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637900.9759Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India. Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.202032155479
348410.9749Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment. Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis (contig Intestine_364647) and Enterococcus faecium (contig Intestine_80272) carrying efrA, efrB and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica (contig Sediment_825143) and Escherichia coli (contig Sediment_188430) carrying mexB and APH(3')-IIa were found in sediments, and Laribacter hongkongensis (contig Water_478168 and Water_369477), Shigella sonnei (contig Water_880246), and Acinetobacter baumannii (contig Water_525520) carrying sul1, sul2, ereA, qacH, OXA-21, and mphD were found in pond water. Mobile genetic elements (MGEs) analysis indicated that horizontal gene transfer (HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.201930952342
987120.9742An Integrative and Conjugative Element (ICE) Found in Shewanella halifaxensis Isolated from Marine Fish Intestine May Connect Genetic Materials between Human and Marine Environments. Integrative and conjugative elements (ICEs) play a role in the horizontal transfer of antibiotic resistance genes (ARGs). We herein report an ICE from Shewanella halifaxensis isolated from fish intestine with a similar structure to both a clinical bacterial ICE and marine bacterial plasmid. The ICE was designated ICEShaJpn1, a member of the SXT/R391 family of ICEs (SRIs). ICEShaJpn1 has a common core structure with SRIs of clinical and fish origins and an ARG cassette with the pAQU1 plasmid of Photobacterium damselae subsp. damselae, suggesting that the common core of SRIs is widely distributed and ARG cassettes are collected from regional bacteria.202236058879
303030.9740Mobile Genomic Island GEI-FN1A in Aeromonas salmonicida FN1 Contributes to the Spread of Antibiotic-Resistance Genes. Antibiotics are used to treat severe bacterial infections. However, owing to excessive antibiotic use, bacteria under high selective pressure for antibiotics develop resistance through spontaneous mutation or by acquiring antibiotic-resistance genes (ARGs) through horizontal gene transfer (HGT). Horizontal transfer of ARGs among bacteria in the environment can lead to the emergence of multidrug-resistant (MDR) bacteria that infect animals and humans, thus causing disease outbreaks. In this study, MDR strain FN1 was isolated from a feces-contaminated soil sample from a chicken farm under pressure from the antibiotic florfenicol (16 mg/L) and identified as Aeromonas salmonicida. Whole-genome sequencing and analysis revealed the 86.8-kb antibiotic-resistant genomic island, GEI-FN1A, in the FN1 genome. Genome annotation revealed that GEI-FN1A carried several ARGs, including two tetracycline-resistance genes [tetR and tet(A)], three aminoglycoside-resistance genes [aph(6), aph(3"), and aac(3)], one trimethoprim-resistance gene (dfrB4), two chloramphenicol/florfenicol-resistance genes (catB3 and floR), three macrolide-resistance genes [mphR(A), mrx(A), and mph(A)] and two sul1 genes. GEI-FN1A also contained genes encoding integrase, transposase, and recombinase, which mediate the horizontal transfer of MDR genes. These findings suggest that GEI-FN1A in A. salmonicida FN1 can potentially spread ARGs among environmental bacteria.202540553200
81640.9739High-Level Nickel Resistance in Alcaligenes xylosoxydans 31A and Alcaligenes eutrophus KTO2. Two new nickel-resistant strains of Alcaligenes species were selected from a large number (about 400) of strains isolated from ecosystems polluted by heavy metals and were studied on the physiological and molecular level. Alcaligenes xylosoxydans 31A is a heterotrophic bacterium, and Alcaligenes eutrophus KTO2 is an autotrophic aerobic hydrogen-oxidizing bacterium. Both strains carry-among other plasmids-a megaplasmid determining resistance to 20 to 50 mM NiCl(2) and 20 mM CoCl(2) (when growing in defined Tris-buffered media). Megaplasmids pTOM8, pTOM9 from strain 31A, and pGOE2 from strain KTO2 confer nickel resistance to the same degree to transconjugants of all strains of A. eutrophus tested but were not transferred to Escherichia coli. However, DNA fragments carrying the nickel resistance genes, cloned into broad-hostrange vector pVDZ'2, confer resistance to A. eutrophus derivatives as well as E. coli. The DNA fragments of both bacteria, TBA8, TBA9, and GBA (14.5-kb BamHI fragments), appear to be identical. They share equal size, restriction maps, and strong DNA homology but are largely different from fragment HKI of nickel-cobalt resistance plasmid pMOL28 of A. eutrophus CH34.199116348590
716250.9737Dissemination of antibiotic resistance genes and human pathogenic bacteria from a pig feedlot to the surrounding stream and agricultural soils. The dissemination of antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and antibiotic-resistant HPB (ARHPB) from animal feedlot to nearby environment poses a potentially high risk to environmental ecology and public health. Here, a metagenomic analysis was employed to explore the dissemination of ARGs, HPB, and ARHPB from a pig feedlot to surrounding stream and agricultural soils. In total, not detectable (ND)-1,628.4 μg/kg of antibiotic residues, 18 types of ARGs, 48 HPB species, and 216 ARB isolates were detected in all samples. Antibiotic residues from pig feedlot mainly migrated into stream sediments and greenhouse soil. The dominant ARGs and HPB species from pig feedlot spread into stream sediments (tetracycline resistance genes, Clostridium difficile, and Mycobacterium tuberculosis), stream water (multidrug resistance (MDR) genes, Shigella flexneri, and Bordetella pertussis), and greenhouse soil (MDR genes, Bacillus anthracis, and Brucella melitensis). It is concerning that 54.4% of 216 ARB isolates from all samples were potential ARHPB species, and genome sequencing and functional annotation of 4 MDR HPB isolates showed 9 ARG types. Our findings revealed the potential migration and dissemination of antibiotic residues, ARGs, HPB, and ARHPB from pig feedlot to surrounding stream and agricultural soils via pig sewage discharge and manure fertilization.201829860105
348760.9735A comparison of antibiotic resistance genes and mobile genetic elements in wild and captive Himalayan vultures. As the most widely distributed scavenger birds on the Qinghai-Tibetan Plateau, Himalayan vultures (Gyps himalayensis) feed on the carcasses of various wild and domestic animals, facing the dual selection pressure of pathogens and antibiotics and are suitable biological sentinel species for monitoring antibiotic resistance genes (ARGs). This study used metagenomic sequencing to comparatively investigate the ARGs and mobile genetic elements (MGEs) of wild and captive Himalayan vultures. Overall, the resistome of Himalayan vultures contained 414 ARG subtypes resistant to 20 ARG types, with abundances ranging from 0.01 to 1,493.60 ppm. The most abundant resistance type was beta-lactam (175 subtypes), followed by multidrug resistance genes with 68 subtypes. Decreases in the abundance of macrolide-lincosamide-streptogramin (MLS) resistance genes were observed in the wild group compared with the zoo group. A total of 75 genera (five phyla) of bacteria were predicted to be the hosts of ARGs in Himalayan vultures, and the clinical (102 ARGs) and high-risk ARGs (35 Rank I and 56 Rank II ARGs) were also analyzed. Among these ARGs, twenty-two clinical ARGs, nine Rank I ARG subtypes, sixteen Rank II ARG subtypes were found to differ significantly between the two groups. Five types of MGEs (128 subtypes) were found in Himalayan vultures. Plasmids (62 subtypes) and transposases (44 subtypes) were found to be the main MGE types. Efflux pump and antibiotic deactivation were the main resistance mechanisms of ARGs in Himalayan vultures. Decreases in the abundance of cellular protection were identified in wild Himalayan vultures compared with the captive Himalayan vultures. Procrustes analysis and the co-occurrence networks analysis revealed different patterns of correlations among gut microbes, ARGs, and MGEs in wild and captive Himalayan vultures. This study is the first step in describing the characterization of the ARGs in the gut of Himalayan vultures and highlights the need to pay more attention to scavenging birds.202439006014
302170.9734Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. Although IncP-1 plasmids are important for horizontal gene transfer among bacteria, in particular antibiotic resistance spread, so far only three plasmids from the subgroup IncP-1α have been completely sequenced. In this study we doubled this number. The three IncP-1α plasmids pB5, pB11 and pSP21 were isolated from bacteria of two different sewage treatment plants and sequenced by a combination of next-generation and capillary sequencing technologies. A comparative analysis including the previously analysed IncP-1α plasmids RK2, pTB11 and pBS228 revealed a highly conserved plasmid backbone (at least 99.9% DNA sequence identity) comprising 54 core genes. The accessory elements of the plasmid pB5 constitute a class 1 integron interrupting the parC gene and an IS6100 copy inserted into the integron. In addition, the tetracycline resistance genes tetAR and the ISTB11-like element are located between the klc operon and the trfA-ssb operon. Plasmid pB11 is loaded with a Tn5053-like mercury resistance transposon between the parCBA and parDE operons and contains tetAR that are identical to those identified in plasmid pB5 and the insertion sequence ISSP21. Plasmid pSP21 harbours an ISPa7 element in a Tn402 transposon including a class 1 integron between the partitioning genes parCBA and parDE. The IS-element ISSP21 (99.89% DNA sequence identity to ISSP21 from pB11), inserted downstream of the tetR gene and a copy of ISTB11 (identical to ISTB11 on pTB11) inserted between the genes pncA and pinR. On all three plasmids the accessory genes are almost always located between the backbone modules confirming the importance of the backbone functions for plasmid maintenance. The striking backbone conservation among the six completely sequenced IncP-1α plasmids is in contrast to the much higher diversity within the IncP-1β subgroup.201121115076
716380.9733Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey. Antibiotic resistance genes (ARGs), human pathogenic bacteria (HPB), and HPB carrying ARGs pose a high risk to soil ecology and public health. Here, we used a metagenomic approach to investigate their diversity and abundance in chicken manures and greenhouse soils collected from Guli, Pulangke, and Hushu vegetable bases with different greenhouse planting years in Nanjing, Eastern China. There was a positive correlation between the levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in manures and greenhouse soils. In total, 156.2–5001.4 μg/kg of antibiotic residues, 22 classes of ARGs, 32 HPB species, and 46 species of HPB carrying ARGs were found. The highest relative abundance was tetracycline resistance genes (manures) and multidrug resistance genes (greenhouse soils). The dominant HPB and HPB carrying ARGs in the manures were Bacillus anthracis, Bordetella pertussis, and B. anthracis (sulfonamide resistance gene, sul1), respectively. The corresponding findings in greenhouse soils were Mycobacterium tuberculosis and M. ulcerans, M. tuberculosis (macrolide-lincosamide-streptogramin resistance protein, MLSRP), and B. anthracis (sul1), respectively. Our findings confirmed high levels of antibiotics, ARGs, HPB, and HPB carrying ARGs in the manured greenhouse soils compared with those in the field soils, and their relative abundance increased with the extension of greenhouse planting years.201525514174
348590.9731Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.202133913739
5133100.9727Draft genome sequence of Marinobacter sp. DUT-3, a manganese-oxidizing and potential antibiotic-resistant bacterium from Bohai coastal sediments. A manganese-oxidizing bacterium, Marinobacter sp. DUT-3, was isolated from Bohai coastal sediments. A total of 24 contigs with GC content of 57.91% and 3,817 protein-coding genes were obtained by genome sequencing. Isolation of this strain suggests potential for synergistic antibiotics removal via biogenic manganese oxides and intrinsic resistance.202541081498
7166110.9727Foam shares antibiotic resistomes and bacterial pathogens with activated sludge in wastewater treatment plants. Foaming is a common operational problem that occurs in activated sludge (AS) from many wastewater treatment plants (WWTPs), but the characteristic of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in foams is generally lacking. Here, we used a metagenomic approach to characterize the profile of ARGs and HPB in foams and AS from full-scale WWTPs receiving pesticide wastewater. No significant difference in the microbial communities was noted between the AS and foam samples. The diversity and abundance of ARGs in the foams were similar to those in the pertinent AS samples. Procrustes analysis suggested that the bacterial community is the major driver of ARGs. Metagenomic assembly also indicated that most ARGs (e.g., multidrug, rifamycin, peptides, macrolide-lincosamide-streptogramin, tetracycline, fluoroquinolone, and beta-lactam resistance genes) were carried by chromosomes rather than mobile genetic elements. Moreover, the relative abundances of HPB, Pseudomonas putida and Mycobacterium smegmatis, were enriched in the foam samples. Nine HPB were identified as carriers of 21 ARG subtypes, of which Pseudomonas aeruginosa could carry 12 ARG subtypes. Overall, this study indicates the prevalence of ARGs, HPB, and ARG-carrying HPB in foams, which highlights the potential risk of foams in spreading ARGs and HPB into the surrounding environments.202133373956
3007120.9726Analysis of the complete nucleotide sequence of an Actinobacillus pleuropneumoniae streptomycin-sulfonamide resistance plasmid, pMS260. pMS260 is an 8.1-kb non-conjugative but mobilizable plasmid that was isolated from Actinobacillus pleuropneumoniae and encodes streptomycin (SM) and sulfonamide (SA) resistances. The analysis of the complete nucleotide sequence of the plasmid revealed a high degree of similarity between pMS260 and the broad-host-range IncQ family plasmids. pMS260 had a single copy of an origin of vegetative replication (oriV). This sequence was identical to a functional oriV of the IncQ-like plasmid pIE1130 that had been exogenously isolated from piggery manure. However, pMS260 did not carry the second IncQ plasmid RSF1010-like oriV region present in pIE1130. A pIE1130-identical transfer origin was also found in pMS260. In addition, the deduced amino acid sequences from 10 open reading frames identified in pMS260 were entirely or nearly identical to those from genes for the replication, mobilization, and SM-SA resistance of pIE1130, indicating that pMS260 belongs to the IncQ-1 gamma subgroup. pMS260 is physically indistinguishable from pIE1130 apart from two DNA regions that contain the chloramphenicol and kanamycin resistance genes (catIII and aphI, respectively) and the second oriV-like region of pIE1130. The codon bias analysis of each gene of pIE1130 and the presence of potential recombination sites in the sulII-strA intergenic regions suggest that pIE1130 seems to have acquired the catIII and aphI genes more recently than the other genes of pIE1130. Therefore, pMS260 may be the ancestor of pIE1130. Information regarding the broad-host-range replicon of pMS260 will be useful in the development of genetic systems for a wide range of bacteria including A. pleuropneumoniae.200414711528
1995130.9726Genomic insights into Shigella species isolated from small ruminants and manure in the North West Province, South Africa. This study investigated Shigella species' antibiotic resistance patterns and genomic characteristics from small ruminants and manure collected in Potchefstroom, North West, South Africa. Whole genome sequencing was used to determine resistome profiles of Shigella flexneri isolates from small ruminants' manure and Shigella boydii from sheep faeces. Comparative genomics was employed on the South African 261 S. flexneri strains available from GenBank, including the sequenced strains in this study, by investigating the serovars, antibiotic resistance genes (ARGs), and plasmid replicon types. The S. flexneri strains could not be assigned to known sequence types, suggesting novel or uncharacterized lineages. S. boydii R7-1A was assigned to sequence type 202 (ST202). Serovar 2A was the most common among South African S. flexneri strains, found in 96% of the 250 compared human-derived isolates. The shared mdf(A) was the most prevalent gene, identified in 99% of 261 S. flexneri genomes, including plasmid replicon types ColRNAI_1 (99%) and IncFII_1 (98%). Both species share a core set of resistance determinants mainly involving β-lactams (ampC1, ampC, ampH), macrolides (mphB), polymyxins (eptA, pmrF), multidrug efflux pumps (AcrAB-TolC, Mdt, Emr, Kpn families), and regulatory systems (marA, hns, crp, baeRS, evgAS, cpxA, gadX). However, S. boydii possesses additional resistance genes conferring resistance to tetracyclines (tet(A)), phenicols (floR), sulphonamides (sul2), and aminoglycosides (APH(3'')-Ib, APH(6)-Id), along with the acrEF efflux pump components (acrE, acrF). In contrast, S. flexneri harboured unique genes linked to polymyxin resistance (ugd) and regulatory functions (sdiA, gadW) that were absent in S. boydii. These findings highlight Shigella strains' genomic diversity and antimicrobial resistance potential in livestock-associated environments. Moreover, S. boydii highlights the potential risk of multidrug-resistant bacteria in farming and environmental routes. KEY POINTS: • First whole genome study of Shigella from manure and small ruminants in South Africa. • Shigella boydii strain carried multiple resistance genes to β-lactams and tetracycline. • Multidrug efflux pump gene mdf(A) was detected in 99% of South African Shigella flexneri strains.202541148367
6381140.9726Occurrence and distribution of antibiotic resistance genes in Elymus nutans silage from different altitudes on the Qinghai-Tibetan Plateau. INTRODUCTION: Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) have attracted more attentions in fermented feed recently. However, little information is available on the occurrence and distribution of ARGs in ensiled forages in the alpine region of the Qinghai-Tibetan plateau (QTP) with an extremely harsh environment. METHODS: The study investigated the distribution and spread mechanism of ARB and ARGs in Elymus nutans silage along 2600 m (low), 3600 m (medium) and 4600 m (high) altitude in the QTP. RESULTS: The major ARG types in Elymus nutans silage were multidrug, aminoglycoside, bacitracin, beta-lactam and polymyxin, while tnpA and IS91 were the dominant mobile genetic elements (MGEs) subtypes in the Elymus nutans silage. The dominant ARGs were mainly carried by Pantoea, Enterobacter, Serratia, and Lelliottia. Although altitudinal gradient had no influence on the diversity or abundance of other ARGs and MGEs in the Elymus nutans silage (p > 0.05), the network co-occurrence patterns among ARGs, MGEs, and bacteria in high-altitude silage were more complex than that in low- and medium-altitude silages. The dominant clinical ARGs in the alpine silage were bacA and acrF, and the abundance of clinical ARGs decreased with prolonged fermentation time. DISCUSSION: This study provides important data on the status of ARGs in ensiled forage from the alpine region of the QTP.202540458713
3019150.9726Identification and Characterization of New Resistance-Conferring SGI1s (Salmonella Genomic Island 1) in Proteus mirabilis. Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.201830619228
1753160.9725Characterization of a Linezolid- and Vancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanG Operons. Linezolid and vancomycin are among the last-resort antimicrobial agents in the treatment of multidrug-resistant Gram-positive bacterial infections. Linezolid- and vancomycin-resistant (LVR) Gram-positive bacteria may pose severe threats to public health. In this study, three optrA- and vanG-positive Streptococcus suis strains were isolated from two farms of different cities. There were only 1 and 343 single-nucleotide polymorphisms in coding region (cSNPs) of HCB4 and YSJ7 to YSJ17, respectively. Mobilome analysis revealed the presence of vanG, erm(B), tet(O/W/32/O), and aadE-apt-sat4-aphA3 cluster on an integrative and conjugative element, ICESsuYSJ17, and erm(B), aphA3, aac(6')-aph(2″), catpC(194), and optrA on a prophage, ΦSsuYSJ17-3. ICESsuYSJ17 exhibited a mosaic structure and belongs to a highly prevalent and transferable ICESa2603 family of Streptococcus species. ΦSsuYSJ17-3 shared conserved backbone to a transferable prophage Φm46.1. A novel composite transposon, IS1216E-araC-optrA-hp-catpC(194)-IS1216E, which can be circulated as translocatable unit (TU) by IS1216E, was integrated on ΦSsuYSJ17-3. Vancomycin resistance phenotype and vanG transcription assays revealed that the vanG operon was inducible. The LVR strain YSJ17 exhibited moderate virulence in a zebrafish infection model. To our knowledge, this is the first report of LVR isolate, which is mediated by acquired resistance genes optrA and vanG operons in Gram-positive bacteria. Since S. suis has been recognized as an antimicrobial resistance reservoir in the spread of resistance genes to major streptococcal pathogens, the potential risks of disseminating of optrA and vanG from S. suis to other Streptococcus spp. are worrisome and routine surveillance should be strengthened.201931551963
3562170.9725Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10. This study examined the potential of bacteria from river epilithon to mobilize a recombinant catabolic plasmid, pD10, encoding 3-chlorobenzoate degradation and kanamycin resistance. Fifty-four mobilizing plasmids were exogenously isolated by triparental matings between strains of Pseudomonas putida and epilithic bacteria from the River Taff (South Wales, United Kingdom). Frequencies for mobilization ranged from 1.7 x 10(-8) to 4.5 x 10(-3) per recipient at 20 degrees C. The sizes of the mobilizing plasmids isolated ranged from 40 kb to over 200 kb, and 19 of 54 were found to encode mercury resistance. Plasmid-encoded resistance to tetracycline and streptomycin was also found but not resistance to UV light or various heavy metals. Eight plasmids of epilithic bacteria, analyzed by comparing restriction fragmentation patterns, showed significant differences between those isolated from different independent matings. Optimal temperatures for mobilization of pD10 were between 15 and 25 degrees C. Four mercury resistance plasmids were found to be broad host range, transferring mercury resistance and mobilizing pD10 readily to representative species of beta- and gamma-purple bacteria. In general, frequencies of pD10 mobilization by plasmids of epilithic bacteria were 2 to 3 orders of magnitude lower than conjugal transfer frequencies. Thus, there is a high potential for exchange of recombinant genes introduced into the epilithon by mobilization between a variety of bacterial species.19921599248
6798180.9725Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health. Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.202539892320
3563190.9725Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup. Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.201425653641