Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector. - Related Documents




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165501.0000Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector. Escherichia coli are gut commensal bacteria and opportunistic pathogens, and the emergence of antimicrobial resistance threatens the safety of the food chain. To know the E. coli strains circulating in the Brazilian poultry sector is important since the country corresponds to a significant chicken meat production. Thus, we analyzed 90 publicly genomes available in a database using web-based tools. Genomic analysis revealed that sul alleles were the most detected resistance genes, followed by aadA, bla(CTX-M), and dfrA. Plasmids of the IncF family were important, followed by IncI1-Iα, Col-like, and p0111. Genes of specific metabolic pathways that contribute to virulence (terC and gad) were predominant, followed by sitA, traT, and iss. Additionally, pap, usp, vat, sfa/foc, ibeA, cnf1, eae, and sat were also predicted. In this regard, 11 E. coli were characterized as avian pathogenic E. coli and one as atypical enteropathogenic E. coli. Phylogenetic analysis confirmed the predominant occurrence of B1 but also A, D, B2, F, E, G, C, and Clade I phylogroups, whereas international clones ST38, ST73, ST117, ST155, and ST224 were predicted among 53 different sequence types identified. Serotypes O6:H1 and:H25 were prevalent, and fimH31 and fimH32 were the most representatives among the 36 FimH types detected. Finally, single nucleotide polymorphisms-based phylogenetic analysis confirmed high genomic diversity among E. coli strains. While international E. coli clones have adapted to the Brazilian poultry sector, the virulome background of these strains support a pathogenic potential to humans and animals, with lineages carrying resistance genes that can lead to hard-to-treat infections.202235864380
165710.9998Occurrence and genomic characterization of ESBL-producing Escherichia coli ST29 strains from swine with abundant virulence genes. Food-production animals were considered to be a major reservoir of antimicrobial-resistant bacteria and clinically relevant pathogens. The potential of commensal Escherichia coli from pigs as a source of opportunistic pathogens associated with extraintestinal infections in humans needs to be assessed. In this study, 13 E. coli isolates from an intensive pig farm in China were analyzed using whole genome sequencing followed by in-depth in silico analysis. Genomic analysis showed comprehensive antimicrobial resistance profiles, with each isolate carrying between 4 and 22 antimicrobial resistance genes. Although these E. coli isolates were assigned to low-virulence phylogroup A and B1, 31 different virulence genes were detected at least once in the 13 sequenced isolates. Extraintestinal pathogenic E. coli-associated virulence genes, including iss, iha, tsh and iroN, were found in commensal E. coli isolates in this study. Of note, a large number of virulence genes (n = 22) were identified in ESBL-producing E. coli sequence type (ST) 29 isolates. Our study revealed the presence of comprehensive antimicrobial resistance and virulence gene profiles in commensal E. coli isolates of pigs. The emerged ESBL-producing E. coli ST 29 isolates harboring a high abundance of VAGs highlighted that this new clonal linage may pose a threat to public health.202032918980
165920.9998Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages. Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging.201222766078
165130.9998Comparative Genomic Analysis of Antimicrobial-Resistant Escherichia coli from South American Camelids in Central Germany. South American camelids (SAC) are increasingly kept in Europe in close contact with humans and other livestock species and can potentially contribute to transmission chains of epizootic, zoonotic and antimicrobial-resistant (AMR) agents from and to livestock and humans. Consequently, SAC were included as livestock species in the new European Animal Health Law. However, the knowledge on bacteria exhibiting AMR in SAC is too scarce to draft appropriate monitoring and preventive programs. During a survey of SAC holdings in central Germany, 39 Escherichia coli strains were isolated from composite fecal samples by selecting for cephalosporin or fluoroquinolone resistance and were here subjected to whole-genome sequencing. The data were bioinformatically analyzed for strain phylogeny, detection of pathovars, AMR genes and plasmids. Most (33/39) strains belonged to phylogroups A and B1. Still, the isolates were highly diverse, as evidenced by 28 multi-locus sequence types. More than half of the isolates (23/39) were genotypically classified as multidrug resistant. Genes mediating resistance to trimethoprim/sulfonamides (22/39), aminoglycosides (20/39) and tetracyclines (18/39) were frequent. The most common extended-spectrum-β-lactamase gene was bla(CTX-M-1) (16/39). One strain was classified as enteropathogenic E. coli. The positive results indicate the need to include AMR bacteria in yet-to-be-established animal disease surveillance protocols for SAC.202236144308
165840.9997Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine. Phenotypic determination of antimicrobial resistance in bacteria is very important for diagnosis and treatment, but sometimes this procedure needs further genetic evaluation. Whole-genome sequencing plays a critical role in deciphering and advancing our understanding of bacterial evolution, transmission, and surveillance of antimicrobial resistance. In this study, whole-genome sequencing was performed on nineteen clinically extraintestinal Escherichia coli isolates from chicken, cows and swine and showing different antimicrobial susceptibility. A total of 44 different genes conferring resistance to 11 classes of antimicrobials were detected in 15 of 19 E. coli isolates (78.9%), and 22 types of plasmids were detected in 15/19 (78.9%) isolates. In addition, whole-genome sequencing of these 19 isolates identified 111 potential virulence factors, and 53 of these VFDB-annotated genes were carried by all these 19 isolates. Twelve different virulence genes were identified while the most frequent ones were gad (glutamate decarboxylase), iss (increased serum survival) and lpfA (long polar fimbriae). All isolates harbored at least one of the virulence genes. The findings from comparative genomic analyses of the 19 diverse E. coli isolates in this study provided insights into molecular basis of the rising multi-drug resistance in E. coli.201830019301
165650.9997Characterisation of Commensal Escherichia coli Isolated from Apparently Healthy Cattle and Their Attendants in Tanzania. While pathogenic types of Escherichia coli are well characterized, relatively little is known about the commensal E. coli flora. In the current study, antimicrobial resistance in commensal E. coli and distribution of ERIC-PCR genotypes among isolates of such bacteria from cattle and cattle attendants on cattle farms in Tanzania were investigated. Seventeen E. coli genomes representing different ERIC-PCR types of commensal E. coli were sequenced in order to determine their possible importance as a reservoir for both antimicrobial resistance genes and virulence factors. Both human and cattle isolates were highly resistant to tetracycline (40.8% and 33.1%), sulphamethazole-trimethoprim (49.0% and 8.8%) and ampicillin (44.9% and 21.3%). However, higher proportion of resistant E. coli and higher frequency of resistance to more than two antimicrobials was found in isolates from cattle attendants than isolates from cattle. Sixteen out of 66 ERIC-PCR genotypes were shared between the two hosts, and among these ones, seven types contained isolates from cattle and cattle attendants from the same farm, suggesting transfer of strains between hosts. Genome-wide analysis showed that the majority of the sequenced cattle isolates were assigned to phylogroups B1, while human isolates represented phylogroups A, C, D and E. In general, in silico resistome and virulence factor identification did not reveal differences between hosts or phylogroups, except for lpfA and iss found to be cattle and B1 phylogroup specific. The most frequent plasmids replicon genes found in strains from both hosts were of IncF type, which are commonly associated with carriage of antimicrobial and virulence genes. Commensal E. coli from cattle and attendants were found to share same genotypes and to carry antimicrobial resistance and virulence genes associated with both intra and extraintestinal E. coli pathotypes.201627977751
84660.9997Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017-2018. Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017-2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure, and performed comparative analysis their pangenome contents. We found 55 Escherichia coli and 19 Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI virulence genes including fimH, iutA, feoA/B/C, mrkD, and foc. We identified 18 different sequence types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli sequence types were ST131 (26%), ST335/1193 (10%), and ST10 (6%). Diverse plasmid types were observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups. Pangenome analysis of each set revealed a total of 2862 and 3464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively. Among these are acquired AMR determinants including fluoroquinolone resistance-conferring genes aac(3)-Ib-cr and other significant genes: aad, tet, sul1, sul2, and cat, which are associated with aminoglycoside, tetracycline, sulfonamide, and chloramphenicol resistance, respectively. Accessory genomes of both species collections were detected several β-lactamase genes, bla(CTX-M), bla(TEM) and bla(OXA,) or bla(NDM). Overall, 93% are multi-drug resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are associated with resistance to three or more antibiotic classes. Our findings illustrate the abundant acquired resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae, which are mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial epidemiology of these important AMR pathogens.202134943759
84570.9997Variants of β-lactamase-encoding genes are disseminated by multiple genetically distinct lineages of bloodstream Escherichia coli. BACKGROUND: Escherichia coli is a major cause of bloodstream infections (BSI), which can lead to life-threatening organ dysfunction. We determined the genomic characteristics of E. coli implicated in BSI and the spread of antimicrobial resistance (AMR). METHODS: We carried out in vitro antimicrobial susceptibility testing and whole genome sequencing of 557 E. coli isolates recovered from BSI at Dartmouth-Hitchcock Medical Center, USA. RESULTS: We identify at least 119 previously recognized sequence types (ST), of which five STs (ST69, ST73, ST95, ST127, ST131) altogether represent 50% of the bloodstream E. coli population. Of the 142 distinct serotypes detected, the most common are O25:H4 and O1:H7. A total of 62 acquired genes are associated with resistance to at least 13 antimicrobial classes. These include the β-lactamase gene families bla(TEM), bla(SHV), bla(OXA), bla(CTX-M), and bla(CMY), which together can be further classified into 15 variants, including seven genes encoding extended-spectrum β-lactamases (ESBL). A total of 210/557 genomes carry at least one bla gene, with bla(TEM-1) being the most prevalent variant. ESBL-related genes are frequently detected in ST131 genomes. Four virulence operons related to iron uptake are differentially distributed among the five dominant STs. The putative IncF-type plasmid is often associated with genes related to AMR and iron uptake. Estimation of core and accessory genome similarity identifies 12 presumptive epidemiological linkages that span anywhere between 2-18 months. CONCLUSIONS: Multiple but genetically distinct E. coli lineages similarly cause BSI and shape AMR dissemination, emphasizing the opportunistic nature of E. coli in invasive infections.202540595425
84780.9997Genome-based characterization of Escherichia coli causing bloodstream infection through next-generation sequencing. Escherichia coli are one of the commonest bacteria causing bloodstream infection (BSI). The aim of the research was to identify the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance of E. coli isolated from bloodstream infection hospitalized patients in Cipto Mangunkusumo National Hospital Jakarta. We used whole genome sequencing methods rather than the conventional one, to characterized the serotypes, MLST (Multi Locus Sequence Type), virulence genes, and antimicrobial resistance (AMR) of E. coli. The composition of E. coli sequence types (ST) was as follows: ST131 (n = 5), ST38 (n = 3), ST405 (n = 3), ST69 (n = 3), and other STs (ST1057, ST127, ST167, ST3033, ST349, ST40, ST58, ST6630). Enteroaggregative E. coli (EAEC) and Extra-intestinal pathogenic E. coli (ExPEC) groups were found dominant in our samples. Twenty isolates carried virulence genes for host cells adherence and 15 for genes that encourage E. coli immune evasion by enhancing survival in serum. ESBL-genes were present in 17 E. coli isolates. Other AMR genes also encoded resistance against aminoglycosides, quinolones, chloramphenicol, macrolides and trimethoprim. The phylogeny analysis showed that phylogroup D is dominated and followed by phylogroup B2. The E. coli isolated from 22 patients in Cipto Mangunkusumo National Hospital Jakarta showed high diversity in serotypes, sequence types, virulence genes, and AMR genes. Based on this finding, routinely screening all bacterial isolates in health care facilities can improve clinical significance. By using Whole Genome Sequencing for laboratory-based surveillance can be a valuable early warning system for emerging pathogens and resistance mechanisms.202033362261
161590.9997Evaluation of the Antibiotic Resistance and Virulence of Escherichia coli Strains Isolated from Chicken Carcasses in 2007 and 2013 from Paraná, Brazil. The frequent use of antimicrobials in commercial poultry production has raised concerns regarding the potential impact of antimicrobials on human health due to selection for resistant bacteria. Several studies have reported similarities between extraintestinal pathogenic Escherichia coli (ExPEC) strains isolated from birds and humans, indicating that these contaminant bacteria in poultry may be linked to human disease. The aim of our study was to analyze the frequency of antimicrobial resistance and virulence factors among E. coli strains isolated from commercial chicken carcasses in Paraná, Brazil, in 2007 and 2013. A total of 84 E. coli strains were isolated from chicken carcasses in 2007, and 121 E. coli strains were isolated in 2013. Polymerase chain reaction was used to detect virulence genes (hlyF, iss, ompT, iron, and iutA) and to determine phylogenetic classification. Antimicrobial susceptibility testing was performed using 15 antimicrobials. The strains were also confirmed as extended-spectrum β-lactamase (ESBL)-producing E. coli with phenotypic and genotypic tests. The results indicated that our strains harbored virulence genes characteristic of ExPEC, with the iutA gene being the most prevalent. The phylogenetic groups D and B1 were the most prevalent among the strains isolated in 2007 and 2013, respectively. There was an increase in the frequency of resistance to a majority of antimicrobials tested. An important finding in this study was the large number of ESBL-producing E. coli strains isolated from chicken carcasses in 2013, primarily for the group 2 cefotaximase (CTX-M) enzyme. ESBL production confers broad-spectrum resistance and is a health risk because ESBL genes are transferable from food-producing animals to humans via poultry meat. These findings suggest that our strains harbored virulence and resistance genes, which are often associated with plasmids that can facilitate their transmission between bacteria derived from different hosts, suggesting zoonotic risks.201525974222
2042100.9997Genome Analysis of Multidrug-Resistant Escherichia coli Isolated from Poultry in Nigeria. Escherichia coli is one of the most common commensal bacteria of the gastrointestinal tract of humans and warm-blooded animals. Contaminated poultry can lead to disease outbreaks in consumers causing massive economic losses in the poultry industry. Additionally, commensal E. coli can harbor antibiotic resistance genes that can be transferred to other bacteria, including pathogens, in a colonized human host. In a previous study on antimicrobial resistance of E. coli from food animals from Nigeria, multidrug-resistant E. coli were detected. Three of those isolates were selected for further study using whole-genome sequencing due to the extensive drug resistance exhibited. All of the isolates carried the extended-spectrum β-lactamase (ESBL) genes, bla(CTX-M15) and bla(TEM-1), whereas one isolate harbored an additional ESBL, bla(OXA-1). All of the tetracycline-resistant isolates carried tet(A). The genes aac3-IIa and aacA4, conferring resistance to aminoglycosides, were identified in an E. coli isolate resistant to gentamicin and tobramycin. In two E. coli isolates, dfrA14, qnrS1, and sulII, were detected conferring resistance to trimethoprim, fluoroquinolones, and sulfonamides, respectively. The third isolate carried dfrA17, no fluoroquinolone resistance gene, an additional sulI gene, and a chloramphenicol resistance gene, catB3. Mutations in candidate genes conferring resistance to fosfomycin and fluoroquinolones were also detected. Several efflux systems were detected in all the E. coli isolates and virulence-associated genes related to serum resistance, motility, and adhesion. E. coli and non-E. coli origin prophages were also identified in the isolates. The results underline the higher resolution power of whole-genome sequencing for investigation of antimicrobial resistance, virulence, and phage in E. coli.202031509034
5729110.9997Virulome 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
1653120.9997Resistance Genes, Plasmids, Multilocus Sequence Typing (MLST), and Phenotypic Resistance of Non-Typhoidal Salmonella (NTS) Isolated from Slaughtered Chickens in Burkina Faso. The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries' residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data are not available. To study the epidemiology of antibiotic resistance in Salmonella, 102 Salmonella strains isolated from slaughtered chickens were subjected to whole-genome sequencing (WGS) to obtain information on antimicrobial resistance (AMR) genes and other genetic factors. Twenty-two different serotypes were identified using WGS, the most prevalent of which were Hato (28/102, 27.5%) and Derby (23/102, 22.5%). All strains analyzed possessed at least one and up to nine AMR genes, with the most prevalent being the non-functional aac(6')-Iaa gene, followed by aph(6)-Id. Multi-drug resistance was found genotypically in 36.2% of the isolates for different classes of antibiotics, such as fosfomycin and β-lactams, among others. Plasmids were identified in 43.1% of isolates (44/102), and 25 plasmids were confirmed to carry AMR genes. The results show that chicken can be considered as a reservoir of antibiotic-resistant Salmonella strains. Due to the prevalence of these drug-resistant pathogens and the potential for foodborne illnesses, poultry processing and cooking should be performed with attention to prescribed safe handling methods to avoid cross-contamination with chicken products.202235740187
2633130.9997Tracking bla(CTX-M) transmission through transposable elements in uropathogenic and commensal E. coli. AIM: To investigate the nucleotide sequences associated with transposable elements carrying bla(CTX-M) allelic variants as potential markers for the transmission of antimicrobial resistance genes between domestic animals, humans and the environment. MATERIALS & METHODS: We conducted whole-genome sequencing and analyzed the nucleotide sequences of most abundant bla(CTX-M) allelic variants (bla(CTX-M-27), bla(CTX-M-55), and bla(CTX-M-65)) in commensal Escherichia coli (n = 20) from household members in Quito and uropathogenic E. coli (UPEC) (n = 149) isolated from nine clinics in Quito, Ecuador. RESULTS: The Ecuadorian commensal E. coli and UPEC displayed identical nucleotide sequences surrounding the bla(CTX-M) gene and the synteny was similar to those found in other parts of the world; however phylogenetic analysis indicated that the genetic environments in Ecuadorian isolates were unique. CONCLUSION: These findings suggest that the nucleotide sequences flanking the bla(CTX-M) genes may be useful for resolving ARG transmission pathways, especially inter-regional analyses.202539880589
1647140.9997Genomic and antimicrobial resistance genes diversity in multidrug-resistant CTX-M-positive isolates of Escherichia coli at a health care facility in Jeddah. BACKGROUND: Whole genome sequencing has revolutionized epidemiological investigations of multidrug-resistant pathogenic bacteria worldwide. Aim of this study was to perform comprehensive characterization of ESBL-positive isolates of Escherichia coli obtained from clinical samples at the King Abdulaziz University Hospital utilizing whole genome sequencing. METHODS: Isolates were identified by MALDI-TOF mass spectrometry. Genome sequencing was performed using a paired-end strategy on the MiSeq platform. RESULTS: Nineteen isolates were clustered into different clades in a phylogenetic tree based on single nucleotide polymorphisms in core genomes. Seventeen sequence types were identified in the extended-spectrum β-lactamase (ESBL)-positive isolates, and 11 subtypes were identified based on distinct types of fimH alleles. Forty-one acquired resistance genes were found in the 19 genomes. The bla(CTX-M-15) gene, which encodes ESBL, was found in 15 isolates and was the most predominant resistance gene. Other antimicrobial resistance genes (ARGs) found in the isolates were associated with resistance to tetracycline (tetA), aminoglycoside [aph(3″)-Ib, and aph(6)-Id], and sulfonamide (sul1, and sul2). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA were commonly found in several genomes. CONCLUSION: Several other ARGs were found in CTX-M-positive E. coli isolates confer resistance to clinically important antibiotics used to treat infections caused by Gram-negative bacteria.202031279801
1856150.9997Whole-Genome Sequencing-Based Species Classification, Multilocus Sequence Typing, and Antimicrobial Resistance Mechanism Analysis of the Enterobacter cloacae Complex in Southern China. Members of the Enterobacter cloacae complex (ECC) are important opportunistic nosocomial pathogens that are associated with a great variety of infections. Due to limited data on the genome-based classification of species and investigation of resistance mechanisms, in this work, we collected 172 clinical ECC isolates between 2019 and 2020 from three hospitals in Zhejiang, China and performed a retrospective whole-genome sequencing to analyze their population structure and drug resistance mechanisms. Of the 172 ECC isolates, 160 belonged to 9 classified species, and 12 belonged to unclassified species based on ANI analysis. Most isolates belonged to E. hormaechei (45.14%) followed by E. kobei (13.71%), which contained 126 STs, including 62 novel STs, as determined by multilocus sequence typing (MLST) analysis. Pan-genome analysis of the two ECC species showed that they have an "open" tendency, which indicated that their Pan-genome increased considerably with the addition of new genomes. A total of 80 resistance genes associated with 11 antimicrobial agent categories were identified in the genomes of all the isolates. The most prevailing resistance genes (12/29, 41.38%) were related to β-lactams followed by aminoglycosides. A total of 247 β-lactamase genes were identified, of which the bla(ACT) genes were the most dominant (145/247, 58.70%), followed by the bla(TEM) genes (21/247, 8.50%). The inherent ACT type β-lactamase genes differed among different species. bla(ACT-2) and bla(ACT-3) were only present in E. asburiae, while bla(ACT-9), bla(ACT-12), and bla(ACT-6) exclusively appeared in E. kobei, E. ludwigii, and E. mori. Among the six carbapenemase-encoding genes (bla(NDM-1), bla(NDM-5), bla(IMP-1), bla(IMP-4), bla(IMP-26), and bla(KPC-2)) identified, two (bla(NDM-1) and bla(IMP-1)) were identified in an ST78 E. hormaechei isolate. Comparative genomic analysis of the carbapenemase gene-related sequences was performed, and the corresponding genetic structure of these resistance genes was analyzed. Genome-wide molecular characterization of the ECC population and resistance mechanism would offer valuable insights into the effective management of ECC infection in clinical settings. IMPORTANCE The presence and emergence of multiple species/subspecies of ECC have led to diversity and complications at the taxonomic level, which impedes our further understanding of the epidemiology and clinical significance of species/subspecies of ECC. Accurate identification of ECC species is extremely important. Also, it is of great importance to study the carbapenem-resistant genes in ECC and to further understand the mechanism of horizontal transfer of the resistance genes by analyzing the surrounding environment around the genes. The occurrence of ECC carrying two MBL genes also indicates that the selection pressure of bacteria is further increased, suggesting that we need to pay special attention to the emergence of such bacteria in the clinic.202236350178
1612160.9997Carriage of antimicrobial resistant Escherichia coli in dogs: Prevalence, associated risk factors and molecular characteristics. Resistance to antimicrobials, in particular that mediated by extended spectrum β-lactamases (ESBL) and AmpC β-lactamases are frequently reported in bacteria causing canine disease as well as in commensal bacteria, which could be a potential health risk for humans they come into contact with. This cross-sectional study aimed to estimate the prevalence and investigate the molecular characteristics of ESBL and plasmid encoded AmpC (pAmpC)-producing E. coli in the mainland UK vet-visiting canine population and, using responses from detailed questionnaires identify factors associated with their carriage. Faecal samples were cultured for antimicrobial resistant (AMR), ESBL and pAmpC-producing E. coli. A subset of ESBL and pAmpC-producing isolates were subjected to multi-locus sequence typing and DNA microarray analyses. Multivariable logistic regression analysis was used to construct models to identify risk factors associated with multidrug resistant (MDR, resistance to three or more antimicrobial classes), fluoroquinolone resistant, ESBL and AmpC-producing E. coli. AMR E.coli were isolated from 44.8% (n=260) of samples, with 1.9% and 7.1% of samples carrying ESBL and pAmpC-producing E. coli, respectively. MDR E. coli were identified in 18.3% of samples. Recent use of antimicrobials and being fed raw poultry were both identified as risk factors in the outcomes investigated. A number of virulence and resistance genes were identified, including genes associated with extra-intestinal and enteropathogenic E. coli genotypes. Considering the close contact that people have with dogs, the high levels of AMR E. coli in canine faeces may be a potential reservoir of AMR bacteria or resistance determinants.201728110781
1650170.9997Multidrug-Resistant Salmonella enterica 4,[5],12:i:- Sequence Type 34, New South Wales, Australia, 2016-2017. Multidrug- and colistin-resistant Salmonella enterica serotype 4,[5],12:i:- sequence type 34 is present in Europe and Asia. Using genomic surveillance, we determined that this sequence type is also endemic to Australia. Our findings highlight the public health benefits of genome sequencing-guided surveillance for monitoring the spread of multidrug-resistant mobile genes and isolates.201829553318
1858180.9997Molecular Characteristics of Antimicrobial Resistance and Virulence in Klebsiella pneumoniae Strains Isolated from Goose Farms in Hainan, China. We retrospectively investigated 326 samples that were collected from goose farms in Hainan Province, China, in 2017. A total of 33 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were identified from 326 samples, and the 33 CRKP isolates were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. All of these 33 CRKP isolates possessed bla(NDM-5), and a single isolate coharbored mcr-1 and bla(NDM-5), while 4 isolates carried multiple virulence and metal tolerance gene clusters. One CRKP strain (CMG-35-2) was selected for long sequence reading. A hybrid plasmid carrying the virulence, resistance, and metal resistance gene in the strain was found. It possessed 2 backbones [IncFIB(K)-IncFII(K)] within a single plasmid that were closely related to K. pneumoniae plasmids from a human-associated habitat in the United States and from a human isolate in Hong Kong. A mouse abdominal infection model indicated that that strain was of the moderate virulence phenotype. This study revealed that K. pneumoniae on goose farms is an important reservoir for bla(NDM-5) and these bacteria are represented by a diversity of sequence types. The heterozygous multiple drug resistance genes carried on plasmids highlighted the genetic complexity of CRKP and the urgent need for continued active surveillance. IMPORTANCE CRKP is one of the most important pathogens, which can cause infection not only in humans but also in waterfowl. The discovery of bla(NDM-5)-producing K. pneumoniae in waterfowl farms in recent years suggests that waterfowl are an important reservoir for bla(NDM-5)-producing Enterobacteriaceae. However, there are few studies on the spread of bla(NDM-5)-producing bacteria in waterfowl farms. Our study showed that the IncX3 plasmid carrying bla(NDM-5) in goose farms is widely present in K. pneumoniae isolates and a large number of resistance genes are accumulated in it. We found a transferable IncFIB-FII hybrid plasmid that combines virulence, resistance, and metal resistance genes, which allow transfer of these traits between bacteria in different regions. The results of this study contribute to a better understanding of the prevalence and transmission of carbapenem-resistant K. pneumoniae in goose farms.202235389252
1654190.9997High frequency of B2 phylogroup among non-clonally related fecal Escherichia coli isolates from wild boars, including the lineage ST131. Wild boars are worldwide distributed mammals which population is increasing in many regions, like the Iberian Peninsula, leading to an increased exposition to humans. They are considered reservoirs of different zoonotic pathogens and have been postulated as potential vectors of antimicrobial-resistant (AMR) bacteria. This study aimed to determine the prevalence of antimicrobial resistance and phylogenetic distribution of Escherichia coli from wild boar feces. Antimicrobial resistance and integron content was genetically characterized and E. coli of B2 phylogroup was further analyzed by molecular typing and virulence genotyping. The prevalence of AMR E. coli was low, with only 7.5% of isolates being resistant against at least one antimicrobial, mainly ampicillin, tetracycline and/or sulfonamide. An unexpected elevated rate of B2 phylogroup (47.5%) was identified, most of them showing unrelated pulsed-field-gel-electrophoresis patterns. ST131/B2 (fimH 22 sublineage), ST28/B2, ST1170/B2, ST681/B2 and ST625/B2 clones, previously described in extraintestinal infections in humans, were detected in B2 isolates, and carried one or more genes associated with extraintestinal pathogenic E. coli (ExPEC). This study demonstrated a low prevalence of antimicrobial resistance in E. coli from wild boars, although they are not exempt of AMR bacteria, and a predominance of genetically diverse B2 phylogroup, including isolates carrying ExPEC which may contribute to the spread of virulence determinants among different ecosystems.201728365752