ResFinder 4.0 for predictions of phenotypes from genotypes

Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations

In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.

Molecular and genomic investigation unveils Pseudomonas putida as an emerging multidrug-resistant pathogen linked to bovine clinical mastitis

Pseudomonas putida is one of the emerging pathogens responsible causing mastitis in lactating animals. This study investigated the prevalence, antimicrobial resistance (AMR), genetic diversity and virulence factor genes (VFGs) to highlight the pathogenic potentials of P. putida strains isolated from milk, feces and farm soil of dairy cows diagnosed with clinical mastitis (CM). A total of 110 samples were collected and analyzed, revealing an overall prevalence of P. putida in dairy farms at 40.90 %, with specific prevalence rates of 42.22 % in milk, 26.67 % in feces, and 31.11 % in farm soil. In vitro antimicrobial assays demonstrated that 76.0 % P. putida isolates exhibited multidrug resistance (MDR, resistance to ≥ 3 antibiotics), particularly showing high resistance to oxacillin, ampicillin, nalidixic acid, and aztreonam. Conversely, P. putida isolates showed the highest susceptibility against imipenem. The genome analysis of three MDR P. putida strains 11CM-M1 (milk), 11CM-F1 (feces) and 11CM-S1 (farm soil), showed a close evolutionary relationship with different strains of Pseudomonas spp. isolated from bovine mastitis milk and feces samples, human stool, and samples sourced from hospital environment. The assembled genomes of three P. putida strains encoded nine antibiotic resistance genes (ARGs), 36 VFGs, and 367 metabolic subsystems, highlighting a complex functional profile and potential for pathogenicity. The detailed analysis of these ARGs and VFGs demonstrated that P. putida strains employ distinct mechanisms of resistance (e.g., efflux pumps), biofilm formation, and virulence factors, including adhesins, secreted toxins, and lipopolysaccharides, which contribute to their pathogenic potential. Given the lack of reports linking P. putida strains to bovine mastitis in Bangladesh, the increasing trend of AMR, along with the presence of significant ARGs and VFGs in the studied strains, underscores the need for more intensive research, including animal model experiment, to better elucidate the pathogenesis and inform treatment decisions for mastitis in dairy animals.

Gene expressions of clinical Pseudomonas aeruginosa harboring RND efflux pumps on chromosome and involving a novel integron on a plasmid

The clinical strain of Pseudomonas aeruginosa XM8 harbored multiple RND-type antibiotic efflux pump genes and a novel integron In4881 on its plasmid pXM8-2, rendering it resistant to nearly all conventional antibiotics except colistin. The resistance was primarily attributed to the inactivation of the oprD gene and overexpression of several efflux pump genes, including mexAB-oprM, mexCD-oprJ, oprN-mexFE, and mexXY. In this study, the XM8 strain was comprehensively characterized using various methods. Antimicrobial susceptibility testing was performed using the BioMerieux VITEK2 system and manual double dilution methods. Gene expression levels of efflux pump-related genes were analyzed via quantitative real-time PCR. The bacterial chromosome and plasmid were sequenced using both Illumina and Nanopore platforms, and bioinformatics tools were employed to analyze mobile genetic elements associated with antibiotic resistance. The pXM8-2 plasmid containsed multiple mobile genetic elements, including integrons (In4881, In334, In413) and transposons (Tn3, TnAs1, TnAs3). Notably, In4881 was reported for the first time in this study. The presence of these elements highlights the potential for horizontal gene transfer and further spread of antibiotic resistance. Given the strong resistance profile of the XM8 strain, effective measures should be implemented to prevent the dissemination and prevalence of such multidrug-resistant bacteria.

Genetic characterization of extensively drug-resistant blaCTX-M-27Shigella sonnei clusters among men who have sex with men in a region of northern Spain

OBJECTIVE

The convergence of globalization with increased sexual risk behaviours has significantly facilitated the dissemination of multidrug-resistant and extensively drug-resistant clusters of Shigella spp. among men who have sex with men, particularly Shigella sonnei and Shigella flexneri. A cluster of S. sonnei carrying blaCTX-M-27 caused a European outbreak in 2020-2021, with more than 30 cases in Spain, including two in our institution. In this study, we conducted a retrospective study from October 2022 to December 2023 that included five additional patients with shigellosis caused by a CTX-M-27-producing S. sonnei.

METHODS

Genetic characterization was assessed by whole-genome sequencing using the MinION Mk1C device (Oxford Nanopore Technologies, Oxford, UK).

RESULTS

All the isolates presented IncB/O/K/Z or IncFII plasmids, which carried genes conferring resistance to second- and third-generation cephalosporins, cotrimoxazole, azithromycin and quinolones. SNP analysis revealed that neither the strains within this study nor the UK cluster were related to each other.

CONCLUSIONS

Different community clusters of extensively drug-resistant S. sonnei strains harbouring blaCTX-M-27 are spreading in our area, mainly associated with sexual transmission among men who have sex with men.

Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment

Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.

Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota

In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.

The evolution of carbapenem-resistant Pseudomonas aeruginosa in the COVID-19 era: A global perspective and regional insights

OBJECTIVE

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a major contributor to healthcare-associated infections globally. The aim of this study was the impact of the COVID-19 pandemic on the genomic characteristics of P. aeruginosa, particularly clinical CRPA isolates.

METHODS

Clinical data of each patient were collected from the clinical and medical record system. Whole-genome sequencing and bioinformatics analyses were performed to characterize the antibiotic resistance genes (ARGs) and evolutionary dynamics of these isolates. Furthermore, big data analysis was employed to elucidate the genomic characteristics of P. aeruginosa genomes across different periods on a global scale. Statistical analyses were applied to ensure the reliability of the findings.

RESULTS

A total of 628 non-duplicate CRPA isolates were collected, with 256 isolates from before the COVID-19 pandemic and 372 during the pandemic. Only 26.59% of isolates carried carbapenemases, predominantly GES-14, and carbapenemase diversity decreased during the pandemic. However, the diversity of CRPA sequence types (STs) increased, with ST235 and ST244 emerging as the most prevalent clones. The Antibiotic resistance genes (ARGs) number carried by CRPA isolates significantly decreased during the pandemic (P < 0.05), with notable differences in 24 ARGs and 14 virulence factors (VFs) between prepandemic and pandemic periods (χ2 test, P < 0.05). O11 was the predominant serotype across all periods. Global analysis revealed a significant reduction in ARGs in strains from China and Australia (P < 0.01) during the pandemic. Analysis of the global epidemic clones ST244 and ST235 indicated that ARGs in ST244 P. aeruginosa increased significantly during the pandemic.

CONCLUSIONS

Our study highlights the critical need for ongoing surveillance of the evolutionary effects of the COVID-19 pandemic on clinical CRPA isolates, offering an essential theoretical basis for the development of effective and rational control strategies in clinical settings.

Genomic characterization of Streptococcus suis serotype 31 isolated from one human and 17 clinically asymptomatic pigs in Thailand

Streptococcus suis is a zoonotic pathogen capable of causing severe diseases in humans and pigs. Frequently, S. suis serotype 31 strains have been isolated from pigs. The first human case of S. suis was reported in Thailand in 2015. In total, 18 strains from one human and 17 clinically asymptomatic pigs in Thailand were analyzed to characterize S. suis serotype 31. In total, 11 different STs were identified, with the major ST being ST2767 (38.89 %; 7/18). The minimum core-genome (MCG) classification revealed that almost all of the serotype 31 strains belonged to MCG7 (94.44 %; 17/18). Genomic analysis revealed that the serotype 31 isolates were major clusters with the porcine-healthy strains from China, Viet Nam, and Thailand. The human serotype 31 ST221 isolate was closely related to S. suis serotype 5 and 24 strains (CC221/234) isolated from Thailand. All serotype 31 strains were multidrug resistant with resistance to azithromycin (100 %; 18/18) and tetracycline (100 %; 18/18). Notably, 10 (55.56 %) of the serotype 31 strains were resistant to penicillin, while 8 strains (44.44 %) showed intermediate resistance to this agent. High substitutions were observed in three penicillin-binding proteins (1 A, 2B, and 2X) of these serotype 31 strains. The most prevalent antimicrobial resistance genes were erm(B) (100 %; 18/18) and tet(O) (66.67 %; 12/18). Overall, 7 strains carried integrative conjugative elements (ICEs) that harbored antimicrobial resistance genes, such as erm(B), tet(O), and tet(W). This study contribute to understanding the genomic diversity and provide valuable information for public health awareness of multidrug-resistant S. suis serotype 31.

Effectiveness of newly isolated bacteriophages targeting multidrug-resistant Extraintestinal Pathogenic Escherichia coli strain (TZ1_3) in food preservation and mice health modulation

Bacteriophages are promising alternatives for combating multidrug-resistant bacterial infections. Two lytic bacteriophages, named P1 and P3, targeting pathogenic Escherichia coli (ExPEC; strain TZ1_3) were isolated and evaluated for their potential ability to control pathogenic numbers either in ExPEC-contaminated food or ExPEC-infected mice. Results showed that phages significantly reduced ExPEC numbers within 6 and 12 h in contaminated water, milk, beef, and chicken when applied at 106 plaque-forming units (PFU). Notably, phage therapy administered via intraperitoneal injection (1012 PFU) effectively reduced ExPEC numbers in the heart, liver, spleen and kidney, restored α-diversity of gut microbes, and increased levels of acetic (13.98 %-37.58 %) and valeric acid (10.27 %-31.51 %) in ExPEC-infected mice. Additionally, phage injections caused no detrimental effects on body weight (which increased by 6.49 %-8.11 %), and on gut microbes in healthy mice. Overall, this study highlights the potential of phages in controlling foodborne microorganisms.

Draft genomic sequences of a rare environmental pathogen, Comamonas kerstersii, from immunocompromised patients with acute gastroenteritis

Comamonas kerstersii is a ubiquitous, aerobic, motile gram-negative bacteria considered commensal but has played a significant role as a potential pathogen causing clinical infections. Here, we report the genomic sequences of five C. kerstersii isolated from immunocompromised patients with acute gastroenteritis.

Draft genome sequence of a multidrug-resistant clinical Serratia marcescens DUEML4 (ST444) isolated from a human tracheal aspirate in Bangladesh

Serratia marcescens is a rare opportunistic nosocomial pathogen. Here, we report the draft genome sequence of S. marcescens DUEML4 (ST444), isolated from the tracheal aspirate of a 68-year-old female patient with respiratory tract infection in a hospital in Dhaka. This is the first public genome sequence of ST444.

Identification of pandemic ST147, ESBL-type β-lactamases, carbapenemases, and virulence factors in Klebsiella pneumoniae isolated from southern Peru

Multidrug-resistant Klebsiella pneumoniae (MDR K. pneumoniae) is a significant pathogen associated with nosocomial infections, often leading to high morbidity and mortality. This resistance is largely due to the efficient horizontal transfer of mobile genetic elements such as plasmids, which carry resistance genes and virulence factors. These elements contribute to the production of extended-spectrum β-lactamases (ESBL) and carbapenemases, which further complicates treatment. Despite the high prevalence of MDR K. pneumoniae in Peruvian hospitals, the genomic characterization of these strains remains limited. This study investigated the phenotypic and molecular identification of extended-spectrum β-lactamases (ESBLs), carbapenemases, and virulence factors in 91 MDR K. pneumoniae strains collected from three hospitals between 2022 and 2023. Phenotypic detection of ESBLs was performed using the Jarlier method, while carbapenemases were identified via double-disk synergy testing with boronic acid, EDTA, and Carba NP test. The positive isolates were further analyzed for resistance genes (blaCTX-M, blaTEM, blaSHV, blaKPC, blaNDM, blaIMP, and blaVIM). Four isolates were subjected to whole-genome sequencing (WGS) for further characterization. All multidrug-resistant K. pneumoniae strains (100%) were ESBL-positive, with 14.3% producing carbapenemases, primarily KPC-type and metallo-β-lactamases (MBLs). The virulence factor analyses revealed that only 7.7% exhibited hypermucoviscosity. Protease activity was detected in 19.8% of the strains, and lipase activity in 1.1%. Regarding biofilm formation, 85.7% of the strains showed moderate adherence. Molecular analysis identified ESBL (blaCTX-M, 78%; blaTEM, 71.4%; blaSHV, 82.4%) and carbapenemase genes (blaKPC 7.7%, blaNDM 4.4%). Genomic analysis revealed various antimicrobial resistance mechanisms, including porin-coding gene mutations, aminoglycoside resistance linked to fluoroquinolone resistance, and multidrug efflux pump regulators. Sequence typing has identified high-risk clones (ST147, ST629, and ST37) associated with hospital outbreaks globally. These findings underscore the considerable concern of MDR and hypervirulent K. pneumoniae in Peruvian hospitals. These findings emphasize the pressing need for sustained genomic surveillance, enhanced infection control measures, and strategies to address the expanding problem of MDR K. pneumoniae.

Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen

BACKGROUND

Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.

RESULTS

Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.

CONCLUSIONS

This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.

Mapping antimicrobial resistance landscape at a city scale sewage network

Wastewater is a valuable source for monitoring contaminants of biotic or abiotic origin. Antimicrobial resistance (AMR) has emerged as a public health threat that consists of the ability of microorganisms to resist the effects of antimicrobial compounds, rendering them very difficult or impossible to eradicate in case of infection. Considering the dissemination of antimicrobial resistance genes (ARGs) to a wide number of ecosystems, there is a need for the identification of hotspots that concentrate antimicrobial resistance determinants. A comprehensive investigation conducted at a city-scale in Sabadell (Barcelona, Spain) has integrated both phenotypic and genotypic methodologies, including metagenomics and culture-based techniques coupled with whole-genome sequencing (WGS), to monitor ARG presence in seven different spots of the sewage system. Metagenomics approach identified 262 ARG variants across analyzed sampling sites, grouped into 15 resistance categories. The most prevalent ARGs were macrolides-lincosamides-class B streptogramins (MLSB) (35.1 %) and beta-lactams (28.7 %), including carbapenems (5.9 %) and cephalosporins (5.3 %). MLSB resistance featured dominant msr(E) and mph(E) genes, the most abundant ARGs in our study. ARGs conferring resistance to beta-lactam were dominated by blaOXA-464, blaOXA-491, and blaNPS. Key genes for carbapenem (blaOXA-372, blaKPC-2) and cephalosporin (blaOXA-10, blaOXA-1) resistance were identified. The hospital sector exhibited the highest relative abundance of ARGs, dominated by beta-lactams, MLSB, and aminoglycosides. Wastewater treatment plant (WWTP) entrance points and residential areas displayed similar ARG profiles, while WWTP effluent and industrial zones had the lowest ARG levels. WWTP significantly reduced ARG presence (93.3 %). The characterization of antibiotic-resistant bacterial isolates found that most abundant ARGs were predominantly plasmid-borne, favoring ARG spread across bacterial genera. This finding confirmed the significant role of plasmids in ARG dissemination, increasing both diversity and prevalence within waterborne bacterial communities. City-scale surveillance programs can play a pivotal role in guiding effective measures to reduce the dissemination of AMR and mitigate their environmental impact.

Genome sequence of antibiotic-resistant Klebsiella quasipneumoniae FSFC0558: a novel sequence type (ST8212)

Klebsiella quasipneumoniae are Gram-negative bacteria of the family Enterobacteriaceae, distinguished from other members of the Klebsiella genus through a chromosomally encoded extended spectrum β-lactamase, blaOKP . Here, we report a hybrid assembled genome of a novel sequence type of K. quasipneumoniae subspecies similipneumoniae isolated from a faecal sample of a patient with sepsis.

Clinical and Microbiological Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Associated Recurrent Urinary Tract Infections

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major pathogen responsible for urinary tract infections (UTIs). However, its role and characteristics in recurrent urinary tract infections (rUTIs) remain poorly understood. Investigating its features in rUTIs may provide insights into effective prevention strategies.

Methods

We analyzed a cohort of patients with rUTIs caused by Klebsiella pneumoniae from April 2020 to April 2024. Antibiotic susceptibility of the isolates was evaluated. Biofilm Formation Assay and Galleria mellonella infection models were employed to assess the virulence of the strains. Polymerase Chain Reaction (PCR) and whole-genome sequencing (WGS) were utilized to determine multilocus sequence typing (MLST) and capsular serotyping, as well as to identify resistance genes, virulence genes, and plasmid replicons. Phylogenetic relationships among the isolates were also established.

Results

A total of 41 patients with rUTIs were included, with 56.1% caused by CRKP. 97.01% of CRKP carry the blaKPC-2 gene. Compared to patients infected with carbapenem-susceptible Klebsiella pneumoniae (CSKP), those infected with CRKP had a higher prevalence of underlying diseases and complications. Both groups of strains exhibited a high degree of antibiotic resistance. CRKP strains demonstrated enhanced biofilm formation capacity and greater lethality in Galleria mellonella infection models. The predominant phenotype of the CRKP strain was ST11 KL64, whereas the CSKP strain showed multiple phenotypes in different patients. Sequencing analyses revealed that both groups of strains carried a wide range of virulence genes, resistance genes, and plasmid replicons. Among the cases of rUTIs, 31 were identified as relapses caused by the same strain, with no significant differences between the initial and final infection strains.

Conclusion

This study demonstrates that patients with rUTIs caused by CRKP present significant complexity in terms of clinical features, strain resistance and virulence properties. When managing UTIs caused by CRKP, special care needs to be taken to manage recurrent infections.

Lactobacillus delbrueckii subsp. allosunkii and lactis as emerging human uropathogens in elderly patients

Lactobacillus delbrueckii has been considered a very rare cause of human urinary tract infections (UTIs). However, little is known about its clinical significance and antimicrobial susceptibility, and genomic data from clinical isolates are lacking. This study aimed at analyzing clinical, microbiological, and genomic data of L. delbrueckii urinary isolates. All L. delbrueckii isolates collected from patients hospitalized in a French university hospital from 2014 to 2016 were included. Clinical and biological data were gathered. Species identification was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and MICs were determined using the broth microdilution method. Whole genome sequencing (WGS) was conducted (Illumina MiSeq 2 × 300 bp), and genomes were compared using three approaches (multilocus sequence typing [MLST], average nucleotide identity [ANI], and core genome single nucleotide polymorphism [SNP]). From 2014 to 2016, 48 isolates of L. delbrueckii were recovered from the urine of 48 patients (mean age = 84 years; sex ratio M/F = 0.04). Nearly half (44%) of patients were diagnosed with a UTI, and all had significant cultures (≥105 CFU/mL) with a positive direct examination in >90% of cases. The majority of isolates were susceptible to most antibiotics (especially β-lactams), whereas they seemed intrinsically resistant to fosfomycin and metronidazole. Subspecies identification was consistent across the three approaches, showing that most L. delbrueckii isolates belonged to subspecies allosunkii (n = 40; 83%), followed by subspecies lactis (n = 8; 17%). Two isolates were resistant to tetracycline (MIC >16 mg/L) and both harbored the tet(W) gene. This study demonstrates the uropathogenic role of L. delbruekii subspecies allosunkii and lactis, particularly in elderly female patients.IMPORTANCEThis largest case series of urinary tract infections (UTIs) caused by Lactobacillus delbrueckii clearly demonstrates the uropathogenic role of this species (especially the subspecies allosunkii) in human UTIs, particularly in elderly female patients and those with underlying comorbidities. This study may change practice in two ways: (i) clinical laboratories, which typically consider lactobacilli from urine samples as contaminants, may need to reassess this practice; (ii) patient care can be improved by prescribing appropriate antibiotics for these underdiagnosed UTIs. L. delbrueckii should be considered an actual pathogen when it is significantly found in the urine of predisposed patients with clinical and/or biological signs of infection. While matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry allows reliable identification of L. delbrueckii, there is also a need for better discrimination between subspecies (especially allosunkii and lactis). Since L. delbrueckii isolates are usually susceptible to many antibiotics, we recommend β-lactams (especially aminopenicillins) for the treatment of those UTIs.

Broiler litter moisture and trace metals contribute to the persistence of Salmonella strains that harbor large plasmids carrying siderophores

Broiler litter sampling has proven to be an effective method for determining the Salmonella status of a broiler chicken flock and understanding the ecology of Salmonella prior to harvest. In this study, we investigated the ecology of Salmonella within the litter (n = 224) from two commercial broiler houses in the United States. We employed culture enrichment methods and quantitative polymerase chain reaction to determine the prevalence and load of Salmonella and utilized antimicrobial susceptibility testing and whole-genome sequencing (WGS) to characterize select isolates. Additionally, we applied machine learning algorithms and in vitro experiments to identify environmental selective pressures that may contribute to the persistence of Salmonella in litter. Our findings indicate that the prevalence and abundance of Salmonella in broiler litter are influenced by the downtime between flocks as well as by the flock raised on the litter. A Decision Tree Classifier model developed demonstrated that the moisture in the caked part of litter was the most influential environmental parameter for predicting the prevalence of viable Salmonella. WGS analysis revealed that Typhimurium, Infantis, and Kentucky strains that harbored large self-conjugative plasmids encoding fitness factors for iron siderophore production were the dominant Salmonella population found in litter, and exposure to iron-limiting and copper-enriched culture media affected Salmonella growth. Our results suggest that trace metals may select for siderophores harbored on plasmids, and interventions that reduce litter moisture can potentially curtail the persistence of Salmonella in pre-harvest environments.IMPORTANCEBroiler chicken meat is the most consumed protein worldwide, and global poultry imports are projected to reach 17.5 million tons by 2031. To raise billions of chickens, litter is reused multiple times by the top global producers and exporters of chicken (Brazil and the United States). Chickens are in continuous contact with litter and depend on it for warmth and coprophagy. Consequently, litter serves as a major route for pathogens such as Salmonella to infect chickens, making it crucial to understand the environmental and genetic selective pressures that might explain why certain Salmonella strains persist on broiler farms more than others. In this study, we demonstrated that Salmonella strains that harbored siderophores on large conjugative plasmids persisted in litter and suggested that reducing litter moisture would significantly control Salmonella prevalence. However, a complete eradication of persisting Salmonella strains will require novel, innovative, and multifaceted approaches.

Evidence of in vitro mecB-mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens

Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376T = CCM 8659T = DSM 111350T) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures. Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.

Establishing Sitafloxacin Epidemiological Cut-off Values (ECOFFs) for Clinical Bacterial Isolates

Objective

To establish the epidemiological cut-off values (ECOFFs) of sitafloxacin against Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, and Streptococcus pneumoniae.

Methods

We collected 2264 clinical isolates from five different labs located in four cities in China. The minimum inhibitory concentrations (MICs) and inhibition zone diameters of sitafloxacin for all isolates were determined by using the broth microdilution method (BMD) and the disk diffusion method according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. MIC ECOFFs were determined using ECOFFinder software, with the 99% calculated ECOFF selected as the initial value. Zone diameter ECOFFs were determined via the visual estimation method. Whole-genome sequencing was performed on E. coli strains exhibiting overlapping MICs between wild-type (WT) and non-wild-type (NWT) groups to analyze resistance mechanisms.

Results

Sitafloxacin MICs ranged from 0.002 to 64 mg/L, while inhibition zone diameters ranged from 6 to 45 mm across the nine species. MIC ECOFFs were determined as 0.032, 0.064, 0.125, 0.5, 0.064, 0.125, 0.5, 0.25, and 0.125 mg/L for E. coli, K. pneumoniae, P. mirabilis (tentative ECOFF), P. aeruginosa, A. baumannii, S. aureus, E. faecalis, E. faecium, and S. pneumoniae, respectively. Except for S. pneumoniae, MICs of the other eight species showed a high correlation with zone diameters (|r| > 0.8, P < 0.0001). Consequently, the zone diameter ECOFFs were established as 26, 25, 24, 24, 25, 26, 21, and 22 for E. coli, K. pneumoniae, P. mirabilis, P. aeruginosa, A. baumannii, S. aureus, E. faecalis, and E. faecium, respectively.

Conclusion

We established MIC and zone diameter ECOFFs for sitafloxacin against the nine species listed above. The MIC ECOFF for P. mirabilis was classified as tentative. For S. pneumoniae, the correlation between zone diameters and MICs was insufficient to establish a zone diameter ECOFF.

Emergence of plasmid-mediated fosfomycin resistance among Escherichia coli harboring fosA4, tet(X4), and mcr-1 genes in wild birds

Fosfomycin represents a last-line reserve antibiotic for the treatment of infections caused by multidrug-resistant (MDR) bacteria. Nevertheless, the advent of plasmid-mediated fosfomycin resistance among bacteria from humans and food animals incurs great concern. This study reports the detection and genomic portrait of the plasmid-mediated fosfomycin resistance gene, fosA4, amid Escherichia coli from wild birds co-harboring plasmid-mediated tigecycline resistance gene, tet(X4), and colistin resistance gene, mcr-1. A total of 100 samples from fecal droppings of wild birds in the urban parks in Faisalabad, Pakistan were subjected for the isolation and characterization of fosfomycin-resistant E. coli. The fosA4 gene was identified in 11 (11%) of the E. coli isolates, and all exhibited an MDR phenotype. Genome sequencing confirmed that all the fosA4-positive isolates also co-harbored the mobile tigecycline resistance tet(X4) gene on a large MDR IncFII plasmid. One isolate PKF8 belonging to ST48 also co-carried the colistin resistance gene mcr-1 on the IncHI2 plasmid. To the extent of our knowledge, this is the first discovery of E. coli isolates in wild birds co-harboring the mcr-1, fosA4, and tet(X4) genes. The emergence of these pivotal antimicrobial resistance genes in wild birds native to South Asia with their close association to humans and animals is alarming. Our findings highlight the urgent need for further surveillance of bacterial resistance to last-resort antibiotics in the clinics, animal farming, and environment with the One Health approach.

IMPORTANCE

The global spread of the plasmid-mediated fosfomycin resistance gene fosA4 bearing Escherichia coli strains incurs a public health concern. However, research focusing on the pervasiveness of fosA4-positive isolates in wild birds is still rare, and to the best of our knowledge, this is the first documentation from South Asia highlighting the concurrent presence of the fosA4, mcr-1, and tet(X4) genes within E. coli isolates recovered from fecal samples of wild birds in Pakistan. This co-existence of ARGs along with phylogenetic analysis revealed that MDR plasmids carried by E. coli isolates have the ability to spread horizontally between wild birds, food animals, and humans. Co-existence of fosA4, tet(X4), and mcr-1-carrying plasmids is worrying and warrants further investigation.

Differences in antimicrobial resistance between exoU and exoS isolates of Pseudomonas aeruginosa

PURPOSES

This study compared antimicrobial resistance between exoU and exoS Pseudomonas aeruginosa strains isolated from microbial keratitis (MK) and examined their resistance genotypes.

METHODS

The presence of exoU and exoS was determined in 187 MK isolates using PCR. Minimum inhibitory concentrations of ciprofloxacin, levofloxacin, gentamicin, and tobramycin were measured. Whole genome sequencing of 39 isolates was used to identify resistance genes via Resfinder. Mutations in key genes, including DNA gyrase, topoisomerase IV, efflux pumps, and DNA repair systems, were analyzed using Geneious Prime. Functional effects of novel SNPs were predicted using SIFT.

RESULTS

Antibiotic resistance was significantly higher in exoU than exoS: 38.2% vs. 20.5% for ciprofloxacin, 29.1% vs. 12.1% for levofloxacin, 40% vs. 23.5% for gentamicin, and 29.1% vs. 14.4% for tobramycin (all p < 0.05). ExoU isolates exclusively had mutations in GyrA (Thr83Ile) and ParC (Ser87Ile), as well as in efflux pump regulators MexZ (Gly89Ser), NalC (Asp79Glu) and MexS (Val73Ala) (p < 0.01). They also more frequently harbored the acquired resistance genes aph(6)-Id (55% vs. 0%) and aph(3'')-Ib (60% vs. 5.3%) and had higher mutation rates in DNA repair genes mutL (70% vs. 15.8%) and mutS (45% vs. 5.3%) (p < 0.01). Mutations in gyrA, parC, efflux pump (mexB, mexD, mexY) and regulator (mexZ, nalC, mexS) genes correlated with fluoroquinolone resistance (R ≥ 0.33; p ≤ 0.04). Possession of aph(3'')-Ib, aph(6)- Id and SNPs in efflux pump regulators mexZ and parR were associated with aminoglycoside resistance.

CONCLUSION

ExoU strains exhibited more resistance genes and mutations, contributing to higher resistance to fluoroquinolones and aminoglycosides.

CIWARS: a web server for antibiotic resistance surveillance using longitudinal metagenomic data

The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://ciwars.cs.vt.edu/.

Whole-genome sequence of Bacillus subtilis TP111, a potential fish probiotic that prevents motile Aeromonas septicemia in Nile tilapia (Oreochromis niloticus)

We report the genome of fish probiotic Bacillus subtilis TP111 strain isolated from the gut of a healthy Nile tilapia (Oreochromis niloticus) in Bangladesh. TP111 has a genome size of 4,174,638 bp, 43.48% guanine-cytosine, 243.0× genome coverage with 4,224 potential coding sequences, and 10 predicted secondary metabolite biosynthetic gene clusters.

Genomic analysis of Proteus mirabilis: Unraveling global epidemiology and antimicrobial resistance dissemination - emerging challenges for public health and biosecurity

Given the escalating public health threat posed byProteus mirabilis(P. mirabilis) and its rapidly evolving drug resistance, it is imperative to elucidate its global epidemiology and resistance mechanisms through a comprehensive genomic lens. As of August 2024, 3,403 high-qualityP. mirabilisgenomes were retrieved from public databases (total 3,752), spanning 58 countries/regions, with the United States showing the highest report rate (52.51 %). Human-derived isolates, particularly from urine (34.47 %), were the primary source. A total of 239 antibiotic resistance genes (ARGs) were identified in P. mirabilis, with β-lactamase and carbapenemase genes being particularly widespread and isolates from China harboring the highest ARG counts. Globally,P. mirabilisisolates were categorized into 17 distinct clusters, with U.S. isolates showing the widest phylogenetic spread. Minimal SNP variations among isolates from different countries and hosts suggest transnational and cross-host clonal propagation. Frequent clonal transmission was also observed among diverse hosts and clinical sources.P. mirabiliscarries numerous integrative and conjugative elements (ICEs), some facilitating ARG dissemination (n = 215). Prophages, though ubiquitous, contributed minimally to ARG spread. Spearman's analysis revealed significant correlations between ARGs and insertion sequences (ISs), replicons, and ICEs. Ancestral state analysis indicated prophages were mainly acquired horizontally, while other mobile genetic elements (MGEs) were largely clonally transmitted. This study provides the first comprehensive genomic analysis ofP. mirabilis's global resistance landscape, highlighting the need to designate it as a novel antimicrobial resistance indicator and implement long-term surveillance.

Ligilactobacillus salivarius Lac45 inhibits MRSA and suppresses inflammation in human keratinocyte

Dysbiosis, an imbalance in skin microflora, is a key contributor to inflammatory skin conditions, including atopic dermatitis (AD), seborrheic dermatitis (SD), and psoriasis. In AD, Staphylococcus aureus colonization of skin lesions is prevalent approximately 70% of cases, with disease severity positively correlating with bacterial presence. Moreover, methicillin-resistant Staphylococcus aureus (MRSA) is found in 10-30% of AD skin lesions, highlighting the need for novel therapeutic strategies that target both microbial imbalance and inflammation. This study evaluates Ligilactobacillus salivarius Lac45 (LS-Lac45), a breast milk-derived bacterial strain, for its antimicrobial and anti-inflammatory potential in dermatology. We assessed its antimicrobial activity against MRSA using an agar disk-diffusion assay and its anti-inflammatory effects in a peptidoglycan (PGN)-induced inflammation model in HaCaT keratinocytes. To elucidate its mechanisms of action, mass spectrometry was used to analyze protein expression changes in LS-Lac45-treated keratinocytes. Our results demonstrate that live LS-Lac45 effectively inhibits MRSA growth. Additionally, heat-killed LS-Lac45 significantly reduces PGN-induced production of pro-inflammatory cytokines IL-6, IL-8, and TNF-α. Proteomic analysis further identifies LS-Lac45-mediated modulation of immune-related proteins, including heat shock protein 60, metallothionein 2A, and antioxidant-1, suggesting a role in inflammatory regulation. These findings highlight LS-Lac45 as a candidate for managing MRSA-associated inflammatory skin conditions, particularly AD. While this study provides key insights into its antimicrobial and immunomodulatory properties, further research is needed to evaluate its probiotic characteristics and clinical applicability in dermatology.

Genome analysis of manure and soil-dwelling Acinetobacter strains indicates potential health risks associated with antibiotic resistance and virulence factors

The genus Acinetobacter includes opportunistic pathogenic species of increasing clinical importance due to their ability to resist multiple antibiotics and to face multiple environmental stresses. Here, comprehensive whole-genome analysis was used to reveal the presence of genes potentially related to pathogenicity in 11 tetracycline-resistant Acinetobacter isolates from manure of dairy cows under tetracycline and amoxicillin prophylaxis and from soils affected by this manure. The isolates were identified as Acinetobacter pseudolwoffii, A. gerneri, A. gandensis, and A. amyesii and screened their genomes for the presence of genes related to host colonization, infection, or environmental persistence. We detected 164 genes of antimicrobial resistance, virulence factors, mobile genetic elements, or biofilm formation. All isolates were predicted to be human pathogens with high probability (0.7-0.8) and the manure isolates identified as A. pseudolwoffii carried a top-risk human-associated aminoglycoside resistance gene. The phenotypic characterization of the isolates showed that they could all grow at 37 °C, some up to 41 °C, and that they showed differential susceptibility to several antibiotics, with one isolate identified as A. gandensis being multi-resistant. Our analyses suggest that environmental Acinetobacter strains from fresh manure and manured soils possess risky antibiotic-resistance genes and phenotypic traits of clinical relevance indicating potential pathogenicity.

Identification of a novel phage depolymerase against ST11 K64 carbapenem-resistant Klebsiella pneumoniae and its therapeutic potential

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a clinical pathogen with a high mortality rate, and its clinical management and infection control have become a serious challenge. Phage-encoded depolymerase cleaves the capsular polysaccharide, a major virulence factor of K. pneumoniae. This study aimed to identify a phage depolymerase targeting ST11 K64 CRKP, evaluate its antimicrobial activity and therapeutic efficacy, and provide new alternative therapeutic strategies for K64 CRKP. Phages were screened from untreated hospital sewage using clinically isolated CRKP as the host bacterium. The host range, efficiency of plaque formation, optimal multiplicity of infection, adsorption efficiency, and one-step growth curve of phage vB_KpnP_IME1309 were determined by the double-layer agar plate culture method. The morphology of the phage was observed by transmission electron microscopy. Phage nucleic acids were extracted for whole-genome sequencing, and the phage-encoded depolymerase gene ORF37 was amplified by polymerase chain reaction. Next, a recombinant plasmid was constructed to induce depolymerase expression, which was verified using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In vitro bactericidal activity was determined using a combined serum assay, and the anti-K. pneumoniae biofilm effect of depolymerase was determined by crystal violet staining. Finally, a Galleria mellonella larvae infection model was established to investigate the therapeutic effect of depolymerase on larvae in vivo. Here, we isolated and characterized a phage vB_KpnP_IME1309 targeting ST11 K64 CRKP, which featured a latent period of 20 min and a burst size of approximately 290 plaque-forming units/cell. It contained 41 predicted open reading frames, of which ORF37 encoded depolymerase. The expressed and purified depolymerase Dep37 cleaved only ST11 K64 CRKP and formed a translucent halo on the agar plate. Dep37 increased the susceptibility of K. pneumoniae B1 to serum killing, inhibited CRKP biofilm formation, and degraded mature biofilms. The combination of Dep37 and kanamycin was significantly more effective in treating CRKP biofilms compared to either Dep37 or kanamycin alone. An injection of Dep37 at 5 min and 2 h after the CRKP infection of Galleria mellonella larvae increased their survival rates by up to 73% and 53%, respectively. Depolymerase Dep37 may be used as a potential method for capsule typing of K. pneumoniae, showing great promise for the development of novel alternative therapeutic strategies against ST11 K64 CRKP.

IMPORTANCE

A novel phage vB_KpnP_IME1309 targeting ST11 K64 carbapenem-resistant Klebsiella pneumoniae (CRKP) was isolated and characterized. The ORF37 encoding depolymerase gene of phage vB_KpnP_IME1309 was successfully expressed and purified. Depolymerase increases the susceptibility of CRKP to serum killing, inhibits CRKP biofilm formation, and degrades mature biofilms. The combination of depolymerase and kanamycin is significantly more effective than either depolymerase or kanamycin alone in the treatment of CRKP biofilm. Depolymerase injection at 5 min and 2 h after CRKP infection of Galleria mellonella larvae increased the survival rate of larvae by up to 73% and 53%, respectively. Depolymerase Dep37 may be used as a method for the development of novel alternative therapeutic strategies against ST11 K64 CRKP.

Genomic analysis and therapeutic efficacy evaluation of bacteriophage PK2420 for pneumonia caused by hypervirulent Klebsiella pneumoniae (K20 serotype)

Hypervirulent Klebsiella pneumoniae (hvKp) strains are increasingly recognized for their aggressive nature, which leads to severe clinical outcomes. The emergence of multidrug-resistant strains constitutes a substantial challenge for clinical management. Phage therapy offers a potential solution to the antibiotic resistance crisis. A multidrug-resistant hvKp strain, K2420 (K20 serotype), was used to isolate bacteriophages from hospital sewage. Phage morphology, biological properties, and genome characteristics were analyzed using transmission electron microscopy, plaque assays, and whole-genome sequencing. Therapeutic safety and efficacy were assessed in an acute pneumonia murine model induced by intratracheal injection of K2420. Assessment parameters included bacterial load, phage titer, body temperature, cytokine levels, histopathological findings, and other relevant indicators. Phage PK2420, a member of the Autographiviridae family and Przondovirus genus, was identified. It rapidly lyses K. pneumoniae (K20 serotype), inhibits biofilm formation, and exhibits a burst size of 37.4 plaque-forming units/cell. The phage is stable at temperatures ranging from 0°C to 40°C and pH values between 6 and 9. Its genome, 41,155 bp in length, contains 46 coding sequences. The phage has no genes associated with antibiotic resistance, virulence, or lysogeny. In vivo, PK2420 substantially reduced K. pneumoniae bacterial loads, improved survival rates, and alleviated pneumonia severity without observable side effects. Phage PK2420 exhibits lytic activity against K. pneumoniae both in vitro and in murine models, providing a promising and safe option for the treatment of hvKp infections.IMPORTANCEOur investigation provides insights into the interaction mechanism among hypervirulent Klebsiella pneumoniae (hvKp) (K20 serotype), phage, and the host in a mouse pneumonia model, offering a valuable reference for future research on phage pharmacokinetics. This study demonstrated that bacteriophage PK2420 exhibits promising biosafety and therapeutic efficacy against hvKp-induced pulmonary infections and dissemination in a murine model. These findings suggest that phage PK2420 may be a potential option for the clinical treatment of hvKp infections.

The genomic characteristics of dominant Salmonella enterica serovars from retail pork in Sichuan province, China

Foodborne Salmonella is the main cause of salmonellosis in China. Porcine animals are a reservoir for this bacterium consequently posing a threat to food safety and public health. In this study, 157 out of 240 pork samples (65.42 %) were identified as Salmonella-positive. From these, after isolation and deduplication, 376 Salmonella isolates were collected. Twenty four serovars were identified based on WGS, among which S. London/ST155 (24.47 %), S. Rissen/ST469 (23.40 %), S. Derby/ST40 (13.56 %), and S. 4,[5],12:i:- (monophasic S. Typhimurium)/ST34 (13.30 %) were dominant. In all, 69.68 % (262/376) of these isolates expressed multidrug resistance (MDR, defined as resistance to compounds in three or more antimicrobial classes) phenotypes with S. London (54.35 %, 50/92) accounting for the highest proportion of these. Notably, the resistance to front-line critically important antimicrobial agents (CIA), including cephalosporins, ciprofloxacin, and azithromycin was 0.80 %. Based on in silico analysis, antimicrobial resistant-encoding genes (ARG) identified in the MDR isolates included aac(3)-IId, aac(6')-Iaa, blaTEM-1B, mph(A), qnrB6, aac(6')-Ib-cr, sul1, sul2, and tet(A), which expressed resistance to aminoglycosides, β-lactams, macrolides, quinolones, sulfonamides, and tetracyclines. Furthermore, diverse biocide and heavy metal resistance-encoding genes were distributed across different serovars with triC encoding triclosan resistance being identified exclusively in S. London. Moreover, monophasic S. 4,[5],12:i:- carried the greatest number of virulence factors and heavy metal resistance genes among the dominant serovars. This study extended our understanding of the genomic epidemiology and multidrug resistance of Salmonella derived from pork and highlighted the potential risk to human health, posed by commonly encountered serovars.

Genomic characterization of plasmids of mcr-1-positive Escherichia coli isolated from cohabiting rats, dairy cattle and pigs

BACKGROUND

Antimicrobial resistance has become a significant global issue impacting humans, animals, and the environment. Currently, the focus of concern has shifted to the environment, which can act as a reservoir and significantly contribute to the spread of resistance genes. This study aimed to elucidate the potential transmission of mcr-1, which confers colistin resistance, among Escherichia coli isolates from pigs, dairy cattle, and co-habiting rodents. In March 2018, 30 fecal samples were collected from three pig farms and one mixed cattle farm, and 31 cecal contents from rats (Rattus norvegicus) captured from the same four animal farms were analyzed.

RESULTS

Out of 26 mcr-1 positive E. coli isolates, 16 came from six rats, 10 from four pigs, and none from dairy cattle. The mcr-1-positive isolates from cohabiting rats and pigs were genetically unrelated, based on different XbaI-PFGE profiles. The plasmid profiles of one isolate per animal from each farm were analyzed by S1-PFGE. E. coli isolates from cohabiting rats and pigs showed plasmid bands of similar sizes (33 or 65 kb). To investigate the horizontal transfer of these plasmids between the animals, two pairs of E. coli isolates from pig farms 1 and 3 were selected for WGS analysis. Three of the isolates (EcoP3-1, EcoC2-1 from pigs, and Eco1266-6 from a rat) belonged to clonal complex 10 (CC10), while the other rat isolate (Eco1284-6) belonged to CC398 (ST398). Eco1266-6 (rat) and EcoC2-1 (pig) from cohabiting animals in pig farm 1 carried IncX4 plasmids with the mcr-1.1 variant. The plasmid sequences were almost identical (99.98% identity), both carrying the mcr-1.1/pap2 segment. pEcoC2-1 had a complete ISVsa5 insertion sequence upstream of the mcr-1 gene. Eco1284-6 (rat) and EcoP3-1 (pig) from pig farm 3 carried IncI2 plasmids with different allelic variants of mcr-1 (mcr-1.5 and mcr-1.1).

CONCLUSIONS

E. coli isolates from cohabiting rats and pigs were genetically distinct, but one pair of isolates had very similar IncX4 plasmids, suggesting the potential for horizontal spread of plasmids carrying mcr genes. These findings suggest a threat of resistant E. coli spreading between cohabiting animals and into the environment. This underscores the importance of conducting integrated One-Health studies.

First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying blaIMI-4 carbapenemase in Costa Rica

OBJECTIVES

All carbapenem-resistant Gram-negative bacterial isolates obtained in the Costa Rican National Network of Bacteriology Laboratories are routinely referred to the National Reference Center for Bacteriology for national-laboratory for surveillance and characterization of their carbapenem-related-mechanism of resistance. As a result of this healthcare-associated infection surveillance, two bacterial isolates with unknown mechanisms for carbapenem resistance were investigated.

METHODS

The isolates were subjected to taxonomic identification, antimicrobial susceptibility testing, whole-genome characterization, using Illumina and Oxford Nanopore technologies, and bioinformatic analyses.

RESULTS

The isolates were identified as Enterobacter roggenkampii and Enterobacter sichuanensis. While the isolates presented different antimicrobial resistance profiles, both were resistant to carbapenems, positive for the modified carbapenem inactivation method (mCIM), and showed inhibition of carbapenem resistance with boronic acid. The full characterization of the isolates' genomes, revealed the presence of the rare chromosomal blaIMI-4 gene inserted within 25-kb integrative mobile elements, closely related to EcloIMEX-2.

CONCLUSIONS

The limited global distribution of the blaIMI-4 variant, along with its identification in two distinct bacterial species in Costa Rica within integrative mobile elements, underscores the critical need for regular antibiotic resistance surveillance using next-generation sequencing technologies. This study demonstrates that this practice allows timely detection of novel or rare mechanisms of antibiotic resistance.

Spread of antimicrobial-resistant clones of the ESKAPEE group: From the clinical setting to hospital effluent

Antimicrobial resistance is a public health concern affecting human, animal, and environmental health. Antimicrobial-resistant pathogens, such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE), the most important microorganisms involved in healthcare-related infections, can be excreted by patients into hospital effluent which then becomes a reservoir for these pathogens. In this context, we characterized and compared resistant microorganisms of the ESKAPEE group, isolated from hospital effluent and clinical samples from patients of the Pequeno Príncipe Hospital, located at Curitiba, Paraná. Out of 345 microorganisms isolated, 208 from the ESKAPEE group were obtained from hospital effluent and 18 were from clinical samples. Among them, K. pneumoniae was the most frequently identified microorganism in both clinical and environmental settings. The genomic context of the resistance of 52 single-clone isolates with satisfactory genome assembly parameters was analyzed. The identified carbapenem resistance genes were blaKPC-2,blaGES-5, and blaNDM-1. Two Enterobacter kobei isolates co-produced the carbapenemases blaKPC-2 and blaGES-5. The samples were defined as polyclonal for K. pneumoniae and E. cloacae complexes and clonal for E. coli isolates. ST392 and ST11 were identified in both clinical and environmental samples of K. pneumoniae that produces Klebsiella pneumoniae carbapenemase (KPC) or New Delhi metallo-β-lactamase (NDM), suggesting the persistence of these microorganisms in hospital effluents. The ESKAPEE group is present in hospitals, and its dissemination through hospital effluents is a significant concern due to its capacity to transfer antimicrobial resistance genes, which poses a risk to public health and food safety.

Draft genomes of Klebsiella pneumoniae and Streptococcus anginosus strains found in the urine of the same female patient

Here, we report the draft genomes of Klebsiella pneumoniae 5008-1 and Streptococcus anginosus 5008-2 strains isolated from a catheterized urine sample obtained from an asymptomatic postmenopausal woman diagnosed with recurrent urinary tract infection and receiving vaginal estrogen cream.

Draft genome sequence of emerging pathogen Morganella morganii strain PS00513 isolated from a chronic surgical wound

We report the draft genome sequence and antimicrobial resistance gene profile of Morganella morganii strain PS00513. This strain was isolated from a chronic surgical wound infection of an adult male patient. The chromosome is 3.87 Mb long and accompanied by a 9.6 kb plasmid, which both contain multiple antibiotic resistance genes.

Draft genomic sequences of Vibrio cholerae strains linked to the cholera outbreak in Kamituga, South Kivu, DRC

Vibrio cholerae is responsible for outbreaks in Africa, but the cause of the outbreaks remains poorly understood. Here, we report the draft genomes of four Vibrio cholerae strains isolated from individuals affected by an outbreak in Kamituga, South Kivu, the Democratic Republic of the Congo, between January and May 2024.

The Klebsiella pneumoniae tellurium resistance gene terC contributes to both tellurite and zinc resistance

Klebsiella pneumoniae is widely recognized as a pathogen responsible for hospital-acquired infections and community-acquired invasive infections. It has rapidly become a significant global public health threat due to the emergence of hypervirulent and multidrug-resistant strains, which have increased the challenges associated with treating life-threatening infections. Tellurium resistance genes are widespread on virulence plasmids in K. pneumoniae isolates. However, the core function of the ter operon (terZABCDEF) in K. pneumoniae remains unclear. In this study, the multidrug-resistant K. pneumoniae P1927 strain was isolated from the sputum of a hospitalized pneumonia patient. The ter operon, along with antimicrobial resistance and virulence genes, was identified on a large hybrid plasmid in K. pneumoniae P1927. We generated a terC deletion mutant and demonstrated that this mutant exhibited reduced virulence in a Galleria mellonella larva infection model. Further physiological functional analysis revealed that terC is not only important for Te(IV) resistance but also for resistance to Zn(II), Mn(II), and phage infection. All genes of the ter operon were highly inducible by Zn(II), which is a stronger inducer than Te(IV), and the terBCDE genes were also induced by Mn(II). Collectively, our study demonstrates novel physiological functions of TerC in Zn(II) resistance and virulence in K. pneumoniae.IMPORTANCEKlebsiella pneumoniae has rapidly become a global threat to public health. Although the ter operon is widely identified in clinical isolates, its physiological function remains unclear. It has been proposed that proteins encoded by the ter operon form a multi-site metal-binding complex, but its exact function is still unknown. TerC, a central component of the tellurium resistance determinant, was previously shown to interact with outer membrane proteins OmpA and KpsD in Escherichia coli, suggesting potential changes in outer membrane structure and properties. Here, we report that TerC confers resistance to Zn(II), Mn(II), and phage infection, and Zn(II) was shown to be a strong inducer of the ter operon. Furthermore, TerC was identified as a novel virulence factor. Taken together, our results expand our understanding of the physiological functions encoded by the ter operon and its role in the virulence of K. pneumoniae, providing deeper insights into the link between heavy metal(loid) resistance determinants and virulence in pathogenic bacteria.

Genomic census of invasive nontyphoidal Salmonella infections reveals global and local human-to-human transmission

Extraintestinal infections caused by Enterobacteriaceae represent a global concern, further exacerbated by the growing prevalence of antimicrobial resistance (AMR). Among these, invasive nontyphoidal Salmonella (iNTS) infections have become increasingly challenging to manage, and their global spread remains poorly understood. Here we compiled 1,115 patient records and generated a comprehensive genomic dataset on iNTS. Age and sex emerged as significant risk factors, with Salmonella Enteritidis identified as a major cause. We observed serovar-specific AMR patterns, with notable resistance to fluoroquinolones and third-generation cephalosporins. A global phylogenomic analysis of Enteritidis revealed three distinct clades, highlighting the accumulation of AMR determinants during its international spread. Importantly, our genomic and transmission analyses suggest that iNTS infections may involve human-to-human transmission, with diarrheal patients acting as potential intermediaries, deviating from typical zoonotic pathways. Collectively, our newly generated cohort and iNTS genomic dataset provide a framework for precise local iNTS burden and underscore emerging transmission trends.

Genome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus Enterococcus and an abundance of safe species

Enterococci are lactic acid bacteria (LAB) that, as their name implies, often are found in the gastrointestinal tract of animals. Like many other gut-dwelling LAB, for example, various lactobacilli, they are frequently found in other niches as well, including plants and fermented foods from all over the world. In fermented foods, they contribute to flavor and other organoleptic properties, help extend shelf life, and some even possess probiotic properties. There are many positive attributes of enterococci; however, they have been overshadowed by the occurrence of antibiotic-resistant and virulent strains, often reported for the two species, Enterococcus faecalis and Enterococcus faecium. More than 40,000 whole-genome sequences covering 64 Enterococcus type species are currently available in the National Center for Biotechnology Information repository. Closer inspection of these sequences revealed that most represent the two gut-dwelling species E. faecalis and E. faecium. The remaining 62 species, many of which have been isolated from plants, are thus quite underrepresented. Of the latter species, we found that most carried no potential virulence and antibiotic resistance genes, an observation that is aligned with these species predominately occupying other niches. Thus, the culprits found in the Enterococcus genus mainly belong to E. faecalis, and a biased characterization has resulted in the opinion that enterococci do not belong in food. Since enterococci possess many industrially desirable traits and frequently are found in other niches besides the gut of animals, we suggest that their use as food fermentation microorganisms is reconsidered.IMPORTANCEWe have retrieved a large number of Enterococcus genome sequences from the National Center for Biotechnology Information repository and have scrutinized these for the presence of virulence and antibiotic resistance genes. Our results show that such genes are prevalently found in the two species Enterococcus faecalis and Enterococcus faecium. Most other species do not harbor any virulence and antibiotic resistance genes and display great potential for use as food fermentation microorganisms or as probiotics. The study contributes to the current debate on enterococci and goes against the mainstream perception of enterococci as potentially dangerous microorganisms that should not be associated with food and health.

Whole genome sequencing of non-aureus Staphylococcus species from poultry barn bioaerosols across Alberta reveals circulation of isolates with multiple antibiotic resistant genes and disinfectant resistant genes

OBJECTIVES

Poultry environment has vast variety of bacterial species and non-aureus Staphylococcus species (NASS) are predominantly found. Various NASS are normal inhabitant of gastrointestinal tract and skin of chickens. The study objective was to isolate and identify NASS from bioaerosols of layer chicken barns across Alberta, leading to the phenotypic and genotypic antimicrobial resistance (AMR) profiling of the isolated bacterial colonies.

METHODS

A total of 15 barns were sampled in this study with an XMX-CV microbial air sampler. Phenotypic AMR profiles were determined using the Sensititre® broth microdilution method on the standard CMV3AGPF plates and whole genome sequencing (WGS) was conducted to confirm the species and AMR genes.

RESULTS

Seven Staphylococcus equorum, 5 Staphylococcus shinii, 1 Staphylococcus pseudoxylosus, 1 Staphylococcus cohnii, and 1 Staphylococcus gallinarum isolates were confirmed and identified by WGS and comparative genomic analysis. One of the S. equorum isolate was genetically highly divergent from the remaining isolates of the study. The phenotypic susceptibility profile showed 73.3% (11/15) of the isolates were resistant to lincomycin, 66.7% (10/15) were resistant to tetracycline, 33.3% (5/15) were resistant to streptomycin, 20% (3/15) were resistant to erythromycin, and 6.3% were resistant to gentamicin. A total of 10 antimicrobial resistance genes (ARGs) for antibiotics and 1 gene encoding resistance to disinfectants were detected among the study isolates by WGS.

CONCLUSIONS

Normal bioaerosol microflora having ARGs may lead to reduced therapeutic effectiveness of antibiotics in poultry and these ARGs can be a source of serious public health concern.

Assessment of Phenotypic Tools for Detection of OXA-48, KPC, and NDM in Klebsiella pneumoniae in Oman

Background: The alarming increase in carbapenemase-producing Enterobacterales is a matter of grave public health concern. The most ubiquitous carbapenemases, Klebsiella pneumoniae carbapenemase (KPC)-, New Delhi metallo-β-lactamase (NDM)-, and oxacillinase (OXA-48)-like enzymes, belong to the Ambler molecular classes A, B, and D, respectively. KPC- and OXA-48-like enzymes have a serine-based hydrolytic mechanism, while NDMs are metallo-β-lactamases that contain zinc in the active site. For the judicious use of reserve drugs and promoting antimicrobial stewardship, timely detection of carbapenemases is essential. While molecular tools are the gold standard for the detection of these enzymes, many laboratories have limited access to them. This study focused on evaluating in-house tools and commercial phenotypic tests for the detection of OXA-48-, KPC-, and NDM-like enzymes in K. pneumoniae, the predominant extremely drug-resistant pathogen in Oman. Methods: In total, 80 GeneXpert/PCR-confirmed (40 OXA-48 and 20 KPC and NDM each) and 37 whole-genome-sequenced (25 OXA-232 and 6 KPC-2, plus NDM-1 and NDM-5) K. pneumoniae were subjected to screening by temocillin (30 μg disk) (MAST Diagnostica, Germany) and D71C (MASTDISCS®). Isolates resistant to temocillin (<11 mm) and D71C were subjected to four tests: an in-house tool (OXA-48 disk test) and three commercial phenotypic tests: (i) the MASTDISCS® Combi (D72C) (MAST Group Ltd., Bootle, UK); (ii) the MASTDISCS® Combi (D73C) (MAST Group Ltd., UK); and (iii) an immunochromatographic assay (ICT), which is the KPC/IMP/NDM/VIM/OXA-48 Combo test kit (Medomics, China), for the detection of OXA-48-, KPC-, and NDM-like carbapenemases. Results: Temocillin exhibited good sensitivity and specificity (100% and 97.50%) compared to D71C (70% and 100%). Among the confirmatory tests, the in-house OXA-48 disk test had 92.50% sensitivity and 100% specificity, while the commercial MAST DISC tests D72C, D73C, and ICT had 97.50%, 95.00%, and 100% sensitivity and 100%, 91.67%, and 95% specificity, respectively. Conclusions: The temocillin disk test is a good screening tool. With high sensitivity and specificity, ease of performance, short turnaround time, and low cost, we recommend the ICT format for routine diagnostic use. In resource-constrained centers, the OXA-48 disk test is an excellent alternative with high sensitivity and specificity.

Antimicrobial resistance in coagulase negative staphylococci: Genome analysis and role of horizontal gene transfer

Coagulase-negative staphylococci (CNS) are emerging as significant contributors to antimicrobial resistance, yet their genomic characteristics remain incompletely understood. This study presents a whole-genome analysis of 12 multidrug-resistant CNS strains (Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis) isolated from blood cultures, focusing on antimicrobial resistance genes, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) mechanisms. We identified 22 resistance genes conferring resistance to 11 antimicrobial classes, many of which were plasmid-associated. Notably, we report the first detection of the ISSha1 insertion sequence in S. hominis, along with novel resistance plasmids, including pGO1 and VRSAp in S. haemolyticus and pAMα1 in S. hominis. The identification of bacteriophage-derived sequences in S. haemolyticus and S. hominis suggests a role for phages in genetic exchange. CRISPR sequences and a Cas gene were detected in S. hominis, suggesting a potential but unconfirmed role in restricting gene transfer. Additionally, pGO1 was identified as a conjugative plasmid, while pAMα1 and VRSAp were determined to be mobilizable, reinforcing the role of CNS in resistance dissemination. These results highlight CNS as reservoirs of antimicrobial resistance genes and emphasize the importance of species-specific genomic surveillance. Proactive monitoring of CNS is crucial for controlling antimicrobial resistance in clinical settings.

Molecular epidemiology of Salmonella Enteritidis in humans and animals in Spain

Salmonella Enteritidis, the most prevalent serovar-causing human gastroenteritis, has been traditionally linked to poultry sources. Although antimicrobial resistance (AMR) is not common in this serovar, increasing levels of resistance to fluoroquinolones and ampicillin have been reported in the last few years. Here, 298 isolates retrieved from different sources (human, livestock, wildlife, food, and environment) and years (2002-2021) in Spain were analyzed to evaluate their diversity, the distribution of AMR-conferring genes (ARGs), and mutations and reconstruct the epidemiology of infection due to this serovar. Isolates were clustered in two major clades (I and II), with strains in clade I (including 61.5% of all human isolates) displaying a pan-susceptible phenotype and not carrying AMR determinants. In contrast, clade II included 80.7% of isolates from animal/food/environmental sources, with the majority (69.8%) harboring mutations in the quinolone resistance determinant regions (QRDR). ARGs, although rare, were mostly found in clade II strains that also carried plasmid replicons, among which IncX1 was the most common. Although higher levels of phenotypic resistance were found in animal isolates, extended-spectrum beta-lactamase, plasmid-mediated AmpC, and carbapenemase-encoding genes were only found among human isolates. In summary, the majority of human and animal isolates from Spanish sources in our collection were classified in different phylogenetic branches, suggesting that additional sources are contributing to the occurrence of foodborne infections in Spain. Furthermore, the different distributions of virulence factors and ARGs in isolates from different sources and their association with specific plasmids suggest the presence of different dynamics contributing to the selection of resistant strains.

Evaluating the safety and efficacy of Lacticaseibacillus paracasei TISTR 2593 as a therapeutic probiotic for obesity prevention

Several recent studies have reported the potential of probiotics in reducing body weight and fat mass and improving glucose and lipid metabolism. Therefore, probiotic administration is considered an alternative approach for treating obesity. The objective of this study was to evaluate the probiotic properties and antiadipogenic potential of the strain TISTR 2593. Through whole-genome sequence analysis, the strain TISTR 2593 was identified as Lacticaseibacillus paracasei. L. paracasei TISTR 2593 exhibited γ-hemolytic activity (nonhemolysis) and demonstrated susceptibility to antibiotics, indicating that it is generally safe for consumption. Additionally, this strain displayed desirable probiotic properties, including tolerance to artificial gastric juice and bile salts, adhesion to Caco-2 cells, and the ability to inhibit pathogens. Furthermore, L. paracasei TISTR 2593 exhibited cholesterol-reducing capability and demonstrated antiadipogenic activity. In 3T3-L1 adipocytes, treatment with 10% (w/v) heated L. paracasei TISTR 2593 cells resulted in an approximately 50% reduction in lipid accumulation, similar to the positive control (quercetin). Moreover, L. paracasei TISTR 2593 heat-killed cells dose-dependently decreased the expression levels of CCAAT/enhancer-binding protein-α and peroxisome proliferator-activated receptor-γ, two vital transcription factors involved in the early stage of adipocyte differentiation. These findings suggest that L. paracasei TISTR 2593 possesses probiotic and functional properties, including antiadipogenic activity, supporting its potential as a therapeutic probiotic supplement for preventing obesity. Overall, the results of this study indicate that L. paracasei TISTR 2593 exhibits promising probiotic characteristics and beneficial effects on adipogenesis modulation, reinforcing its potential as a therapeutic option in obesity prevention.

Potential genetic markers of biofilm formation ability by Listeria monocytogenes isolated from fresh agricultural products

The ability of Listeria monocytogenes to form biofilms is the key to its persistence in the food industry. Biofilm phenotype assessment is mainly based on physical and chemical methods, which are time-consuming. The aim of this study was to analyze genetic differences in the biofilm-forming ability of L. monocytogenes, found potential genetic markers, and quickly determined the biofilm phenotype. In particular, 103 strains of L. monocytogenes from agricultural products, were evaluated through multilocus sequence typing and their biofilm formation assays. The genetic characteristics of 12 representative strains were analyzed by comparative genomics, and the relevant genetic characteristics of the 103 strains were verified by polymerase chain reaction technology. The 103 strains were divided into 22 sequence types (STs), and top six types were ranked from high to low according to the median of biofilm biomass as follows: ST91, ST87, ST8, ST9, ST121, ST155, and all of them exhibited 2-3 biofilm phenotypes (strong, medium and weak). Comparative genomics analysis and verification identified the vip gene as a preliminary genetic marker for biofilm phenotypes, and the accuracy of determination can be improved by combining vip with 1-3 genes (srmB, cycB, and uvrB) or STs (ST8, ST87, and ST121). In addition, the smc_4, srmB-inlH, inlH and ssbA genes could accurately distinguish the phenotypes of ST9, ST155, ST91 and other STs. These genetic markers could be used as key targets for rapid determination of the biofilm phenotype of L. monocytogenes, thereby providing useful guidance for the optimization of disinfection processes in the food industry.

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

BACKGROUND

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

OBJECTIVES

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Insights towards the impact of subinhibitory chlorhexidine on antimicrobial susceptibility and horizontal gene transfer in Enterococcus faecium

Enterococcus faecium, a human and animal commensal broadly distributed in the environment, is currently one of the most challenging multidrug-resistant (MDR) healthcare-associated pathogens worldwide. It is often exposed to chlorhexidine (CHX), a broad-spectrum antiseptic, extensively used in healthcare, domestic, and food production settings, and a diffused polluter. However, the impact of gradients of CHX concentrations, including at subinhibitory levels, on E. faecium adaptation to various antimicrobials remains unclear. Our study aimed to explore the effects of subinhibitory CHX concentrations on biocides and antibiotics susceptibility as well as in the transfer of clinically relevant antibiotic resistance genes among E. faecium (n = 11) from diverse sources and clonal backgrounds. Serial exposure to increasing CHX concentrations resulted in strain-specific MICCHX and MBCCHX changes among six E. faecium studied. These strains presented different CHX genotypes, namely the P102H mutation in DNA-binding response regulator ChtR in two strains showing twofold increased MICCHX and/or MBCCHX, and an absent EfrEF transporter in a strain exhibiting increased CHX susceptibility after exposure. Whole-genome comparison between parental and CHX-adapted strains found no alterations in genes with a recognized role in CHX reduced susceptibility. Additionally, in a different assay, subinhibitory CHX exposure enhanced the transfer (up to 12.5-fold) of vancomycin or linezolid resistance genes among most E. faecium strains tested, except one lacking a functional EfrEF transporter. Our data suggest that subinhibitory CHX concentrations could have a role in Enterococcus adaptation to CHX and in the spread of antibiotic resistance through horizontal transfer events. Further investigation is warranted to elucidate the underlying mechanisms driving these phenomena in E. faecium, ensuring the continued effectiveness of both CHX and antibiotics, and safeguarding Public Health.

Genetic Comparison of Enterococcus Species Isolated from Osteomyelitis Lesions and the Barn Environment of Successive Broiler Chicken Flocks

Osteomyelitis caused by Enterococcus cecorum is an emerging disease in broiler chickens in Canada. Other Enterococcus species have been reported as causative agents in certain outbreaks. The epidemiology of this disease is unknown, but contaminated barns are affected by recurring episodes. A broiler chicken flock located in Quebec, Canada, exhibited osteomyelitis lesions positive for E. cecorum and Enterococcus faecalis. Surprisingly, the following lot, in the same barn, revealed the presence of E. faecalis- and Enterococcus raffinosus-positive lesions but no E. cecorum. To better understand the epidemiology of these two outbreaks, verify the persistence of pathogenic isolates in the barn, and identify the possible transfer of genetic material between the Enterococcus species isolated from both events, 16 isolates (1 E. cecorum, 13 E. faecalis, and 2 E. raffinosus isolates) were sequenced, and their genomes were compared. Interestingly, more than one Enterococcus species could be isolated from the same lesion, while other lesions also revealed several nonclonal isolates from the same species. This might suggest the opportunistic nature of Enterococcus spp. as there was no predominant isolate in the lesions. The number of virulence genes varied from 1 to 34 across three Enterococcus species with no common virulence gene. The number and nature of antimicrobial resistance genes among those isolates were worrisome because they indicate the presence of multidrug resistance on the farm. Both plasmids and phages were shared by different Enterococcus species, which suggests potential horizontal gene transfer of mobile genetic elements within this enterococci population.

Molecular epidemiology and emergence of sequence type 25 hypervirulent Klebsiella pneumoniae in pigs in the Netherlands (2013-2020): a global comparative analysis with human and pig isolates

Klebsiella pneumoniae (Kp), a ubiquitous pathogen found in diverse ecological niches, poses a threat to human and animal health. Hypervirulent Kp (hvKp) is concerning for its acquisition of virulence and antimicrobial resistance genes through plasmids. This study investigates hvKp as a cause of septicaemia in piglets in the Netherlands and examines the role of plasmids in virulence and host association. We collected 41 Kp isolates cultured from necropsies submitted from 15 different farms (2013-2020) and sequenced them using long-read sequencing. We identified sequence type (ST) 25 as the dominant Kp (67%, 10/15 farms) associated with septicaemia in pigs in the Netherlands. ST25 isolates displayed a hypervirulent profile, including the K2 hyper-capsule type and carried an iuc3 virulence plasmid. Further analysis revealed two ST25 clonal groups: CG25 and CG3804, a novel porcine clone. Multidrug resistance was identified in CG25 isolates from five pig farms. There was one colistin-resistant isolate carrying mcr-1 on a plasmid. Comparative genomic analysis was performed by including a large dataset of related publicly available Kp genomes from ST25 humans (n=230) and pigs (n=12) of all STs for phylogenetic and plasmid analysis. Pangenomic analysis revealed significantly higher iuc3 prevalence in global CG25 pig isolates (98%, 40/41) compared to humans (10%, 24/234) correlating with their enhanced virulence (scores 3-4 vs 0-1). The study highlights ST25 hvKp causing septicaemia in piglets in the Netherlands for the first time. Aerobactin lineage iuc3 on a plasmid is associated with infections in pigs and is responsible for an increased virulence score.

Transmission of a plasmid harboring NDM-1 gene between Salmonella Typhimurium and Escherichia coli strains in an infant

BACKGROUND

NDM-1 has been frequently identified in Enterobacteriaceae strains from clinical samples, but its occurrence in Salmonella Typhimurium (S. Typhimurium) is uncommon. Moreover, reports on the transmission of a plasmid harboring NDM-1 between different species in clinical samples are rare.

METHODS

Two S. Typhimurium strains and an Escherichia coli (E. coli) strain were isolated from a 14-month-old infant presenting with diarrhea. The resistance phenotypes were determined using the VITEK 2 Compact System. Genomic DNA was extracted from the isolated strains and whole genome sequencing was performed. The transmissibility of plasmids was validated by a conjugation experiment.

RESULTS

The subsequently isolated S. Typhimurium and E. coli strains exhibited resistance to imipenem, and whole genomic analysis revealed that each strain harbored a plasmid harboring NDM-1 and Qnrs1 genes. The two plasmids were nearly identical based on their sequences and could transfer to recipient strains. A genomic region containing several genes encoding phosphoribosylanthranilate isomerase, bleomycin binding protein, subclass B1 metallo-beta-lactamase, and IS30-like element ISAba125 family transposase was surrounded by the two flanking IS26 elements.

CONCLUSION

The transfer of plasmid harboring NDM-1 between S. Typhimurium and E. coli strains within patients highlights the potential for widespread transmission between different species. Continuous monitoring these strains may be important for preventing extensive transmission of resistance genes.