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Heliyon Mar 2024The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and...
The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and the environment. In Ecuador, previous research indicates a high prevalence of antimicrobial resistant (AMR) bacteria in surface waters affected by human activities, including irrigation channels. In this study, we analyzed sediment samples collected from an irrigation channel utilized for agricultural purposes in northern Ecuador, using microbiological techniques and whole-genome sequencing (WGS). Our investigation revealed the first documented occurrence of in Ecuador and the initial report of environmental ST2070. Furthermore, we identified the coexistence of OXA-10-type class D β-lactamase and KPC-2-type class A β-lactamase in the isolate (UTA41), representing the first report of such a phenomenon in this species. Additionally, we detected various antibiotic resistance genes in the UTA41 isolate, including , , , , , and , as well as virulence genes such as bacterial efflux pump and siderophore biosynthesis genes. We also identified two intact prophage regions (Entero_186 and Klebsi_phiKO2) in the isolate. Our study presents the first evidence of isolate containing two carbapenemase-encoding genes in environmental samples from Latin America. This finding indicates the potential spread of critical-priority bacteria in water samples originating from anthropogenic sources, such as urban wastewater discharges and livestock facilities.
PubMed: 38449644
DOI: 10.1016/j.heliyon.2024.e26379 -
Microbiology Spectrum Apr 2024" Liberibacter asiaticus" (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known...
Integrated bacterial transcriptome and host metabolome analysis reveals insights into " Liberibacter asiaticus" population dynamics in the fruit pith of three citrus cultivars with different tolerance.
" Liberibacter asiaticus" (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known about the biological processes and phytochemical substances that are vital for CLas colonization and growth in fruit pith. In this study, CLas-infected fruit pith of three citrus cultivars ("Shatangju" mandarin, "Guanxi" pomelo, and "Shatian" pomelo) exhibiting different tolerance to CLas were collected and used for dual RNA-Seq and untargeted metabolome analysis. Comparative transcriptome analysis found that the activation of the CLas noncyclic TCA pathway and pathogenic-related effectors could contribute to the colonization and growth of CLas in fruit pith. The pre-established Type 2 prophage in the CLas genome and the induction of its CRISPR/ system could enhance the phage resistance of CLas and, in turn, facilitate CLas population growth in fruit pith. CLas infection caused the accumulation of amino acids that were correlated with tolerance to CLas. The accumulation of most sugars and organic acids in CLas-infected fruit pith, which could be due to the phloem blockage caused by CLas infection, was thought to be beneficial for CLas growth in localized phloem tissue. The higher levels of flavonoids and terpenoids in the fruit pith of CLas-tolerant cultivars, particularly those known for their antimicrobial properties, could hinder the growth of CLas. This study advances our understanding of CLas multiplication in fruit pith and offers novel insight into metabolites that could be responsible for tolerance to CLas or essential to CLas population growth.IMPORTANCECitrus Huanglongbing (HLB, also called citrus greening disease) is a highly destructive disease currently threatening citrus production worldwide. HLB is caused by an unculturable bacterial pathogen, " Liberibacter asiaticus" (CLas). However, the mechanism of CLas colonization and growth in citrus hosts is poorly understood. In this study, we utilized the fruit pith tissue, which was able to maintain the CLas at a high abundance, as the materials for dual RNA-Seq and untargeted metabolome analysis, aiming to reveal the biological processes and phytochemical substances that are vital for CLas colonization and growth. We provided a genome-wide CLas transcriptome landscape in the fruit pith of three citrus cultivars with different tolerance and identified the important genes/pathways that contribute to CLas colonization and growth in the fruit pith. Metabolome profiling identified the key metabolites, which were mainly affected by CLas infection and influenced the population dynamic of CLas in fruit pith.
Topics: Citrus; Rhizobiaceae; Transcriptome; Fruit; Metabolome; Population Dynamics; Phytochemicals; Plant Diseases; Liberibacter
PubMed: 38440971
DOI: 10.1128/spectrum.04052-23 -
Frontiers in Microbiology 2024is an important opportunistic pathogen with the potential to develop resistance against last-line antibiotics, such as carbapenems, limiting the treatment options....
is an important opportunistic pathogen with the potential to develop resistance against last-line antibiotics, such as carbapenems, limiting the treatment options. Here, we investigated the antibiotic resistance profiles of 10 strains isolated from patient samples in the intensive-care unit of a Brazilian tertiary hospital using conventional PCR and a comprehensive genomic characterization of a specific strain (CRK317) carrying both the and genes simultaneously. All isolates were completely resistant to β-lactam antibiotics, including ertapenem, imipenem, and meropenem with differencing levels of resistance to aminoglycosides, quinolones, and tigecycline also observed. Half of the strains studied were classified as multidrug-resistant. The carbapenemase-producing isolates carried many genes of interest including: β-lactams (, , , group, group and in 20-80% of the strains), aminoglycoside resistance genes [ and (, 70 and 80%], a fluoroquinolone resistance gene (, 80%), a sulfonamide resistance gene (, 80%) and a multidrug efflux system transporter (, 70%) while all strains carried the efflux pumps (subunit A) and . Moreover, we performed a comprehensive genomic characterization of a specific strain (CRK317) carrying both the and genes simultaneously. The draft genome assembly of the CRK317 had a total length of 5,462,831 bp and a GC content of 54.8%. The chromosome was found to contain many essential genes. analysis identified many genes associated with resistance phenotypes, including β-lactamases (, , , , , ), the bleomycin resistance gene (), an erythromycin resistance methylase (), aminoglycoside-modifying enzymes [-, -, ], a sulfonamide resistance enzyme (), a chloramphenicol acetyltransferase (like), a plasmid-mediated quinolone resistance protein (), a glutathione transferase (), PEtN transferases (, ) and a glycosyltransferase (). We also detected 22 genomic islands, eight families of insertion sequences, two putative integrative and conjugative elements with a type IV secretion system, and eight prophage regions. This suggests the significant involvement of these genetic structures in the dissemination of antibiotic resistance. The results of our study show that the emergence of carbapenemase-producing , co-harboring and , is a worrying phenomenon which highlights the importance of developing strategies to detect, prevent, and control the spread of these microorganisms.
PubMed: 38426065
DOI: 10.3389/fmicb.2024.1352851 -
BioRxiv : the Preprint Server For... Feb 2024Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is...
Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.
PubMed: 38410456
DOI: 10.1101/2024.02.09.579689 -
PeerJ 2024Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with... (Review)
Review
Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.
Topics: Bacteriophages; Microbiota; Metagenome; Prophages; Mouth; Bacteria
PubMed: 38406289
DOI: 10.7717/peerj.16947 -
BioRxiv : the Preprint Server For... Feb 2024Endolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as...
Endolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as highly specific lytic proteins with a low chance of bacterial resistance. The diversity in lysin sequences and domain organization can be staggering. analysis of bacteriophage and prophage genomes can help identify endolysins exhibiting unique features and high antibacterial activity, hence feeding the pipeline of narrow-spectrum protein antibiotics. Mycobacteriophage lysis cassettes mostly have two lytic enzymes, LysinA and LysinB. The enzyme LysinA targets peptidoglycan in the cell wall and possesses a modular architecture. LysinB typically contains a single domain and acts upon the mycolyl ester linkages in mycolyl-arabinogalactan-peptidoglycan (Payne et al., 2010). This study aimed to find novel LysinBs against . After a detailed characterization of lysis cassettes from three prophages, we chose to work on a LysinB (hereafter described as LysinB_MF) found in an incomplete prophage (phiE1336, 9.4 kb in strain E1336). LysinB_MF showed low sequence similarity with any other endolysins in the database and formed a separate clade on phylogenetic analysis. LysinB_MF's structure, extracted from the AlphaFold Protein Structure Database, demonstrated a modular architecture with two structurally distinct domains: a peptidoglycan-binding domain (PGBD) at the N-terminal and the characteristic alpha/beta hydrolase domain connected via a linker peptide. We found the alpha/beta hydrolase domain, which is the enzyme-active domain (EAD), contains the conserved Ser-Asp-His catalytic triad with a tunnel-like topology and forms intermolecular hydrogen bonds. The PGBD shows structural similarity to the cell-wall binding domain of an amidase from , hinting at its acquisition due to domain mobility. Our electrostatic potential analysis suggested that PGBD might be essential to the enzyme activity. This was experimentally validated by generating a truncated version of the enzyme, which demonstrated about six-fold decreased activity compared to its native form. The antimycobacterial activity of this enzyme was also compromised in its absence. Based on our analysis, PGBD emerged as an integral constituent of enzymes with diverse functional properties and is predicted to be a conserved cross-kingdom. Overall, this study highlights the importance of mining mycobacterial prophages as a novel endolysin source. It also provides unique insights into the diverse architecture of mycobacteriophage-encoded endolysins and the importance of functional domains for their catalytic activities.
PubMed: 38405724
DOI: 10.1101/2024.02.15.580446 -
Microorganisms Feb 2024In recent years, subsp. serovar Mbandaka ( Mbandaka) has been increasingly isolated from laying hens and shell eggs around the world. Moreover, this serovar has been...
In recent years, subsp. serovar Mbandaka ( Mbandaka) has been increasingly isolated from laying hens and shell eggs around the world. Moreover, this serovar has been identified as the causative agent of several salmonellosis outbreaks in humans. Surprisingly, little is known about the characteristics of this emerging serovar, and therefore, we investigated antimicrobial resistance, virulence, and prophage genes of six selected Brazilian strains of Mbandaka using Whole Genome Sequencing (WGS). Multi-locus sequence typing revealed that the tested strains belong to Sequence Type 413 (ST413), which has been linked to recent multi-country salmonellosis outbreaks in Europe. A total of nine resistance genes were detected, and the most frequent ones were , , , , , and . A point mutation in ParC at the 57th position (threonine → serine) associated with quinolone resistance was present in all investigated genomes. A 112,960 bp IncHI2A plasmid was mapped in 4/6 strains. This plasmid harboured tetracycline (ACDR) and mercury () resistance genes, genes contributing to conjugative transfer, and genes involved in plasmid maintenance. Most strains (four/six) carried genomic island 1 (SGI1). All Mbandaka genomes carried seven pathogenicity islands (SPIs) involved in intracellular survival and virulence: SPIs 1-5, 9, and C63PI. The virulence genes , , , , (two/six), and (one/six) were absent in some of the genomes; conversely, , , and were present in all of them. Five bacteriophage sequences (with homology to phage phiV10, phage Fels-2, phage HK542, phage ST64T, phage SW9) were identified, with protein counts between 31 and 54, genome lengths of 24.7 bp and 47.7 bp, and average GC content of 51.25%. In the phylogenetic analysis, the genomes of strains isolated from poultry in Brazil clustered into well-supported clades with a heterogeneous distribution, primarily associated with strains isolated from humans and food. The phylogenetic relationship of Brazilian . Mbandaka suggests the presence of strains with high epidemiological significance and the potential to be linked to foodborne outbreaks. Overall, our results show that isolated strains of Mbandaka are multidrug-resistant and encode a rather conserved virulence machinery, which is an epidemiological hallmark of strains that have successfully disseminated both regionally and globally.
PubMed: 38399716
DOI: 10.3390/microorganisms12020312 -
Microorganisms Jan 2024Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function,...
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
PubMed: 38399658
DOI: 10.3390/microorganisms12020255 -
Comparative Genome Analysis of Two Serotype 8 Strains Identifies Two New Virulence-Associated Genes.Animals : An Open Access Journal From... Feb 2024is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, serotype 8 has distinctive...
is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, serotype 8 has distinctive characteristics such as a high detection rate and causing multi-host infection. There is no complete genome of serotype 8 strains so far. In this study, the complete genome of two serotype 8 strains, virulent strain 2018WUSS151 and non-virulent strain WUSS030, were sequenced. Comparative genomic analysis showed that the homology of the two genomes reaches 99.68%, and the main difference is the distinctive prophages. There are 83 genes unique to virulent strain 2018WUSS151, including three putative virulence-associated genes (PVGs). Two PVGs, and are passenger genes in ISSsu2 family transposons that are able to form circular DNA intermediates during transposition, indicating the possibility of horizontal transmission among strains. The deletion mutant of PVGs or attenuated the virulence of serotype 2 virulent SC070731 in a mouse infection model, confirming their role in virulence. These findings contribute to clarifying the genomic characterization of serotype 8 and pathogenesis.
PubMed: 38396540
DOI: 10.3390/ani14040572 -
Toxins Feb 2024Cattle are the primary reservoir for STEC O157, with some shedding >10 CFU/g in feces, a phenomenon known as super-shedding (SS). The mechanism(s) responsible for SS are...
Cattle are the primary reservoir for STEC O157, with some shedding >10 CFU/g in feces, a phenomenon known as super-shedding (SS). The mechanism(s) responsible for SS are not understood but have been attributed to the environment, host, and pathogen. This study aimed to compare genetic characteristics of STEC O157 strains from cattle in the same commercial feedlot pens with SS or low-shedding (LS) status. Strains from SS (n = 35) and LS (n = 28) collected from 11 pens in three feedlots were analyzed for virulence genes, Shiga toxin-carrying bacteriophage insertion sites, and phylogenetic relationships. In silico analysis showed limited variation regarding virulence gene profiles. -encoding prophage insertion sites and for and , respectively, were all occupied, but two isolates had fragments of the -carrying phage in and loci without and . All strains screened for lineage-specific polymorphism assay (LSPA-6) were 111111, lineage I. Of the isolates, 61 and 2 were clades 1 and 8, respectively. Phylogenetic analysis revealed that pens with more than one SS had multiple distantly related clusters of SS and LS isolates. Although virulence genes and lineage were largely similar within and across feedlots, multiple genetic origins of strains within a single feedlot pen illustrate challenges for on-farm control of STEC.
Topics: Animals; Cattle; Escherichia coli O157; Phylogeny; Shiga Toxin; Virulence; Cattle Diseases; Bacteriophages; Escherichia coli Infections; Shiga-Toxigenic Escherichia coli; Feces
PubMed: 38393164
DOI: 10.3390/toxins16020086