kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Fusobacterium sphaericum sp. nov., isolated from a human colon tumor adheres to colonic epithelial cells and induces IL-8 secretion

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. An analysis of the prevalence and abundance of Fs in > 20,000 human metagenomic samples shows that it is a rarely detected member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche and given its in vitro interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae

To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.

Genome-based assessment of antimicrobial resistance of Escherichia coli recovered from diseased swine in eastern China for a 12-year period

The global rise of antimicrobial resistance (AMR), driven by antibiotic use in healthcare and agriculture, poses a major public health threat. While AMR in clinical settings is well studied, there is a gap in understanding the resistance profiles of Escherichia coli from diseased livestock, particularly regarding zoonotic transmission. This study analyzes 114 E. coli isolates from diseased swine over 12 years, revealing that 99.12% were multidrug-resistant. Resistance was highest for ampicillin and amoxicillin/clavulanic acid (100%), followed by ciprofloxacin (96.49%) and tetracycline (94.74%). Furthermore, 21.05% of isolates were resistant to colistin, and 1.75% to tigecycline. A total of 76 antimicrobial resistance genes (ARGs) were identified, with mcr-1 found in 18.42%, mcr-3 in 4.39%, and tet(X4) in 1.75%. Significant co-occurrence of ARGs and plasmids suggests potential for co-selective dissemination. This study is the first to report enterotoxigenic E. coli (ETEC) strains carrying both mcr-1 and mcr-3 genes. After the 2017 colistin ban in China, mcr-1 detection rates significantly decreased, while florfenicol resistance rates increased in 2018-2021 (94.29%) compared to 2010-2017 (79.55%). This work provides valuable insights into the AMR profiles of E. coli from diseased swine and highlights trends that can inform strategies for monitoring and controlling public health risks associated with zoonotic E. coli transmission.IMPORTANCEThis study highlights the critical role of diseased and deceased swine in the spread of antimicrobial resistance (AMR), providing new insights into the transmission of resistance genes in zoonotic contexts. By analyzing E. coli from diseased swine, we identify key resistance genes such as mcr-1, mcr-3, and tet(X4), which pose significant public health risks, especially regarding last-resort antibiotics like colistin. Moreover, the study identifies novel transmission patterns of mcr genes, including ETEC strains carrying the mcr-3 gene and strains harboring both mcr-1 and mcr-3 genes. The role of plasmids in horizontal gene transfer is also revealed, facilitating rapid AMR spread across species. The long-term persistence of resistant strains highlights the challenges in controlling AMR in livestock. These findings underscore the need for enhanced surveillance and a One Health approach to mitigate AMR risks across animal, human, and environmental health.

Phylogenomics of Brucella abortus isolated from African Buffalo in Kruger National Park: New perspectives on wildlife-cattle disease dynamics

In South Africa, Brucella abortus biovar 1 is the primary cause of bovine brucellosis, significantly impacting cattle production and trade. Serological studies have revealed brucellosis in African wildlife, complicating control efforts due to limited epidemiological data. In 1977, B. abortus biovar 1 was isolated from an African buffalo fetus in Kruger National Park (KNP), raising speculation that buffalo may serve as reservoir hosts. This study investigated Brucella spp. in free-ranging buffalo in KNP using serological, molecular, and bacteriological methods. Brucella abortus bv 1 was isolated from lymph nodes and spleens of three sub-adult buffalo in 2022, marking the first documented recurrence in 50 years. Phylogenomic analyses revealed connections between buffalo isolates and cattle strains from South Africa and South America, suggesting spillover and shared origins from Europe. Further genomic and epidemiological surveillance is required to clarify the role of buffalo as reservoir hosts for brucellosis.

Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health

Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence of new and increasingly virulent foodborne pathogens. Traditional methods of detecting these outbreaks, including culture-based techniques, serotyping and molecular methods such as real-time PCR, are still widely used. However, these approaches often lack the precision and resolution required to definitively trace the source of an outbreak and distinguish between closely related strains of pathogens. Whole genome sequencing (WGS) has emerged as a revolutionary tool in outbreak investigations, providing high-resolution, comprehensive genetic data that allows accurate species identification and strain differentiation. WGS also facilitates the detection of virulence and antimicrobial resistance (AMR) genes, providing critical insight into the potential pathogenicity, treatment/control options and risks of spreading foodborne pathogens. This capability enhances outbreak surveillance, source tracing and risk assessment, making WGS an increasingly integrated component of public health surveillance systems. Despite its advantages, the widespread implementation of WGS faces several pressing challenges, including high sequencing costs, the need for specialized bioinformatics expertise, limited computational infrastructure in resource-constrained settings, and the standardization of data-sharing frameworks across regulatory and public health agencies. Addressing these barriers is crucial to maximizing the impact of WGS on foodborne disease surveillance. Even so, WGS is emerging as a vital tool in food safety and public health, and its potential to become the gold standard in outbreak detection has been recognized by public health authorities in the USA, the European Union, Australia and China, for example. This review highlights the role of WGS in foodborne outbreak investigations, its implementation challenges, and its impact on public health surveillance.

Cefiderocol activity against planktonic and biofilm forms of β-lactamase-producing pseudomonas aeruginosa from people with cystic fibrosis

OBJECTIVES

Chronic Pseudomonas aeruginosa infections are a leading cause of acute pulmonary exacerbations in people with cystic fibrosis (pwCF). Intrinsic antibiotic resistance and biofilm formation complicate treatment. This study investigates the genomic diversity and cefiderocol efficacy against planktonic and biofilm-associated forms of P. aeruginosa isolates from pwCF.

METHODS

Eight P. aeruginosa clinical isolates and three laboratory strains underwent whole genome sequencing (WGS). Biofilm formation was assessed through biomass, cell count, metabolic activity, and extracellular DNA (eDNA). The minimum bactericidal concentration (MBC90) and biofilm eradication concentration (MBEC90) were also determined.

RESULTS

WGS revealed significant genomic diversity, identifying ten distinct sequence types (STs). Antibiotic susceptibility testing (AST) showed that 10/11 strains were susceptible to cefiderocol, with one isolate (MPA9) displaying resistance linked to the blaOXA486 gene. Adding the β-lactamase inhibitor avibactam (AVI) restored susceptibility in this resistant strain. Although iron metabolism genes were highly conserved across isolates, MPA9 lacked the fpvA iron receptor, potentially contributing to cefiderocol resistance. Biofilm formation significantly increased tolerance to cefiderocol, with an 8-fold rise in MBEC90 compared to MBC90.

CONCLUSION

These findings highlight the genomic diversity and adaptive potential of P. aeruginosa in pwCF. Cefiderocol shows promise against planktonic and biofilm-associated P. aeruginosa, and combining it with AVI may counteract β-lactamase-mediated resistance.

Salmonella enterica serovar Braenderup shows clade-specific source associations and a high proportion of molecular epidemiological clustering

Salmonella enterica serovar Braenderup (S. enterica ser. Braenderup) is an important clinical serovar in the United States. This serovar was reported by the CDC in 2017 as the fifth most common Salmonella enterica serovar associated with outbreaks in the United States, which have been linked to both fresh produce and food animal products. The goals of this study were to compare the relatedness of human clinical isolates from southeastern USA (Tennessee (n = 106), Kentucky (n = 48), Virginia (n = 252), South Carolina (n = 109), Georgia (n = 159), Alabama (n = 8), Arkansas (n = 26), and Louisiana (n = 91)) and global clinical (n = 5,153) and nonclinical (n = 1,053) isolates obtained from the NCBI. Additionally, we also examined the population structure of S. enterica ser. Braenderup strains (n = 3,131) on EnteroBase and found that all the strains of this serovar are associated with a single cgMLST eBurst group (ceBG 185), confirming that this serovar is monophyletic. We divided the S. enterica ser. Braenderup population into two clades (Clade I and Clade II) and one clade group (Clade Group III). The composition of distinct environmental isolates in the clades differed: Clade I was significantly associated with produce (90.7%; P < 0.0001) and water, soil, and sediment (76.9%; P < 0.0001), and Clade II was significantly associated with poultry environments (62.8%; P < 0.0001). The clade-specific gene associations (e.g., Clade I-associated competence proteins and cytochrome_c_asm protein and Clade II-associated heme-exporter protein and dimethyl sulfoxide [DMSO] reductase-encoding genes) provide potential insights into possible mechanisms driving environmental adaptation and host-pathogen interaction. Phylogenetic analyses identified 218 molecular epidemiological clusters in the current study, which represented a greater proportion of potentially outbreak-related isolates than previously estimated.

IMPORTANCE

This study provides insights into the genomic diversity of S. enterica ser. Braenderup by revealing distinct clade-specific source attribution patterns and showing that a greater proportion of isolates were associated with epidemiological clusters based on the genomic relatedness than previously estimated. Specifically, we analyzed the diversity of human clinical isolates from southeastern USA and compared them with the global clinical and nonclinical isolates. Our analysis showed different clades of S. enterica ser. Braenderup linked to different environments, providing insights on the potential source of human sporadic infection and outbreaks. These findings can enhance public health surveillance and response strategies targeting S. enterica serovar Braenderup by expanding our understanding of potential transmission pathways and the genomic diversity of clinical and environmental isolates.

Increased Proportions of Invasive Pneumococcal Disease Cases Among Adults Experiencing Homelessness Sets the Stage for New Serotype 4 Capsular-Switch Recombinants

BACKGROUND

The Centers for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) identified increased serotype 4 invasive pneumococcal disease (IPD), particularly among adults experiencing homelessness (AEH).

METHODS

We quantified increased proportions of IPD cases in AEH during 2016-2022. Employing genomic-based characterization of IPD isolates, we identified serotype-switch variants. Recombinational analyses were used to identify the genetic donor and recipient strain that generated a serotype 4 progeny strain. We performed phylogenetic analyses of the serotype 4 progeny and of the serotype 12F genetic recipient to determine genetic distances.

RESULTS

We identified a cluster of 30 highly related (0-21 nucleotide differences) IPD isolates recovered during 2022-2023, corresponding to a serotype 4 capsular-switch variant. This strain arose through a multifragment recombination event between serotype 4/ST10172 and serotype 12F/ST220 parental strains. Twenty-five of the 30 cases occurred in Oregon. Of 29 cases with known residence status, 16 occurred in AEH. Variant emergence coincided with a 2.6-fold increase (57 to 148) of cases caused by the serotype 4/ST10172 donor lineage in 2022 compared to 2019 and its first appearance in Oregon. Most serotypes showed sequential increases of AEH IPD/all IPD ratios during 2016-2022 (eg, for all serotypes combined, 247/2198, 11.2% during 2022 compared to 405/5317, 7.6% for 2018-2019, P < .001). Serotypes 4 and 12F each caused more IPD than any other serotype in AEH during 2020-2022 (207 combined case isolates accounting for 38% of all IPD in AEH).

CONCLUSIONS

Expansion and increased transmission of serotypes 4 and 12F among adults potentially led to recent genesis of an impactful hybrid serotype-switch variant.

Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis

BACKGROUND

Antimicrobial resistance in Enterobacterales represents a substantial threat in modern clinical practice and the collection of data on the efficacy of new molecules is of paramount importance. Our study aimed to analyse the in vitro activity of imipenem/cilastatin/relebactam (IMI/REL) against KPC-producing Klebsiella pneumoniae (KPC-Kp) and investigate the genetic determinants of resistance to this agent.

METHODS

A total of 603 KPC-Kp strains, which were randomly collected during a multicentre study in northern Italy in the period 2016-2018, were analysed retrospectively. Antibiotic susceptibility testing was performed using a commercial broth microdilution. IMI-REL-resistant KPC-Kp strains were further analysed by whole genome sequencing to identify resistance determinants.

RESULTS

Ninety-eight percent of KPC-Kp (591/603) showed in vitro susceptibility to IMI/REL, with a minimum inhibitory concentration below the EUCAST cut-off. Different mutations in OmpK36 were found in all 12 IMI/REL-resistant strains, which belonged to MLST STs 258 (3 isolates), 307 (8 isolates) and 512 (1 isolate), but no clonal relatedness was detected by the minimum spanning tree analysis, except for 2 strains isolated in the same hospital. Equal distribution of blaKPC-2 (6/12) and blaKPC-3 (6/12) was found, and in 11 isolates the presence of genetic variants associated with the production of beta-lactamases was also identified. KPC-Kp resistant to IMI/REL retained susceptibility to meropenem/vaborbactam (MVB, 12/12, 100%) and ceftazidime/avibactam (CZA, 11/12, 91.7%). Only one strain of 603 was resistant to either MVB and CZA but susceptible to IMI/REL with a MIC of 2 mg/L; 4/603 (0.7%) were resistant to CZA but susceptible to IMI/REL and MVB.

CONCLUSIONS

IMI/REL showed good in vitro activity against the KPC-Kp strains analysed. All the IMI/REL-resistant strains displayed a mutation in porin OmpK36 and produced carbapenemases, with KPC-2 and KPC-3 being equally distributed. MVB and CZA maintained good activity against IMI/REL resistant isolates.

Acquired Amphotericin B Resistance Attributed to a Mutated ERG3 in Candidozyma auris

First identified in 2009, Candidozyma auris (formerly Candida auris ) is an emerging multidrug resistant fungus that can cause invasive infections with a crude mortality rate ranging from 30-60%. Currently, 30-50% of C. auris isolates are intrinsically resistant to amphotericin B. In this work, we characterized a clinical case of acquired amphotericin B resistance using whole genome sequencing, a large-scale phenotypic screen, comprehensive sterol profiling, and genotypic reversion using CRISPR. Data obtained in this work provides evidence that a deletion resulting in a frameshift in ERG3 contributes to the observed resistant phenotype. Characterization of this isolate also revealed a fitness cost is associated with the abrogation of ergosterol production and its replacement with other late-stage sterols. This article presents a clinical case description of amphotericin B resistance from a frameshift mutation in ERG3 in C. auris and marks an advancement in the understanding of antifungal resistance in this fungal pathogen.

Molecular epidemiology and β-lactam resistance mechanisms of Enterobacter cloacae complex isolates obtained from bloodstream infections, Kyoto, Japan

The Enterobacter cloacae complex (ECC) comprises multiple species that require genomic analysis for precise identification. They produce inducible AmpC β-lactamase and may carry acquired β-lactamases, which are responsible for cefotaxime and cefepime resistance. To determine the molecular epidemiology, antimicrobial resistance, and β-lactam resistance mechanisms of the ECC, we conducted whole-genome sequencing analysis, antimicrobial susceptibility testing, and mutation analysis on bloodstream ECC isolates from patients in Kyoto, Japan. In 194 ECC isolates, 13 species and six unnamed taxa were identified, with Enterobacter xiangfangensis (36%) being the most common. A total of 38% of the isolates were nonsusceptible to cefotaxime and presented relatively high nonsusceptibility rates to all antimicrobial agents tested. Among the different species, Enterobacter hoffmannii presented the highest nonsusceptibility rates to both β-lactams and non-β-lactams. Among the cefotaxime-nonsusceptible isolates, 16% harbored genes encoding extended-spectrum β-lactamases (ESBLs), carbapenemase, and/or plasmid-mediated AmpC, and ampC derepression was the predominant resistance mechanism in the remaining isolates. The prevalent sequence types (STs) in cefotaxime-susceptible and cefotaxime-nonsusceptible isolates were different, although some STs were shared by both groups. Cefepime nonsusceptibility was detected in 7% of the isolates and was associated with E. hoffmannii ST78 and E. xiangfangensis ST93, which carry ESBLs. Sixty-four mutants, experimentally obtained from eight cefotaxime-susceptible isolates, had various ampD mutations, and 42% and 99% of the mutants were nonsusceptible to cefepime and piperacillin/tazobactam, respectively, indicating the risks associated with the use of these antimicrobials. Continuous surveillance via genomic and phenotypic analyses is needed to combat antimicrobial resistance in the ECC.IMPORTANCEThe Enterobacter cloacae complex (ECC) is a group of pathogenic bacteria that cause nosocomial infections. The ECC produces chromosomal inducible AmpC β-lactamases, which is associated with treatment failure despite initial susceptibility to third-generation cephalosporins in selected ampC-derepressed mutants. The complex antimicrobial resistance mechanisms of the ECC and challenges in species identification have complicated our understanding of the ECC and the selection of appropriate treatment. In this study, we performed phenotypic, whole-genome sequencing, and mutation analyses among ECC isolates from patients with bloodstream infections to determine the precise molecular-based epidemiology, resistance mechanisms to third-/fourth-generation cephalosporins, specific species and clones that contribute to antimicrobial resistance, and acquisition rates of fourth-generation cephalosporin resistance in ampC-derepressed mutants. These data will help elucidate the local epidemiology and complex β-lactam resistance mechanisms in the ECC and guide appropriate antimicrobial therapy and infection control strategies for ECC-related infections.

Phylodynamic analysis of a prolonged meningococcal epidemic reveals multiple introductions and pre-epidemic expansion

Neisseria meningitidis is the causative agent of invasive meningococcal disease (IMD), a form of bacterial meningitis and septicaemia, leading to isolated cases, outbreaks, and epidemics worldwide. Between 1991 and 2008, Aotearoa/New Zealand (NZ) experienced a prolonged hyperendemic group B IMD outbreak caused by the NZMenB epidemic strain, belonging to clonal-complex 41/44 (cc41/44) and identified by the PorA variant P1.7-2,4 (B:4:P1.7-2,4:cc41/44). NZMenB continues to account for approximately one-quarter of group B meningococcal disease cases in NZ. To understand NZMenB origin and initiation we used phylodynamic tools to analyse approximately 97 % of all NZMenB isolates submitted to the NZ Meningococcal Reference Laboratory from 1990 to 2019. We found NZMenB can be divided into three major clades: clade41, clade154, and clade42, each with distinct origins and expansion patterns. Our evidence from molecular dating and clonal expansion analysis suggests that NZMenB was circulating and had expanded before the epidemic. Comparison with international data showed multiple importations and re-introductions of NZMenB into NZ, while not suggesting close relationships with international variants. The recent COVID-19 health emergency and differing governmental responses have brought societal and environmental contributions to epidemics and pandemics into focus. We propose the NZMenB epidemic may have been triggered by increasing societal inequality and household crowding resulting from government policies at the time.

Mystique, a broad host range Acinetobacter phage, reveals the impact of culturing conditions on phage isolation and infectivity

With the global rise of antimicrobial resistance, phage therapy is increasingly re-gaining traction as a strategy to treat bacterial infections. For phage therapy to be successful however, we first need to isolate appropriate candidate phages for both clinical and experimental research. Acinetobacter baumannii is an opportunistic pathogen known for its ability to rapidly evolve resistance to antibiotics, making it a prime target for phage therapy. Yet phage isolation may be hampered by A. baumannii's ability to rapidly switch between capsular states. Here, we report the discovery and structural characterisation of a novel lytic phage, Mystique. This phage was initially isolated against the wild-type AB5075: a commonly used clinical model strain. When screening Mystique on 103 highly diverse isolates of A. baumannii, we found that it has a broad host range, being able to infect 85.4% of all tested strains when tested on bacterial lawns - a host range that expanded to 91.3% when tested in liquid culture. This variation between solid and liquid culturing conditions on phage infectivity was also observed for several other phages in our collection that were assumed unable to infect AB5075, and some capsule negative mutants that seemed resistant to Mystique proved susceptible when assayed in liquid. This highlights how differences in culturing conditions can drastically impact phage infectivity, with important consequences for phage isolation and characterisation efforts. Finally, Mystique was found to be able to infect other species of Acinetobacter, making it a multi-species phage with broad applicability for further research.

Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data

Antimicrobial resistance is a global health concern, and methicillin-resistant Staphylococcus aureus (MRSA) is one of the highest-priority organisms exhibiting this phenotype. Here, we performed a national surveillance integrating patient clinical data of S. aureus isolated from bloodstream infections. We performed genome sequencing, standardized antimicrobial susceptibility testing, and collected clinical metadata of 580 S. aureus isolates collected during 2019-2020. We focused on three predominant clonal complexes (CC1, CC5, and CC8) and assesses their microbiological and clinical significance, as well as their distribution across eastern and western Japan. Furthermore, we conducted a genomic comparison of the isolates of 2019-2000 with those of 1994-2000 and investigated the evolutionary trajectory of emerging clones from the three dominant clonal complexes. We revealed that the emerging MRSA ST764-SCCmecII showed the highest mortality rate within 30 days of hospitalization. This high-risk clone diverged from the New York/Japan clone (ST5-SCCmecII), which was inferred to have undergone repeated infections with phages carrying superantigen toxin genes and acquired antimicrobial resistance genes via mobile genetic elements, leading to its emergence around 1994. Overall, we provide a blueprint for a national genomic surveillance study that integrates clinical data and enables the identification and evolutionary characterization of a high-risk clone.

Comparative Genomic Analysis of Three Paenibacillus polymyxa Strains Isolated from Termitarium and Identification of Novel Biosynthetic Gene Clusters

The emergence of multidrug-resistant (MDR) pathogens poses a significant global threat in healthcare settings, emphasizing the critical need for novel antibiotic discovery. Consequently, international efforts are continuously directed towards identifying new antibiotics from diverse microbial sources. We investigated the biosynthetic potential of three Paenibacillus polymyxa strains isolated from a termitarium, WGTm-28, WGTm-93, and WGTm-147. These strains exhibited a broad-spectrum of antimicrobial activity against clinical and plant pathogens. Whole-genome sequencing using the Illumina platform and subsequent annotation revealed 112 biosynthetic gene clusters (BGCs) responsible for synthesizing diverse secondary metabolites. Notably, BGCs encoding polymyxin, fusaricidin B, and tridecaptin were identified in all three strains. Anabaenopeptin NZ857/nostamide A was found in WGTm-28 and WGTm-93, while paenibacillin and paenilan were found only in WGTm-93. A BGC coding for rhizomideA/B/C was exclusively present in WGTm-147. BGCs encoding marthiapeptide A, aurantinin B/C/D, cerecidin, paenibacterin, paenicidin B, and calyculin A were identified with lower identity (from 28 to 60%) with previously reported organisms. Interestingly, 33 putative NRPS BGCs, hybrid clusters, and PKSs BGC were discovered with ≤ 25% or no identity to known antibiotics, suggesting the potential of synthesizing novel antimicrobial agents by these strains.

Identification of Elizabethkingia species by MALDI-TOF MS proteotyping

Elizabethkingia species, isolated from clinical and environmental samples, are emerging opportunistic bacterial pathogens with a high mortality rate in clinical settings worldwide. Taxonomically, Elizabethkingia comprises seven species: E. anophelis, E. argenteiflava, E. bruuniana, E. meningoseptica, E. miricola, E. ursingii, and E. occulta. In this study, we identified useful biomarker proteins, including ribosomal L29, L30, S21, and the YtxH domain-containing proteins, for distinguishing Elizabethkingia species using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiles. Evaluation of 29 clinical and environmental Elizabethkingia strains revealed that these species could be separated by MALDI-TOF MS profiles into six groups-E. anophelis, E. argenteiflava, E. bruuniana/E. miricola, E. meningoseptica, E. ursingii, and E. occulta-based on the four biomarker protein peaks. This study demonstrates the potential of routine MALDI-TOF MS -based examination methods for the early detection of Elizabethkingia species in clinical laboratories.

IMPORTANCE

Elizabethkingia species are groups of emerging opportunistic bacterial pathogens with a high mortality rate, causing healthcare-associated outbreaks worldwide. Rapid identification of Elizabethkingia species is important becausethese species show intrinsically carbapenem resistance and there are few data for using appropriate antibiotics. Until now, only whole-genome sequencing could accurately identify the seven Elizabethkingia species. Therefore, establishing rapid and accurate identification methods for Elizabethkingia species in clinical laboratories is vital. In this study, we developed new methods for identifying Elizabethkingia species using four biomarker protein peaks-ribosomal L29, L30, S21, and the YtxH domain-containing proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) proteotyping. This study demonstrates the potential of routine MALDI-TOF MS -based laboratory examination for the early identification of Elizabethkingia species.

Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut

Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.

A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species

Bacterial vaginosis (BV) is a prevalent condition associated with an imbalance in the vaginal microbiota, often involving species of Gardnerella . The taxonomic complexity and inconsistent nomenclature of Gardnerella have impeded progress in understanding the role of specific species in health and disease. In this study, we conducted a comprehensive genomic and pangenomic analysis to resolve taxonomic ambiguities and elucidate metabolic and virulence potential across Gardnerella species. We obtained complete, closed genomes for 42 Gardnerella isolates from women with BV and curated publicly available genome sequences (n = 291). Average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), and the cpn60 gene sequences identified nine species and eleven subspecies within Gardnerella , for which we refined species and subspecies boundaries and proposed updated nomenclature. Pangenome analysis revealed species-specific gene clusters linked to metabolic pathways, virulence factors, and niche adaptations, distinguishing species specialized for mucin degradation in the vaginal environment from those potentially adapted to urinary tract colonization. Notably, we identified lineage-specific evolutionary divergence in gene clusters associated with biofilm formation, carbohydrate metabolism, and antimicrobial resistance. We further discovered the first cryptic plasmids naturally present within the Gardnerella genus. Our findings provide a unified framework for Gardnerella taxonomy and nomenclature, and enhance our understanding of species-specific functional capabilities, with implications for Gardnerella research, diagnostics, and targeted therapeutics in BV.

Comparative genomic analysis reveals the emergence and dissemination of different Salmonella enterica serovar Gallinarum biovar Gallinarum lineages in Brazil

RESEARCH HIGHLIGHTS

Fowl typhoid (FT) is a concerning poultry disease caused by S. Gallinarum.Five S. Gallinarum lineages (I to V) were demonstrated in South American farms.S. Gallinarum lineages have specific antimicrobial resistance / virulence genomic profiles.Main FT outbreaks in Brazil have been caused by the specific lineage II.

Outbreak of Serotype 1 Invasive Pneumococcal Disease, Kibera Urban Informal Settlement, Nairobi, Kenya, 2023

Use of 10-valent pneumococcal conjugate vaccine in Kenya has led to substantial reductions in vaccine-type pneumococcal carriage and invasive pneumococcal disease. However, analysis of recent surveillance data indicates an outbreak of vaccine-type serotype 1 in 2023 in Kibera, Kenya. Continued monitoring of invasive pneumococcal disease in Kenya is warranted.

Discovery and engineering of the antibody response to a prominent skin commensal

The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8+ T cell response pre-emptively, in the absence of an infection1. However, the scope and purpose of this anticommensal immune programme are not well defined, limiting our ability to harness it therapeutically. Here, we show that this colonist also induces a potent, durable and specific antibody response that is conserved in humans and non-human primates. A series of S. epidermidis cell-wall mutants revealed that the cell surface protein Aap is a predominant target. By colonizing mice with a strain of S. epidermidis in which the parallel β-helix domain of Aap is replaced by tetanus toxin fragment C, we elicit a potent neutralizing antibody response that protects mice against a lethal challenge. A similar strain of S. epidermidis expressing an Aap-SpyCatcher chimera can be conjugated with recombinant immunogens; the resulting labelled commensal elicits high antibody titres under conditions of physiologic colonization, including a robust IgA response in the nasal and pulmonary mucosa. Thus, immunity to a common skin colonist involves a coordinated T and B cell response, the latter of which can be redirected against pathogens as a new form of topical vaccination.

Characterisation and comparison of Mycoplasma bovis strain types from Irish and Scottish bovine isolates in a global context

Infection with Mycoplasma bovis (M. bovis) can present as a range of clinical manifestations of varying severity in beef and dairy cattle worldwide and can seriously impact cattle health and welfare. The objectives of this study were to characterise the strains and genetic diversity within isolates of M. bovis collected from bovine clinical samples in Ireland and Scotland, and to provide place these isolates a global phylogenetic context. We performed Illumina whole genome sequencing 19 M. bovis strains from 19 unique Irish animals and 5 M. bovis strains from 4 unique Scottish animals. The strains were then analysed against 117 downloaded Genbank assemblies to create a phylogenetic tree. The Irish strains clustered into 2 main groups which were identifiable as sequence type 29 (Group 1) and sequence type 21 (Group 2) using the pubMLST system. The Scottish strains all fell within Group 1 of our analysis and were identifiable as sequence type 29 using the pubMLST system. No novel sequence types were found. The Irish and Scottish strains are similar to the genetic variation of M. bovis currently seen in Europe and may suggest separate introductions. The impact of disease associated with M. bovis in cattle emphasises the importance of within and between herd biosecurity as well as the global nature of infectious disease due to widespread international cattle movement.

Convergence of Hypervirulence and Multidrug-Resistance in Burkholderia cepacia Complex Isolates from Patients with COVID-19

Purpose

Burkholderia is a conditioned pathogen in the medical setting and mainly affects patients with cystic fibrosis. We found co-infection with Burkholderia cepacia complex (Bcc) in many patients with respiratory tract infections, including H7N9 and COVID-19. However, previous studies have not focused on co-infections with BCC and respiratory viruses. Therefore, this study attempted to clarify the evolution of COVID-19-Bcc and H7N9-Bcc in terms of genetic background, antibiotic resistance, and virulence phenotypes.

Methods

This study retrospectively collected 49 Bcc isolated from patients with H7N9 and COVID-19 in a tertiary hospital of Zhejiang Province, of which 42 isolates were isolated from patients with H7N9, seven isolates were isolated from patients with COVID-19. The collected isolates were tested for antibiotic susceptibility, Galleria mellonella infection model, and whole-genome COVID-19-Bcc Characterization.

Results

The test results of 49 strains of Bcc showed that the strains isolated from COVID-19 patients accounted for 57.1% of multidrug-resistance resistant strains. Statistical analysis of the median lethal time of G. mellonella showed that the median fatal time for COVID-19-Bcc was shorter and more virulent than that of H7N9-Bcc (P<0.05). The results of phylogenetic analysis indicated that COVID-19-Bcc may have evolved from H7N9-Bcc.

Conclusion

In this study, co-infection with BCC in many patients with respiratory tract infections, including H7N9 and COVID-19, was first identified and clarified that COVID-19-Bcc may have evolved from H7N9-Bcc and has the characteristics of hypervirulence and multidrug resistance.

Genomic characterization of ST11-KL25 hypervirulent KPC-2-producing multidrug-resistant Klebsiella pneumoniae from China

The global prevalence of ST11 hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) isolates has been increasingly documented, yet genomic characterization of this clone remains insufficiently explored. Here, we report a clinical ST11-KL25 hv-CRKP strain (KP156) that exhibited resistance to multiple antibiotics and demonstrated hypervirulence in a mouse infection model. Whole-genome sequencing revealed that KP156 harbored one virulence plasmid (pKP156-Vir) and two resistance plasmids (pKP156-KPC and pKP156-tetA). The pKP156-Vir contains several virulence factors, including rmpA2 and iucABCD, which are critical contributors to its hypervirulence. The bla KPC-2 and bla CTX-M-65 genes, located within the Tn6296 transposon of pKP156-KPC, along with a multidrug-resistant (MDR) region containing multiple transposons and conjugative elements in pKP156-tetA, are associated with the transfer of resistance genes. Phylogenetic analysis indicates that KP156 shares high homology with other ST11 hv-CRKPs, suggesting potential transmission of this clone. Our study informs the development of genomic surveillance and control strategies for this strain.

Sequential use of capsular typing and whole-genome sequencing-based analysis for transmission of carbapenem-resistant Acinetobacter baumannii in a tertiary medical center

BACKGROUND

During the COVID-19 pandemic, there has been an increasing trend in healthcare-associated infections (HAIs) caused by carbapenem-resistant Acinetobacter baumannii (CRAB), posting a global public health concern. The heightened sensitivity of whole-genome sequencing (WGS) renders it an optimal and potent tool for monitoring outbreaks and tracing the transmission routes of nosocomial pathogens.

METHOD

We collected CRAB isolates from March 1, 2023, to April 6, 2023 in Chang Gung Memorial Hospital Lin Kou branch, a tertiary medical center in northern Taiwan. Any two or more isolates with the same identifiable capsular K-locus (KL) types were selected, and analyzed via WGS to identify putative transmission clusters, combined with epidemiologic and retrospective analysis on medical records to confirm risk factors and hidden transmission chains.

RESULT

A total of 48 non-redundant CRAB isolates were collected, belonging to ST2 of Pasteur MLST scheme and identifiable KL types of KL2, KL3, KL9, KL10, KL22, KL52. Excluding the KL types that was only found in 1 case, KL2 (n = 9, 22.5 %), KL3 (n = 24, 60 %), KL9 (n = 3, 7.5 %), and KL10 (n = 4, 10 %) were selected for further WGS analysis. Four distinct transmission clusters comprised of 2, 3, 10, and 23 cases were identified on a basis of phylogenetic status. 12 probable transmission chains were revealed, and 2 hidden transmission routes can be speculated.

CONCLUSION

This study referred to some hidden transmission chains that may be missed from traditional surveillance measures. Despite its low prevalence and high cost currently, implementing WGS could be a efficient, prompt, and unequivocal option for future MDRO infection control.

Expanding the Stenotrophomonas maltophilia complex: phylogenomic insights, proposal of Stenotrophomonas forensis sp. nov. and reclassification of two Pseudomonas species

A novel Stenotrophomonas species was isolated as a contaminant in viral transport media at the District of Columbia Department of Forensic Sciences Public Health Laboratory. Phylogenomic and biochemical analyses of the isolate determined that it represented a novel species within Stenotrophomonas. Related strains in public genome databases suggested that this novel species is associated with clinically acquired infections, similar to closely related Stenotrophomonas maltophilia. The name Stenotrophomonas forensis sp. nov. is proposed. Comparative genomic and phylogenetic analyses of the S. maltophilia complex reveal that Stenotrophomonas africana is an independent species and is not a later heterotypic synonym of S. maltophilia. We also propose the transfer of two misclassified Pseudomonas species into Stenotrophomonas as Stenotrophomonas beteli comb. nov. and Stenotrophomonas hibiscicola comb. nov. The type strain for S. forensis sp. nov. is DFS-20110405T (=ATCC TSD-272T=NCTC 14893T).

Genome sequencing and comparative genomic analysis of bovine mastitis-associated non-aureus staphylococci and mammaliicocci (NASM) strains from India

We describe the whole-genome sequencing and comparative genomic analysis of 22 mastitis-associated NASM strains isolated from India. The mean genome size of the strains was 2.55 Mbp, with an average GC content of 32.2%. We identified 14 different sequence types (STs) among the 22 NASM strains. Of these, ST1 and ST6 of S. chromogenes were exclusively associated with bovine mastitis. Genome-wide SNP-based minimum spanning tree revealed the intricate phylogenetic relationships among NASM strains from India, categorizing them into five major clades. Interestingly, mastitis-associated strains formed separate subclades in all the NASM species studied, indicating distinct host-specific co-evolution. The study identified 32 antimicrobial resistance (AMR) genes and 53 virulence-associated genes, providing insights into the genetic factors that could contribute to the pathogenicity of NASM species. Some virulence and AMR genes were found in the predicted genomic islands, suggesting possible horizontal transfer events.

Utilizing whole-genome sequencing to characterize Listeria spp. persistence and transmission patterns in a farmstead dairy processing facility and its associated farm environment

Farmstead dairy processing facilities may be particularly susceptible to Listeria spp. contamination due to the close physical proximity of their processing environments (PE) to associated dairy farm environments (FE). In this case study, we supported the implementation of interventions focused on improving (1) cleaning and sanitation efficacy, (2) hygienic zoning, and (3) sanitary equipment and facility design and maintenance in a farmstead dairy processing facility, and evaluated their effect on Listeria spp. detection in the farmstead's PE over 1 yr. Detection of Listeria spp. in the farmstead's PE was numerically reduced from 50% to 7.5% after 1 yr of intervention implementation, suggesting that these interventions were effective at improving Listeria spp. control. In addition, environmental samples were also collected from the farmstead's FE to evaluate the risk of the FE as a potential source of Listeria spp. in the PE. Overall, detection of Listeria spp. was higher in samples collected from the FE (75%, 27/36) compared with samples collected from the PE (24%, 29/120). Whole-genome sequencing performed on select isolates collected from the PE and FE supported the identification of 6 clusters (range of 3 to 15 isolates per cluster) that showed ≤ 50 high-quality single nucleotide polymorphism differences. Of these 6 clusters, 3 (i.e., clusters 2, 4, and 5) contained isolates that were collected from both the PE and FE, suggesting that transmission between these 2 environments was likely. Moreover, all cluster 2 isolates represented a clonal complex of L. monocytogenes commonly associated with dairy farm environmental reservoirs (i.e., CC666), which may support that the farmstead's FE represented an upstream source of the cluster 2 isolates that were found in the PE. Overall, our data underscore that although the FE can represent a potential upstream source of Listeria spp. contamination in a farmstead dairy processing facility, implementation of targeted interventions can help effectively minimize Listeria spp. contamination in the PE.

Chromosomal Type II Toxin-Antitoxin Systems May Enhance Bacterial Fitness of a Hybrid Pathogenic Escherichia coli Strain Under Stress Conditions

The functions of bacterial plasmid-encoded toxin-antitoxin (TA) systems are unambiguous in the sense of controlling cells that fail to inherit a plasmid copy. However, its role in chromosomal copies is contradictory, including stress-response-promoting fitness and antibiotic treatment survival. A hybrid pathogenic Escherichia coli strain may have the ability to colonize distinct host niches, facing contrasting stress environments. Herein, we determined the influence of multiple environmental stress factors on the bacterial growth dynamic and expression profile of previously described TA systems present in the chromosome of a hybrid atypical enteropathogenic and extraintestinal E. coli strain. Genomic analysis revealed 26 TA loci and the presence of five type II TA systems in the chromosome. Among the tested stress conditions, osmotic and acid stress significantly altered the growth dynamics of the hybrid strain, enhancing the necessary time to reach the stationary phase. Using qPCR analyses, 80% of the studied TA systems were differentially expressed in at least one of the tested conditions, either in the log or in the stationary phase. These data indicate that type II TA systems may contribute to the physiology of pathogenic hybrid strains, enabling their adaptation to different milieus.

Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software.

Salmonella associated with agricultural animals exhibit diverse evolutionary rates and show evidence of recent clonal expansion

Most foodborne salmonellosis outbreaks are linked to agricultural animal products with a few serovars accounting for most Salmonella isolated from specific animal products, suggesting an adaptation to the corresponding animal hosts and their respective environments. Here, we utilized whole-genome sequence (WGS) data to analyze the evolution and population genetics of seven serovars frequently isolated from ground beef (Montevideo, Cerro, and Dublin), chicken (Kentucky, Infantis, and Enteritidis), and turkey (Reading) in the United States. In addition, publicly available metadata were used to characterize major clades within each serovar with regard to public health significance. Except for Dublin, all serovars were polyphyletic, comprising 2-6 phylogenetic groups. Further partitioning of the phylogenies identified 25 major clades, including 12 associated with animal or environmental niches. These 12 clades differed in evolutionary parameters (e.g., substitution rates) as well as public health relevant characteristics (e.g., association with human illness, antimicrobial resistance). Overall, our results highlight several critical trends: (i) the Salmonella generation time appears to be more dependent on source than serovar and (ii) all serovars contain clades and sub-clades that are estimated to have emerged after the year 1940 and that are enriched for isolates associated with humans, agricultural animals, antimicrobial resistance (AMR), and/or specific geographical regions. These findings suggest that serotyping alone does not provide enough resolution to differentiate isolates that may have evolved independently, present distinct geographic distribution and host association, and possibly have distinct public health significance.

IMPORTANCE

Non-typhoidal Salmonella are major foodborne bacterial pathogens estimated to cause more than one million illnesses, thousands of hospitalizations, and hundreds of deaths annually in the United States. More than 70% of Salmonella outbreaks in the United States have been associated with agricultural animals. Certain serovars include persistent strains that have repeatedly contaminated beef, chicken, and turkey, causing outbreaks and sporadic cases over many years. These persistent strains represent a particular challenge to public health, as they are genetically clonal and widespread, making it difficult to differentiate distinct outbreak and contamination events using whole-genome sequence (WGS)-based subtyping methods (e.g., core genome allelic typing). Our results indicate that a phylogenetic approach is needed to investigate persistent strains and suggest that the association between a Salmonella serovar and an agricultural animal is driven by the expansion of clonal subtypes that likely became adapted to specific animals and associated environments.

Genetic mutations in Cryptococcus neoformans pyrimidine salvage pathway enzymes contribute to reduced susceptibility against 5-fluorocytosine

Cryptococcal meningitis is a high-mortality infection. Adding 5-fluorocytosine (5-FC) to its treatment improves outcomes, but resistance to 5-FC presents a significant challenge. We conducted whole-genome sequencing on seven C. neoformans isolates with varying 5-FC susceptibility, along with proteomic and in silico analyses. Our findings indicate that mutations in genes of the pyrimidine salvage pathway are responsible for 5-FC resistance. Specifically, we identified an E64G missense mutation in the FUR1 gene, a large deletion in the FCY1 gene, and a point mutation in FCY1 leading to a truncated protein. The proteomic data indicated that these mutations resulted in the absence or reduction of crucial enzymes in resistant isolates. Genetic transformations confirmed the association between these mutations and 5-FC resistance. Resistance to 5-FC can develop during treatment and is closely tied to mutations in key metabolic enzymes. Understanding in vivo resistance development is crucial for combating resistance and enhancing patient outcomes.

Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne blaOXA-23

Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a significant threat to hospitalized patients as effective therapeutic options are scarce. Based on the genomic characteristics of the CRAB strain AB2877 harboring chromosome-borne blaOXA-23, which was isolated from the bronchoalveolar lavage fluid (BALF) of a patient in a respiratory intensive care unit (RICU), we systematically analyzed antibiotic resistance genes (ARGs) and the genetic context associated with ARGs carried by CRAB strains harboring chromosome-borne blaOXA-23 worldwide. Besides blaOXA-23, other ARGs were detected on the chromosome of the CRAB strain AB2877 belonging to ST208/1806 (Oxford MLST scheme). Several key genetic contexts associated with the ARGs were identified on the chromosome of the CRAB strain AB2877, including (1) the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph(6)-Id (2); the resistance island AbGRI3 harboring armA and mph(E)-msr(E) (3); the Tn3-like composite transposon containing blaTEM-1D and aph(3')-Ia; and (4) the structure "ISAba1-blaADC-25." The first two genetic contexts were most common in ST195/1816, followed by ST208/1806. The last two genetic contexts were found most frequently in ST208/1806, followed by ST195/1816.IMPORTANCEThe blaOXA-23 gene can be carried by plasmid or chromosome, facilitating horizontal genetic transfer and increasing carbapenem resistance in healthcare settings. In this study, we focused on the genomic characteristics of CRAB strains harboring the chromosome-borne blaOXA-23 gene, and the important genetic contexts associated with blaOXA-23 and other ARGs were identified, and their prevalent clones worldwide were determined. Notably, although the predominant clonal CRAB lineages worldwide containing the MDR region associated with blaOXA-23, tet(B)-tetR(B), aph(3'')-Ib, and aph (6)-Id was ST195/1816, followed by ST208/1806, the CRAB strain AB2877 in our study belonged to ST208/1806. Our findings contribute to the knowledge regarding the dissemination of CRAB strains and the control of nosocomial infection.

Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, adheres to colonic epithelial cells and induces IL-8 secretion

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. ( Fs ), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome

Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.

Comparative Genomics Revealing the Genomic Characteristics of Klebsiella variicola Clinical Isolates in China

Klebsiella variicola is an opportunistic pathogen often misidentified as Klebsiella pneumoniae, leading to misdiagnoses and inappropriate treatment in clinical settings. The genetic and molecular characteristics of clinically isolated K. variicola remain largely unexplored. We aim to fill this knowledge gap by examining the genomic properties of and evolutionary relationships between clinical isolates of K. variicola. The genomic data of 70 K. variicola strains were analyzed using whole-genome sequencing. A phylogenetic tree was generated based on the gene sequences from these K. variicola strains and public databases. Among the K. variicola strains, the drug resistance genes with the highest carrying rates were beta-lactamase and aminoglycoside. Locally isolated strains had a higher detection rate for virulence genes than those in public databases, with yersiniabactin genes being the most prevalent. The K locus types and MLST subtypes of the strains exhibited a dispersed distribution, with O3/O3a being the predominant subtype within the O category. In total, 28 isolates carried both IncFIB(K)_Kpn3 and IncFII_pKP91 replicons. This study underscores the importance of developing more effective diagnostic tools and therapeutic strategies for K. variicola infections. The continued surveillance and monitoring of K. variicola strains is essential for understanding the epidemiology of infections and informing public health strategies.

Whole-genome sequencing-based genetic diversity, transmission dynamics, and drug-resistant mutations in Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia

Background

Extrapulmonary tuberculosis (EPTB) refers to a form of Tuberculosis (TB) where the infection occurs outside the lungs. Despite EPTB being a devastating disease of public health concern, it is frequently overlooked as a public health problem. This study aimed to investigate genetic diversity, identify drug-resistance mutations, and trace ongoing transmission chains.

Methods

A cross-sectional study was undertaken on individuals with EPTB in western Ethiopia. In this study, whole-genome sequencing (WGS) was employed to analyze Mycobacterium tuberculosis (MTB) samples obtained from EPTB patients. Out of the 96 genomes initially sequenced, 89 met the required quality standards for genetic diversity, and drug-resistant mutations analysis. The data were processed using robust bioinformatics tools.

Results

Our analysis reveals that the majority (87.64%) of the isolates can be attributed to Lineage-4 (L4), with L4.6.3 and L4.2.2.2 emerging as the predominant sub-lineages, constituting 34.62% and 26.92%, respectively. The overall clustering rate and recent transmission index (RTI) were 30 and 17.24%, respectively. Notably, 7.87% of the isolates demonstrated resistance to at least one anti-TB drug, although multi-drug resistance (MDR) was observed in only 1.12% of the isolates.

Conclusions

The genetic diversity of MTBC strains in western Ethiopia was found to have low inter-lineage diversity, with L4 predominating and exhibiting high intra-lineage diversity. The notably high clustering rate in the region implies a pressing need for enhanced TB infection control measures to effectively disrupt the transmission chain. It's noteworthy that 68.75% of resistance-conferring mutations went undetected by both GeneXpert MTB/RIF and the line probe assay (LPA) in western Ethiopia. The identification of resistance mutations undetected by both GeneXpert and LPA, along with the detection of mixed infections through WGS, emphasizes the value of adopting WGS as a high-resolution approach for TB diagnosis and molecular epidemiological surveillance.

OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

Application of Environmental Monitoring Programs and Root Cause Analysis to Identify and Implement Interventions to Reduce or Eliminate Listeria Populations in Apple Packinghouses

Controlling Listeria in produce packinghouses can be challenging due to the large number of potential contamination routes. For example, repeated isolation of the same Listeria subtype in a packinghouse could indicate persistence in the packinghouse or reintroduction of the same Listeria from an upstream source. To improve understanding of Listeria transmission patterns in packinghouses, we performed a longitudinal study in four apple packinghouses, including testing of 1,339 environmental sponges and whole genome sequencing (WGS)-based characterization of 280 isolates. Root cause analysis and subsequent intervention implementation were also performed and assessed for effectiveness. Listeria prevalence among environmental sponges collected from the four packinghouses was 20% (range of 5-31% for individual packinghouses). Sites that showed high Listeria prevalence included drains, forklift tires and forks, forklift stops, and waxing area equipment frames. A total of 240/280 WGS-characterized isolates were represented in 41 clusters, each containing two or more isolates that differed by ≤50 high-quality single nucleotide polymorphisms (hqSNPs); 21 clusters were isolated from one packinghouse over ≥2 samplings (suggesting persistence or possibly reintroduction), while 11 clusters included isolates from >2 packinghouses, suggesting common upstream sources. Some interventions successfully (i) reduced Listeria detection on forklift tires and forks (across packinghouses) and (ii) mitigated packinghouse-specific Listeria issues (e.g., in catch pans). However, interventions that lacked enhanced equipment disassembly when persistence was suspected typically appeared to be unsuccessful. Overall, while our data suggest a combination of intensive environmental sampling with subtyping and root cause analysis can help identify effective interventions, implementation of effective interventions continues to be a challenge in packinghouses.

Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia

BACKGROUND

The lineage 4 (L4) of Mycobacterium tuberculosis (MTB) is not only globally prevalent but also locally dominant, surpassing other lineages, with lineage 2 (L2) following in prevalence. Despite its widespread occurrence, factors influencing the expansion of L4 and its sub-lineages remain poorly understood both at local and global levels. Therefore, this study aimed to conduct a pan-genome and identify genomic signatures linked to the elevated prevalence of L4 sublineages among extrapulmonary TB (EPTB) patients in western Ethiopia.

METHODS

A cross-sectional study was conducted at an institutional level involving confirmed cases of extrapulmonary tuberculosis (EPTB) patients from August 5, 2018, to December 30, 2019. A total of 75 MTB genomes, classified under lineage 4 (L4), were used for conducting pan-genome and genome-wide association study (GWAS) analyses. After a quality check, variants were identified using MTBseq, and genomes were de novo assembled using SPAdes. Gene prediction and annotation were performed using Prokka. The pan-genome was constructed using GET_HOMOLOGUES, and its functional analysis was carried out with the Bacterial Pan-Genome Analysis tool (BPGA). For GWAS analysis, Scoary was employed with Benjamini-Hochberg correction, with a significance threshold set at p-value ≤ 0.05.

RESULTS

The analysis revealed a total of 3,270 core genes, predominantly associated with orthologous groups (COG) functions, notably in the categories of '[R] General function prediction only' and '[I] Lipid transport and metabolism'. Conversely, functions related to '[N] Cell motility' and '[Q] Secondary metabolites biosynthesis, transport, and catabolism' were primarily linked to unique and accessory genes. The pan-genome of MTB L4 was found to be open. Furthermore, the GWAS study identified genomic signatures linked to the prevalence of sublineages L4.6.3 and L4.2.2.2.

CONCLUSIONS

Apart from host and environmental factors, the sublineage of L4 employs distinct virulence factors for successful dissemination in western Ethiopia. Given that the functions of these newly identified genes are not well understood, it is advisable to experimentally validate their roles, particularly in the successful transmission of specific L4 sublineages over others.

Presence and Role of the Type 3 Fimbria in the Adherence Capacity of Enterobacter hormaechei subsp. hoffmannii

Enterobacter hormaechei, one of the species within the Enterobacter cloacae complex, is a relevant agent of healthcare-associated infections. In addition, it has gained relevance because isolates have shown the capacity to resist several antibiotics, particularly carbapenems. However, knowledge regarding colonization and virulence mechanisms of E. hormaechei has not progressed to the same extent as other Enterobacteriaceae species as Escherichia coli or Klebsiella pneumoniae. Here, we describe the presence and role of the type 3 fimbria, a chaperone-usher assembled fimbria, which was first described in Klebsiella spp., and which has been detected in other representatives of the Enterobacteriaceae family. Eight Chilean E. cloacae isolates were examined, and among them, four E. hormaechei isolates were found to produce the type 3 fimbria. These isolates were identified as E. hormaechei subsp. hoffmannii, one of the five subspecies known. A mutant E. hormaechei subsp. hoffmannii strain lacking the mrkA gene, encoding the major structural subunit, displayed a significantly reduced adherence capacity to a plastic surface and to Caco-2 cells, compared to the wild-type strain. This phenotype of reduced adherence capacity was not observed in the mutant strains complemented with the mrkA gene under the control of an inducible promoter. Therefore, these data suggest a role of the type 3 fimbria in the adherence capacity of E. hormaechei subsp. hoffmannii. A screening in E. hormaechei genomes contained in the NCBI RefSeq Assembly database indicated that the overall presence of the type 3 fimbria is uncommon (5.94-7.37%), although genes encoding the structure were detected in representatives of the five E. hormaechei subspecies. Exploration of complete genomes indicates that, in most of the cases, the mrkABCDF locus, encoding the type 3 fimbria, is located in plasmids. Furthermore, sequence types currently found in healthcare-associated infections were found to harbor genes encoding the type 3 fimbria, mainly ST145, ST78, ST118, ST168, ST66, ST93, and ST171. Thus, although the type 3 fimbria is not widespread among the species, it might be a determinant of fitness for a subset of E. hormaechei representatives.

Coexistence of a novel NDM-1-encoding MDR plasmid and an IMP-4-encoding IncN-IncU hybrid plasmid in a clinical isolate of Citrobacter freundii BC73

Objectives

To investigate the genetic characteristics and transmission mechanism of the NDM-1-, IMP-4-, and SHV-12-producing multidrug-resistant (MDR) clinical isolate, Citrobacter freundii BC73.

Methods

C. freundii BC73 was isolated from a urine specimen of a urological patient diagnosed with bladder cancer at a Chinese teaching hospital. Antimicrobial susceptibility testing was carried out using DL-120E susceptibility cards and DL-96A system. Whole genome sequencing (WGS) of the isolate was performed using the Illumina and Oxford Nanopore platforms to analyze the genetic context of drug resistance genes and plasmid characteristics. The phylogenetic tree was constructed and visualized by KSNP3.0 software and iTOL5.0 online database.

Results

C. freundii isolate BC73 co-carrying bla NDM-1, bla IMP-4 and bla SHV-12 were multidrug-resistant. bla NDM-1 and bla IMP-4 were located on a novel IncFIB-like plasmid, pCFBC1, and an IncN-IncU hybrid plasmid, pCFBC2, respectively. The transferability of bla NDM-1 and bla IMP-4 from C. freundii BC73 to E. coli J53 was successfully demonstrated. The genetic context of the bla NDM-1 and bla IMP-4 genes were ISCR27-groEL-∆groES-cutA-dsbD-trpF-ble MBL-bla NDM-1-∆ISAba125-IS3000 and intI1-bla IMP-4-Kl.pn.13-mobC-IS6100, respectively. Additionally, two extensive transposition units (MGE1 in pCFBC1, MGE2 in pCFBC2) were identified and numerous antimicrobial resistance genes were discovered on it.

Conclusion

To our knowledge, our study represents the first characterization of a ST22 C. freundii isolate co-harboring bla NDM-1, bla IMP-4, and bla SHV-12, obtained from a urine sample. The dissemination of this MDR isolate should be of close concern in future clinical surveillance.

Genomic Study of High-Risk Clones of Enterobacter hormaechei Collected from Tertiary Hospitals in the United Arab Emirates

Enterobacter hormaechei has emerged as a significant pathogen within healthcare settings due to its ability to develop multidrug resistance (MDR) and survive in hospital environments. This study presents a genome-based analysis of carbapenem-resistant Enterobacter hormaechei isolates from two major hospitals in the United Arab Emirates. Eight isolates were subjected to whole-genome sequencing (WGS), revealing extensive resistance profiles including the blaNDM-1, blaOXA-48, and blaVIM-4 genes. Notably, one isolate belonging to ST171 harbored dual carbapenemase genes, while five isolates exhibited colistin resistance without mcr genes. The presence of the type VI secretion system (T6SS), various adhesins, and virulence genes contributes to the virulence and competitive advantage of the pathogen. Additionally, our isolates (87.5%) possessed ampC β-lactamase genes, predominantly blaACT genes. The genomic context of blaNDM-1, surrounded by other resistance genes and mobile genetic elements, highlights the role of horizontal gene transfer (HGT) in the spread of resistance. Our findings highlight the need for rigorous surveillance, strategic antibiotic stewardship, and hospital-based WGS to manage and mitigate the spread of these highly resistant and virulent pathogens. Accurate identification and monitoring of Enterobacter cloacae complex (ECC) species and their resistance mechanisms are crucial for effective infection control and treatment strategies.

What's on a prophage: analysis of Salmonella spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions

The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 Salmonella spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse Salmonella. On average, prophages accounted for 3.7% (0.1%-8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the Salmonella genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. enterica genomes, 7.5% (median; range: 1.1%-47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host Salmonella cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of Salmonella.

IMPORTANCE

Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of Salmonella, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse Salmonella prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping Salmonella's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.

Genomic and immunocyte characterisation of bloodstream infection caused by Klebsiella pneumoniae

OBJECTIVES

The aim of this study was to evaluate the characteristics of immunocyte associated with bloodstream infection (BSI) caused by Klebsiella pneumoniae (Kpn).

METHODS

Patients with BSI-Kpn were included from 2015 to 2022 in our hospital. Immunocyte subpopulations of enrolled BSI-Kpn patients were tested on the same day of blood culture using multicolor flow cytometry analysis. Antibiotic susceptibility test was determined by agar dilution or broth dilution method. All included isolates were subjected to whole genome sequencing and comparative genomics analysis. Clinical and genetic data were integrated to investigate the risk factors associated with clinical outcome.

RESULTS

There were 173 patients with non-duplicate BSI-Kpn, including 81 carbapenem-resistant Kpn (CRKP), 30 extended-spectrum β-lactamases producing Kpn (ESBL-Kpn), 62 none CRKP or ESBL-Kpn (S-Kpn). Among 68 ST11-CRKP isolates, ST11-O2v1:KL64 was the most common serotypes cluster (77.9%, 53/68), followed by ST11-OL101: KL47 (13.2%, 9/68). Compared with CSKP group, subpopulations of immunocyte in patients with CRKP were significantly lower (P < 0.01). In patients with ST11-O2v1:KL64 BSI-Kpn, the level of cytotoxic T lymphocytes (CD3 + CD8 +) is the highest, while the B lymphocytes (CD3-CD19 +) was the least. In addition, the level of immunocyte in patients with Kpn co-harbored clpV-ybtQ-qacE were lower than that in patients with Kpn harbored one of clpV, ybtQ or qacE and without these three genes. Furthermore, co-existence of clpV-ybtQ-qacE was independently associated with a higher risk for 30-day mortality.

CONCLUSIONS

The results demonstrate that patients with BSI-CRKP, especially for ST11-O2v1:KL64, exhibit lower leukomonocyte counts. In addition, BSI-Kpn co-harbored clpV-ybtQ-qacE is correlated to higher 30-day mortality.

Genomic characterization of Staphylococcus aureus isolated from patients admitted to intensive care units of a tertiary care hospital: epidemiological risk of nasal carriage of virulent clone during admission

We conducted a molecular epidemiological study of Staphylococcus aureus using whole-genome sequence data and clinical data of isolates from nasal swabs of patients admitted to the intensive care unit (ICU) of Hiroshima University hospital. The relationship between isolate genotypes and virulence factors, particularly for isolates that caused infectious diseases during ICU admission was compared with those that did not. The nasal carriage rates of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in patients admitted to the ICU were 7.0% and 20.1%, respectively. The carriage rate of community-acquired (CA)-MRSA was 2.3%, accounting for 32.8% of all MRSA isolates. Whole-genome sequencing analysis of the MRSA isolates indicated that most, including CA-MRSA and healthcare-associated (HA)-MRSA, belonged to clonal complex (CC) 8 [sequence type (ST) 8] and SCCmec type IV. Furthermore, results for three disease foci (pneumonia, skin and soft tissue infection, and deep abscess) and the assessment of virulence factor genes associated with disease conditions [bacteremia, acute respiratory distress syndrome (ARDS), disseminated intravascular coagulopathy (DIC), and septic shock] suggested that nasal colonization of S. aureus clones could represent a risk for patients within the ICU. Particularly, MRSA/J and MSSA/J may be more likely to cause deep abscess infection; ST764 may cause ventilation-associated pneumonia, hospital-acquired pneumonia and subsequent bacteremia, and ARDS, and tst-1-positive isolates may cause DIC onset.IMPORTANCENasal colonization of MRSA in patients admitted to the intensive care unit (ICU) may predict the development of MRSA infections. However, no bacteriological data are available to perform risk assessments for Staphylococcus aureus infection onset. In this single-center 2-year genomic surveillance study, we analyzed all S. aureus isolates from nasal swabs of patients admitted to the ICU and those from the blood or lesions of in-patients who developed infectious diseases in the ICU. Furthermore, we identified the virulent clones responsible for causing infectious diseases in the ICU. Herein, we report several virulent clones present in the nares that are predictive of invasive infections. This information may facilitate the design of preemptive strategies to identify and eradicate virulent MRSA strains, reducing nosocomial infections within the ICU.

Genome sequence-based species classification of Enterobacter cloacae complex: a study among clinical isolates

Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, "E. xiangfangensis," "E. hoffmanii." While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates.

IMPORTANCE

Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.

In vitro, in planta, and comparative genomic analyses of Pseudomonas syringae pv. syringae strains of pepper (Capsicum annuum var. annuum)

Pseudomonas syringae pv. syringae (Pss) is an emerging phytopathogen that causes Pseudomonas leaf spot (PLS) disease in pepper plants. Pss can cause serious economic damage to pepper production, yet very little is known about the virulence factors carried by Pss that cause disease in pepper seedlings. In this study, Pss strains isolated from pepper plants showing PLS symptoms in Ohio between 2013 and 2021 (n = 16) showed varying degrees of virulence (Pss populations and disease symptoms on leaves) on 6-week-old pepper seedlings. In vitro studies assessing growth in nutrient-limited conditions, biofilm production, and motility also showed varying degrees of virulence, but in vitro and in planta variation in virulence between Pss strains did not correlate. Comparative whole-genome sequencing studies identified notable virulence genes including 30 biofilm genes, 87 motility genes, and 106 secretion system genes. Additionally, a total of 27 antimicrobial resistance genes were found. A multivariate correlation analysis and Scoary analysis based on variation in gene content (n = 812 variable genes) and single nucleotide polymorphisms within virulence genes identified no significant correlations with disease severity, likely due to our limited sample size. In summary, our study explored the virulence and antimicrobial gene content of Pss in pepper seedlings as a first step toward understanding the virulence and pathogenicity of Pss in pepper seedlings. Further studies with additional pepper Pss strains will facilitate defining genes in Pss that correlate with its virulence in pepper seedlings, which can facilitate the development of effective measures to control Pss in pepper and other related P. syringae pathovars.

IMPORTANCE

Pseudomonas leaf spot (PLS) caused by Pseudomonas syringae pv. syringae (Pss) causes significant losses to the pepper industry. Highly virulent Pss strains under optimal environmental conditions (cool-moderate temperatures, high moisture) can cause severe necrotic lesions on pepper leaves that consequently can decrease pepper yield if the disease persists. Hence, it is important to understand the virulence mechanisms of Pss to be able to effectively control PLS in peppers. In our study, in vitro, in planta, and whole-genome sequence analyses were conducted to better understand the virulence and pathogenicity characteristics of Pss strains in peppers. Our findings fill a knowledge gap regarding potential virulence and pathogenicity characteristics of Pss in peppers, including virulence and antimicrobial gene content. Our study helps pave a path to further identify the role of specific virulence genes in causing disease in peppers, which can have implications in developing strategies to effectively control PLS in peppers.

Multidrug-resistant Klebsiella pneumoniae clinical isolates producing NDM- and OXA-type carbapenemase in Nepal

OBJECTIVES

The emergence of multidrug-resistant Klebsiella pneumoniae has become a serious problem in medical settings worldwide.

METHODS

A total of 46 isolates of multidrug-resistant K. pneumoniae were obtained from 2 hospitals in Nepal from October 2018 to April 2019.

RESULTS

Most of these isolates were highly resistant to carbapenems, aminoglycosides, and fluoroquinolones with the minimum inhibitory concentrations (MICs) of more than 64 µg/mL. These isolates harboured carbapenemase-encoding genes, including blaNDM-1, blaNDM-5, blaOXA-181 and blaOXA-232, and 16S rRNA methyltransferase-encoding genes, including armA, rmtB, rmtC, and rmtF. Multilocus sequence typing revealed that 44 of 46 isolates were high-risk clones such as ST11 (2%), ST14 (4%), ST15 (11%), ST37 (2%), ST101 (2%), ST147 (28%), ST231 (13%), ST340 (4%), and ST395 (28%). In particular, ST395 isolates, which spread across medical settings in Nepal, co-harboured blaNDM-5 and rmtB on IncFII plasmids and co-harboured blaOXA-181/-232 and rmtF on ColKP3 plasmids. Several isolates harboured blaOXA-181 or blaNDM-5 on their chromosomes and multi-copies of blaNDM-1 or genes encoding 16S rRNA methyltransferases on their plasmids.

CONCLUSIONS

The presented study demonstrates that the high-risk clones of multidrug-resistant K. pneumoniae spread in a clonal manner across hospitals in Nepal.

First whole genome sequencing data of a Mycobacterium tuberculosis STB-T1A strain isolated from a spinal tuberculosis patient in Sabah, Malaysia

Spinal tuberculosis, also referred to as Pott's disease, presents a significant risk of severe paralysis if not promptly detected and treated, owing to complications such as spinal cord compression and deformity. This article presents the genetic analysis of a Mycobacterium tuberculosis STB-T1A strain, isolated from the spine of a 29-year-old female diagnosed with spinal tuberculosis. Genomic DNA was extracted from pure culture and subjected to sequencing using the Illumina NovaSeq 6000 sequencing system. The genome of the M. tuberculosis STB-T1A strain spans 4,367,616 base pairs with a G+C content of 65.56 % and 4174 protein-coding genes. Comparative genomic analysis, conducted via single nucleotide polymorphism (SNP)-based phylogenetic analysis using the Maximum Likelihood method, revealed that the strain falls within the Indo-Oceanic lineage (Lineage 1). It clusters with the M. tuberculosis 43-16836 strain, which was isolated from the cerebrospinal fluid of a patient with tuberculous meningitis in Thailand. The complete genome sequence has been deposited at the National Center for Biotechnology Information (NCBI) GenBank database with the accession number JBBMVZ000000000.