic E. coli isolates from surveillance of broiler chicken and feedlot cattle feces, retail meat, wastewater, and well water were whole-genome sequenced. Phylogroup designation and screening for two amino acid substitutions in PmrB putatively linked to colistin resistance (Y358N, E123D) were performed in silico. Three additional data sets of publicly available E. coli assemblies were similarly scrutinized: (i) E. coli isolates from studies identifying the Y358N or E123D substitutions, (ii) colistin-susceptible E. coli isolates reported in the literature, and (iii) a random sampling of 14,700 E. coli assemblies available in the National Center for Biotechnology Information public database. Within all data sets, ≥95% of phylogroup B1 and C isolates have the PmrB Y358N variation. The PmrB E123D amino acid substitution was only identified in phylogroup B2 isolates, of which 94%-100% demonstrate the substitution. Both PmrB amino acid variations were infrequent in other phylogroups. Among published colistin susceptible isolates, colistin minimum inhibitory concentrations (MICs) were not higher in isolates bearing the E123D and Y358N amino acid variations than in isolates without these PmrB substitutions. The E123D and Y358N PmrB amino acid substitutions in E. coli appear strongly associated with phylogroup. The previously observed associations between Y358N and E123D amino acid substitutions in PmrB and colistin resistance in E. coli may be spurious.

IMPORTANCE

Colistin is a critical last-resort treatment for extensively drug-resistant Gram-negative infections in humans. Therefore, accurate identification of the genetic mechanisms of resistance to this antimicrobial is crucial to effectively monitor and mitigate the spread of resistance. Examining over 16,000 whole-genome sequenced Escherichia coli isolates, this study identifies that PmrB E123D and Y358N amino acid substitutions previously associated with colistin resistance in E. coli are strongly associated with phylogroup and are alone not sufficient to confer a colistin-resistant phenotype. This is a critical clarification, as both substitutions are identified as putative mechanisms of colistin resistance in many publications and a common bioinformatic tool. Given the potential spurious nature of initial associations of these substitutions with colistin resistance, this study's findings emphasize the importance of appropriate experimental design and consideration of relevant biological factors such as phylogroup when ascribing causal mechanisms of resistance to chromosomal variations.

Four New Sequence Types and Molecular Characteristics of Multidrug-Resistant Escherichia coli Strains from Foods in Thailand

The presence of antibiotic-resistant Escherichia coli in food is a serious and persistent problem worldwide. In this study, 68 E. coli strains isolated from Thai food samples were characterized. Based on antibiotic susceptibility assays, 31 of these isolates (45.59%) showed multiple antibiotic resistance (MAR) index values > 0.2, indicating high exposure to antibiotics. Among these, strain CM24E showed the highest resistance (it was resistant to ten antibiotics, including colistin and imipenem). Based on genome sequencing, we identified four isolates (namely, CF25E, EF37E, NM10E1, and SF50E) with novel Achtman-scheme multi-locus sequence types (STs) (ST14859, ST14866, ST14753, and ST14869, respectively). Clermont phylogrouping was used to subtype the 68 researched isolates into five Clermont types, mainly A (51.47%) and B1 (41.18%). The blaEC gene was found only in Clermont type A, while the blaEC-13 gene was predominant in Clermont type B1. A correlation between genotypes and phenotypes was found only in Clermont type B1, which showed a strong positive correlation between the presence of an afa operon and yersiniabactin-producing gene clusters with the colistin resistance phenotype. Strain SM47E1, of Clermont type B2, carried the highest number of predicted virulence genes. In summary, this study demonstrates the pressing problems posed by the prevalence and potential transmission of antimicrobial resistance and virulence genes in the food matrix.

BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata

Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.

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

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

Molecular characterization, virulence and antimicrobial and biocidal susceptibility of selected bacteria isolated from the cloaca of nestling ospreys (Pandion haliaetus) from Mono Lake, California, USA

In the present study, the presence of the Enterobacterales, Staphylococcus spp., Mammaliicoccus spp., and Enterococcus spp. in cloacal samples of nestling ospreys (Pandion haliaetus), a fish-eating specialist, from Mono Lake, California, USA was examined by a multiphasic approach, including antimicrobial and biocide susceptibility testing, genotyping, and whole genome sequencing of selected isolates. The most commonly detected species was Escherichia coli, followed by Mammaliicoccus sciuri, Staphylococcus delphini, Enterococcus faecalis, Enterococcus faecium, Hafnia alvei, Klebsiella pneumoniae, Citrobacter braakii and single isolates of Edwardsiella tarda, Edwardsiella albertii, Klebsiella aerogenes, Plesiomonas shigelloides and Staphylococcus pseudintermedius. Multi-drug resistance (MDR) was observed in two E. coli isolates and in an Enterococcus faecium isolate. The MDR blaCTX-M-55-positive E. coli belonged to the pandemic clone ST58. The results of the present study suggest that nestling ospreys are exposed to MDR bacteria, possibly through the ingestion of contaminated fish. Ospreys may be good biosentinels for the presence of these microorganisms and antibiotic resistance in the local environment and the risk for other wildlife, livestock and humans.

The genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria

INTRODUCTION

The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets.

METHODS

This descriptive integrated typing study included 252 human isolates, 53 dog isolates and 10 cat isolates collected from 2019 to 2022 at the Charité University Hospital in Berlin, Germany. CgMLST was performed to characterize methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant gram-negative bacteria. The genetic diversity of the MDROs of the different host populations was determined and compared based on sequence type and core genome complex type.

RESULTS

Within this study the majority of samples from pets and humans was genetically distinct. However, for some isolates, the number of allelic differences identified by cgMLST was low. Two cases of putative household transmission or shared source of VR E. faecium and MDR E. coli between humans and pets were documented.

CONCLUSIONS

The interaction between humans and their pets appears to play a minor role in the spread of the MDROs studied. However, further research is needed. This study emphasizes the importance of comprehensive molecular surveillance and a multidisciplinary One Health approach to understand and contain the spread of MDROs in human and animal populations.

TRIAL REGISTRATION

The study is registered with the German Clinical Trials Register (DRKS00030009).

Sequence Types and Antimicrobial Resistance Profiles of Salmonella Typhimurium in the Food Chain in Singapore

Salmonella remains a significant foodborne pathogen globally with S. Typhimurium presenting as a frequently occurring serovar. This study aimed to characterize 67 S. Typhimurium isolates from humans, food, farms, and slaughterhouses collected in Singapore from 2016 to 2017. Using whole-genome sequencing analysis, the isolates were found to belong to either ST19 (n = 33) or ST36 (n = 34). ST36 predominated in human intestinal and chicken isolates, while human extra-intestinal and non-chicken food isolates belonged to ST19. Plasmids were predicted in 88.1% (n = 59) of the isolates with the most common incompatibility group profiles being IncFIB(S), IncFII(S) and IncQ1. IncFIB(S) (adjusted p-value < 0.05) and IncFII(S) (adjusted p-value < 0.05) were significantly more prevalent in ST19 isolates, while Col156 (adjusted p-value < 0.05) was more significantly found in ST36 isolates. ST36 isolates exhibited higher resistance to multiple antibiotic classes such as penicillins, phenicols, folate pathway inhibitors, aminoglycosides, β-lactam/β-lactamase inhibitor combinations, tetracyclines, and fluoroquinolones. Phylogenetics analysis suggested potential shared routes of transmission among human, chicken, farm and slaughterhouse environments. Taken together, this study offers a cross-sectional epidemiological insight into the genomic epidemiology and antimicrobial landscape of S. Typhimurium isolates in Singapore, informing strategies for future public health and food safety surveillance.

Genotypic and phenotypic characterisation of asymptomatic bacteriuria (ABU) isolates displaying bacterial interference against multi-drug resistant uropathogenic E. Coli

Escherichia coli can colonise the urogenital tract of individuals without causing symptoms of infection, in a condition referred to as asymptomatic bacteriuria (ABU). ABU isolates can protect the host against symptomatic urinary tract infections (UTIs) by bacterial interference against uropathogenic E. coli (UPEC). The aim of this study was to investigate the genotypic and phenotypic characteristics of five ABU isolates from midstream urine samples of adults. Comparative genomic and phenotypic analysis was conducted including an antibiotic resistance profile, pangenome analysis, and a putative virulence profile. Based on the genome analysis, the isolates consisted of one from phylogroup A, three from phylogroup B2, and one from phylogroup D. Two of the isolates, PUTS 58 and SK-106-1, were noted for their lack of antibiotic resistance and virulence genes compared to the prototypic ABU strain E. coli 83,972. This study provides insights into the genotypic and phenotypic profiles of uncharacterised ABU isolates, and how relevant fitness and virulence traits can impact their potential suitability for therapeutic bacterial interference.

Genomic insights into the antimicrobial resistance and virulence of Helicobacter pylori isolates from gastritis patients in Pereira, Colombia

BACKGROUND

Helicobacter pylori infects the stomach and/or small intestines in more than half of the human population. Infection with H. pylori is the most common cause of chronic gastritis, which can lead to more severe gastroduodenal pathologies such as peptic ulcer, mucosa-associated lymphoid tissue lymphoma, and gastric cancer. H. pylori infection is particularly concerning in Colombia in South America, where > 80% of the population is estimated to be infected with H. pylori and the rate of stomach cancer is one of the highest in the continent.

RESULTS

We compared the antimicrobial susceptibility profiles and short-read genome sequences of five H. pylori isolates obtained from patients diagnosed with gastritis of varying severity (chronic gastritis, antral erosive gastritis, superficial gastritis) in Pereira, Colombia sampled in 2015. Antimicrobial susceptibility tests revealed the isolates to be resistant to at least one of the five antimicrobials tested: four isolates were resistant to metronidazole, two to clarithromycin, two to levofloxacin, and one to rifampin. All isolates were susceptible to tetracycline and amoxicillin. Comparative genome analyses revealed the presence of genes associated with efflux pump, restriction modification systems, phages and insertion sequences, and virulence genes including the cytotoxin genes cagA and vacA. The five genomes represent three novel sequence types. In the context of the Colombian and global populations, the five H. pylori isolates from Pereira were phylogenetically distant to each other but were closely related to other lineages circulating in the country.

CONCLUSIONS

H. pylori from gastritis of different severity varied in their antimicrobial susceptibility profiles and genome content. This knowledge will be useful in implementing appropriate eradication treatment regimens for specific types of gastritis. Understanding the genetic and phenotypic heterogeneity in H. pylori across the geographical landscape is critical in informing health policies for effective disease prevention and management that is most effective at local and country-wide scales. This is especially important in Colombia and other South American countries that are poorly represented in global genomic surveillance studies of bacterial pathogens.

Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia

The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.

Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA

Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.

Data sharing considerations to maximize the use of pathogen biological and genomics resources data for public health

Public sector data associated with health are a highly valuable resource with multiple potential end-users, from health practitioners, researchers, public bodies, policy makers, and industry. Data for infectious disease agents are used for epidemiological investigations, disease tracking and assessing emerging biological threats. Yet, there are challenges in collating and re-using it. Data may be derived from multiple sources, generated and collected for different purposes. While public sector data should be open access, providers from public health settings or from agriculture, food, or environment sources have sensitivity criteria to meet with ethical restrictions in how the data can be reused. Yet, sharable datasets need to describe the pathogens with sufficient contextual metadata for maximal utility, e.g. associated disease or disease potential and the pathogen source. As data comprise the physical resources of pathogen collections and potentially associated sequences, there is an added emerging technical issue of integration of omics 'big data'. Thus, there is a need to identify suitable means to integrate and safely access diverse data for pathogens. Established genomics alliances and platforms interpret and meet the challenges in different ways depending on their own context. Nonetheless, their templates and frameworks provide a solution for adaption to pathogen datasets.

Enteroaggregative Escherichia coli: Frequent, yet underdiagnosed pathotype among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic

Enteroaggregative Escherichia coli (EAEC) strains including those of serogroup O111 are important causes of diarrhea in children. In the Czech Republic, no information is available on the etiological role of EAEC in pediatric diarrhea due to the lack of their targeted surveillance. To fill this gap, we determined the proportion of EAEC among E. coli O111 isolates from children with gastrointestinal disorders ≤ 2 years of age submitted to the National Reference Laboratory for E. coli and Shigella during 2013-2022. EAEC accounted for 177 of 384 (46.1 %) E. coli O111 isolates, being the second most frequent E. coli O111 pathotype. Most of them (75.7 %) were typical EAEC that carried aggR, usually with aaiC and aatA marker genes; the remaining 24.3 % were atypical EAEC that lacked aggR but carried aaiC and/or aatA. Whole genome sequencing of 11 typical and two atypical EAEC O111 strains demonstrated differences in serotypes, sequence types (ST), virulence gene profiles, and the core genomes between these two groups. Typical EAEC O111:H21/ST40 strains resembled by their virulence profiles including the presence of the aggregative adherence fimbriae V (AAF/V)-encoding cluster to such strains from other countries and clustered with them in the core genome multilocus sequence typing (cgMLST). Atypical EAEC O111:H12/ST10 strains lacked virulence genes of typical EAEC and differed from them in cgMLST. All tested EAEC O111 strains displayed stacked-brick aggregative adherence to human intestinal epithelial cells. The AAF/V-encoding cluster was located on a plasmid of 95,749 bp or 93,286 bp (pAAO111) which also carried aggR, aap, aar, sepA, and aat cluster. EAEC O111 strains were resistant to antibiotics, in particular to aminopenicillins and cephalosporins; 88.3 % produced AmpC β-lactamase, and 4.1 % extended spectrum β-lactamase. We conclude that EAEC are frequent among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. To reliably assess the etiological role of EAEC in pediatric diarrhea, a serotype-independent, PCR-based pathotype surveillance system needs to be implemented in the future.

Genes associated with fitness and disease severity in the pan-genome of mastitis-associated Escherichia coli

Introduction

Bovine mastitis caused by Escherichia coli compromises animal health and inflicts substantial product losses in dairy farming. It may manifest as subclinical through severe acute disease and can be transient or persistent in nature. Little is known about bacterial factors that impact clinical outcomes or allow some strains to outcompete others in the mammary gland (MG) environment. Mastitis-associated E. coli (MAEC) may have distinctive characteristics which may contribute to the varied nature of the disease. Given their high levels of intraspecies genetic variability, virulence factors of commonly used MAEC model strains may not be relevant to all members of this group.

Methods

In this study, we sequenced the genomes of 96 MAEC strains isolated from cattle with clinical mastitis (CM). We utilized clinical severity data to perform genome-wide association studies to identify accessory genes associated with strains isolated from mild or severe CM, or with high or low competitive fitness during in vivo competition assays. Genes associated with mastitis pathogens or commensal strains isolated from bovine sources were also identified.

Results

A type-2 secretion system (T2SS) and a chitinase (ChiA) exported by this system were strongly associated with pathogenic isolates compared with commensal strains. Deletion of chiA from MAEC isolates decreased their adherence to cultured bovine mammary epithelial cells.

Discussion

The increased fitness associated with strains possessing this gene may be due to better attachment in the MG. Overall, these results provide a much richer understanding of MAEC and suggest bacterial processes that may underlie the clinical diversity associated with mastitis and their adaptation to this unique environment.

Detection of Salmonella Mbandaka Carrying the blaCTX-M-8 Gene Located on IncI1 Plasmid Isolated from a Broiler Flock Environment

Salmonella Mbandaka is one of the most globally widespread serovars, occurring in many sources and included among twenty serovars that contribute to human salmonellosis in Europe. In Poland, it has been noted in non-human sources since 1996, being found firstly in feeds and later in waterfowl and chicken. Over the years, it gained epidemiological importance, being isolated from a wide range of animal species, including livestock. Generally, it is characterized by sensitivity to most antimicrobials and the ability to form biofilms. The occurrence of cephalosporin-resistant Salmonella in non-human sources is an extremely rare phenomenon in Poland. In this report, we characterized the full genome of the ESBL-producing S. Mbandaka strain isolated from a broiler farm environment (boot swab sample) in Poland in 2022. The isolate was serotyped as S. Mbandaka according to the White-Kaufmann-Le Minor scheme. Antimicrobial susceptibility testing performed with the microbroth dilution method showed its resistance to ampicillin, cefotaxime, ceftazidime, ciprofloxacin, and nalidixic acid. The whole-genome sequence was reconstructed using short and long reads and assembled into the complete chromosome and three plasmids: IncI1 pST113 (89,439 bp), Col(pHAD28) (2699 bp), and Col440 (2495 bp). The strain belonged to sequence type ST413. Plasmid analysis showed blaCTX-M-8 mobilization on IncI1(alpha) surrounded with insertion sequences. The analyzed genome content draws attention to the possibility of the horizontal spread of the resistance genes. To the best of our knowledge, this is the first report of blaCTX-M-8-positive Salmonella in Poland.

Epidemiology of and risk factors associated with third-generation cephalosporin-resistant Escherichia coli carriage in children: A comparison between regions in Taiwan

BACKGROUND

The increasing prevalence of antimicrobial-resistant Escherichia coli (E. coli) in the community is a global public health challenge. This study investigated the prevalence of third-generation cephalosporin-resistant (3GCR) E. coli fecal carriage in children, identified associated risk factors, and determined antimicrobial resistance patterns of E. coli across three regions of Taiwan.

METHODS

Stool samples from children aged 0-18 years were collected in southern, northern, and eastern Taiwan from community or outpatient clinics between July 2022 and May 2023. E. coli colonies were selected and examined for antimicrobial susceptibility and multilocus sequence typing. Participant demographic data and potential risk factors for carrying resistant E. coli were surveyed using a questionnaire.

RESULTS

Of the 246 children surveyed, 59.3% carried multidrug-resistant (MDR) E. coli, and 37.4% carried 3GCR E. coli. The prevalence of 3GCR E. coli carriage was highest in southern Taiwan (42.7%), followed by northern Taiwan (35.5%) and eastern Taiwan (28.4%). The study identified several risk factors which may be associated with the fecal carriage of 3GCR E. coli, such as having lower paternal education levels, being overweight or obese, having a nonvegetarian diet, and consuming eggs, with variations observed across regions.

CONCLUSION

This study documented elevated fecal carriage rates of 3GCR and MDR E. coli across regions of Taiwan. The study also identified numerous demographic and environmental factors that require implementing comprehensive strategies to address this public health challenge.