Fig 1 - available via license: Creative Commons Attribution-NonCommercial 4.0 International
Content may be subject to copyright.
Schematic circular representation of complete genome sequences of KPC-2-producing A. hydrophila GSH8-2. Short paired-end whole-genome sequencing was performed using an Illumina NextSeq 500 platform with a 300-cycle NextSeq 500 Reagent Kit v2 (2 × 150-mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long-read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al., 2017), minimap version 0.2-r124 (Li, 2016), racon version 1.1.0 (Vaser et al., 2017) and circulator version 1.5.3 (Hunt et al., 2015). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al., 2014). Annotation was performed in Prokka version 1.11 (Seemann, 2014), InterPro v49.0 (Finn et al., 2017) and NCBI-BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al., 2010). AMR genes were identified by homology searching against the ResFinder database (Zankari et al., 2012). The class 1 integron was assigned in the INTEGRALL database (http://integrall.bio.ua.pt/) (Moura et al., 2009). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al., 2011). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5-7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1); slot 8, prophage; slot 9, notable ARGs or ARG-related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
Source publication
Aeromonas hydrophila and Aeromonas caviae adapt to saline water environments, and are the most predominant Aeromonas species isolated from estuaries. Here, we isolated antimicrobial‐resistant (AMR) Aeromonas strains (A. hydrophila GSH8‐2 and A. caviae GSH8M‐1) carrying the carabapenemase blaKPC‐2 gene from a wastewater treatment plant (WWTP) efflue...
Contexts in source publication
Context 1
... information regarding the complete chromosome and plasmid sequences for Aeromonas isolates GSH8-2 ( Fig. 1) and GSH8M-1 ( Fig. 2) are shown in Table 2. Multilocus sequence typing (MLST) based on the genomic data assigned both strains to novel sequence types (ST), classifying GSH8-2 and GSH8M-1 as ST558 and ST13 respectively (Table ...
Context 2
... core genome of the A. hydrophila strains constituted 48.95% of the total genome based on 491 764 SNVs (Supporting Information Fig. S1). The phylogeny placed GSH8-2 in one of multiple clusters, unrelated to previously identified clinical and environmental isolates (Supporting Information Fig. S1). ...
Context 3
... core genome of the A. hydrophila strains constituted 48.95% of the total genome based on 491 764 SNVs (Supporting Information Fig. S1). The phylogeny placed GSH8-2 in one of multiple clusters, unrelated to previously identified clinical and environmental isolates (Supporting Information Fig. S1). No pathogenic fish clonal cluster was observed among isolates from the United States or China. ...
Context 4
... hydrophila GSH8-2. Aeromonas hydrophila GSH8-2 harbours a 39.1-kb IncP-6 replicon plasmid, pGSH8-2, carrying bla KPC-2 (Table 2 and Fig. 1). In addition, the strain was found to carry multiple β-lactamase genes [cepS (FOX/MOX family class C β-lactamase, 95% identity), cphA2 (CphA family subclass B2 metallo-β-lactamase, 98% identity), bla OXA-726 (class D β-lactamase)] on its chromosome. These are intrinsic ARGs in A. hydrophila ...
Context 5
... it also carried chromosomal copies of macrolide 2 0 -phosphotransferase [mph(A)] and tetracycline efflux MFS transporter [tet(E)], which were found within a potential prophage (2805-2905 kb, shown in Fig. 1). BLASTatlas analysis suggested that these horizontally acquired phage elements are GSH8-2 strain-specific, and are similar to elements from the ATCC 7966 type strain WCHAH045096 (isolated from sewage in China in 2015, bla KPC-2 positive) and ZYAH75 (isolated from a human wound in China in 2015) (slots 5-7 in Fig. 1). The detection of ...
Context 6
... (2805-2905 kb, shown in Fig. 1). BLASTatlas analysis suggested that these horizontally acquired phage elements are GSH8-2 strain-specific, and are similar to elements from the ATCC 7966 type strain WCHAH045096 (isolated from sewage in China in 2015, bla KPC-2 positive) and ZYAH75 (isolated from a human wound in China in 2015) (slots 5-7 in Fig. 1). The detection of mph(A) and tet(E) on a prophage in the chromosome of GSH8-2 could contribute to the reduced susceptibility to azithromycin and tetracycline respectively (Table ...
Context 7
... of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al., 2011). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5-7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1); slot 8, prophage; slot 9, notable ARGs or ARG-related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour. ...
Context 8
... pGSH8M-1-2 was found to carry an additional elements, the first of which is a Tn3 family transposon (inverted repeats at nt 27 425-34 564: GGGGATGTAAGCCGGAACCCCAGAAATTTCCGTCAC-CCTAG -CTGGGCTGACGGAAATTTCTGGGATTCCGG CGTACAACCCC), and the second is the IS26-mediated composite transposon carrying mph(A) family macrolide 2 0 -phosphotransferase (Fig. 1B). A Blastp homology search indicated that this Mph(A) shares 100% identity with those found in 39 E. coli, 14 Klebsiella pneumoniae, 1 Salmonella Typhimurium and 1 Shigella flexneri strains. In addition, IS26 is a ubiquitous IS in Enterobacteriaceae, indicating that mph(A) acquisition could take place through IS26-mediated recombination ...
Context 9
... characterize the single effect of each KPC-2-positive plasmid (pGSH8-2 or pGSH8M-1-2), electro-transformants carrying the KPC-2-plasmid under an E. coli DH10B T1 R . Genes for bla KPC-2 , ARGs, transposase, methionine sulfoxide reductase/oxidoreductase, and others are highlighted with red, magenta, blue, green, and grey, respectively, as shown in Fig. 1. strain background were obtained (see detailed experimental methods in the Supporting Information), and the MIC values were determined (Table 1). These electro-transformants exhibited significantly reduced susceptibility to all tested β-lactams but not to other antimicrobials except for azithromycin. pGSH8M-1-2 carries mph(A) (Fig. 2), ...
Context 10
... proteins, two 3-ketoacyl-CoA thiolases and other oxidoreductases (green highlighted ORFs in Fig. 2). In total, four sets of redundant MsrA/B were identified in A. caviae GSH8M-1 (one on its chromosome, two on pGSH8M-1-1 and one on pGSH8M-1-2). Likewise, A. hydrophila GSH8-2 plasmid pGSH8M-1-2 also carries GST and MsrA/B reductase (Fig. 1). Such multiple sulfo-related reductase enzymes might contribute to adaptation to oxidative stresses encountered in WWTP environments or during antiseptic ...
Citations
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacterae-mia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii. In this study, we analysed the pan-genome of 233 A. veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii. Single molecule real-time sequencing was applied to identify the motif methyl-ated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.
... and Aeromonas spp. isolates were recovered from WWTPs, hospital sewage, and river and seawater samples in the USA, Brazil and China [118][119][120]122,123,125]. In addition, the GES-31 carbapenemase was first described in an Aeromonas punctata isolate recovered from a Brazilian river [121] de Araujo et al. and Xu et al. have reported the isolation of KPC-2-producing Aeromonas hydrophila from rivers in Brazil and China, respectively [121,127]. ...
Medicinal activities carried out within hospitals lead to a high consumption of antibiotics and subsequently result in a high excretion rate of antibiotic residues. These antibiotics consumed in human medicine are not fully absorbed by the body and are often discharged into the environment as biological waste from infected human patients. The significant water consumption in hospitals and the pharmaceutical impact on wastewater from healthcare facilities facilitate the emergence and spread of antibiotic-resistant bacteria and antibiotic-resistant genes in the environment. Hospital effluents could be doubly involved in the dissemination of antibiotic molecules and multidrug-resistant bacteria in various ecosystems. The objective of this study is to characterize hospital effluents by assessing antibiotic concentrations and the diversity of antibiotic-resistant bacteria in these hospital wastewaters and within the environment (aquatic environments; rivers), as well as to inventory the bacteria present and those carrying antibiotic resistance in both hospital wastewater and the environment.
... isolates were recovered from WWTPs, hospital sewage, and river and seawater samples in the USA, Brazil and China [118][119][120]122,123,125]. In addition, the GES-31 carbapenemase was first described in an Aeromonas punctata isolate recovered from a Brazilian river [121] de Araujo et al. and Xu et al. have reported the isolation of KPC-2-producing Aeromonas hydrophila from rivers in Brazil and China, respectively [121,127]. Recently, KPC-2-producing A. hydrophilia and Aeromonas caviae were recovered from river water and WWTP effluents [124,126]. ...
Medicinal activities carried out within hospitals lead to a high consumption of antibiotics and subsequently result in a high excretion rate of antibiotic residues. These antibiotics consumed in human medicine are not fully absorbed by the body and are often discharged into the environment as biological waste from infected human patients. The significant water consumption in hospitals and the pharmaceutical impact on wastewater from healthcare facilities facilitate the emergence and spread of antibiotic-resistant bacteria and antibiotic-resistant genes in the environment. Hospital effluents could be doubly involved in the dissemination of antibiotic molecules and multidrug-resistant bacteria in various ecosystems. The objective of this study is to characterize hospital effluents by assessing antibiotic concentrations and the diversity of antibiotic-resistant bacteria in these hospital wastewaters and within the environment (aquatic environments, rivers), as well as to inventory the bacteria present and those carrying antibiotic resistance in both hospital wastewater and the environment.
... In a previous investigation, bla KPC2 was initially identified in a WWTP in Japan, despite its absence in clinical isolates. They proposed that the surveillance of AMR through WWTP could aid identifying the continuous dissemination of AMR in the environment and potentially serve as an early indicator of its spread in clinical settings and communities [38,39]. In another study conducted in Jeddah city, Saudi Arabia, researchers identified the presence of the carbapenemase gene bla NDM-1 in an E. coli strain (ST101) in wastewater for the first time. ...
Wastewater treatment plants (WWTPs) are recognized as important niches of antibiotic-resistant bacteria that can be easily spread to the environment. In this study, we collected wastewater samples from the WWTP of A Coruña (NW Spain) from April 2020 to February 2022 to evaluate the presence of Gram-negative bacteria harboring carbapenemase genes. Bacteria isolated from wastewater were classified and their antimicrobial profiles were determined. In total, 252 Gram-negative bacteria carrying various carbapenemase genes were described. Whole-genome sequencing was conducted on 55 selected carbapenemase producing isolates using Oxford Nanopore technology. This study revealed the presence of a significant population of bacteria carrying carbapenemase genes in WWTP, which constitutes a public health problem due to their risk of dissemination to the environment. This emphasizes the usefulness of WWTP monitoring for combating antibiotic resistance. Data revealed the presence of different types of sequences harboring carbapenemase genes, such as blaKPC-2, blaGES-5, blaGES-6, blaIMP-11, blaIMP-28, blaOXA-24, blaOXA-48, blaOXA-58, blaOXA-217, and blaVIM-2. Importantly, the presence of the blaKPC-2 gene in wastewater, several months before any clinical case was detected in University Hospital of A Coruña, suggests that wastewater-based epidemiology can be used as an early warning system for the surveillance of antibiotic-resistant bacteria.
... Tn6840-related IMEs comprise four IMEs, namely Tn6840 from cWCHAH045096, Tn6841 from c628330 (a novel Aeromonas strain identified in this study), Tn6842 from c17ISAe, and Tn6843 from cGSH8-2 ( Figure 5). Tn6840, Tn6842, and Tn6843 sequences were sourced from the GenBank [39,40]. The lengths of these IMEs vary from 15,792 bp to 78,805 bp ( Table 2). ...
The emergence of antibiotic-resistant Aeromonas strains in clinical settings has presented an escalating burden on human and public health. The dissemination of antibiotic resistance in Aeromonas is predominantly facilitated by chromosome-borne accessory genetic elements, although the existing literature on this subject remains limited. Hence, the primary objective of this study is to comprehensively investigate the genomic characteristics of chromosome-borne accessory genetic elements in Aeromonas. Moreover, the study aims to uncover novel genetic environments associated with antibiotic resistance on these elements. Aeromonas were screened from nonduplicated strains collected from two tertiary hospitals in China. Complete sequencing and population genetics analysis were performed. BLAST analysis was employed to identify related elements. All newly identified elements were subjected to detailed sequence annotation, dissection, and comparison. We identified and newly designated 19 chromosomal elements, including 18 integrative and mobilizable elements (IMEs) that could be classified into four categories: Tn6737-related, Tn6836-related, Tn6840-related, and Tn6844a-related IMEs. Each class exhibited a distinct pattern in the types of resistance genes carried by the IMEs. Several novel antibiotic resistance genetic environments were uncovered in these elements. Notably, we report the first identification of the blaOXA-10 gene and blaVEB-1 gene in clinical A. veronii genome, the first presence of a tetA(E)–tetR(E) resistance gene environment within the backbone region in IMEs, and a new mcr-3.15 resistance gene environment. The implications of these findings are substantial, as they provide new insights into the evolution, structure, and dissemination of chromosomal-borne accessory elements.
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
... The genomes of 19 other A. veronii strains were obtained from the NCBI Genome database using the NCBI Datasets command-line tool with the parameters 'datasets download genome taxon "aeromonas veronii" --assembly-level complete_genome --assemblysource refseq --dehydrated' in November 2021. RefSeq assembly accession numbers are provided as follows: GCF_000204115.1 [43], GCF_000464515.2 [44], GCF_001593245.1, GCF_002803925.1, GCF_002803945.1, GCF_003491365.1, GCF_003722175.1, GCF_008693705.1 [45], GCF_009755745.1, GCF_009834065.1, GCF_011045495.1, GCF_013415825.1, GCF_014168715.1 [46], GCF_014168995.1 [46], GCF_014169795.1 [46], GCF_014169835.1 [46], GCF_014169875.1 [46], GCF_017310275.1 and GCF_020172765.2 [47]. To ensure the timeliness and comprehensiveness of the data, we also removed the restriction of assembly level and downloaded 232 A. veronii genomes on 28 July 2023. ...
Aeromonas veronii is an opportunistic pathogen that affects both fish and mammals, including humans, leading to bacteraemia, sepsis, meningitis and even death. The increasing virulence and drug resistance of A. veronii are of significant concern and pose a severe risk to public safety. The Type I restriction-modification (RM) system, which functions as a bacterial defence mechanism, can influence gene expression through DNA methylation. However, little research has been conducted to explore its origin, evolutionary path, and relationship to virulence and drug resistance in A. veronii . In this study, we analysed the pan-genome of 233 A . veronii strains, and the results indicated that it was 'open', meaning that A. veronii has acquired additional genes from other species. This suggested that A. veronii had the potential to adapt and evolve rapidly, which might have contributed to its drug resistance. One Type I methyltransferase (MTase) and two complete Type I RM systems were identified, namely AveC4I, AveC4II and AveC4III in A. veronii strain C4, respectively. Notably, AveC4I was exclusive to A. veronii C4. Phylogenetic analysis revealed that AveC4I was derived from horizontal gene transfer from Thiocystis violascens and exchanged genes with the human pathogen Comamonas kerstersii . Single molecule real-time sequencing was applied to identify the motif methylated by AveC4I, which was unique and not recognized by any reported MTases in the REBASE database. We also annotated the functions and pathways of the genes containing the motif, revealing that AveC4I may control drug resistance in A. veronii C4. Our findings provide new insight on the mechanisms underlying drug resistance in pathogenic bacteria. By identifying the specific genes and pathways affected by AveC4I, this study may aid in the development of new therapeutic approaches to combat A. veronii infections.
... In addition, the xHYB method could be limited to detecting only ARG target genes; therefore, the potential ARB organism should be investigated by conducting either conventional mDNA-Seq or bacterial isolation for antimicrobial agent selection. [13][14][15] This study demonstrated that mDNA-seq with the multiplex xHYB method could be a suitable evaluation standard for deep-dive detection to monitor increasing ARB trends in WWTP-specific areas, and could aid in monitoring potential ongoing dissemination in the overall community. Even with proper treatment, urban WWTP effluents may increase the AMR burden, with a high frequency of ARGs acquired in the environment. ...
Metagenomic sequencing (mDNA-seq) is one of the best approaches to address antimicrobial resistance (AMR) issues and characterize AMR genes (ARGs) and their host bacteria (ARB); however, the sensitivity provided is insufficient for the overall detection in wastewater treatment plant (WWTP) effluents because the effluent is well treated. This study investigated the multiplex hybrid capture (xHYB) method (QIAseq × HYB AMR Panel) and its potential to increase AMR assessment sensitivity. The mDNA-Seq analysis suggested that the WWTP effluents had an average of 104 reads per kilobase of gene per million (RPKM) for the detection of all targeted ARGs, whereas xHYB significantly improved detection at 601,576 RPKM, indicating an average 5,805-fold increase in sensitivity. For instance, sul1 was detected at 15 and 114,229 RPKM using mDNA-seq and xHYB, respectively. The blaCTX-M, blaKPC, and mcr gene variants were not detected by mDNA-Seq but were detected by xHYB at 67, 20, and 1,010 RPKM, respectively. This study demonstrates that the multiplex xHYB method could be a suitable evaluation standard with high sensitivity and specificity for deep-dive detection, highlighting a broader illustration of ongoing dissemination in the entire community.
... The RPKM value of bla IMP in this study was higher than that of bla CTX-M , while fewer patients had MBL producers than ESBL producers. This finding may be attributed to the fact that many MBL producers, such as P. aeruginosa, Acinetobacter spp., and Aeromonas spp., are opportunistic pathogens with wide environmental distribution, including in wastewater, and are not part of the human flora, unlike Enterobacterales, to which ESBL producers mainly belong (15,16). Contamination of wastewater systems with ARB indicates a potential transmission risk to inpatients (17). ...
Wastewater can be useful in monitoring the spread of antimicrobial resistance (AMR) within a hospital. The abundance of antibiotic resistance genes (ARGs) in hospital effluent was assessed using metagenomic sequencing (mDNA-seq) and hybrid capture (xHYB). mDNA-seq analysis and subsequent xHYB targeted enrichment were conducted on two effluent samples per month from November 2018 to May 2021. Reads per kilobase per million (RPKM) values were calculated for all 1,272 ARGs in the constructed database. The monthly numbers of patients with presumed extended-spectrum β-lactamase (ESBL)-producing and metallo-β-lactamase (MBL)-producing bacteria, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE) were compared with the monthly RPKM values of bla CTX-M , bla IMP , mecA , vanA , and vanB by xHYB. The average RPKM value for all ARGs detected by xHYB was significantly higher than that of mDNA-seq (665, 225, and 328, respectively, and P < 0.05). The average number of patients with ESBL producers and RPKM values of bla CTX-M-1 genes in 2020 were significantly higher than that in 2019 (17 and 13 patients per month and 921 vs 232 per month, respectively, both P < 0.05). The average numbers of patients with MBL-producers, MRSA, and VRE were 1, 28, and 0 per month, respectively, while the average RPKM values of bla IMP , mecA , vanA , and vanB were 6,163, 6, 0, and 126 per month, respectively. Monitoring ARGs in hospital effluent using xHYB was found to be more useful than conventional mDNA-seq in detecting ARGs including bla CTX-M , bla IMP, and vanB , which are important for infection control.
IMPORTANCE
Environmental ARGs play a crucial role in the emergence and spread of AMR that constitutes a significant global health threat. One major source of ARGs is effluent from healthcare facilities, where patients are frequently administered antimicrobials. Culture-independent methods, including metagenomics, can detect environmental ARGs carried by non-culturable bacteria and extracellular ARGs. mDNA-seq is one of the most comprehensive methods for environmental ARG surveillance; however, its sensitivity is insufficient for wastewater surveillance. This study demonstrates that xHYB appropriately monitors ARGs in hospital effluent for sensitive identification of nosocomial AMR dissemination. Correlations were observed between the numbers of inpatients with antibiotic-resistant bacteria and the ARG RPKM values in hospital effluent over time. ARG surveillance in hospital effluent using the highly sensitive and specific xHYB method could improve our understanding of the emergence and spread of AMR within a hospital.
... According to Liang et al. (2021), A. dhakensis is a gram-negative waterborne pathogen that can cause gastroenteritis, being considered more virulent than other Aeromonas species. According to Sekizuka et al. (2019), A. caviae is one of the Aeromonas species most adapted to saline water environments, predominant in estuaries and which has often been isolated from environmental sources, such as sewage treatment plants. ...
Milk is a rich food, source of several indispensable nutrients, much consumed by the population. Its quality and microbiota are influenced by several factors. The objective of the present study was to determine the microbiota of refrigerated raw milk and processed milk in dairy products in Vale do Taquari - RS, through genetic sequencing. Three types of milk were analyzed in two dairies in the region: raw refrigerated milk, which arrives at the dairies by means of tank trucks, pasteurized milk and milk treated by Ultra High Temperature (UHT). The determination of the milk microbiota was performed through sequencing of the 16S rRNA gene. The results showed that refrigerated raw milk has the highest number of microorganisms in the two dairy products, followed by pasteurized milk and milk sterilized by the UHT process, successively. Dairy processing 2 proved to be more efficient, especially for UHT treated milk, considerably reducing the microbiota. Eighty-seven species of the Bacteria Kingdom were identified and the samples showed considerable microbiological diversity. Psychrotrophic microorganisms such as Kurthia gibsonii were expressive in the samples. Lactic acid bacteria such as Streptococcus macedonicus were found in refrigerated raw milk and pasteurized milk and Streptococcus thermophilus in sterilized milk. Harmful species such as Bacillus cereus group, Aeromonas dhakensis and Acinetobacter haemolyticus were found in UHT treated milk from both dairy products, in addition to Aeromonas caviae, Enterobacter mori and Viridibacillus arenosi.
Index terms:
Microorganisms; metagenomics; genetic sequencing; milk quality; milk production
... The majority of A. caviae (37/38), A. hydrophila (7/8), and A. media (6/7) that were resistant to at least one of the carbapenem antibiotics tested produced carbapenemases and mainly possessed the bla KPC-2 gene. Previous studies have demonstrated the presence of bla KPC-2 in Aeromonas strains from natural waters in Brazil [42,43] and from wastewater in Brazil [3], the United States [30], China [20], and Japan [18]. Besides the present study, only one previous study detected bla KPC-2 in Aeromonas sp. from activated sludge in Europe (Poland) [14]. ...
... Our carbapenem-resistant Aeromonas isolates carrying these plasmids were also positive for bla KPC-2 , bla VIM-2 , or bla NDM-1 genes, suggesting possible mobilization of these genes by plasmid-mediated transfer. The plasmid replicons ColE and IncR have been associated with the carriage of bla KPC-2 in Enterobacterales isolates [45][46][47] while IncU (also known as IncP-6 [48]) has been associated with the transfer of bla KPC-2 from Aeromonas to E. coli [18]. In addition to bla KPC-2 , other carbapenamase genes such as bla NDM-1 and bla OXA-48 [49,50] and ESBL genes such as bla CTX-M-15 [51] have also been found on the ColE plasmid in enterobacteria. ...
Antibiotic resistance (AR) remains one of the greatest threats to global health, and Aeromonas species have the potential to spread AR in the aquatic environment. The spread of resistance to antibiotics important to human health, such as third-generation cephalosporins (3GCs) and carbapenems, is of great concern. We isolated and identified 15 cefotaxime (3GC)- and 51 carbapenem-resistant Aeromonas spp. from untreated hospital and treated municipal wastewater in January 2020. The most common species were Aeromonas caviae (58%), A. hydrophila (17%), A. media (11%), and A. veronii (11%). Almost all isolates exhibited a multidrug-resistant phenotype and harboured a diverse plasmidome, with the plasmid replicons ColE, IncU, and IncR being the most frequently detected. The most prevalent carbapenemase gene was the plasmid-associated blaKPC-2 and, for the first time, the blaVIM-2, blaOXA-48, and blaIMP-13 genes were identified in Aeromonas spp. Among the 3GC-resistant isolates, the blaGES-5 and blaMOX genes were the most prevalent. Of the 10 isolates examined, three were capable of transferring carbapenem resistance to susceptible recipient E. coli. Our results suggest that conventionally treated municipal and untreated hospital wastewater is a reservoir for 3GC- and carbapenem-resistant, potentially harmful Aeromonas spp. that can be introduced into aquatic systems and pose a threat to both the environment and public health.
