In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing

Genomic characterisation of an extended-spectrum β-Lactamase-producing Klebsiella pneumoniae isolate assigned to a novel sequence type (6914)

BACKGROUND

Cow milk, which is sometimes consumed raw, hosts a plethora of microorganisms, some of which are beneficial, while others raise food safety concerns. In this study, the draft genome of an extended-spectrum β-lactamase-producing Klebsiella pneumoniae subsp. pneumoniae strain Cow102, isolated from raw cow milk used to produce traditional foods in Nigeria, is reported.

RESULT

The genome has a total length of 5,359,907 bp, with 70 contigs and a GC content of 57.35%. A total of 5,244 protein coding sequences were detected with 31% mapped to a subsystem, and genes coding for amino acids and derivatives being the most prevalent. Multilocus sequence typing revealed that the strain had new allelic profile assigned to the novel 6914 sequence type possessing capsular and lipopolysaccharide antigen K locus 122 with an unknown K type (KL122) and O locus O1/O2v2 with type O2afg, respectively. A total of 28 resistance-related genes, 98 virulence-related genes, two plasmids and five phages were identified in the genome. The resistance genes oqxA, oqxB and an IS3 belonging to cluster 204 were traced to bacteriophage Escher 500,465. Comparative analysis predicted one strain specific orthologous group comprising three genes.

CONCLUSION

This report of a novel sequence type (ST6914) in K. pneumoniae presents a new allelic profile, indicating ongoing evolution and diversification within the species. Its uniqueness suggests it may represent a locally evolved lineage, although further sampling would be necessary to confirm this hypothesis. The strain's multidrug resistance, virulence gene repertoire, and isolation from animal milk render it a potentially significant public health concern, underscoring the importance of genomic surveillance in non-clinical settings to detect emerging strains. Further research is required to fully characterise the capsular K type of ST6914.

Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach

Pathogenic Escherichia coli (PEC) are important foodborne bacteria that can cause severe illness in humans. The PECs thrive within the intestines of humans as well as animals and may contaminate multiple ecosystems, including food and water, via faecal transmission. Abattoir and farm employees are at high risk of PEC exposure, which could translate to community risk through person-to-person contact. To determine the epidemiology and resistome of PECs in Gauteng and Limpopo provinces of South Africa, 198 swine faecal samples, 220 poultry cloacal swabs, 108 human hand swabs, 11 run-off water samples from abattoirs and farms were collected from four swine and five poultry commercial abattoirs and two swine farms. One effluent sample each was collected from four wastewater treatment plants (WWTP) and a tertiary hospital setting. Phenotypic and genotypic techniques were used including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Results showed EHEC and EPEC prevalence was 4.1 % (22/542) and 20.8 % (113/542), respectively, with the O26 serogroup detected the most in PEC isolates. According to the PFGE dendrogram, isolates from poultry, human hand swabs and run-off water clustered together. Diverse virulence factors such as the novel stx2k subtype and eae genes were detected among the 36 representative PEC isolates according to WGS. The results showed that 66.7 % (24/36) of sequenced PECs presented with multi-drug resistance (MDR) to β-lactamase 13.9 % (5/36), aminoglycoside 61.1 % (22/36), tetracycline 41.7 % (15/36) and quinolones 38.9 % (14/36). No colistin nor carbapenem resistance was detected. Sequence types (STs) associated with MDR in this study were: ST752, ST189, ST206, ST10, ST48 and ST38. The findings highlight the threat of zoonotic pathogens to close human contacts and the need for enhanced surveillance to mitigate the spread of MDR foodborne PECs.

Genomic characteristics of Salmonella enterica serovar Blockley

Non-typhoidal Salmonella (NTS) is a significant cause of foodborne illness worldwide, with increasing antimicrobial resistance posing a public health concern. Salmonella enterica serovar Blockley (S. Blockley) is relatively uncommon, and its antimicrobial resistance profile and population structure have been understudied. This study presents a comprehensive genomic analysis of 264 S. Blockley isolates from diverse geographical regions to elucidate antimicrobial resistance patterns and population structure. Bayesian analysis classified these genomes into 10 distinct groups (BAPS A to BAPS J), further categorized into two lineages, R and S. Lineage R comprised six BAPS clusters (BAPSs A-F), predominantly found in Asia and Africa, all of which harbored the azithromycin resistance gene mph(A) and other resistance determinants. In contrast, lineage S, lacking mph(A), comprised the remaining four BAPS clusters, which were primarily found in Europe and the Americas. Several types of mutations in gyrA were found in lineage R, which were specific to BAPS clusters. These BAPS clusters exhibited distinct geographic distributions, with BAPS B, BAPS D, and BAPS E unique to China, Taiwan, and Japan, respectively, while BAPS H and BAPS I were predominantly found in the United States. Temporal phylogenetic analysis suggested that lineage R diverged in the 1980s, with notable microevolutionary changes. The presence of a genomic island with mph(A), aph(3')-Ia, aph(3")-Ib, aph(6)-Id, and tet(A) in lineage R underscores the public health threat, highlighting a need for continuous surveillance.IMPORTANCEAntimicrobial resistance in Salmonella is a global public health concern. In this study, we focused on serovar Blockley, and a whole-genome analysis revealed its global population structure. The results revealed the existence of azithromycin-resistant strains, which were characterized both phylogenetically and geographically. The resistance genes were transmitted via genomic islands, and their micro-scale evolution was also revealed. Our findings are the first to reveal the dissemination of antimicrobial resistance genes, including azithromycin, in serovar Blockley, and provide valuable insights into understanding the spread of antimicrobial resistance.

Detection of drug resistance in Escherichia coli from calves with diarrhea in the Tongliao region: an analysis of multidrug-resistant strains

Introduction

Escherichia coli is a major pathogen responsible for calf diarrhea, which has been exacerbated by the irrational and unscientific use of antimicrobial drugs, leading to significant drug resistance.

Methods

This study focused on the isolation and identification of E. coli from calf diarrhea samples in the Tongliao area of China. Isolation was conducted using selective media, Gram staining, and 16S rRNA sequencing. The minimum inhibitory concentration (MIC) of E. coli was determined through the microbroth dilution method. Additionally, the presence of antibiotic-resistant genes was detected, and multidrug-resistant strains were selected for whole-genome sequencing (WGS).

Results

The results revealed that all 40 isolated strains of E. coli exhibited resistance to sulfadiazine sodium, enrofloxacin, and ciprofloxacin, with 90% of the strains being susceptible to polymyxin B. Notably, strains 11, 23, and 24 demonstrated severe resistance. The detection rates of the antibiotic resistance genes TEM-1, TEM-206, strA, strB, qacH, and blaCTX were 100%, indicating a high prevalence of these genes. Moreover, the majority of strains carried antibiotic resistance genes consistent with their resistance phenotypes. WGS of strains 11, 23, and 24 revealed genome sizes of 4,897,185 bp, 4,920,234 bp, and 4,912,320 bp, respectively. These strains carried two, one, and two plasmids, respectively. The prediction of antibiotic resistance genes showed a substantial number of these genes within the genomes, with strain 24 harboring the highest number, totaling 77 subspecies containing 88 antibiotic resistance genes.

Discussion

In conclusion, all 40 isolated strains of E. coli from calf diarrhea in this study were multidrug-resistant, exhibiting a broad distribution of antibiotic resistance genes and mobile components. This poses a significant risk of horizontal gene transfer, highlighting the critical situation of antibiotic resistance in this region.

Complete genome sequence of a high-risk Escherichia coli ST10 isolated from avian feces in Pakistan

We present the complete genome sequence of Escherichia coli strain PEC1009 isolated from avian feces in Pakistan. The strain belongs to sequence type (ST) 10, a high-risk clone. The strain possesses two plasmids, and various plasmid-borne antibiotic resistance genes and chromosome-borne virulence factor genes were identified in its genome.

Draft genome of a Pseudovibrio sp. isolated from the skeleton of Pachyseris speciosa from a Singaporean reef

A Pseudovibrio sp. was isolated from the skeleton of the heat resilient coral Pachyseris speciosa. Genome analysis revealed the presence of the complete denitrification pathway and potential dimethylsulfoniopropionate metabolism which enhance coral resilience and production of tropodithietic acid, an antibiotic implicated in host defense.

Emergence of hypervirulent and carbapenem-resistant Klebsiella pneumoniae from 2014 - 2021 in Central and Eastern China: a molecular, biological, and epidemiological study

BACKGROUND

In recent years, the hypervirulent and carbapenem-resistant Klebsiella pneumoniae has been increasingly reported worldwide. The objective of this study was to compare the antibiotic resistance and virulence profiles of carbapenem-resistant hypervirulent K.pneumoniae (CR-hvKP) and hypervirulent carbapenem-resistant K.pneumoniae (hv-CRKP) and identify the prevailing strain in clinical settings.

METHODS

In this study, hv-CRKP or CR-hvKP were identified based on the results of whole-genome analysis (WGS), multilocus sequence typing (MLST) and the antimicrobial susceptibility testing. We then compared antibiotic resistance and virulence profiles between CR-hvKP and hv-CRKP through the antimicrobial susceptibility testing and a series of virulence experiments including biofilm formation ability detection method, the resistance test against human serum, siderophore production test, neutrophil phagocytosis assay and Galleria mellonella infection model. Additionally, pathway enrichment analysis was conducted to assess the effect of SNPs on the phenotype.

RESULTS

In this study, we categorized 17.4% of hypervirulent and carbapenem-resistant K. pneumoniae strains as CR-hvKP and 82.6% as hv-CRKP. Among them, 84.2% (16/19) of CR-hvKP strains harboring carbapenemase genes exhibited lower imipenem and meropenem MIC values compared to hv-CRKP strains. The virulence potential of hv-CRKP and CR-hvKP was confirmed by using virulence experiments in vitro and in vivo, showing that virulence of the CR-hvKP strains was comparable to that of hv-CRKP strains. Notably, the 90 hv-CRKP strains were classified into 3 different ST types and 8 capsule types, each showing varying degrees of resistance and virulence. We observed that subclonal replacement was within the predominant hv-CRKP clone, with the ST11-KL64 strain, characterized by high-level resistance and virulence emerging as the currently prevailing subclone, replacing ST11-KL47. KEGG enrichment analysis showed that pathways associated with the citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, two-component regulatory system, and folate metabolism were significantly enriched among the group expressing different levels of capsular polysaccharides.

CONCLUSIONS

The hv-CRKP strains exhibited a greater survival advantage in the hospital environment than CR-hvKP strains. Notably, the ST11-KL64 hv-CRKP strain which displayed a high level of resistance and hypervirulence, warrants the most clinical vigilance.

CLINICAL TRIAL NUMBER

Not applicable.

Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence

BACKGROUND

Following a one-health approach, we sought to determine reservoirs of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-PE), other than Escherichia coli or Klebsiella pneumoniae complex species (i.e., low-abundant species), and their associated ESBL genes and plasmid-replicon profiles.

METHODS

From 06/2017-05/2019, ESBL-PE isolates were recovered from clinical samples routinely collected at the University Hospital Basel (Basel, Switzerland), as well as from wastewater and foodstuffs collected monthly at predefined locations throughout the city of Basel. Whole-genome sequencing was performed for characterization of ESBL-PE isolates.

RESULTS

Among 1634 isolates recovered, 114 (7%) belonged to 17 low-abundant ESBL-PE species. Seven species originated from more than one compartment, mainly from clinical and wastewater samples (6/17). Sixteen different ESBL genes were identified, with blaCTX-M-15 (27%), blaFONA-6 (23%) and blaSHV-12 (16%) being most frequent. The blaCTX-M-1 gene was the only ESBL gene recovered from all three compartments. Putative plasmids constituted 60% of ESBL gene-containing contigs, while chromosomes comprised 40%. Foodstuff isolates showed the highest proportion (91%, 41/45) of ESBL genes located on chromosomes, whereas wastewater isolates had the highest proportion (95%, 37/39) of putative plasmids. Multi-replicon combinations were identified in 81% of the isolates. Epidemiological links were found among some clinical and wastewater isolates.

CONCLUSIONS

The dominance of blaCTX-M-15 among low-abundant ESBL-PE species supports its species-independent transmission potential beyond the E. coli and K. pneumoniae complex, and blaCTX-M-1 may be transmitted between strains recovered from different compartments. The substantial overlap between low-abundant ESBL-PE present in wastewater and clinical samples supports the utility of wastewater surveillance for antibiotic resistance monitoring.

Comparative genomic analysis provides new insights into non-typhoidal Salmonella population structure in Peru

Non-typhoidal Salmonella (NTS) is one of the leading causes of foodborne outbreaks worldwide, especially in low- and middle-income countries such as Peru. To understand the dynamics of NTS serotypes circulating in the country, the whole genomes of 1122 NTS strains from 1998 to 2018 were analyzed using phylogenomic and comparative genomics tools. A total of 40 different Sequences Type (STs) were identified, the five most frequent being ST-32 (S. Infantis, 37.25%), ST-11 (S. Enteritidis, 23.8%), ST-19 (S. Typhimurium, 14.17%), ST-31 (S. Newport, 6.77%), and ST-413 (S. Mbandaka, 4.72%). Furthermore, the maximum likelihood phylogeny showed high clonality between strains from the same ST recovered from different isolation sources, as well as a variable recombination rate, when comparing each ST individually. Moreover, several virulence factors involved in adherence and invasion, as well as plasmids and prophages, are strongly associated with the most frequent STs, while multidrug resistance markers are mostly linked to ST-32. This work provides an overview of the main genomic characteristics linked to the high-frequency ST, which have undergone few genetic modifications over time, suggesting a high adaptation of these NTS circulating clones in Peru.

Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in Gauteng South Africa

Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient's urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.

Investigating the changing taxonomy and antimicrobial resistance of bacteria isolated from door handles in a new infectious disease ward pre- and post-patient admittance

Healthcare-associated infections (HAIs) are a significant burden to health systems, with antimicrobial resistance (AMR) further compounding the issue. The hospital environment plays a significant role in the development of HAIs, with microbial surveillance providing the foundation for interventions. We sampled 40 door handles at a newly built hospital prior to patients being admitted and then 6 and 12 months after this date. We utilized 16S rDNA sequencing to identify unique colonies, disc diffusion assays to assess the antibiotic resistance of Staphylococcus spp., and whole-genome sequenced (WGS) multidrug-resistant (MDR) isolates. Before patient admission, 43% of sites harbored Staphylococcus spp., increasing to 55% and 65% at six and 12 months, respectively, while Bacillus spp. saw a large increase from 3% to 68% and 85%, respectively. No ESKAPE pathogens were identified. Staphylococcus spp. showed relatively low resistance to all antibiotics except cefoxitin (56%) before patient admittance. Resistance was highest after 6 months of ward use, with an increase in isolates susceptible to all antibiotics after 12 months (11% and 54% susceptibility, respectively). However, MDR remained high. WGS revealed blaZ (25/26), and mecA (22/26) and aac6-aph2 (20/26) were the most abundant resistance genes. Two Staphylococcus hominis isolates identified at the first two time points, respectively, and three Staphylococcus epidermidis isolates identified at all three time points, respectively, were believed to be clonal. This study highlighted the prevalence of a resistant reservoir of bacteria recoverable on high-touch surfaces and the long-term persistence of Staphylococcus spp. first introduced prior to patient admission.

IMPORTANCE

Healthcare-associated infections (HAIs) are a significant burden to health systems, conferring increased morbidity, mortality, and financial costs to hospital admission. Antimicrobial resistance (AMR) further compounds the issue as viable treatment options are constrained. Previous studies have shown that environmental cleaning interventions reduced HAIs. To ensure the effectiveness of these, it is important to analyze the hospital environment at a microbial level, particularly high-touch surfaces which see frequent human interaction. In addition to identifying infectious microorganisms, it is also beneficial to assess typically non-infectious organisms, as traits including AMR can be transferred between the two. Our study identified that there were high levels of antibiotic resistance in typically non-infectious organisms found on high touch surfaces on a hospital ward. However, the organisms identified suggested that the cleaning protocols in place were sufficient, with their presence being due to repeated recolonization events through human interaction after cleaning had taken place.

Investigation of Citrobacter freundii clinical isolates in a Chinese hospital during 2020-2022 revealed genomic characterization of an extremely drug-resistant C. freundii ST257 clinical strain GMU8049 co-carrying blaNDM-1 and a novel blaCMY variant

The emergence of multidrug-resistant Citrobacter freundii poses a significant threat to public health. C. freundii isolates were collected from clinical patients in a Chinese hospital during 2020-2022. An unusual strain, GMU8049, was not susceptible to any of the antibiotics tested, including the novel β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam. Whole-genome sequencing (WGS) revealed that GMU8049 harbors a circular chromosome belonging to the rare ST257 and an IncX3 resistance plasmid. Genomic analysis revealed the coexistence of two β-lactamase genes, including plasmid-mediated blaNDM-1 and chromosomal blaCMY encoding a novel CMY variant, combined with an outer membrane porin deficiency, which may account for the extreme resistance to β-lactams. Conjugation experiment confirmed that the blaNDM-1 resistance gene located on pGMU8049 could be successfully transferred to Escherichia coli EC600. The novel CMY variant had an amino acid substitution at position 106 (N106S) compared to the closely related CMY-51. Additionally, a GMU8049-specific truncation in an OmpK37 variant that produces a premature stop codon. Moreover, a variety of chromosome-located efflux pump coding genes and virulence-related genes were also identified. Analysis of strain GMU8049 in the context of other C. freundii strains reveals an open pan-genome and the presence of mobile genetic elements that can mediate horizontal gene transfer of antimicrobial resistance and virulence genes. Our work provides comprehensive insights into the genetic mechanisms of highly resistant C. freundii, highlighting the importance of genomic surveillance of this opportunistic pathogen as a high-risk population for emerging resistance and pathogenicity.IMPORTANCEEmerging pathogens exhibiting multi-, extremely, and pan-drug resistance are a major concern for hospitalized patients and the healthcare community due to limited antimicrobial treatment options and the potential for spread. Genomic technologies have enabled clinical surveillance of emerging pathogens and modeling of the evolution and transmission of antimicrobial resistance and virulence. Here, we report the genomic characterization of an extremely drug-resistant ST257 Citrobacter freundii clinical isolate. Genomic analysis of GMU8049 with a rare ST type and unusual phenotypes can provide information on how this extremely resistant clinical isolate has evolved, including the acquisition of blaNDM-1 via the IncX3 plasmid and accumulation through chromosomal mutations leading to a novel CMY variant and deficiency of the outer membrane porin OmpK37. Our work highlights that the emergence of extremely resistant C. freundii poses a significant challenge to the treatment of clinical infections. Therefore, great efforts must be made to specifically monitor this opportunistic pathogen.

Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments

This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.

Antibiotic resistance plasmids in Enterobacteriaceae isolated from fresh produce in northern Germany

In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system.

IMPORTANCE

This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.

Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence

Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.

Enterobacter adelaidei sp. nov. Isolation of an extensively drug resistant strain from hospital wastewater in Australia and the global distribution of the species

BACKGROUND

Enterobacter species are included among the normal human gut microflora and persist in a diverse range of other environmental niches. They have become important opportunistic nosocomial pathogens known to harbour plasmid-mediated multi-class antimicrobial resistance (AMR) determinants. Global AMR surveillance of Enterobacterales isolates shows the genus is second to Klebsiella in terms of frequency of carbapenem resistance. Enterobacter taxonomy is confusing and standard species identification methods are largely inaccurate or insufficient. There are currently 27 named species and a total of 46 taxa in the genus distinguishable via average nucleotide identity (ANI) calculation between pairs of genomic sequences. Here we describe an Enterobacter strain, ECC3473, isolated from the wastewater of an Australian hospital whose species could not be determined by standard methods nor by ribosomal RNA gene multi-locus typing.

AIM

To characterise ECC3473 in terms of phenotypic and genotypic antimicrobial resistance, biochemical characteristics and taxonomy as well as to determine the global distribution of the novel species to which it belongs.

METHODS

Standard broth dilution and disk diffusion were used to determine phenotypic AMR. The strain's complete genome, including plasmids, was obtained following long- and short read sequencing and a novel long/short read hybrid assembly and polishing, and the genomic basis of AMR was determined. Phylogenomic analysis and quantitative measures of relatedness (ANI, digital DNA-DNA hybridisation, and difference in G+C content) were used to study the taxonomic relationship between ECC3473 and Enterobacter type-strains. NCBI and PubMLST databases and the literature were searched for additional members of the novel species to determine its global distribution.

RESULTS

ECC3473 is one of 21 strains isolated globally belonging to a novel Enterobacter species for which the name, Enterobacter adelaidei sp. nov. is proposed. The novel species was found to be resilient in its capacity to persist in contaminated water and adaptable in its ability to accumulate multiple transmissible AMR determinants.

CONCLUSION

E. adelaidei sp. nov. may become increasingly important to the dissemination of AMR.

Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks

For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.

Genomic surveillance detects interregional spread of New Delhi metallo-beta-lactamase-1-producing Providencia stuartii in hospitals, Romania, December 2021 to September 2023

BackgroundNew Delhi metallo-beta-lactamase (NDM)-producing Providencia stuartii has been reported from European Union/European Economic Area (EU/EEA) countries with increasing frequency. During 2018 to 2022, 355 cases of NDM-producing P. stuartii were detected in seven hospitals reporting on NDM-production in Enterobacterales in Romania.AimOur aim was to determine the extent of spread of NDM-producing P. stuartii in hospitals in Romania.MethodsWe analysed whole genome sequences and epidemiological data of 74 P. stuartii isolates collected in six hospitals from December 2021 to September 2023.ResultsWe identified four multi-hospital clusters including isolates detected over more than a year, indicating sustained spread of bla NDM-1-carrying P. stuartii within the healthcare system. These clusters consisted of isolates from up to four hospitals and three regions. Three multi-hospital clusters were caused by a specific multidrug-resistant P. stuartii sequence type 46 lineage carrying bla NDM-1 and a large set of additional resistance markers. Investigation in an international context showed that this lineage had already been detected in nine countries (Bulgaria, France, Germany, Ireland, the Netherlands, Romania, Switzerland, United Kingdom, United States) since 2015.ConclusionOur results alert about the risk of carbapenem-resistant P. stuartii transmission in healthcare settings. Enhanced infection prevention and control measures should be instituted as soon as cases are detected in healthcare facilities. National surveillance systems in EU/EEA countries should, in addition to carbapenem-resistant and/or carbapenemase-producing Klebsiella pneumoniae and Escherichia coli, consider reporting carbapenem-resistant and/or carbapenemase-producing P. stuartii and other Enterobacterales where relevant.

Genomic characterization of third-generation cephalosporin-resistant Escherichia coli strains isolated from diseased dogs and cats: Report from Japanese Veterinary Antimicrobial Resistance Monitoring

This study investigates the genomic characteristics of canine and feline cefotaxime (CTX, a third-generation cephalosporin)-resistant Escherichia coli using the JVARM, Japanese Veterinary Antimicrobial Resistance Monitoring System, a nationwide monitoring. In this study, whole-genome sequencing (WGS) was performed on 51 canine and 45 feline CTX-resistant E. coli isolates, with certain isolates subjected to pulsed-field gel electrophoresis with S1 nuclease for plasmid-chromosome separation. The most common blaCTX-M genes were blaCTX-M-27 (dogs: 11/51 [21.6 %]; cat: 10/45 [22.2 %]), followed by blaCTX-M-14 (dogs: 10/51 [19.6 %]; cats: 10/45 [22.2 %]), and blaCTX-M-15 (dogs: 9/51 [17.6 %]; cats: 5/45 [11.1 %]). Besides β-lactamase genes, all isolates harbored mdf(A), a multidrug efflux pump, with resistance genes for aminoglycosides, sulfonamides, trimethoprims, macrolides and tetracyclines. None of the isolates had carbapenemase genes, such as blaOXA-48, blaNDM, and blaIMP, whereas most of the isolates showed double mutations in gyrA and parC, which affected quinolone resistance. For the isolates separately analyzed for plasmid and chromosomal DNA via WGS, the majority of CTX-M genes were present on the plasmids. Some plasmids also harbored the same combination of resistance genes and plasmid replicon type, although they differed from isolates derived from different areas of Japan. The predominant plasmids were blaCTX-M-27,aadA5, aph(6)-Id, aph(3")-Ib, sul1, sul2, tet(A), dfrA17, and mph(A) on IncF. The predominant combination of ST131, O25:H4, and B2 isolates comprised the largest cluster in the minimum spanning tree and the ST131 E. coli harboring blaCTX-M-27 from human in Japan was closely related to these isolates. The results indicated that CTX-resistant canine and feline E. coli harbored multiple plasmids carrying the same combination of resistance genes and emphasizes the need to prevent the spread. DATA AVAILABILITY: All raw short-read sequence data have been deposited in the DNA Data Bank of Japan. (DRR Run No, DRR335726-335821).

Genomic epidemiology and phenotypic characterisation of Salmonella enterica serovar Panama in Victoria, Australia

Salmonella enterica serovar Panama, a causative agent of non-typhoidal salmonellosis (NTS), is one of several serovars that causes invasive NTS disease (iNTS) in humans. S. Panama is an understudied pathogen, with its pathobiology poorly understood. It is a predominant iNTS serovar in Australia, a high-income country with high rates of salmonellosis, where S. Panama has been documented to have a high odds ratio (13.9-15.26) for causing iNTS. This study investigates the genomic epidemiology and antimicrobial resistance profiles of all S. Panama isolates recovered in Victoria, Australia, between 2000 and 2021. We examined the infection dynamics of S. Panama in seven isolates, representing the genetic diversity of the study population. Two sub-lineages, encompassed within a previously described Asian lineage, were identified. Multi-drug resistance (resistance to ≥3 drug classes) was detected in 46 (51.7%) Australian isolates. The plasmid-mediated colistin resistance gene, mcr1.1, was detected in one Australian S. Panama isolate, carried by an IncI plasmid previously reported in Salmonella and Escherichia coli isolates collected from poultry in South-East Asia. Examination of the intracellular replication dynamics of S. Panama isolates demonstrated diverse phenotypes. In THP-1 derived macrophages, despite low host cell uptake, S. Panama showed higher replication rates over time compared to S. enterica serovar Typhimurium. However, a causative genotype could not be identified to explain this observed phenotype. This study provides insights into the S. Panama isolates circulating in Australia over two-decades, finding that 78% were linked to international travel suggesting importation in Australia. It shows MDR was common in this iNTS serovar, and colistin resistance reported for the first time. It provides the first data on the host-pathogen interactions of S. Panama in Australia, which will aid our collective understanding of the pathobiology of S. Panama and iNTS serovars more broadly.

First report and genomic characterization of Escherichia coli O111:H12 serotype from raw mussels in Türkiye

BACKGROUND

This study aimed to assess the prevalence and genomic characteristics of Shiga-toxigenic (STEC) and Enteroaggregative E. coli (EAEC) strains in raw mussels and ready-to-eat (RTE)-stuffed mussels, focusing on potential public health implications for identifying virulence and antimicrobial resistance genes.

RESULTS

The genome sequence analysis identified the E. coli strain named 23EM as serotype O111:H12, with adhesion (fimH-54) and fumarate hydratase (fumC-11) genes. The draft genome (4.9 Mb, 50.6% GC content, 111 contigs, 4,688 genes) is available in NCBI GenBank (accession JAWXVJ000000000). The strain, classified as ST292 and CC ST10, showed high similarity to nonpathogenic E. coli MG1655 but was distinct from pathogenic strains such as EAEC and ExPEC. In silico serotyping revealed the presence of O111-antigen flippase (wzx) and H12-antigen flagellin (fliC) genes. The strain harbors an IncFII (pCoo) plasmid with 96.95% identity. PathogenFinder predicted a 92% probability of being a human pathogen, supported by 720 pathogenic protein families. CRISPR analysis identified one high-evidence sequence with nine spacers and six low-evidence sequences. Phylogenetic analysis using RAxML positioned 23EM close to nonpathogenic E. coli but distant from other pathogenic strains. Antimicrobial resistance genes across multiple classes, including macrolides, fluoroquinolones, and aminoglycosides, were identified. The strain also contains several virulence factors, such as adhesins (e.g., ECP, ELF, TIF, type IV pili), and autotransporter genes (espP, pic), highlighting its significant pathogenic potential and public health risk.

CONCLUSIONS

This study highlights the ability of the detection of E. coli strains harboring virulence and antimicrobial resistance genes in mussels, thus emphasizing the importance of ongoing surveillance and careful consideration of the potential risks associated with the consumption of these shellfish.

Escherichia coli from six European countries reveals differences in profile and distribution of critical antimicrobial resistance determinants within One Health compartments, 2013 to 2020

BackgroundAntimicrobial resistance (AMR) is a global threat. Monitoring using an integrated One Health approach is essential to detect changes in AMR occurrence.AimWe aimed to detect AMR genes in pathogenic and commensal Escherichia coli collected 2013-2020 within monitoring programmes and research from food animals, food (fresh retail raw meat) and humans in six European countries, to compare vertical and horizontal transmission.MethodsWe whole genome sequenced (WGS) 3,745 E. coli isolates, detected AMR genes using ResFinder and performed phylogenetic analysis to determine isolate relatedness and transmission. A BLASTn-based bioinformatic method compared draft IncI1 genomes to conserved plasmid references from Europe.ResultsResistance genes to medically important antimicrobials (MIA) such as extended-spectrum cephalosporins (ESC) were widespread but predicted resistance to MIAs authorised for human use (carbapenem, tigecycline) was detected only in two human and three cattle isolates. Phylogenetic analysis clustered E. coli according to phylogroups; commensal animal isolates showed greater diversity than those from human patients. Only 18 vertical animal-food and human-animal transmission events of E. coli clones were detected. However, IncI1 plasmids from different sources and/or countries carrying resistance to ESCs were conserved and widely distributed, although these variants were rarely detected in human pathogens.ConclusionUsing WGS we demonstrated AMR is driven vertically and horizontally. Human clinical isolates were more closely related, but their IncI1 plasmids were more diverse, while animal or food isolates were less similar with more conserved IncI1 plasmids. These differences likely arose from variations in selective pressure, influencing AMR evolution and transmission.

The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China

AIMS

Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP), coharboring hypervirulence and carbapenem-resistance genes mediated by plasmids, causes infections with extremely high mortality and seriously impacts public health. Exploring the transfer mechanisms of virulence/carbapenem-resistance plasmids, as well as the formation and evolution pathway of hv-CRKP is of great significance to the control of hv-CRKP infections.

METHODS

In this study, we identified the predominant clone of hv-CRKP in China and elucidated its genomic characteristics and formation route based on 239 multicenter clinical K. pneumoniae isolates and 1014 GenBank genomes by using comparative genomic analysis. Further, we revealed the factors affecting the transfer of virulence plasmids, and explained the genetic foundation for the prevalence of Chinese predominant hv-CRKP clone.

RESULTS

ST11-KL64 is the predominant clone of hv-CRKP in China and primarily evolved from ST11-KL64 CRKP by acquiring the pLVPK-like virulence plasmid from hvKP. Significantly, the virulence gene cluster iroBCDN was lost in the virulence plasmid of ST11-KL64 hv-CRKP but existed in that of hvKP. Moreover, the absence of iroBCDN didn't decrease the virulence of hv-CRKP, which was proved by bacterial test, cell-interaction test and mice infection model. On the contrary, loss of iroBCDN was observed to regulate virulence/carbapenem-resistance plasmid transfer and oxidative stress-related genes in strains and thus promoted the mobilization of nonconjugative virulence plasmid from hvKP into ST11-KL64 CRKP, forming hv-CRKP which finally had elevated antioxidant capacity and enhanced survival capacity in macrophages. The loss of iroBCDN increased the survival ability of hv-CRKP without decreasing its virulence, endowing it with an evolutionary advantage.

CONCLUSIONS

Our work provides new insights into the key role of iroBCDN loss in convergence of CRKP and hvKP, and the genetic and biological foundation for the widespread prevalence of ST11-KL64 hv-CRKP in China.

The drainome: longitudinal metagenomic characterization of wastewater from hospital ward sinks to characterize the microbiome and resistome and to assess the effects of decontamination interventions

BACKGROUND

Hospital drains and water interfaces are implicated in nosocomial transmission of pathogens. Metagenomics can assess the microbial composition and presence of antimicrobial resistance genes in drains ('the drainome') but studies applying these methods longitudinally and to assess infection control interventions are lacking.

AIM

To apply long-read metagenomics coupled with microbiological measurements to investigate the drainome and assess the effects of a peracetic-acid-containing decontamination product.

METHODS

Twelve-week study in three phases: a baseline phase, an intervention phase of enhanced decontamination with peracetic acid, and a post-intervention phase. Five hospital sink drains on an intensive care unit were sampled twice weekly. Each sample had: (1) measurement of total viable count (TVC); (2) metagenomic analyses including (i) taxonomic classification of bacteria and fungi (ii), antibiotic resistance gene detection, (iii) plasmid identification; and (3) immunochromatographic detection of antimicrobial residues.

FINDINGS

Overall TVCs remain unchanged in the intervention phase (+386 cfu/mL, SE 705, P = 0.59). There was a small but significant increase in the microbial diversity in the intervention phase (-0.07 in Simpson's index, SE 0.03, P = 0.007), which was not sustained post-intervention (-0.05, SE 0.03, P = 0.08). The intervention was associated with increased relative abundance of the Pseudomonas genus (18.3% to 40.5% (+22.2%), SE 5.7%, P < 0.001). Extended spectrum β-lactamases were found in all samples, with NDM-carbapenemase found in three drains in six samples. Antimicrobial residues were detected in a large proportion of samples (31/115, 27%), suggesting use of sinks for non-handwashing activities.

CONCLUSION

Metagenomics and other measurements can determine the composition of the drainome and assess the effectiveness of decontamination interventions.

Hazard Characterization of Antibiotic-resistant Aeromonas spp. Isolated from Mussel and Oyster Shellstock Available for Retail Purchase in Canada

Surveillance and monitoring of foods for the presence of antimicrobial-resistant (AMR) bacteria are required to assess the risks these bacteria pose to human health. Frequently consumed raw or lightly cooked, live bivalve shellfish such as mussels and oysters can be a source of exposure to AMR bacteria. This study sought to determine the prevalence of third-generation cephalosporin (3GC) and carbapenem-resistant bacteria in live mussel and oyster shellstock available for retail purchase through the course of one calendar year. Just over half of the 180 samples (52%) tested positive for the presence of 3GC-resistant bacteria belonging to thirty distinct bacterial species. Speciation of the isolates was carried out using the Bruker MALDI Biotyper. Serratia spp., Aeromonas spp., and Rahnella spp. were the most frequently isolated groups of bacteria. Antibiotic resistance testing confirmed reduced susceptibility for 3GCs and/or carbapenems in 15 of the 29 Aeromonas isolates. Based on AMR patterns, and species identity, a subset of ten Aeromonas strains was chosen for further characterization by whole genome sequence analysis. Genomic analysis revealed the presence of multiple antibiotic resistance and virulence genes. A number of mobile genetic elements were also identified indicating the potential for horizontal gene transfer. Differences in gene detection by the bioinformatic tools and databases used (ResFinder. CARD RGI, PlasmidFinder, and MobSuite) are discussed. This study highlights the strengths and limitations of using genomics tools to perform hazard characterization of diverse foodborne bacterial species.

First Detection of High-Level Aminoglycoside-Resistant Klebsiella pneumoniae and Enterobacter cloacae Isolates Due to 16S rRNA Methyltransferases with and Without blaNDM in Uruguay

BACKGROUND

The increase in antimicrobial resistance includes emerging mechanisms such as 16S ribosomal RNA methylases, which confer high-level resistance to aminoglycosides. In this regard, the most predominant genes observed worldwide are rmtB and armA, but their presence in Uruguay is unknown.

OBJECTIVES

We describe the genomic characterization of isolates carrying rmtB and rmtC, together with blaNDM-5 and blaNDM-1, respectively, and rmtD in our country. Methology: Five isolates from patients admitted to three hospitals were studied. Identification and antibiotic susceptibility testing were performed using the Vitek2 System. Whole Genome Sequencing was conducted, and hybrid assembly was performed with Unicycler. In silico analysis using the Center for Genomic Epidemiology's tools was undertaken to predict antibiotic resistance determinants, plasmid incompatibility groups, and sequence types.

RESULTS

We report three K. pneumoniae ST307 isolates with an IncR plasmid carrying blaNDM-5/blaCTX-M-15/blaTEM-1B/rmtB/dfrA14/dfrA12/sul1/qacEΔ1/ermB/mphA, one K. pneumoniae ST258 harboring an IncC plasmid containing rmtC/blaNDM-1/blaCMY-6/aac(6')-Ib/sul1, and one E. cloacae ST88 isolate with an IncFIB/II plasmid hosting rmtD, within a novel Tn21-like transposon named Tn7825, alongside blaOXA-101/sul1/tet(G)/floR, and a new variant of blaTEM assigned as blaTEM-258. One of the strains, named UH_B2, also carried an IncM1 plasmid encoding qnrE1/blaTEM-1/blaCTX-M-8 associated with ISEcp1.

CONCLUSIONS

This is the first description of plasmids harboring 16S rRNA methyltransferases in Uruguay. The association and dissemination of diverse antibiotic-resistant genes underpin the health threat they represent, highlighting the lack of available antibiotics effective against multidrug-resistant microorganisms.

Real-time plasmid transmission detection pipeline

The spread of antimicrobial resistance among bacteria by horizontal plasmid transmissions poses a major challenge for clinical microbiology. Here, we evaluate a new real-time plasmid transmission detection pipeline implemented in the SeqSphere+ (Ridom GmbH, Münster, Germany) software. Within the pipeline, a local Mash plasmid database is created, and Mash searches with a distance threshold of 0.001 are used to trigger plasmid transmission early warning alerts (EWAs). Clonal transmissions are detected using core-genome multi-locus sequence typing allelic differences. The tools MOB-suite, NCBI AMRFinderPlus, CGE MobileElementFinder, pyGenomeViz, and MUMmer, integrated in SeqSphere+, are used to characterize plasmids and for visual pairwise plasmid comparisons, respectively. We evaluated the pipeline using published hybrid assemblies (Oxford Nanopore Technology/Illumina) of a surveillance and outbreak data set with plasmid transmissions. To emulate prospective usage, samples were imported in chronological order of sampling date. Different combinations of the user-adjustable parameters sketch size (1,000 vs 10,000) and plasmid size correction were tested, and discrepancies between resulting clusters were analyzed with Quast. When using a sketch size of 1,000 with size correction turned on, the SeqSphere+ pipeline agreed with the published data and produced the same clonal and carbapenemase-carrying plasmid clusters. EWAs were in the correct chronological order. In summary, the developed pipeline presented here is suitable for integration into clinical microbiology settings with limited bioinformatics knowledge due to its automated analyses and alert system, which are combined with the GUI-based SeqSphere+ platform. Thus, with its integrated sample database, (near) real-time plasmid transmission detection is within reach in bacterial routine-diagnostic settings when long-read sequencing is employed.

IMPORTANCE

Plasmid-mediated spread of antimicrobial resistance is a major challenge for clinical microbiology, and monitoring of potential plasmid transmissions is essential to combat further dissemination. Whole-genome sequencing is often used to surveil nosocomial transmissions but usually limited to the detection of clonal transmissions (based on chromosomal markers). Recent advances in long-read sequencing technologies enable full reconstruction of plasmids and the detection of very similar plasmids, but so far, easy-to-use bioinformatic tools for this purpose have been missing. Here, we present an evaluation of an innovative real-time plasmid transmission detection pipeline. It is integrated into the GUI-based SeqSphere+ software, which already offers core-genome multi-locus sequence typing-based pathogen outbreak detection. It requires very limited bioinformatics knowledge, and its database, automated analyses, and alert system make it well suited for prospective clinical application.

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.

Segatella clades adopt distinct roles within a single individual's gut

Segatella is a prevalent genus within individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on its genetic diversity, the lack of available isolates from this genus has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of Segatella. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to Segatella isolates either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related Segatella isolates, extending this to host-microbe interactions.

Carriage and antimicrobial susceptibility of commensal Neisseria species from the human oropharynx

Commensal Neisseria (Nc) mainly occupy the oropharynx of humans and animals. These organisms do not typically cause disease; however, they can act as a reservoir for antimicrobial resistance genes that can be acquired by pathogenic Neisseria species. This study characterised the carriage and antimicrobial susceptibility profiles of Nc from the oropharynx of 50 participants. Carriage prevalence of Nc species was 86% with 66% of participants colonised with more than one isolate. Isolates were identified by MALDI-ToF and the most common species was N. subflava (61.4%). Minimum inhibitory concentrations (MICs) to penicillin, ceftriaxone, ciprofloxacin, azithromycin, tetracycline, and gentamicin were determined by agar dilution and E-test was used for cefixime. Using Ng CLSI/EUCAST guidelines, Nc resistance rates were above the WHO threshold of 5% resistance in circulating strains for changing the first line treatment empirical antimicrobial: 5% (CLSI) and 13 (EUCAST) for ceftriaxone and 29.3% for azithromycin. Whole genome sequencing of 30 Nc isolates was performed, which identified AMR genes to macrolides and tetracycline. Core gene MLST clustered Nc into three main groups. Gonococcal DNA uptake sequences were identified in two Nc clusters. This suggests that Nc have the potential AMR gene pool and transfer sequences that can result in resistance transfer to pathogenic Neisseria within the nasopharyngeal niche.

Whole-genome sequencing of clinical isolates of Klebsiella michiganensi in China carrying blaIPM-4 and blaNDM-1

AIM

This study aimed to analyze the prevalence, phenotypes, and carriage of resistance genes of carbapenem-resistant Klebsiella michiganensis strains isolated in our hospital.

METHOD

ology: Four K. michiganensis strains were collected from January 2015 to December 2023. Antimicrobial susceptibility was tested using 21 antibiotics with the BD Phoenix™ M50 System. Whole-genome sequencing of the four strains was performed on an Illumina NovaSeq 6000 platform. Species identification was performed using Kleborate software, sequence type (ST) was performed using MLST, and prediction of antibiotic resistance genes and virulence genes were performed using ABRicate. PlasmidFinder was used to search for plasmids. Whole genome data from 211 strains of carbapenem-resistant K. michiganensis were downloaded from the NCBI database; together with the strains in this study, these data were used to construct an phylogenetic tree using genome single nucleotide polymorphisms (SNP).

RESULTS

Antimicrobial susceptibility showed that K. michiganensis was highly resistant to β-lactams. For the three carbapenems, strain WF0046 was only resistant to ertapenem, while WF0047, WF0052, and WF0053 were resistant to all three carbapenems tested. The four strains of K. michiganensis only showed complete sensitivity to polymyxin E and tigecycline. The four K. michiganensis strains were found to have 43 resistance genes, and all carried carbapenem resistance genes; WF0046 carried the carbapenem resistance gene blaIMP-4, while the other three strains carried blaNDM-1. Among the other resistance genes, β-lactam resistance genes were predicted most (11 types), followed by eight types of aminoglycoside resistance genes. Of the strains characterized in this study, WF0046 belonged to ST158, WF0047 belonged to ST40, WF0052 belonged to ST533, and WF0053 belonged to ST13. These four strains, along with 211 carbapenem-resistant K. michiganensis strains downloaded from NCBI, were divided into five clades; WF0052 belonged to clade A, WF0046 belonged to clade C, and WF0047 and WF0053 both belonged to clade D. The four strains had relatively distant genetic relationships; WF0046, WF0047, and WF0053 were closely related to strains of human origin from other regions of China, while WF0052 was genetically close with a strain of K. michiganensis isolated in the United States.

CONCLUSION

The strains of K. michiganensis from our hospital were resistant to multiple antibiotics, and all strains carried carbapenem resistance genes along with multiple other antibiotic resistance genes. The phylogenetic results showed that these four strains had distant genetic relationships and different ST types, indicating that they came from different sources and the possibility of polyclonal transmission.

Agarose Degrading Potential and Whole Genome Sequence Analysis of Marine Bacterium Aliagarivorans sp. Strain DM1 Isolated from the Arabian Sea

In recent years, agar-degrading bacteria have gained significant interest due to their biotechnological, environmental, microbiological, and industrial applications. Agar poses challenges such as marine waste accumulation, difficult industrial processing, limited natural degradability, and sustainability concerns due to high demand and overharvesting of red algae. The present study addresses the need for efficient agar-degrading microorganisms by isolating Aliagarivorans sp. strain DM1 from biofilm on fabric surfaces in the intertidal regions of the Arabian Sea, India. Phylogenetic analysis revealed that strain DM1 is closely related to Aliagarivorans taiwanensis AAT1T, and it exhibited significant agar-degrading activity on Zobell marine agar plates. Whole genome sequencing of Aliagarivorans sp. strain DM1, conducted using the Illumina NovaSeq platform, yielded a genome size of 4,898,415 bp with an average G + C content of 53.3%. The genome includes 4,518 predicted protein-coding genes (CDS), 86 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes, with thirteen predicted agarases identified. The highest enzyme activity recorded was 51.00 U mL-1 on the 6th day of incubation using 10% inoculum, with optimal conditions of pH 8-9, 0.8 M NaCl, and temperatures between 50 and 60 °C. These findings underscore the promise of Aliagarivorans sp. strain DM1 in developing efficient enzymatic processes that can be applied in various biotechnological and industrial fields, including waste management and agaro-oligosaccharide production. Furthermore, strain DM1 possesses several key characteristics that enhance its adaptability and utility in marine and industrial applications, surpassing closely related strains in enzyme stability, environmental tolerance, and industrial versatility.

Genomic insight on Klebsiella variicola isolated from wastewater treatment plant has uncovered a novel bacteriophage

Klebsiella variicola is considered an emerging pathogen, which may colonize a variety of hosts, including environmental sources. Klebsiella variicola investigated in this study was obtained from an influent wastewater treatment plant in the North-West Province, South Africa. Whole genome sequencing was conducted to unravel the genetic diversity and antibiotic resistance patterns of K. variicola. Whole genome core SNP phylogeny was employed on publicly available 170 genomes. Furthermore, capsule types and antibiotic resistance genes, particularly beta-lactamase and carbapenems genes were investigated from the compared genomes. A 38 099 bp bacteriophage was uncovered alongside with K. variicola genome. Whole genome sequencing revealed that the extended beta-lactamase blaLEN (75.3%) of the beta-lactamase is dominant among compared K. variicola strains. The identified IncF plasmid AA035 confers resistance genes of metal and heat element subtypes, i.e., silver, copper, and tellurium. The capsule type KL107-D1 is a predominant capsule type present in 88.2% of the compared K. variicola genomes. The phage was determined to be integrase-deficient consisting of a fosB gene associated with fosfomycin resistance and clusters with the Wbeta genus Bacillus phage group. In silico analysis showed that the phage genome interacts with B. cereus as opposed to K. variicola strain T2. The phage has anti-repressor proteins involved in the lysis-lysogeny decision. This phage will enhance our understanding of its impact on bacterial dissemination and how it may affect disease development and antibiotic resistance mechanisms in wastewater treatment plants. This study highlights the need for ongoing genomic epidemiological surveillance of environmental K. variicola isolates.

Genomic Characterization and Probiotic Properties of Lactiplantibacillus pentosus Isolated from Fermented Rice

The aim of the study was the preliminary genetic and phenotypic characterization of a potential probiotic strain of Lactiplantibacillus pentosus (strain krglsrbmofpi2) obtained from traditionally fermented rice. Genome sequencing revealed that the strain has a 3.7-Mb genome with a GC content of 46 and a total of 3192 protein-coding sequences. Using bioinformatic methods, we have successfully identified phage genes, plasmids, pathogenicity, antibiotic resistance and a variety of bacteriocins. Through comprehensive biochemical and biophysical analyses, we have gained valuable insights into its auto-aggregation, co-aggregation, antibiotic resistance, hydrophobicity, antioxidant activity and tolerance to simulated gastrointestinal conditions. The safety evaluation of the isolated L. pentosus was performed on the basis of its haemolytic activity. Our studies have shown that this strain has a strong antagonistic activity against the priority pathogens identified by the World Health Organization such as Vibrio cholerae, Clostridium perfringens, Salmonella enterica subsp. enterica ser. Typhi, Escherichia coli, Listeria monocytogenes and Staphylococcus aureus. It is essential to fully understand the genetic and functional properties of the L. pentosus strain before considering its use as a useful probiotic in the food industry.

The interplay between mobilome and resistome in Staphylococcus aureus

Antibiotic resistance genes (ARGs) in Staphylococcus aureus can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in S. aureus favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000 S. aureus genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the S. aureus resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in S. aureus, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.IMPORTANCEThe research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by Staphylococcus aureus, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals. S. aureus has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of S. aureus genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between S. aureus populations, bypassing host barriers. Given that multidrug-resistant S. aureus strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.

mNGS-identified cellulitis due to quinolone-resistant Edwardsiella tarda: a case report

Edwardsiella tarda is frequently isolated from aquatic animals and environments. While human infections caused by E. tarda are rare, some extraintestinal infections can be severe. This case report describes a patient with cellulitis of the right upper extremity of unknown origin. Metagenomic next-generation sequencing (mNGS) indicated that the patient was infected with E. tarda. Antimicrobial susceptibility testing revealed that the isolate was resistant to quinolones and trimethoprim/sulfamethoxazole. The isolate, positive for four virulence genes (fimA, gadB, mukF, and sodB), was confirmed to be virulent using the Galleria mellonella larvae model. Following early pus drainage and a 9-day course of imipenem, the patient ultimately recovered. This case report aimed to illustrate the presentation, diagnosis, and management of uncommon cellulitis caused by drug-resistant, virulent E. tarda.

Whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens

BACKGROUND

The burden of sepsis worsens due to the continuation of emerging pathogens such as multidrug-resistant Pantoea species.

METHODS

A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central, southern, and northern parts of Ethiopia. A total of 1416 sepsis patients were recruited and blood cultures were performed. At each study site, positive cultures were characterized by their colony characteristics, gram stain, and conventional biochemical tests. All Pantoea species were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF) and subjected to whole genome sequencing (WGS) using Illumina HiSeq 2500. The phylogeny structure of Pantoea isolates was calculated using IQ-TREE v1.6.12 from single-nucleotide polymorphisms detected by Snippy v.4.6.0 and filtered by Gubbins v.2.3.4. Average nucleotide identity was estimated by using OrthoANI v.0.93.1 on Shovill v.1.1.0 assemblies. Antimicrobial resistance genes and plasmid replicons were detected using ARIBA v.2.14.6. Phylogenetic trees were visualized using iTOLv.6.5.2.

RESULTS

Multiple Pantoea species include: P. dispersa (n = 19), P. septica (n = 1), and a novel Pantoea spp. (n = 1), were identified among sepsis patients. All P. dispersa isolates and the novel Pantoea species were isolated at Dessie Referral Hospital and displayed phylogenetic clonality, including the ubiquity of an IncM1 plasmid and identical antimicrobial resistance (AMR) gene profiles, encoding blaCTX-M-15, blaTEM-1D, blaSCO-1, and aac(3)-lla. The novel Pantoea spp. isolate harboured blaCTX-M-9 and blaTEM-1D and carried an IncN3 plasmid replicon. The P. septica was isolated at Tikur Anbessa Specialized Hospital in Addis Ababa and carried no detectable acquired AMR genes.

CONCLUSION

The emerging Pantoea spp. carrying multiple AMR genes were identified from sepsis patients. Implementation of strong infection prevention strategies and building surveillance capacity with advanced bacteriology laboratories capable of identifying multidrug-resistant emerging pathogens is strongly recommended.

An outbreak of blaKPC-4- and blaVIM-1-producing Klebsiella pneumoniae and Klebsiella variicola at a single hospital in South Korea

BACKGROUND

The dissemination of Klebsiella spp. producing multiple carbapenemases has been increasingly recognized. Between July 2019 and August 2021, ten patients were found to carry Klebsiella spp. co-harboring blaKPC-4 and blaVIM-1 across multiple wards at a Korean hospital, and one isolate was recovered from a hand-washing sink, more than a year after the outbreak. This study aimed to investigate the outbreak and conduct a genomic study of these isolates.

METHODS

Whole-genome sequencing, including long-read sequencing, was performed to analyze plasmid structures and mobile genetic elements (MGEs). Bioinformatics analyses were performed to trace clonal transmission chains and horizontal gene transfer.

RESULTS

The findings suggested that the inter-ward spread of Klebsiella spp. seemed to be facilitated by healthcare worker contact or patient movement. Of the nine isolates collected (eight clinical and one environmental), seven (including the environmental isolate) were identified as K. pneumoniae (ST3680) and two were K. variicola (single-locus variant of ST5252). These isolates showed high genetic relatedness within their species and harbored the IncHI5B plasmid carrying both blaKPC-4 and blaVIM-1 (pKPCVIM.1). On this plasmid, blaVIM-1 was located in the Class 1 integron associated with IS1326::IS1353 (In2), and Tn4401b carrying blaKPC-4 was inserted into IS1326::IS1353, creating a novel MGE construct (In2_blaVIM-1-Tn4401b_blaKPC-4).

CONCLUSION

The hospital-wide spread of blaKPC-4 and blaVIM-1 was facilitated by clonal spread and horizontal plasmid transfer. The persistence of this strain in the hospital sink suggests a potential reservoir of the strain. Understanding the transmission mechanisms of persistent pathogens is important for improving infection control strategies in hospitals.

Genomic Characterization of 16S rRNA Methyltransferase-Producing Enterobacterales Reveals the Emergence of Klebsiella pneumoniae ST6260 Harboring rmtF, rmtB, blaNDM-5, blaOXA-232 and blaSFO-1 Genes in a Cancer Hospital in Bulgaria

Background: Acquired 16S rRNA methyltransferases (16S-RMTases) confer high-level resistance to aminoglycosides and are often associated with β-lactam and quinolone resistance determinants. Methods: Using PCR, whole-genome sequencing and conjugation experiments, we conducted a retrospective genomic surveillance study of 16S-RMTase-producing Enterobacterales, collected between 2006 and 2023, to explore transmission dynamics of methyltransferase and associated antibiotic resistance genes. Results: Among the 10,731 consecutive isolates, 150 (1.4%) from 13 species carried armA (92.7%), rmtB (4.7%), and rmtF + rmtB (2.7%) methyltransferase genes. The coexistence of extended-spectrum β-lactamase (blaCTX-M-3/15, blaSHV-12, blaSFO-1), carbapenemase (blaNDM-1/5, blaVIM-1/4/86, blaOXA-48), acquired AmpC (blaCMY-2/4/99, blaDHA-1, blaAAC-1), and plasmid-mediated quinolone resistance (qnrB, qnrS, aac(6')-Ib-cr) genes within these isolates was also detected. Methyltransferase genes were carried by different plasmids (IncL/M, IncA/C, IncR, IncFIB, and IncFII), suggesting diverse origins and sources of acquisition. armA was co-transferred with blaCTX-M-3/15, blaNDM-1, blaVIM-4/86, blaOXA-48, blaCMY-4, aac(6')-Ib-cr, qnrB, and qnrS, while rmtF1 was co-transferred with blaSFO-1, highlighting the multidrug-resistant nature of these plasmids. Long-read sequencing of ST6260 K. pneumoniae isolates revealed a novel resistance association, with rmtB1 and blaNDM-5 on the chromosome, blaOXA-232 on a conjugative ColKP3 plasmid, and rmtF1 with blaSFO-1 on self-transmissible IncFIB and IncFII plasmids. Conclusions: The genetic plasticity of plasmids carrying methyltransferase genes suggests their potential to acquire additional resistance genes, turning 16S-RMTase-producing Enterobacterales into a persistent public health threat.

Comprehensive analysis of distribution characteristics and horizontal gene transfer elements of blaNDM-1-carrying bacteria

The worldwide dissemination of New Delhi metallo-β-lactamase-1 (NDM-1), which mediates resistance to almost all clinical β-lactam antibiotics, is a major public health problem. The global distribution, species, sources, and potential transfer risk of blaNDM-1-carrying bacteria are unclear. Results of a comprehensive analysis of literature in 2010-2022 showed that a total of 6002 blaNDM-1 carrying bacteria were widely distributed around 62 countries with a high trend in the coastal areas. Opportunistic pathogens or pathogens like Klebsiella sp., Escherichia sp., Acinetobacter sp. and Pseudomonas sp. were the four main species indicating the potential microbial risk. Source analysis showed that 86.45 % of target bacteria were isolated from the source of hospital (e.g., Hospital patients and wastewater) and little from surface water (5.07 %) and farms (3.98 %). A plasmid-encoded blaNDM-1Acinetobacter sp. with the resistance mechanisms of antibiotic efflux pump, antibiotic target change and antibiotic degradation was isolated from the wastewater of a typical tertiary hospital. Insertion sequences (IS3 and IS30) located in the adjacent 5 kbp of blaNDM-1-bleMBL gene cluster indicating the transposon-mediated horizontal gene transfer risk. These results showed that the worldwide spread of blaNDM-1-carrying bacteria and its potential horizontal gene transfer risk deserve good control.

First draft genome sequence of a Pectobacterium polaris strain isolated in South Africa from potato tuber affected by soft rot

A phytopathogenic strain of Pectobacterium polaris (designated SRB2) was isolated for the first time in South Africa from a potato tuber affected by soft rot. The draft genome of strain SRB2 encodes various plant cell wall-degrading enzymes and genes associated with biofilm formation and virulence. Antibiotic resistance genes were not detected.

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer

Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping community interactions, but offer little toward controlling them-an important step in the translation of synthetic strains into natural contexts. Toxin-antitoxin (TA) systems serve as ubiquitous and diverse agents of selection; however, their utility is limited by their erratic distribution in hosts. Here we examine the heterogeneous distribution of TAs as a consequence of their mobility. By systematically mapping TA systems across a 10,000 plasmid network, we find HGT communities have unique and predictable TA signatures. We propose these TA signatures arise from plasmid competition and have further potential to signal the degree to which plasmids, hosts, and phage interact. To emphasize these relationships, we construct an HGT network based solely on TA similarity, framing specific selection markers in the broader context of bacterial communities. This work both clarifies the evolution of TA systems and unlocks a common framework for manipulating community interactions through TA compatibility.

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.

Coexistence of plasmid-mediated tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in Klebsiella quasipneumoniae

Klebsiella quasipneumoniae is a potential pathogen that has not been studied comprehensively. The emergence of multidrug-resistant (MDR) K. quasipneumoniae, specifically strains resistant to tigecycline and carbapenem, presents a significant challenge to clinical treatment. This investigation aimed to characterize MDR K. quasipneumoniae strain FK8966, co-carrying tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 by plasmids. It was observed that FK8966's MDR was primarily because of the IncHI1B-like plasmid co-carrying tmexCD2-toprJ2 and blaIMP-4, and an IncFIB(K)/IncFII(K) plasmid harboring blaNDM-1. Furthermore, the phylogenetic analysis revealed that IncHI1B-like plasmids carrying tmexCD2-toprJ2 were disseminated among different bacteria, specifically in China. Additionally, according to the comparative genomic analysis, the MDR regions indicated that the tmexCD2-toprJ2 gene cluster was inserted into the umuC gene, while blaIMP-4 was present in transposon TnAs3 linked to the class 1 integron (IntI1). It was also observed that an ΔTn3000 insertion with blaNDM-1 made a novel blaNDM-1 harboring IncFIB(K)/IncFII(K) plasmid. The antimicrobial resistance prevalence and phylogenetic analyses of K. quasipneumoniae strains indicated that FK8966 is a distinct MDR branch of K. quasipneumoniae. Furthermore, CRISPR-Cas system analysis showed that many K. quasipneumoniae CRISPR-Cas systems lacked spacers matching the two aforementioned novel resistance plasmids, suggesting that these resistance plasmids have the potential to disseminate within K. quasipneumoniae. Therefore, the spread of MDR K. quasipneumoniae and plasmids warrants further attention.IMPORTANCEThe emergence of multidrug-resistant K. quasipneumoniae poses a great threat to clinical care, and the situation is exacerbated by the dissemination of tigecycline- and carbapenem-resistant genes. Therefore, monitoring these pathogens and their resistance plasmids is urgent and crucial. This study identified tigecycline- and carbapenem-resistant K. quasipneumoniae strain, FK8966. Furthermore, it is the first study to report the coexistence of tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 in K. quasipneumoniae. Moreover, the CRISPR-Cas system of many K. quasipneumoniae lacks spacers that match the plasmids carried by FK8966, which are crucial for mediating resistance against tigecycline and carbapenems, indicating their potential to disseminate within K. quasipneumoniae.

Occurrence, genetic diversity, and antimicrobial resistance of methicillin-resistant Staphylococcus spp. in hospitalized and non-hospitalized cats in Brazil

Methicillin-resistant Staphylococci (MRS) cause infections at various sites and exhibit multidrug resistance. Despite their importance in veterinary medicine, only little is known about Staphylococcus spp. colonizing and infecting cats. Therefore, in this study, we aimed to isolate and identify Staphylococcus spp. colonizing hospitalized and non-hospitalized domestic cats and analyze their antimicrobial resistance profiles, genetic diversity, and risk factors associated with MRS colonization. A total of 218 oral and axillary swabs were obtained from 109 cats, including 77 non-hospitalized and 32 hospitalized cats. After plating on selective media, the isolates were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and rpoB and 16S rRNA gene sequencing. Subsequently, antimicrobial sensitivity of the strains was assessed, and they were screened for mecA gene. Methicillin-resistant S. haemolyticus (MRSH) isolates were subjected to multilocus sequence typing, whereas methicillin-resistant S. pseudintermedius (MRSP) and S. felis isolates were subjected to whole genome sequencing. S. felis was most commonly isolated from non-hospitalized cats (28.1%), whereas S. pseudintermedius and MRS were commonly isolated from hospitalized cats (25%). MRSH isolates from hospitalized animals were classified as ST3. The identified MRSP strains belonged to two well-known sequence types, ST551 and ST71. Moreover, antimicrobial use (p = 0.0001), hospitalization (p = 0.0141), and comorbidities (p = 0.002) were associated with increased MRS prevalence in cats.

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.

High prevalence and genomic features of multidrug-resistant Salmonella enterica isolated from chilled broiler chicken on retail sale in the United Arab Emirates

Non-typhoidal Salmonella represents a significant global concern for food safety and One Health. Despite the United Arab Emirates (UAE) being a leading consumer of chicken meat globally, there is a lack of comprehensive understanding regarding the prevalence and genomic characteristics of Salmonella within the country. This study aims to address this gap by conducting a thorough analysis of Salmonella prevalence, antimicrobial resistance, and genomic profiles of isolates obtained from whole broiler carcasses retailed under chilled conditions in the UAE. Our findings reveal that Salmonella was detected in 41.2 % (130/315) of the sampled chilled broiler carcasses, with notable variability observed among samples sourced from six different companies. Phenotypic antimicrobial resistance (AMR) testing, among 105 isolates, highlighted high resistance rates to tetracycline (97.1 %), nalidixic acid (93.3 %), ampicillin (92.4 %), azithromycin (75.2 %), ciprofloxacin (63.8 %), and ceftriaxone (54.3 %). Furthermore, a concerning 99 % (104/105) of the isolates exhibited multidrug resistance. Whole-genome sequencing (WGS) of 60 isolates identified five serovars, with S. infantis/Sequence Type (ST) 32 (55 %) and S. Minnesota/ST-458 (28.3 %) being the most prevalent. WGS analysis unveiled 34 genes associated with antimicrobial resistance, including mcr-1.1 (only in two isolates), conferring resistance to colistin. The two major serovars, Infantis and Minnesota, exhibited significant variation (P-values <0.001) in the distribution of major AMR genes (aadA1, blaCMY-2, blaSHV-12, qnrB19, qnrS1, sul1, and sul2). Notably, the gene qacEdelta, conferring resistance to quaternary ammonium compounds commonly found in disinfectants, was universally present in all S. Infantis isolates (n = 33), compared to only one S. Minnesota isolate. Additionally, all S. Infantis isolates harbored the IncFIB (pN55391) plasmid replicon type. Major serovars exhibited distinct distributions of antimicrobial resistance genes, underscoring the importance of serovar-specific surveillance. These findings emphasize the critical need for continuous surveillance and intervention measures to address Salmonella contamination risks in poultry products, providing valuable insights for public health and regulatory strategies not only in the UAE but also globally.

Genomic epidemiology and resistant genes of Acinetobacter baumannii clinical strains in Vietnamese hospitals

Introduction. Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections worldwide, including Vietnam.Hypothesis. Analysis of crucial genetic factors may link to epidemiological characteristics and antibiotic resistance of A. baumannii clinical strains in Vietnamese hospitals.Methodology. Fifty-one A. baumannii clinical strains from six different tertiary hospitals in Vietnam were analysed using whole genome sequencing (WGS), between 2017 and 2019.Results. Eleven sequence types (STs) were identified, including four STs reported for the first time in Vietnam based on the PubMLST database and three new STs not previously documented. ST1336, ST1260 and ST575 were found exclusively in Vietnam. These STs were widely distributed in all hospitals in Vietnam, with ST2 and ST571 being the most dominant. Resistant rates to eight antibiotics, belonging to four antibiotic groups, were very high (72.5-94.1 %) with high MIC values, while resistance to colistin was 29.4%. Fifty-one isolates were identified as MDR, with 100% (51/51) isolates carrying antimicrobial-resistant (AMR) genes, and 52 antibiotic-resistant genes were detected among these strains, including β-lactam (22 genes), chloramphenicol (5 genes), lincosamide (2 genes), aminoglycoside (11 genes), rifampicin (1 gene), quinolone (2 genes), sulfonamide and trimethoprim (4 genes) and tetracycline (5 genes) resistance. The most commonly found mobile structures carried partial or complete transposons: ISaba24/ISEc29/ISEc35 contains a series of antibiotic-resistant genes.Conclusion. The WGS results of the 51 strains of A. baumannii provided important information regarding the distribution of STs and associated antibiotic-resistant genes among A. baumannii strains.

Applying rearrangement distances to enable plasmid epidemiology with pling

Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological analysis. Typical approaches are either low resolution (replicon typing) or use shared k-mer content to define a genetic distance. However, this distance can both overestimate plasmid relatedness by ignoring rearrangements, and underestimate by over-penalizing gene gain/loss. Therefore a model is needed which captures the key components of how plasmid genomes evolve structurally - through gene/block gain or loss, and rearrangement. A secondary requirement is to prevent promiscuous transposable elements (TEs) leading to over-clustering of unrelated plasmids. We choose the 'Double Cut and Join Indel' (DCJ-Indel) model, in which plasmids are studied at a coarse level, as a sequence of signed integers (representing genes or aligned blocks), and the distance between two plasmids is the minimum number of rearrangement events or indels needed to transform one into the other. We show how this gives much more meaningful distances between plasmids. We introduce a software workflow pling (https://github.com/iqbal-lab-org/pling), which uses the DCJ-Indel model, to calculate distances between plasmids and then cluster them. In our approach, we combine containment distances and DCJ-Indel distances to build a TE-aware plasmid network. We demonstrate superior performance and interpretability to other plasmid clustering tools on the 'Russian Doll' dataset and a hospital transmission dataset.