ISCR elements: novel gene-capturing systems of the 21st century?

Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia

Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.

Emergence of carbapenem-resistant Citrobacter spp. across human, animal, and water environments in China

OBJECTIVE

With the rise of carbapenem-resistant Citrobacter spp. (CRC), it is essential to investigate their distribution and resistance characteristics across diverse ecological niches. This study aims to collect CRCs from humans, animals, and water environments to analyze their epidemiology, genetic characteristics, and resistance mechanisms, providing insights into transmission dynamics.

METHODS

CRCs were isolated from different samples using methods including filtration, enrichment, screening, and purification. Antimicrobial susceptibility tests were conducted using the broth microdilution method. Transconjugation experiments were performed through filter mating. Whole genome sequencing and bioinformatics analysis were carried out to analyze genomic features of CRCs.

RESULTS

Total of 171 CRCs were isolated from diverse Chinese provinces between 2016 and 2023. All strains are classified into seven Citrobacter species. Citrobacter freundii is the most common (76.02%), with ST116 and ST22 being the predominant strains. Among all strains, 63.16% carried blaNDM-1, and 41.52% carried blaKPC-2. Hospital wastewater was the primary source of CRCs harbouring two carbapenemase genes, with the most prevalent combination being blaNDM-1 and blaKPC-2 (85.71%, 24/28). All strains showed multi-drug resistance, with over 95% resistant to various carbapenems. Transconjugation experiments showed that carbapenemase genes in the majority of CRCs were located on the plasmids and can be transferred to the recipient strains. Phylogenetic analysis displayed that clonal transmission was observed among a few CRCs.

CONCLUSIONS

Multiple mobile genetic elements mediate the spread and prevalence of carbapenem resistance in Citrobacter spp. Monitoring carbapenemase genes and CRCs across ecological niches is needed to controlling carbapenem resistance, particularly in high-risk sources like hospital wastewater.

Different fates between extracellular and intracellular antimicrobial resistome in full-scale activated sludge and membrane bioreactor processes

Treated effluent of wastewater treatment plants (WWTPs) are major sources of extracellular antimicrobial resistance genes (eARGs) into aquatic environments. This study aimed to clarify the fate and origins of eARGs from influent to treated effluent at a full-scale WWTP. The compositions of eARG and intracellular ARG (iARG) were acquired via shotgun metagenomic sequencing in influent wastewater, activated sludge, and treated effluent of the target WWTP, where identical wastewater was treated by conventional activated sludge (CAS) and membrane bioreactor (MBR) processes. The proportion of eARGs to iARGs increased from influent to effluent in both processes, reaching almost half of the total ARG. Most eARGs in influent were associated with clinically important antimicrobials, whereas eARGs in sludge and effluent were dominated by aminoglycoside resistance genes of aadA and APH variants. Although the eARGs composition in influent wastewater mirrored that of iARGs, a substantial shift occurred in activated sludge and effluent, highlighting the presence of distinct dissemination and reduction mechanisms between eARGs and iARGs. Notably, the origin of eARGs in treated effluent was mainly iARGs in the effluent rather than the carryover of eARG from activated sludge, which were substantially reduced in MBR, compared to CAS. Consequently, these differences in selective mechanisms led to different fates between eARG and iARG during wastewater treatment.

Extended-spectrum β-lactamase-producing Escherichia coli isolated from captive primates: characteristics and horizontal gene transfer ability analysis

The rapid spread of extended-spectrum β-lactamases (ESBLs)-producing Escherichia coli (ESBL-EC) around the world has become a significant challenge for humans and animals. In this study, we aimed to examine the characteristics and horizontal gene transfer (HGT) capacity of ESBL-EC derived from captive primates. We screened for ESBL-EC among a total of 444 multidrug-resistant (MDR) E. coli strains isolated from 13 zoos in China using double-disk test. ESBL genes, mobile genetic elements (MGEs), and virulence-associated genes (VAGs) in ESBL-EC were detected through polymerase chain reaction (PCR). Furthermore, conjugation experiments were conducted to examine the HGT capacity of ESBL-EC, and the population structure (phylogenetic groups and MLST) was determined. Our results showed that a total of 69 (15.54%, 69/444) ESBL-EC strains were identified, and 5 variants of blaCTX and 3 variants of blaTEM were detected. The highest detection rate was blaCTX-M-55 (49.28%, 34/69), followed by blaCTX-M-15 (39.13%, 27/69). Ten MGEs were detected and the most prevalent was IS26 (78.26%, 54/69), followed by ISEcp1 (60.87%, 42/69). Eighteen combinations of MGEs were detected, in which ISEcp1 + IS26 was predominant (18.84%, n = 13). A total of 15 VAGs were detected and the most prevalent was fimC (84.06%, 58/69), followed by sitA (78.26%, 54/69). Furthermore, HGT ability analysis results showed that 40.58% (28/69) of ESBL-EC strains exhibited the ability to engage in conjugative transfer. Plasmid typing revealed that IncFIB (78.57%, 22/28) had the highest detection rates. Furthermore, antibiotic resistance genes (ARGs) of blaTEM-135, tetA and qnrS; MGEs of IS26, trbC and ISCR3/14 showed high rates of conjugative transfer. The population structure analysis showed that the phylogroup B1 and ST2161 were the most prevalent. ESBL-EC poses a potential threat to captive primates and may spread to other animals, humans, and the environment. It is imperative to implement measures to prevent the transmission of ESBL-EC among captive primates.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Integrons are key players in the spread of beta-lactamase-encoding genes

Integrons mediate the acquisition and expression of gene cassettes (GCs). The production of beta-lactamases (BLs) is the most relevant mechanism of beta-lactams resistance. To explore the role of integrons in BL genes dissemination, sequences and metadata were retrieved from the INTEGRALL database and a literature review performed. Integrons (mostly class 1) carrying ≥1 BL-encoding genes (n = 1981) were detected in 37 bacterial genera and encoded BLs from 18 families. A total of 159 BL-encoding gene cassettes (BLGCs) were identified, representing all Ambler classes, with blaOXA-, blaVIM- and blaIMP-carrying integrons the most prevalent. blaGES, blaBEL and most metallo-BLs were exclusively associated with integrons. BL genes from 13 families were identified as genes captured by ISCR1 in complex integrons (n = 234), namely blaNDM, blaCTX-M and blaTEM. Frequently co-detected GCs encoded resistance to all major classes of antibiotics, namely aminoglycosides, phenicols and trimethoprim. Most BLGCs encoded resistance to carbapenems (n = 90) and Pseudomonas aeruginosa was the most frequent host. Most bla-carrying integrons were from clinical contexts and wastewater was the richest environmental compartment. The frequent association of BLs and integrons indicates a significant role in dissemination of beta-lactams resistance. Considering that integrons are (i) low-cost structures often associated with other mobile elements, and (ii) often carry multiple GCs (interchangeable according to environmental stimuli), the association of BL genes with integrons should always be considered a risk factor for the spread of beta-lactam resistance when performing surveillance and epidemiological studies. Further studies monitoring prevalence and diversity of integrons, particularly across non-clinical environments, will draw a more comprehensive picture of integron-associated dissemination of beta-lactams resistance.

Whole genome analysis revealed the role of blaOXA-23 and blaOXA-66 genes in carbapenem resistance of Acinetobacter baumannii strains

Acinetobacter baumannii is a multidrug-resistant bacterium that has emerged as a significant nosocomial pathogen globally and renowned for its ability to acquire antimicrobial resistance (AMR) genes. However, understanding of its resistance mechanisms to certain drug classes remains limited. This study focused on four bacterial strains (AB863, AB889, AB930, and AB960) exhibiting carbapenem resistance. They demonstrated high minimum inhibitory concentration (MIC) (128 mg/L) to meropenem and were categorized as extensively drug-resistant strains. Subsequently, they were identified as A. baumannii through 16S rRNA gene sequence analysis and species-specific PCR targeting the blaOXA51-like gene. Three strains were sequenced for their genomes to study the genetic determinants and functional relevance of carbapenem resistance. The draft genome length of the strains ranged from 3.8 to 4.0 Mbp. A total of 16 antibiotic resistance genes including the genes blaOXA-23 and blaOXA-66 which mediate carbapenem resistance were identified in the genomes. A comprehensive multilocus sequence typing analysis involving 95 A. baumannii strains from different Asian countries assigned the four strains to sequence type 2 (ST2), the most predominant ST circulating in Asia. Comparative genome analysis also revealed blaOXA-66 as the most dominant variant of blaOXA-51-like gene and also a widespread distribution of blaOXA-23 gene. In addition, various mobile genetic elements associated with AMR genes and three efflux pumps families were detected in the genomes of the strains. Transformation of blaOXA-23 and blaOXA-66 genes resulted in meropenem resistance in the transformant which exhibited a MIC of 2 mg/L, thus confirming direct involvement of both genes in carbapenem resistance.

From Metagenomes to Functional Expression of Resistance: floR Gene Diversity in Bacteria from Salmon Farms

Background. The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. Methods. Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover floR gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. Results. Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The floR gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference floR. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the floR sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. Conclusions. This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.

Spreading Ability of Tet(X)-Harboring Plasmid and Effect of Tetracyclines as a Selective Pressure

Tigecycline is a last-resort antimicrobial in humans. Tetracyclines are the most widely used antimicrobials in livestock. Mobile tigecycline resistance genes [tet(X)] are disseminated worldwide, and tetracycline use may have promoted the selection of tet(X) genes. Thus, the selective pressure on tet(X) genes and their plasmids in livestock must be elucidated. We performed a retrospective study to clarify the prevalence of tigecycline-resistant Escherichia coli from pigs in Thailand. Screening for tigecycline resistance was performed on 107 E. coli strains from 25 samples, and tet(X)-carrying plasmids were characterized. tet(X) genes were cloned and expressed in E. coli. Bacterial growth rate in the presence of tetracycline as a result of the presence of tet(X) genes was also evaluated. Thirty-two tet(X4)-harboring tigecycline-resistant E. coli strains were detected in 10/25 samples (40%). The tet(X4) genes were carried on various Inc-type plasmids and flanked by ISCR2. The tet(X)-carrying plasmids were transferred to E. coli and Klebsiella pneumoniae. Acquisition of tet(X) genes and their plasmids improved bacterial growth in the presence of tetracycline. In summary, tetracycline use exerts selective pressure on tet(X) genes and their various backbone plasmids; therefore, a reduced amount of tetracycline use is important to limit the spreading of tet(X) genes.

Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics

The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3--N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.

Effect of Nk-lysin peptides on bacterial growth, MIC, antimicrobial resistance, and viral activities

NK-lysins from chicken, bovine and human are used as antiviral and antibacterial agents. Gram-negative and gram-positive microorganisms, including Streptococcus pyogenes, Streptococcus mutans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella oxytoca, Shigella sonnei, Klebsiella pneumoniae and Salmonella typhimurium, are susceptible to NK-lysin treatment. The presence of dominant TEM-1 gene was noted in all untreated and treated bacteria, while TOHO-1 gene was absent in all bacteria. Importantly, β-lactamase genes CTX-M-1, CTX-M-8, and CTX-M-9 genes were detected in untreated bacterial strains; however, none of these were found in any bacterial strains following treatment with NK-lysin peptides. NK-lysin peptides are also used to test for inhibition of infectivity, which ranged from 50 to 90% depending on NK-lysin species. Chicken, bo vine and human NK-lysin peptides are demonstrated herein to have antibacterial activity and antiviral activity against Rotavirus (strain SA-11). On the basis of the comparison between these peptides, potent antiviral activity of bovine NK-lysin against Rotavirus (strain SA-11) is particularly evident, inhibiting infection by up to 90%. However, growth was also significantly inhibited by chicken and human NK-lysin peptides, restricted by 80 and 50%, respectively. This study provided a novel treatment using NK-lysin peptides to inhibit expression of β-lactamase genes in β-lactam antibiotic-resistant bacterial infections.

Emergence and Characterization of the High-Level Tigecycline Resistance Gene tet(X4) in Salmonella enterica Serovar Rissen from Food in China

The plasmid-mediated tet(X4) gene has exhibited a high-level resistance to tigecycline (TGC), which has raised concerns globally regarding antibiotic resistance. Although the widespread tet(X4) has been found widely in Escherichia coli, it is scarcely found in other Enterobacteriaceae. This study aimed to characterize a ST469 Salmonella enterica serovar Rissen (S. Rissen) isolate harboring tet(X4) from pork, which was identified and characterized via antimicrobial susceptibility testing, conjugation assays, plasmid curing testing, whole-genome sequencing, and bioinformatic analysis. Ten ST469 S. Rissen isolates of 223 Salmonella spp. isolates were isolated from food samples in China during 2021-2023. One of 10 S. Rissen isolates, SM2301, carrying tet(X4) conferred high-level resistance to TGC (minimum inhibitory concentration > 8 µg/mL). The tet(X4) could be conjugated into different recipients, including E. coli, S. enteritidis, and K. pneumoniae isolates. Plasmid curing confirmed that tet(X4) was plasmid-mediated. Genetic analysis revealed that the tet(X4) in the SM2301 isolate was located in the IncFIA(HI1)-IncHI1A-IncHI1B(R27) hybrid plasmid, and the structure of tet(X4) was abh-tet(X4)-ISCR2. To the best of our knowledge, this is the first report of a tet(X4)-positive food-derived S. Rissen isolate. The extending bacterial species of tet(X4)-bearing plasmids suggested the increasing transmission risk of the mobile TGC resistance gene tet(X4) beyond E. coli. This study highlights the emerging and evolution risk of novel resistance genes across various bacterial species. Therefore, further surveillance is warranted to monitor the prevalence of tet(X4) in Salmonella spp. and other bacterial species.

Capture of armA by a novel ISCR element, ISCR28

ISCR28 is a fully functional and active member of the IS91-like family of insertion sequences. ISCR28 is 1,708-bp long and contains a 1,293-bp long putative open reading frame that codes a transposase. Sixty ISCR28-containing sequences from GenBank generated 27 non-repeat genetic contexts, all of which represented naturally occurring biological events that had occurred in a wide range of gram-negative organisms. Insertion of ISCR28 into target DNA preferred the presence of a 5'-GXXT-3' sequence at its terIS (replication terminator) end. Loss of the first 4 bp of its oriIS (origin of replication) likely caused ISCR28 to be trapped in ISApl1-based transposons or similar structures. Loss of terIS and fusion with a mobile element upstream likely promoted co-transfer of ISCR28 and the downstream resistance genes. ArmA and its downstream intact ISCR28 can be excised from recombinant pKD46 plasmids forming circular intermediates, further elucidating its activity as a transposase.

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.

A 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.

Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe

OBJECTIVES

To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19.

METHODS

WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments.

RESULTS

mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids.

CONCLUSIONS

Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Distribution and spread of tigecycline resistance gene tet(X4) in Escherichia coli from different sources

Tigecycline serves as a last-resort antimicrobial agent against severe infections caused by multidrug-resistant bacteria. Tet(X) and its numerous variants encoding flavin-dependent monooxygenase can confer resistance to tigecycline, with tet(X4) being the most prevalent variant. This study aims to investigate the prevalence and characterize tigecycline resistance gene tet(X) in E. coli isolates from various origins in Yangzhou, China, to provide insights into tet(X) dissemination in this region. In 2022, we tested the presence of tet(X) in 618 E. coli isolates collected from diverse sources, including patients, pig-related samples, chicken-related samples, and vegetables in Yangzhou, China. The antimicrobial susceptibility of tet(X)-positive E. coli isolates was conducted using the agar dilution method or the broth microdilution method. Whole genome sequencing was performed on tet(X)-positive strains using Illumina and Oxford Nanopore platforms. Four isolates from pig or pork samples carried tet(X4) and exhibited resistance to multiple antimicrobial agents, including tigecycline. They were classified as ST542, ST10, ST761, and ST48, respectively. The tet(X4) gene was located on IncFIA8-IncHI1/ST17 (n=2), IncFIA18-IncFIB(K)-IncX1 (n=1), and IncX1 (n=1) plasmids, respectively. These tet(X4)-carrying plasmids exhibited high similarity to other tet(X4)-bearing plasmids with the same incompatible types found in diverse sources in China. They shared related genetic environments of tet(X4) associated with ISCR2, as observed in the first identified tet(X4)-bearing plasmid p47EC. In conclusion, although a low prevalence (0.65%) of tet(X) in E. coli strains was observed in this study, the horizontal transfer of tet(X4) among E. coli isolates mediated by pandemic plasmids and the mobile element ISCR2 raises great concerns. Thus, heightened surveillance and immediate action are imperative to curb this clinically significant resistance gene and preserve the efficacy of tigecycline.

Genomic characterization revealing the high rate of tet(X4)-positive Escherichia coli in animals associated with successful genetic elements

Introduction

The rapid spread of plasmid-mediated tet(X4) conferring high tigecycline resistance poses a significant threat to public health. Escherichia coli as the most common pathogen which carries tet(X4) has been widely disseminated in China. Thus, comprehensive investigations are required to understand the mechanism of transmission of tet(X4)-positive E. coli.

Methods

In this study, a total of 775 nonduplicate samples were collected in Guangdong, China from 2019 to 2020. We screened for tet(X4)-positive E. coli by PCR amplification and species identification. Furthermore, we analyzed the phylogenetics and genetic context of tet(X4)-positive E. coli through whole-genome sequencing and long-reads sequencing.

Results

Overall, 146 (18.84%) tet(X4)-positive E. coli were isolated, comprising 2 isolates from humans and 144 isolates from pigs. The majority of tet(X4)-positive E. coli exhibited resistance to multiple antibiotics but all of them were susceptible to amikacin and colistin. Phylogenetic analysis showed that ST877, ST871, and ST195 emerged as the predominant sequence types in tet(X4)-positive E. coli. Further analysis revealed various genetic environments associated with the horizontal transfer of tet(X4). Notably, a 100-kbp large fragment insertion was discovered downstream of tet(X4), containing a replicon and a 40-kbp gene cluster for the bacterial type IV secretion system.

Discussion

The high colonization rate of tet(X4)-positive E. coli in animals suggests that colonization as a key factor in its dissemination to humans. Diverse genetic context may contribute to the transfer of tet(X4). Our findings underline the urgent need for controlling the spread of plasmid-mediated tigecycline resistance.

Genetics of resistance to trimethoprim in cotrimoxazole resistant uropathogenic Escherichia coli: integrons, transposons, and single gene cassettes

Cotrimoxazole, the combined formulation of sulfamethoxazole and trimethoprim, is one of the treatments of choice for several infectious diseases, particularly urinary tract infections. Both components of cotrimoxazole are synthetic antimicrobial drugs, and their combination was introduced into medical therapeutics about half a century ago. In Gram-negative bacteria, resistance to cotrimoxazole is widespread, being based on the acquisition of genes from the auxiliary genome that confer resistance to each of its antibacterial components. Starting from previous knowledge on the genotype of resistance to sulfamethoxazole in a collection of cotrimoxazole resistant uropathogenic Escherichia coli strains, this work focused on the identification of the genetic bases of the trimethoprim resistance of these same strains. Molecular techniques employed included PCR and Sanger sequencing of specific amplicons, conjugation experiments and NGS sequencing of the transferred plasmids. Mobile genetic elements conferring the trimethoprim resistance phenotype were identified and included integrons, transposons and single gene cassettes. Therefore, strains exhibited several ways to jointly resist both antibiotics, implying different levels of genetic linkage between genes conferring resistance to sulfamethoxazole (sul) and trimethoprim (dfrA). Two structures were particularly interesting because they represented a highly cohesive arrangements ensuring cotrimoxazole resistance. They both carried a single gene cassette, dfrA14 or dfrA1, integrated in two different points of a conserved cluster sul2-strA-strB, carried on transferable plasmids. The results suggest that the pressure exerted by cotrimoxazole on bacteria of our environment is still promoting the evolution toward increasingly compact gene arrangements, carried by mobile genetic elements that move them in the genome and also transfer them horizontally among bacteria.

Genomic Insights into the First Emergence of blaNDM-5-Carrying Carbapenem-Resistant Salmonella enterica Serovar London Strain in China

Carbapenem-resistant Salmonella enterica (S. enterica) pose a significant threat to public health, causing gastroenteritis and invasive infections. We report the first emergence of a carbapenem-resistant S. enterica serovar London strain, A132, carrying the blaNDM-5 gene in China. Whole-genome sequencing and bioinformatics analysis assigned A132 to be ST155, a multidrug-resistant clone frequently reported in China. The strain A132 exhibited resistance to multiple antibiotics, with 20 acquired antibiotic resistance genes (ARGs) identified, predominantly located on the IncFIB plasmid (pA132-1-NDM). Notably, the blaNDM-5 gene was located within an IS26 flanked-class 1 integron-ISCR1 complex, comprising two genetic cassettes. One cassette is the class 1 integron, which may facilitate the transmission of the entire complex, while the other is the blaNDM-5-containing ISCR1-IS26-flanked cassette, carrying multiple other ARGs. Genbank database search based on the blaNDM-5-carrying cassette identified a similar genetic context found in transmissible IncFIA plasmids from Escherichia coli (p91) and Enterobacter hormaechei (p388) with a shared host range, suggesting the potential for cross-species transmission of blaNDM-5. To our knowledge, this is the first reported case of Salmonella serovar London ST155 harboring blaNDM-5 gene. Phylogenetic analysis indicated a close relationship between A132 and eight S. London ST155 strains isolated from the same province. However, A132 differed by carrying the blaNDM-5 gene and four unique ARGs. Given the high transmissibility of the F-type plasmid harboring blaNDM-5 and 18 other ARGs, it is imperative to implement vigilant surveillance and adopt appropriate infection control measures to mitigate the threat to public health.

First detection in Spain of NDM-1-producing Pseudomonas aeruginosa in two patients transferred from Ukraine to a university hospital

OBJECTIVES

Carbapenemase-mediated carbapenem resistance in Pseudomonas aeruginosa is a relevant health problem. We detected for the first time in Spain two clinical NDM-producing P. aeruginosa (NDM-Pa) isolates in two Ukrainian patients admitted to our hospital between April and August 2022.

METHODS

Antimicrobial susceptibility was studied by microdilution and MIC gradient strips (EUCAST-2022 criteria). Carbapenemase genes were detected by the Xpert Carba-R and immunochromatography assays. WGS (Illumina and Oxford-Nanopore) was also performed.

RESULTS

In May 2022, we detected an NDM-Pa in a sternotomy wound in a patient. In June-2022, a second NDM-Pa along with an OXA-48-Klebsiella pneumoniae (OXA-48-Kp) isolate was detected in a mandibular abscess from an unrelated patient. Moreover, an NDM+OXA-48-K. pneumoniae (NDM+OXA-48-Kp) was also found in a rectal sample of this patient. Both patients had undergone surgery in Ukraine before their transfer to our hospital. NDM-Pa isolates were resistant to all tested antimicrobials with the exception of aztreonam (MIC = 8 mg/L), colistin (MIC =2 mg/L) and cefiderocol (MIC range = 0.75-2 mg/L). WGS confirmed that both P. aeruginosa isolates were NDM-1 producers, belonged to ST773 and shared an identical resistome. blaNDM-1 was located on a ∼117-Kb chromosomally integrated integrative conjugative element (ICE). OXA-48-Kp and NDM+OXA-48-Kp belonged to ST147 and contained blaOXA-48 on an identical ∼300-Kb IncHIB-plasmid. blaNDM-1 was located on a 51-Kb IncFIB-plasmid only found in NDM+OXA-48-Kp.

CONCLUSIONS

This is the first description of NDM-Pa in Spain. We highlight the threat of further cross-border dissemination of NDM-1 through P. aeruginosa along with K. pneumoniae high-risk clones also carrying OXA-48, which draws a complex epidemiological scenario.

Abatement of antibiotics and resistance genes during catalytic ozonation enhanced sludge dewatering process: Synchronized in volume and hazardousness reduction

Based on the efficiency of the catalytic ozonation techniques (HDWS+O3 and MnFe2O4 @SBC+O3) in enhancing the sludge dewaterability, the effectiveness in synchronized abatement antibiotics and antibiotic resistance genes (ARGs) was conducted to determine. The results revealed that catalytic ozonation conditioning altered the distribution of target antibiotics (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) in the dewatered filtrate, the dewatered sludge cake and the extra-microcolony/cellular polymers (EMPS/ECPS) layers, achieving the redistribution from solid-phase adsorption to liquid-phase dissolution. The total degradation rate was over 90% for TC and OTC, 72-78% for NOR and OFL; the abatement efficiency of eleven ARGs reached 1.47-3.01 log and 1.64-3.59 log, respectively, and more than four eARGs were eliminated. The effective abatement of the absolute abundance of Mobile genetic elements (MGEs) (0.91-1.89 log) demonstrated that catalytic ozonation conditioning could also significantly inhibit horizontal gene transfer (HGT). The abundance of resistant bacteria was greatly reduced and the signal transduction of the typical ARGs host bacteria was inhibited. The highly reactive oxidation species (ROS) generated were responsible for the abatement of antibiotics and ARGs. These findings provided new insights into the sludge conditioning for ideal and synchronized reduction in volume and hazardousness by catalytic ozonation processes in sludge treatment.

Responses of antibiotic resistance genes in the enhanced biological phosphorus removal system under various antibiotics: Mechanisms and implications

The effects of antibiotics on the proliferation of antibiotic resistant genes (ARGs) in WWTPs have drawn great attention in recent years. The effects of antibiotics on ARGs in the enhanced biological phosphorus removal (EBPR) system and its mechanisms, however, are still not well understood. In this study, EBPR systems were constructed using activated sludge to investigate the effects of ten commonly detected antibiotics in the environment on the proliferation of ARGs and the mechanisms involved. The results showed that the total abundance of ARGs increased to varying degrees with the addition of different antibiotics (0.05 mmol/L), and the top 30 ARGs increased by 271.1 % to 370.0 %. Mobile genetic elements (MGEs), functional modules, and the bacteria community were consistently related to the changes in ARGs. Refractory antibiotics, in particular, have a stronger promoting effect on transduction in the EBPR system. The insertion sequence common region (ISCR) and transposon (Tnp) were identified as crucial factors in the proliferation of ARGs. Moreover, the risk of polyphosphate accumulating organisms (PAOs) carrying ARGs in the presence of antibiotics should not be ignored. Our findings emphasize the potential efficacy of employing strategies that target the reduction of MGEs, regulation of cellular communication, and management of microbial communities to effectively mitigate the risks associated with ARGs.

Decoding the enigma: unveiling the molecular transmission of avian-associated tet(X4)-positive E. coli in Sichuan Province, China

Tigecycline is considered one of the "last resort antibiotics" for treating complex infections caused by multidrug-resistant (MDR) bacteria, especially for combating clinical resistant strains that produce carbapenemases. However, the tet(X4) gene, which carried by different plasmids can mediate high levels of bacterial resistance to tigecycline, was first reported in 2019. Here, we report the emergence of the plasmid-mediated tet(X4) in avian environment of Sichuan Province. A total of 21 tet(X4)-positive Escherichia coli (E. coli) strains were isolated and identified from avian samples in selected regions, with an isolation rate of 1.6% (21/1,286), and all of them were MDR strains. Multilocus Sequence Typing (MLST) method was used to classify the 21 tet(X4)-positive E. coli into the ST206, ST761, ST155, ST1638, ST542, and ST767 types, which also belong to the 3 phylogenetic subgroups A, B1, and C. Tet(X4) is located on mobile plasmids that can be efficiently and stably propagated. The results of fitness cost experiments showed that tet(X4)-positive plasmids may incur some fitness cost to host bacteria, but different tet(X4)-positive plasmids bring about differential fitness costs. Whole-genome sequencing further confirmed the tet(X4) gene can be located on IncX1-type plasmids and the core genetic structures are ISVsa3-rdmc-tet(X4) or rdmc-tet(X4)-ISVsa3, the former is a 7 copies tandem repeat structure. In this study, we isolated and identified tet(X4)-positive E. coli from the avian origin in Sichuan, analyzed the mobility of the tet(X4) by conjugational transfer and S1-PFGE, and evaluated the biological characteristics of the tet(X4)-positive plasmid using the results of conjugational frequency, plasmid stability, and fitness costs. Finally, combined with the third-generation whole-genome sequencing analysis, the molecular transmission characteristics of the tet(X4) were preliminarily clarified, providing a scientific basis for guiding veterinary clinical use in this area, as well as risk assessment and prevention of the transfer and spread of tigecycline resistant strains or genes.

Characterization of a novel Tn6485h transposon carrying both blaIMP-45 and blaAFM-1 integrated into the IncP-2 plasmid in a carbapenem-resistant Pseudomonas aeruginosa

OBJECTIVES

To characterize a carbapenem-resistant Pseudomonas aeruginosa (CRPA) with an IncP-2 plasmid containing a novel transposon, Tn6485h, which carries both blaIMP-45 and blaAFM-1.

METHODS

Antimicrobial susceptibility testing and filter mating experiment were performed on PA942. The stability of the plasmid carrying both blaIMP-45 and blaAFM-1 was carried out. We determined the growth rate of the transconjugant to investigate fitness cost. Additionally, whole-genome sequencing and genomic analysis were performed on PA942.

RESULTS

PA942 strain was resistant to most antibiotics except for ciprofloxacin and colistin. Bioinformatics analysis confirmed that PA942 contains an IncP-2 plasmid with a novel transposon Tn6485h carrying both blaIMP-45 and blaAFM-1. The plasmid pPA942-IMP45 can be transferred into recipient bacteria PAO1Rif with an efficiency of 2.2 × 10-7 and the transconjugant PAO1Rif/ pPA942-IMP45 can be stably inherited for 10 generations in the absence of antibiotics.

CONCLUSION

We report a carbapenem-resistant P. aeruginosa strain with an IncP-2 plasmid containing a novel transposon, Tn6485h, which carries both blaIMP-45 and blaAFM-1. The IncP-2 plasmid and transposon Tn6485h may contribute to the spread of MBL genes. Therefore, effective measures to prevent the spread of these plasmids should be taken.

Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen

Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.

Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

BACKGROUND

The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague.

RESULTS

To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and bla_GMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity.

CONCLUSIONS

This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.

IncHI1 plasmids are epidemic vectors that mediate transmission of tet(X4) in Escherichia coli isolated from China

Introduction

This study aimed to investigate the genetic factors promoting widespread Q6 dissemination of tet(X4) between Escherichia coli and to characterize the genetic contexts of tet(X4).

Methods

We isolated E. coli from feces, water, soil and flies collected across a large-scale chicken farm in China in 2020. Antimicrobial susceptibility testing and PFGE typing were used to identify tigecycline resistance and assess clonal relationships among isolates. Plasmids present and genome sequences were analyzed by conjugation, S1 pulsed-field gel electrophoresis (PFGE), plasmid stability testing and whole-genome sequencing.

Results

A total of 204 tigecycline-resistant E. coli were isolated from 662 samples. Of these, we identified 165 tet(X4)-carrying E. coli and these strains exhibited a high degree of multidrug resistance. Based on the geographical location distribution of the sampled areas, number of samples in each area and isolation rate of tigecycline-resistant strains and tet(X4)-carrying isolates, 72 tet(X4)-positive isolates were selected for further investigation. Tigecycline resistance was shown to be mobile in 72 isolates and three types of tet(X4)-carrying plasmids were identified, they were IncHI1 (n = 67), IncX1 (n = 3) and pO111-like/IncFIA(HI1) (n = 2). The pO111-like/IncFIA(HI1) is a novel plasmid capable of transferring tet(X4). The transfer efficiency of IncHI1 plasmids was extremely high in most cases and IncHI1 plasmids were stable when transferred into common recipient strains. The genetic structures flanked by IS1, IS26 and ISCR2 containing tet(X4) were complex and varied in different plasmids.

Discussion

The widespread dissemination of tigecycline-resistant E. coli is a major threat to public health. This data suggests careful use of tetracycline on farms is important to limit spread of resistance to tigecycline. Multiple mobile elements carrying tet(X4) are in circulation with IncHI1 plasmids the dominant vector in this setting.

Impact of different organic matters on the occurrence of antibiotic resistance genes in activated sludge

The occurrence of antibiotic resistance genes (ARGs) in various environments has drawn worldwide attention due to their potential risks. Previous studies have reported that a variety of substances can enhance the occurrence and dissemination of ARGs. However, few studies have compared the response of ARGs under the stress of different organic matters in biological wastewater treatment systems. In this study, seven organic pollutants were added into wastewater treatment bioreactors to investigate their impacts on the ARG occurrence in activated sludge. Based on high-throughput sequencing, it was found that the microbial communities and ARG patterns were significantly changed in the activated sludge exposed to these organic pollutants. Compared with the non-antibiotic refractory organic matters, antibiotics not only increased the abundance of ARGs but also significantly changed the ARG compositions. The increase of Gram-negative bacteria (e.g., Archangium, Prosthecobacter and Dokdonella) carrying ARGs could be the main cause of ARG proliferation. In addition, significant co-occurrence relationships between ARGs and mobile genetic elements were also observed in the sludge samples, which may also affect the ARG diversity and abundance during the organic matter treatment in the bioreactors. Overall, these findings provide new information for better understanding the ARG occurrence and dissemination caused by organic pollutants in wastewater treatment systems.

Effect of hydrochar on antibiotic-resistance genes and relevant mechanisms during chicken manure composting

The reduction of enhanced antibiotic resistance genes (ARGs) in compost is important to mitigate the risk of ARG transmission in agricultural production. Hydrochar is used in many applications as a functional carbon material with adsorption and catalytic properties. This study investigated the effects of hydrochar addition on bacterial communities, mobile genetic elements (MGEs), and ARGs in chicken manure composting. The addition of 2%, 5%, and 10% hydrochar (dry weight) reduced the total numbers of target ARGs and MGEs in the compost products by 40.13-55.33% and 23.63-37.23%, respectively. Hydrochar changed the succession of the bacterial population during composting, lowering the abundance of potential pathogens and promoting microbial activity in amino acid and carbohydrate metabolism. A significant possible microbial host for ARGs was found to be Firmicutes. Hydrochar was found to affect the host microorganisms and MGEs directly by altering environmental factors that indirectly impacted the ARG profiles, as shown by partial least squares pathway modeling analysis. In conclusion, the addition of hydrochar to compost is a simple and effective method to promote the removal of ARGs.

Complete Genetic Analysis of Plasmids Carrying Multiple Resistance, Virulence, and Phage-Like Genes in Foodborne Escherichia coli Isolate

Bacterial antimicrobial resistance, especially phenotypic resistance to multiple drugs (MDR), has posed a serious threat to public health worldwide. To clarify the mechanism of transmission of multidrug resistance encoding plasmids in Enterobacterales, all seven plasmids of an Escherichia coli (E. coli) strain 1108 obtained from a chicken meat sample were extracted and sequenced by Illumina Nextseq 500 and MinION platforms. Plasmids in strain 1108 possessed 16 known antimicrobial resistance genes, with p1108-NDM (~97K) being the most variable plasmid. The multidrug resistance region of p1108-NDM was punctuated by eight IS26 insertion sequences; thus, four MDR regions were found in the backbone of this plasmid. The plasmid p1108-MCR (~65K) was found to lack the ISApl1 element and harbor the blaCTX-M-64-ISEcp1 transposition unit. Moreover, the ISEcp1-blaCMY-2 transposition unit was found in plasmid p1108-CMY2 (~98K), whereas plasmid p1108-emrB (~102K) was associated with resistance to erythromycin (emrB) and streptomycin (aadA22). p1108-IncY (96K) was a phage P1-like plasmid, while p1108-IncFIB (~194K) was found to harbor a virulence region similar to ColV plasmids, and they were found to encode a conserved conjugative transfer protein but harbor no resistance genes. Finally, no mobile element and resistant genes were found in p1108-ColV (~2K). Carriage of mcr-1-encoding elements in carbapenemase-producing Escherichia coli will potentially render all antimicrobial treatment regimens ineffective. Enhanced surveillance and effective intervention strategies are urgently needed to control the transmission of such multidrug resistance plasmids. IMPORTANCE Antimicrobial resistance (AMR) has been increasingly prevalent in agricultural and clinical fields. Understanding the genetic environment involved in AMR genes is important for preventing transmission and developing mitigation strategies. In this study, we investigated the genetic features of an E. coli strain (1108) isolated from food product and harboring 16 AMR genes, including blaNDM-1 and mcr-1 genes encoding resistance to last line antibiotics, meropenem, and colistin. Moreover, this strain also carried virulence genes such as iroBCDEN, iucABCD, and iutA. Our findings confirmed that multiple conjugative plasmids that were formed through active recombination and translocation events were associated with transmission of AMR determinants. Our data warrant the continuous monitoring of emergence and further transmission of these important MDR pathogens.

Spread of blaCTX-M-9 and Other Clinically Relevant Resistance Genes, Such as mcr-9 and qnrA1, Driven by IncHI2-ST1 Plasmids in Clinical Isolates of Monophasic Salmonella enterica Serovar Typhimurium ST34

The monophasic 4,[5],12:i:-variant of Salmonella enterica serovar Typhimurium with sequence type ST34 has become one of the most prevalent non-typhoidal salmonellae worldwide. In the present study, we thoroughly characterized seven isolates of this variant detected in a Spanish hospital and selected based on cefotaxime resistance and cefoxitin susceptibility, mediated by blaCTX-M-9. For this, conventional microbiological techniques, together with whole genome sequencing performed with the Illumina platform, were applied. All selected isolates carried the resistance region RR or variants therein, and most also contained the SGI-4 genomic island. These chromosomal elements, typically associated with monophasic S. Typhimurium ST34, confer resistance to traditional antibiotics (ampicillin, streptomycin, sulfonamides, and tetracycline) and tolerance to heavy metals (mercury, silver, and copper). In addition, each isolate carried a large IncHI2-ST1 conjugative plasmid containing additional or redundant resistance genes. All harbored the blaCTX-M-9 gene responsible for cefotaxime resistance, whereas the qnrA1 gene mediating fluoroquinolone resistance was detected in two of the plasmids. These genes were embedded in ISCR1-bearing complex class 1 integrons, specifically In60-like and In36-like. The mcr-9 gene was present in all but one of the IncHI2-ST1 plasmids found in the analyzed isolates, which were nevertheless susceptible to colistin. Most of the resistance genes of plasmid origin clustered within a highly complex and variable region. The observed diversity results in a wide range of resistance phenotypes, enabling bacterial adaptation to selective pressure posed by the use of antimicrobials.

Association of ISVsa3 with Multidrug Resistance in Salmonella enterica Isolates from Cattle (Bos taurus)

Salmonella enterica is, globally, an important cause of human illness with beef being a significant attributable source. In the human patient, systemic Salmonella infection requires antibiotic therapy, and when strains are multidrug resistant (MDR), no effective treatment may be available. MDR in bacteria is often associated with the presence of mobile genetic elements (MGE) that mediate horizontal spread of antimicrobial resistance (AMR) genes. In this study, we sought to determine the potential relationship of MDR in bovine Salmonella isolates with MGE. The present study involved 111 bovine Salmonella isolates obtained collectively from specimens derived from healthy cattle or their environments at Midwestern U.S. feedyards (2000–2001, n = 19), or specimens from sick cattle submitted to the Nebraska Veterinary Diagnostic Center (2010–2020, n = 92). Phenotypically, 33/111 isolates (29.7%) were MDR (resistant to ≥3 drug classes). Based on whole-genome sequencing (WGS; n = 41) and PCR (n = 111), a MDR phenotype was strongly associated (OR = 186; p < 0.0001) with carriage of ISVsa3, an IS91-like Family transposase. In all 41 isolates analyzed by WGS ((31 MDR and 10 non-MDR (resistant to 0–2 antibiotic classes)), MDR genes were associated with carriage of ISVsa3, most often on an IncC type plasmid carrying blaCMY-2. The typical arrangement was floR, tet(A), aph(6)-Id, aph(3″)-Ib, and sul2 flanked by ISVsa3. These results suggest that AMR genes in MDR S. enterica isolates of cattle are frequently associated with ISVsa3 and carried on IncC plasmids. Further research is needed to better understand the role of ISVsa3 in dissemination of MDR Salmonella strains.

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.

Whole-Genome Analysis of blaNDM-Bearing Proteus mirabilis Isolates and mcr-1-Positive Escherichia coli Isolates Carrying blaNDM from the Same Fresh Vegetables in China

The global spread of colistin or carbapenem-resistant Enterobacteriaceae (CRE) has been a pressing threat to public health. Members of Enterobacteriaceae, especially Proteus mirabilis and Escherichia coli, have been prevalent foodborne pathogens and such pathogens from fresh vegetables have triggered foodborne illness in China. However, reports about CRE, especially P. mirabilis from fresh vegetables, are still lacking. In this study, we identified five bla_NDM-positive P. mirabilis and five bla_NDM-positive generic E. coli concurrently from five fresh vegetables in two markets from China, and four of the five E. coli also carried mcr-1. The 10 isolates were characterized with methods including antimicrobial susceptibility testing, conjugation, whole-genome sequencing and phylogenetic analysis. All 10 isolates were multidrug-resistant (MDR). bla_NDM-5 in five E. coli isolates and one P. mirabilis carrying bla_NDM-5 was located on similarly transferable IncX3 plasmids, while transferably untypable plasmids were the carriers of bla_NDM-1 in four P. mirabilis isolates from different types of vegetables/markets. mcr-1 in the four bla_NDM-₅-positive E. coli was located on similarly non-conjugative IncHI2 MDR plasmids lacking transfer region. Notably, ISCR1 complex class 1 integron capable of capturing bla_NDM-1 was found on all untypable plasmids from P. mirabilis, and five copies of ISCR1 complex class 1 integron containing bla_NDM-1 even occurred in one P. mirabilis, which showed high-level carbapenem resistance. Plasmid and phylogenetic analysis revealed that the bla_NDM-positive P. mirabilis and E. coli from fresh vegetables might be derived from animals and transmitted to humans via the food chain. The concurrence of bla_NDM-positive P. mirabilis and E. coli carrying both mcr-1 and bla_NDM in different types of fresh vegetables eaten raw is alarming and threatens food safety. Sustained surveillance of these foodborne pathogens among fresh vegetables is urgent to ensure the health of food consumers. We report for the first time the concurrence of bla_NDM-positive P. mirabilis and mcr-1-bearing E. coli carrying bla_NDM from the same fresh vegetables.

Epidemiological characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic analysis of Aeromonas caviae isolated from extra-intestinal infections

Objective

Aeromonas caviae (A. caviae) is one of the major etiological agents in human intestinal infections reported to be associated with a broad spectrum of extra-intestinal infections with increasing incidence over recent years. Although previous studies have established its significance as a causative agent of both bloodstream and gastrointestinal infections, the characteristics of A. caviae that cause extra-intestinal infections remain unilluminated.In this single-center retrospective study, we investigated epidemiological characteristics, antimicrobial resistance genes and phenotypes, virulence genes, and phyloevolution of 47 clinical A. caviae isolated from patients with extra-intestinal infections from 2017 to 2020.

Methods

A. caviae strains were identified by biochemical tests and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/MS), ultimately confirmed to species level by whole-genome sequencing (WGS). Antimicrobial resistance and virulence genes were identified using the Comprehensive Antibiotic Resistance Database (CARD) and the virulence factor database (VFDB), respectively. Phylogenetic analysis of 47 clinical strains was performed by combining with 521 A. caviae strains from NCBI database.

Results

A. caviae was an opportunistic pathogen in immunocompromised patients, especially those with underlying hepatobiliary diseases and malignancies. 19 out of 47 isolates were identified as multidrug resistance (MDR) strains. Piperacillin-tazobactam, levofloxacin, gentamicin, amikacin with a resistance rate of less than 10% remained as options to treat extra-intestinal infections. 24 out of 47 isolates exhibited non-susceptibility to cephalosporins and cephamycins, all of which carried β-lactamase gene, including bla _MOX, bla _PER-3, bla _OXA, bla _NDM, and bla _CphA. Most stains (98%, 46/47) carried at least one of the virulence genes, but extra-intestinal infections had a low mortality rate. Phylogenetic analysis indicated the risk of nosocomial transmission but revealed no outbreak. However, the emergence of MDR and β-lactamase resistance genes in extra-intestinal isolates of A. caviae is becoming an increasing risk to public health and requires attention.

Conclusions

This study strengthen our understanding of A.caviae isolated from extra-intestinal infections. It may contribute to the management of extra-intestinal infections as well as the prevention and control of drug resistance.

Structural Basis of PER-1-Mediated Cefiderocol Resistance and Synergistic Inhibition of PER-1 by Cefiderocol in Combination with Avibactam or Durlobactam in Acinetobacter baumannii

Cefiderocol is a novel siderophore cephalosporin that displays activity against Gram-negative bacteria. To establish cefiderocol susceptibility levels of Acinetobacter baumannii strains from China, we performed susceptibility testing and genomic analyses on 131 clinical isolates. Cefiderocol shows high activity against the strains. The production of PER-1 is the key mechanism of cefiderocol resistance. In silico studies predicted that avibactam and durlobactam could inhibit cefiderocol hydrolysis by PER-1, which was confirmed by determining cefiderocol MICs in combination with inhibitors.

Tandem Repeat of bla NDM-1 and Clonal Dissemination of a fosA3 and bla KPC-2 Co-Carrying IncR-F33: A-: B- Plasmid in Klebsiella pneumoniae Isolates Collected in a Southwest Hospital in China, 2010-2013

Introduction

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has been widespread in coastal cities of eastern China since 2009. However, how CRKP spreads and evolves in southwest China is unclear.

Aim

We investigated the genetic characteristics and dissemination mechanisms of carbapenemase genes in forty-one non-repetitive CRKP isolates collected from a southwest hospital, Kunming, Yunnan, during 2010-2013.

Methodology

Drug susceptibilities were analyzed by using VITEK 2 compact system. Genetic relationships were ascertained based on multilocus sequence typing (MLST) and Pulsed-field gel electrophoresis (PFGE) analysis. Genetic backgrounds of bla _KPC-2 and bla _NDM-1 were revealed by DNA walking and high-throughput sequencing.

Results

All isolates were highly resistant to common antibiotics except for tigecycline. In total, 34 bla _KPC-2, 3 bla _NDM-1, 1 bla _IMP-4 and 3 bla _IMP-26 genes were identified and KP67 plasmid 1 co-harbored bla _NDM-1 and bla _IMP-26. Five sequence types, namely ST11, ST290, ST340, ST395 and ST437, were recognized by MLST. Surprisingly, bla _KPC-2 was only detected in ST11 strains. We described a clonal dissemination of fosA3-positive IncR-IncF33:A-:B- multireplicon plasmid carrying the gene cassettes IS26-ΔTn3-ISKpn27-bla _KPC-2-ΔISKpn6-korC-klcA-ΔrepB-Tn1721 in all ST11 isolates. Three bla _NDM-1 positive isolates belonged to three different ST types and their bla _NDM-1 genetic backgrounds were also distinct. Interestingly, the flanking regions of bla _NDM-1 in KP67 and KP72 were duplicated into one to five copies in a form of tandem repeat by the transposition of IS91 like element. The bla _NDM-1 of KP82 was carried on a common IncX3 plasmid.

Conclusion

This study described the early epidemiological characteristics of bla _KPC-2/bla _NDM-1-carrying CRKP, and reported a new tandem repeat pattern of bla _NDM-1 cluster in Yunnan. These findings extend our knowledge on the carbapenemase gene evolutions.

Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination

Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.

Investigating changes in the characteristics of antibiotic resistance genes at different reaction stages of high solid anaerobic digestion with pig manure

Contamination of antibiotic resistance genes (ARGs) from animals is a serious issue as they may spread to human pathogenic bacteria. The reduction of ARG contamination from livestock waste is thus essential. High solid anaerobic digestion (HSAD) is a new and effective technology although some aspects, such as change characteristics of ARGs at different reaction stages, have not been fully investigated. This study focused firstly on the variations in ARGs at different reaction stages in HSAD systems with five different starting methods: 1 natural start (the control) and 4 rapid starts by changing leachate reflux forms. The results showed that the rapid starting methods could accelerate start-up and increase biogas production by 312.5%. The starting and acidification stages showed higher microbial richness and diversity compared with the other stages. ARGs found to be reduced at acidification stage. Variation in ARGs at the starting and acidification stages was mainly driven by a combination of microbial community, mobile genetic elements (MGEs), and environmental factors; while the main contributory factors at the gas production stage were biomass and several unexplained factors. At the ending stage, the main driving factors were biomass and microbial communities. Most of the potential hosts (16/20) of the ARGs belonged to the Firmicutes phylum, which showed the lowest connections with the ARGs at the gas production stage.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Plasmid-Borne AFM Alleles in Pseudomonas aeruginosa Clinical Isolates from China

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a pathogen of global concern due to the fact that therapeutic drugs are limited. Metallo-β-lactamase (MBL)-producing P. aeruginosa has become a critical part of CRPA. Alcaligenes faecalis metallo-β-lactamase (AFM) is a newly identified subclass B1b MBL. In this study, 487 P. aeruginosa strains isolated from patients and the environment in an intensive care unit were screened for AFM alleles. Five AFM-producing strains were identified, including four AFM-2-producing strains (ST262) and one AFM-4-producing strain (ST671). AFM-2-producing strains were isolated from rectal and throat swabs, and AFM-4-producing strains were isolated from the water sink. The bla_AFM-2 carrying plasmids belonged to the IncP-2 type, while the bla_AFM-4 carrying plasmid pAR19438 was a pSTY-like megaplasmid. Plasmid pAR19438 was acquired bla_AFM-4 by the integration of the Tn1403-like transposon. All bla_AFM genes were embedded in an ISCR29-bla_AFM unit core module flanked by class 1 integrons. The core module of bla_AFM-2 was ISCR29-ΔgroL-bla_AFM-2-ble_MBL-ΔtrpF-ΔISCR, while the core module of bla_AFM-4 was ISCR29-ΔgroL-bla_AFM-2-ble_MBL-ΔtrpF-ISCR-msrB-msrA-yfcG-corA-ΔISCR. The flanking sequences of ISCR29-bla_AFM units also differed. The expression of AFM-2 and AFM-4 in DH5α and PAO1 illustrated the same effect for the evaluation of the MICs of β-lactams, except for aztreonam. Identification of AFM-4 underscores that the quick spread and emerging development of mutants of MBLs require continuous surveillance in P. aeruginosa. IMPORTANCE Acquiring metallo-β-lactamase genes is one of the important carbapenem resistance mechanisms of P. aeruginosa. Alcaligenes faecalis metallo-β-lactamase is a newly identified metallo-β-lactamase, the prevalence and genetic context of which need to be explored. In this study, we identified AFM-producing P. aeruginosa strains among clinical isolates and found a new mutant of AFM, AFM-4. The bla_AFM-4 carrying plasmid pAR19438 was a pSTY-like megaplasmid, unlike the plasmids encoding other bla_AFM alleles. The genetic context of bla_AFM-4 was also different. However, AFM-2 and AFM-4 had the same impacts on antibiotic susceptibility. The presence and transmission of AFM alleles in P. aeruginosa pose a challenge to clinical practice.

Fate of resistome components and characteristics of microbial communities in constructed wetlands and their receiving river

Currently, most researches focus on that constructed wetlands (CWs) achieve desirable removal of antibiotics, antibiotic resistance genes (ARGs) and human pathogens. However, few studies have assessed the fate of resistome components, especially the behavior and cooccurrence of ARGs, mobile genetic elements (MGEs) and virulence factors (VFs). Therefore, characteristics of microbial communities (MCs) in CWs and their receiving rivers also deserve attention. These factors are critical to water ecological security. This study used two CWs to explore the fate of resistome components and characteristics of MCs in the CWs and their receiving river. Eleven samples were collected from the two CWs and their receiving river. High-throughput profiles of ARGs and microbial taxa in the samples were characterized. 31 ARG types consisting of 400 subtypes with total relative abundance 42.63-84.94× /Gb of sequence were detected in CWs, and 62.07-88.08× /Gb of sequence in river, evidencing that ARG pollution covered CWs and the river, and implying huge potential risks from ARGs. MGEs and VFs were detected, and tnpA, IS91 and intI1 were the three dominant MGEs, while Flagella. Type IV pili and peritrichous flagella were main VFs. Both CWs can remove ARGs, MGEs and VFs efficiently. However, some ARGs were difficult to remove, such as sul1 and sul2, and certain ARGs remained in the effluent of the CWs. The co-occurrence of ARGs, MGEs, and VFs implies the risk of antibiotic resistance and dissemination of ARGs. Eighty-five types of human pathogen were detected in the river samples, particularly Pseudomonas aeruginosa, Bordetella bronchiseptica, Aeromonas hydrophila and Helicobacter pylori. Correlation analysis indicated that MCs had significant effects on the profiles of ARGs in the water environment. This study reveals potential risks of the reuse of reclaimed water, and illustrates the removal ability of ARGs and related elements by CWs. This study will be helpful for monitoring and managing resistomes in water environments.

Characterization of a genomic Island carrying the tet(X4) gene in porcine Acinetobacter towneri co-harboring plasmid-borne blaNDM−1 and blaOXA−58 genes

Tigecycline and carbapenems are last-resort antimicrobial agents to treat serious infections caused by multi-drug resistant bacterial pathogens. However, the co-occurrence of tigecycline and carbapenem resistance determinants challenges the clinical efficacy of these antimicrobial agents. In this study, we report the co-existence of tet(X4), bla_NDM−1 and bla_OXA−58 genes in the porcine Acinetobacter towneri isolate 19110F47. Sequence analysis revealed that tet(X4) gene, along with the florfenicol resistance gene floR, was flanked by three copies of IS91-like elements, which can form three different translocatable units (TUs), and were located in a 41,098-bp multidrug resistance region (MDRR) within a novel 100,354-bp genomic island (GI) region. TUs comprising floR-virD2-ISVsa3, hp-abh-tet(X4)-ISVsa3 and virD2-floR-ISVsa3-hp-abh-tet(X4)-ISVsa3 can be looped out from the chromosomal DNA and facilitate the transfer of the TU-based resistance genes into other plasmidic or chromosomal sites. In addition, the carbapenemase genes bla_NDM−1 and bla_OXA−58 were found on different non-conjugative multiresistance plasmids in this isolate, with the genetic contexts ISAba125-bla_NDM−1-ble_MBL-tnpR and ΔISAba3-bla_OXA−58-ISAba3, respectively. The simultaneous occurrence of tet(X4), bla_NDM−1 and bla_OXA−58 in the same porcine A. towneri isolate emphasizes the importance of antimicrobial resistance surveillance in food-producing animals.

CTX-M-Producing Bacteria Isolated from a Highly Polluted River System in Portugal

Enterobacteriaceae resistant to third-generation cephalosporins are a great concern for public health, as these are first-line drugs to treat infections. The production of carbapenemases and extended spectrum beta-lactamases (ESBLs) and/or the overexpression of AmpC β-lactamases are the main mechanisms of resistance to these antibiotics. Among the ESBLs, CTX-M β-lactamases are the most prevalent worldwide. Our aims were to determine the prevalence of cefotaxime-resistant Enterobacteriaceae along a heavily polluted river and characterize bla_CTX-M carriers. River water was collected in 11 sites along the main course and tributaries, in two sampling moments. Water quality was evaluated and a collection of cefotaxime-resistant isolates was obtained. bla_CTX-M carriers were characterized regarding phylogenetic affiliation, clonality, antibiotic susceptibility, gene diversity, and context. Water presented very low quality in all sites. From 147 cefotaxime-resistant isolates, 46% carried bla_CTX-M and were affiliated with Escherichia, Klebsiella, Enterobacter, and Citrobacter. Molecular typing revealed clonal isolates in different sites and over the two years, suggesting survival of the strains in the river or continuous pollution inputs from the same sources. Eight variants of bla_CTX-M were found, with bla_CTX-M-15 being the most prevalent (52.5%). Sites with a lower water quality showed the highest resistance rates and prevalence of bla_CTX-M, suggesting that river water may embody human health risks.

An 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.

Dissemination of antimicrobial-resistant isolates of Salmonella spp. in wild boars and its relationship with management practices

Antimicrobial resistance (AMR) is a global concern and controlling its spread is critical for the effectiveness of antibiotics. Members of the genus Salmonella are broadly distributed, and wild boar may play an important role in its circulation between peri-urban areas and the environment, due to its frequent interactions both with livestock or human garbage. As the population of these animals is rising due to management on certain hunting estates or the absence of natural predators, the aim of the present work is to identify the mechanisms of AMR present and/or expressed in Salmonella spp. from wild boar populations and to determine the possible role of management-related factors applied to different game estates located in central Spain. The detection of Salmonella spp. was carried out in 121 dead wild boar from 24 game estates, and antimicrobial resistance traits were determined by antibiotic susceptibility testing and screening for their genetic determinants. The effects of feeding supplementation, the proximity of livestock, the existence of a surrounding fence and the density of wild boar on the AMR of the isolates were evaluated. The predominant subspecies and serovar found were S. enterica subsp. enterica (n = 69) and S. choleraesuis (n = 33), respectively. The other subspecies found were S. enterica subsp. diarizonae, S. enterica subsp. salamae and S. enterica subsp. houtenae. AMR was common among isolates (75.2%) and 15.7% showed multi drug resistance (MDR). Resistance to sulphonamides was the most frequent (85.7%), as well as sul1 which was the AMR determinant most commonly found. Plasmids appeared in 38.8% of the isolates, with IncHI1 being the replicon detected with the highest prevalence. The AMR of the isolates increased when the animals were raised with feeding supplementation and enclosed by fences around the estates.

A blaSIM-1 and mcr-9.2 harboring Klebsiella michiganensis strain reported and genomic characteristics of Klebsiella michiganensis

As a newly emerging Klebsiella pathogen, more and more Klebsiella michiganensis drug resistant strains have been reported in recent years, which posed serious threats to public health. Here we first reported a multidrug-resistant K. michiganensis strain 12084 with two blaSIM-1 and one mcr-9.2 genes isolated from the sputum specimen of a patient in the Second Affiliated Hospital of Zhejiang University School of Medicine and analyzed its genetic basis and drug-resistance phenotypes. Genetic analysis showed that this strain harbored three different incompatibility groups (IncHI2, IncHI5, and IncFIIpKPHS2:IncFIB-4.1) of plasmids (p12084-HI2, p12084-HI5, and p12084-FII). A total of 26 drug-resistance genes belonging to 12 classes of antibiotics were identified, most of which (24) were located on two plasmids (p12084-HI2 and p12084-HI5). Interestingly, two blaSIM-1 genes were identified to locate on p12084-HI2 and p12084-HI5, respectively, both of which were embedded in In630, indicating their genetic homogeny. It was noting that one blaSIM-1 gene was situated in a novel unit transposon (referred to as Tn6733) on the p12084-HI5 plasmid. We also discovered an mcr-9.2 gene on the p12084-HI2 plasmid. To the best of our knowledge, this is the first report of a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain. We then investigated the population structure/classification, and antibiotic resistance for all 275 availably global K. michiganensis genomes. Population structure revealed that K. michiganensis could be divided into two main clades (Clade 1 and Clade 2); the most popular ST29 was located in Clade 1, while other common STs (such as ST50, ST27, and ST43) were located in Clade 2. Drug-resistance analysis showed 25.5% of the K. michiganensis strains (70/275) harboring at least one carbapenemase gene, indicating severe drug resistance of K. michiganensis beyond our imagination; this is a dangerous trend and should be closely monitored, especially for ST27 K. michiganensis with the most drug-resistant genes among all the STs. Overall, we reported a blaSIM-1 and mcr-9.2 harboring K. michiganensis strain, and further revealed the population structure/classification, and drug-resistance of K. michiganensis, which provided an important framework, reference, and improved understanding of K. michiganensis.

The integrase of genomic island GIsul2 mediates the mobilization of GIsul2 and ISCR-related element CR2-sul2 unit through site-specific recombination

In the worldwide health threat posed by antibiotic-resistant bacterial pathogens, mobile genetic elements (MGEs) play a critical role in favoring the dissemination of resistance genes. Among them, the genomic island GIsul2 and the ISCR-related element CR2-sul2 unit are believed to participate in this dissemination. However, the mobility of the two elements has not yet been demonstrated. Here, we found that the GIsul2 and CR2-sul2 units can excise from the host chromosomal attachment site (attB) in Shigella flexneri. Through establishing a two-plasmid mobilization system composed of a donor plasmid bearing the GIsul2 and a trap plasmid harboring the attB in recA-deficient Escherichia coli, we reveal that the integrase of GIsul2 can perform the excision and integration of GIsul2 and CR2-sul2 unit by site-specific recombination between att core sites. Furthermore, we demonstrate that the integrase and the att sites are required for mobility through knockout experiments. Our findings provide the first experimental characterization of the mobility of GIsul2 and CR2-sul2 units mediated by integrase. They also suggest a potential and unappreciated role of the GIsul2 integrase family in the dissemination of CR2-sul2 units carrying various resistance determinants in between.