Plasmid-associated antimicrobial resistance and virulence genes in Escherichia coli in a high arctic reindeer subspecies. - Related Documents




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197401.0000Plasmid-associated antimicrobial resistance and virulence genes in Escherichia coli in a high arctic reindeer subspecies. OBJECTIVES: In extreme environments, such as the Arctic region, the anthropogenic influence is low and the presence of antimicrobial-resistant bacteria is unexpected. In this study, we screened wild reindeer (Rangifer tarandus platyrhynchus) from the Svalbard High Arctic Archipelago for antimicrobial-resistant Escherichia coli and performed in-depth strain characterisation. METHODS: Using selective culturing of faecal samples from 55 animals, resistant E. coli were isolated and subjected to minimum inhibitory concentration (MIC) determination, conjugation experiments and whole-genome sequencing. RESULTS: Twelve animals carried antimicrobial-resistant E. coli. Genomic analysis showed IncF plasmids as vectors both for resistance and virulence genes in most strains. Plasmid-associated genes encoding resistance to ampicillin, sulfonamides, streptomycin and trimethoprim were found in addition to virulence genes typical for colicin V (ColV)-producing plasmids. Comparison with previously reported IncF ColV plasmids from human and animal hosts showed high genetic similarity. The plasmids were detected in E. coli sequence types (STs) previously described as hosts for such plasmids, such as ST58, ST88 and ST131. CONCLUSION: Antimicrobial-resistant E. coli were detected from Svalbard reindeer. Our findings show that successful hybrid antimicrobial resistance-ColV plasmids and their host strains are widely distributed also occurring in extreme environmental niches such as arctic ecosystems. Possible introduction routes of resistant bacterial strains and plasmids into Svalbard ecosystems may be through migrating birds, marine fish or mammals, arctic fox (Vulpes lagopus) or via human anthropogenic activities such as tourism.202134216807
159510.9997Anthropogenic antibiotic resistance genes mobilization to the polar regions. Anthropogenic influences in the southern polar region have been rare, but lately microorganisms associated with humans have reached Antarctica, possibly from military bases, fishing boats, scientific expeditions, and/or ship-borne tourism. Studies of seawater in areas of human intervention and proximal to fresh penguin feces revealed the presence of Escherichia coli strains least resistant to antibiotics in penguins, whereas E. coli from seawater elsewhere showed resistance to one or more of the following antibiotics: ampicillin, tetracycline, streptomycin, and trim-sulfa. In seawater samples, bacteria were found carrying extended-spectrum β-lactamase (ESBL)-type CTX-M genes in which multilocus sequencing typing (MLST) showed different sequence types (STs), previously reported in humans. In the Arctic, on the contrary, people have been present for a long time, and the presence of antibiotic resistance genes (ARGs) appears to be much more wide-spread than was previously reported. Studies of E coli from Arctic birds (Bering Strait) revealed reduced susceptibility to antibiotics, but one globally spreading clone of E. coli genotype O25b-ST131, carrying genes of ESBL-type CTX-M, was identified. In the few years between sample collections in the same area, differences in resistance pattern were observed, with E. coli from birds showing resistance to a maximum of five different antibiotics. Presence of resistance-type ESBLs (TEM, SHV, and CTX-M) in E. coli and Klebsiella pneumoniae was also confirmed by specified PCR methods. MLST revealed that those bacteria carried STs that connect them to previously described strains in humans. In conclusion, bacteria previously related to humans could be found in relatively pristine environments, and presently human-associated, antibiotic-resistant bacteria have reached a high global level of distribution that they are now found even in the polar regions.201627938628
562120.9997Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes. Background/Objectives: The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Methods: Using a large-scale screening approach, we analyzed 3107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5α and performed whole-genome sequencing on 37 representative isolates. Results: Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread (92% of isolates carried one or more bacteriocin gene clusters), with colicins and microcins dominating the profiles. Notably, we identified an hcp-et3-4 gene cluster encoding an effector linked to a Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain (strain D96). Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Conclusions: Our study highlights the co-occurrence of bacteriocin genes, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications.202541009839
197830.9997Antibiotic resistance plasmids in Enterobacteriaceae isolated from fresh produce in northern Germany. In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system. IMPORTANCE: This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.202439287384
204140.9997Carrier flies of multidrug-resistant Escherichia coli as potential dissemination agent in dairy farm environment. The life cycle of synanthropic flies and their behavior, allows them to serve as mechanical vectors of several pathogens. Given that flies can carry multidrug-resistant (MDR) bacteria, this study aimed to investigate the spread of genes of antimicrobial resistance in Escherichia coli isolated from flies collected in two dairy farms in Brazil. Besides antimicrobial resistance determinants, the presence of virulence genes related to bovine colibacillosis was also assessed. Of 94 flies collected, Musca domestica was the most frequently found in the two farms. We isolated 198 E. coli strains (farm A=135 and farm B=63), and >30% were MDR E. coli. We found an association between bla(TEM) and phenotypical resistance to ampicillin, or chloramphenicol, or tetracycline; and bla(CTX-M) and resistance to cefoperazone. A high frequency (86%) of phylogenetic group B1 among MDR strains and the lack of association between multidrug resistance and virulence factors suggest that antimicrobial resistance possibly is associated with the commensal bacteria. Clonal relatedness of MDR E. coli performed by Pulsed-Field Gel Electrophoresis showed wide genomic diversity. Different flies can carry clones, but with distinct antimicrobial resistance pattern. Sanger sequencing showed that the same class 1 integron arrangement is displayed by apparently unrelated strains, carried by different flies. Our conjugation results indicate class 1 integron transfer associated with tetracycline resistance. We report for the first time, in Brazil, that MDR E. coli is carried by flies in the milking environment. Therefore, flies can act as carriers for MDR strains and contribute to dissemination routes of antimicrobial resistance.201829758886
204350.9997Antimicrobial Resistance Genotypes and Mobile Genetic Elements of Poultry-Derived Escherichia coli: A Retrospective Genomic Study from the United States. The presence of antibiotic resistance in commensal bacteria may be an influential factor in the persistence of resistance in pathogens. This is especially critical for Escherichia coli that consumers may be exposed to through the consumption of uncooked meat. In this study, E. coli isolates previously recovered from poultry in the US between 2001 and 2012 were whole-genome sequenced to identify their antibiotic resistance genes and mobile genetic elements. The genomes of 98 E. coli isolates from poultry carcass rinsates and 2 isolates from poultry diagnostic samples with multidrug resistance or potential extended-spectrum β-lactam (ESBL)-producing phenotypes as well as the genetic variabilities among the E. coli were assessed. All E. coli isolates were positive for at least one antibiotic resistance gene and plasmid replicon, with 37 resistance genes and 27 plasmid replicons detected among the isolates. While no ESBL genes were detected, bla(CMY-2) was the most common β-lactamase gene, and bla(TEM) and bla(CARB-2) were also identified. Most isolates (95%) harbored at least one intact phage, and as many as seven intact phages were identified in one isolate. These results show the occurrence of antibiotic resistance genes and mobile genetic elements in these 100 poultry-associated E. coli isolates, which may be responsible for the resistance phenotypes exhibited by the isolates. This retrospective study also enables comparisons of resistance genes and mobile genetic elements from more recent E. coli isolates associated with poultry to aid in understanding the trends of both antibiotic resistance phenotypes and genotypes in the poultry setting over time.202540872236
557660.9997First insights into antimicrobial resistance among faecal Escherichia coli isolates from small wild mammals in rural areas. Wild rodents can be carriers of antimicrobial resistant Escherichia coli. As rodents are known to be involved in the transmission of bacteria of human and animal health concern, they could likewise contribute to the dissemination of antimicrobial resistant bacteria in the environment. The aim of this study was therefore to get first insights into the antimicrobial resistance status among E. coli isolated from wild small mammals in rural areas. We tested 188 faecal isolates from eight rodent and one shrew species originating from Germany. Preselected resistant isolates were screened by minimal inhibitory concentration (MIC) testing or agar diffusion test and subsequent PCR analysis of resistance genes. The prevalence of antimicrobial resistant isolates was low with only 5.5% of the isolates exhibiting resistant phenotypes against at least one antimicrobial compound including beta-lactams, tetracyclines, aminoglycosides and sulfonamides. These results suggest a minor role of wild rodents from rural areas in the cycle of transmission and spread of antimicrobial resistant E. coli into the environment. Nevertheless E. coli with multiple antimicrobial resistances were significantly more often detected in wildlife rodents originating from areas with high livestock density suggesting a possible transmission from livestock to wild rodents.201020569968
197270.9997Draft Genome Sequences of Multidrug-Resistant Escherichia coli Isolated from River Water. The spread of antibiotic resistance poses a critical challenge worldwide. Contaminated environments can become reservoirs, spreading antibiotic-resistant bacteria and genetic determinants of resistance to humans directly or indirectly. Here, we report the draft genome sequence, the resistome, virulence genes, and sequence types of seven multidrug-resistant Escherichia coli strains isolated from river water.202236222705
197380.9997Draft Genome Sequences of Multidrug-Resistant Escherichia coli Strains Isolated from River Water in Malaysia. Antimicrobial resistance has become a primary concern in clinical and public health. Escherichia coli is one of the bacteria that carries and disseminates antimicrobial resistance genes to the community. Here, we report the draft genome sequence of three multidrug-resistant E. coli strains that were isolated from river water in Malaysia.202235678586
198090.9997Genotypic analyses of IncHI2 plasmids from enteric bacteria. Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N = 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.202438684834
1894100.9997Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China. Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and bla(TEM-1) genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.202235467399
1979110.9997Diverse Fluoroquinolone Resistance Plasmids From Retail Meat E. coli in the United States. Fluoroquinolones are used to treat serious bacterial infections, including those caused by Escherichia coli and Salmonella enterica. The emergence of plasmid-mediated quinolone resistance (PMQR) represent a new challenge to the successful treatment of Gram-negative infections. As part of a long-term strategy to generate a reference database of closed plasmids from antimicrobial resistant foodborne bacteria, we performed long-read sequencing of 11 E. coli isolates from retail meats that were non-susceptible to ciprofloxacin. Each of the isolates had PMQR genes, including qnrA1, qnrS1, and qnrB19. The four qnrB19 genes were carried on two distinct ColE-type plasmids among isolates from pork chop and ground turkey and were identical to plasmids previously identified in Salmonella. Seven other plasmids differed from any other sequences in GenBank and comprised IncF and IncR plasmids that ranged in size from 48 to 180 kb. These plasmids also contained different combinations of resistance genes, including those conferring resistance to beta-lactams, macrolides, sulfonamides, tetracycline, and heavy metals. Although relatively few isolates have PMQR genes, the identification of diverse plasmids in multiple retail meat sources suggests the potential for further spread of fluoroquinolone resistance, including through co-selection. These results highlight the value of long-read sequencing in characterizing antimicrobial resistance genes of public health concern.201931866986
1977120.9997Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. INTRODUCTION: Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. OBJECTIVES: In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. RESULTS: The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. CONCLUSION: This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.202133717039
5738130.9997Unveiling the Genomic Landscape of Understudied Salmonella enterica Serovars from Poultry and Human: Implications for Food Safety. Despite the bacteria of the genus Salmonella are pathogens of zoonotic importance, the factors associated with some serovars genetic diversity remain unclear. We investigated genotypic profiles of antimicrobial resistance, plasmid replicons, and virulence factors in 301 S. enterica genomes from human and animal sources, supplemented by ten sequenced genomes from fecal samples of laying hens in Brazil. Many antimicrobial resistance genes have been detected across various Salmonella serovars; with a limited number of unique resistance genes predicted in poultry isolates compared to human isolates. Specifically, among the 52 antimicrobial resistance genes identified, 48% were shared between poultry and human isolates, while 21.1% were exclusive to poultry isolates and 30.7% were exclusive to human isolates. Chromosomal mutations in the gyrA and parC genes were also predicted. To the best of our knowledge, this is the first work to report S. Braenderup carrying the SPI-10. SGI-1 was detected in a few isolates of S. Schwarzengrund from poultry and the CS54 island was solely noticed in genomes referring to the serovars S. Saintpaul and S. Braenderup. Among the serovars analyzed, S. Saintpaul showed the lowest plasmid diversity. A total of 161 (161/271) virulence genes were common to all serovars, the remaining genes were exclusively identified within specific serovars, revealing a distinct distribution pattern within the S. enterica population. Overall, our study brings to light the genetic potential of Salmonella serovars frequently neglected in poultry production, which threatens public health, particularly due to multidrug-resistant profiles against active principles used to treat human infections.202540327155
1895140.9997Comparative Genome Analysis of Livestock and Human Colistin-Resistant Escherichia coli Isolates from the Same Household. BACKGROUND: Emergence and dissemination of colistin-resistant bacteria that harbor mobile colistin resistance (mcr) genes pose a dire challenge for the treatment of intractable infections caused by multidrug-resistant bacteria. Current findings on colistin-resistant bacteria in both humans and livestock of the same households highlight the need to identify the dissemination mechanisms of colistin-resistant bacteria. METHODS: In this study, a comparative genome analysis of colistin-resistant Escherichia coli isolates from livestock and humans of the same household was performed to clarify the possible dissemination mechanism of mcr genes among bacteria. Pulsed-field gel electrophoresis and whole-genome sequencing followed by sequence typing of the isolates were performed for assessment of the samples. RESULTS: The study revealed that two colistin-resistant E. coli isolates, one each from a pig and a chicken, were phylogenetically similar but not identical to the human isolates obtained from the same household. The comparative genome analysis revealed that the chicken isolate and a human isolate shared the same IncHl2 plasmid harboring the mcr transposon (mcr-1-PAP2). The pig isolate and the other human isolate retained the mcr-1 transposon on the chromosome, with the pig isolate carrying the complete mcr transposon (ISApl1-mcr-1-PAP2-ISApl1) and the human isolate carrying the incomplete mcr transposon (ISApl1-mcr-1-PAP2). CONCLUSION: The results of the study confirm the distribution of colistin-resistant bacteria and subsequent transmission of the resistance gene-carrying transposon between livestock and humans of the same household. To the best of our knowledge, this is the first report on genomic analysis of colistin-resistant E. coli isolates obtained from livestock and residents of the same household.202133688219
1930150.9997Changes in dominant Escherichia coli and antimicrobial resistance after 24 hr in fecal matter. Intestinal bacteria carry antimicrobial resistance (AMR) genes in mobile genetic elements which have the potential to spread to bacteria in other animal hosts including humans. In fecal matter, Escherichia coli can continue to multiply for 48 hr after being excreted, and in certain environments, E. coli survive long periods of time. It is unclear the extent to which AMR in E. coli changes in the environment outside of its host. In this study, we analyzed changes in the population structure, plasmid content, and AMR patterns of 30 E. coli isolates isolated from 6 chickens (cloacal swabs), and 30 E. coli isolates from fecal samples (from the same 6 chickens) after 24 hr of incubation. Clonality of isolates was screened using the fumC gene sequence and confirmed in a subset of isolates (n = 14) by multi-locus sequence typing. Major shifts in the population structure (i.e., sequence types) and antibiotic resistance patterns were observed among the numerically dominant E. coli isolates after 24 hr. Four E. coli clones isolated from the cloaca swabs and the corresponding fecal samples (after 24 hr incubation) showed different antibiotic resistance patterns. Our study reveals that fecal matter in the environment is an intermediate habitat where rapid and striking changes occur in E. coli populations and antibiotic resistance patterns.201929896865
5726160.9997Extra-Intestinal Fluoroquinolone-Resistant Escherichia coli Strains Isolated from Meat. Extra-intestinal E. coli are emerging as a global threat due to their diffusion as opportunistic pathogens and, above all, to their wide set of antibiotic resistance determinants. There are still many gaps in our knowledge of their origin and spread pathways, although food animals have been adjudicated vehicles for passing mult-drug resistant bacteria to humans. This study analyzed 46 samples of meat purchased from retail stores in Palermo in order to obtain quinolone-resistant E. coli isolates. Strains were screened for their phylogenetic groups, ST131-associated single nucleotide polymorphisms (SNPs), and then typed by ERIC-PCR. Their set of virulence factors, namely, kpsMII, papA, sfaS, focG, iutA, papC, hlyD, and afa genes, were investigated and their fluoroquinolone-resistance determinants evaluated. The data obtained show a dramatically high prevalence of multidrug resistance patterns in the Palermo area, with 28% of the isolates having virulence factor genes typical of ExPEC strains. No B2 group or ST131 strains were detected. Moreover, 20% of our isolates showed positivity to all the plasmid-mediated quinolone resistance (PMQR) determinants, showing a potential to transfer these genes among other bacteria. Therefore, these data underline the possibility that food animals and, specifically, poultry in particular may be a significant source of resistant bacterial strains, posing a potential zoonotic risk.201830581870
1600170.9996Simultaneous Carriage of mcr-1 and Other Antimicrobial Resistance Determinants in Escherichia coli From Poultry. The use of antimicrobial growth promoters (AGPs) in sub-therapeutic doses for long periods promotes the selection of resistant microorganisms and the subsequent risk of spreading this resistance to the human population and the environment. Global concern about antimicrobial resistance development and transference of resistance genes from animal to human has been rising. The goal of our research was to evaluate the susceptibility pattern to different classes of antimicrobials of colistin-resistant Escherichia coli from poultry production systems that use AGPs, and characterize the resistance determinants associated to transferable platforms. E. coli strains (n = 41) were obtained from fecal samples collected from typical Argentine commercial broiler farms and susceptibility for 23 antimicrobials, relevant for human or veterinary medicine, was determined. Isolates were tested by PCR for the presence of mcr-1, extended spectrum β-lactamase encoding genes and plasmid-mediated quinolone resistance (PMQR) coding genes. Conjugation and susceptibility patterns of the transconjugant studies were performed. ERIC-PCR and REP-PCR analysis showed a high diversity of the isolates. Resistance to several antimicrobials was determined and all colistin-resistant isolates harbored the mcr-1 gene. CTX-M-2 cefotaximase was the main mechanism responsible for third generation cephalosporins resistance, and PMQR determinants were also identified. In addition, co-transference of the qnrB determinant on the mcr-1-positive transconjugants was corroborated, which suggests that these resistance genes are likely to be located in the same plasmid. In this work a wide range of antimicrobial resistance mechanisms were identified in E. coli strains isolated from the environment of healthy chickens highlighting the risk of antimicrobial abuse/misuse in animals under intensive production systems and its consequences for public health.201830090095
5729180.9996Virulome and genome analyses identify associations between antimicrobial resistance genes and virulence factors in highly drug-resistant Escherichia coli isolated from veal calves. Food animals are known reservoirs of multidrug-resistant (MDR) Escherichia coli, but information regarding the factors influencing colonization by these organisms is lacking. Here we report the genomic analysis of 66 MDR E. coli isolates from non-redundant veal calf fecal samples. Genes conferring resistance to aminoglycosides, β-lactams, sulfonamides, and tetracyclines were the most frequent antimicrobial resistance genes (ARGs) detected and included those that confer resistance to clinically significant antibiotics (blaCMY-2, blaCTX-M, mph(A), erm(B), aac(6')Ib-cr, and qnrS1). Co-occurrence analyses indicated that multiple ARGs significantly co-occurred with each other, and with metal and biocide resistance genes (MRGs and BRGs). Genomic analysis also indicated that the MDR E. coli isolated from veal calves were highly diverse. The most frequently detected genotype was phylogroup A-ST Cplx 10. A high percentage of isolates (50%) were identified as sequence types that are the causative agents of extra-intestinal infections (ExPECs), such as ST69, ST410, ST117, ST88, ST617, ST648, ST10, ST58, and ST167, and an appreciable number of these isolates encoded virulence factors involved in the colonization and infection of the human urinary tract. There was a significant difference in the presence of multiple accessory virulence factors (VFs) between MDR and susceptible strains. VFs associated with enterohemorrhagic infections, such as stx, tir, and eae, were more likely to be harbored by antimicrobial-susceptible strains, while factors associated with extraintestinal infections such as the sit system, aerobactin, and pap fimbriae genes were more likely to be encoded in resistant strains. A comparative analysis of SNPs between strains indicated that several closely related strains were recovered from animals on different farms indicating the potential for resistant strains to circulate among farms. These results indicate that veal calves are a reservoir for a diverse group of MDR E. coli that harbor various resistance genes and virulence factors associated with human infections. Evidence of co-occurrence of ARGs with MRGs, BRGs, and iron-scavenging genes (sit and aerobactin) may lead to management strategies for reducing colonization of resistant bacteria in the calf gut.202235298535
3557190.9996Characterization of the variable region in the class 1 integron of antimicrobial-resistant Escherichia coli isolated from surface water. Fecal bacteria are considered to be a potential reservoir of antimicrobial resistance genes in the aquatic environment and could horizontally transfer these genes to autochthonous bacteria when carried on transferable and/or mobile genetic elements. Such circulation of resistance genes constitutes a latent public health hazard. The aim of this study was to characterize the variable region of the class 1 integron and relate its genetic content to resistance patterns observed in antimicrobial-resistant Escherichia coli isolated from the surface waters of Patos Lagoon, Southern Brazil. Genetic diversity of the isolates and presence of the qacEΔ1 gene, which confers resistance to quaternary ammonium compounds, were also investigated. A total of 27 isolates were analyzed. The variable region harbored dfrA17, dfrA1 and dfrA12 genes, which confer resistance to trimethoprim, and aadA1, aadA5 and aadA22 genes that encode resistance to streptomycin/spectinomycin. Most of the isolates were considered resistant to quaternary ammonium compounds and all of them carried the qacEΔ1 gene at the 3' conserved segment of the integron. ERIC-PCR analyses of E. coli isolates that presented the integrons showed great genetic diversity, indicating diverse sources of contamination in this environment. These results suggest that fecal bacteria with class 1 integrons in aquatic environments are potentially important reservoirs of antibiotic-resistance genes and may transfer these elements to other bacteria that are capable of infecting humans.201626991286