Characterization of IncI1 sequence type 71 epidemic plasmid lineage responsible for the recent dissemination of CTX-M-65 extended-spectrum β-lactamase in the Bolivian Chaco region

Characterization of IS26-bracketed blaCTX-M-65 resistance module on IncI1 and IncX1 plasmids in Escherichia coli ST224 isolated from a chicken in China

Antimicrobial resistance (AMR) poses a significant global health threat, particularly due to increasing bacterial resistance to β-lactam and aminoglycoside antibiotics, primarily mediated by extended-spectrum β-lactamases (ESBLs) and 16S rRNA methylases in Enterobacteriaceae. In this study, a multidrug resistant (MDR) E. coli strain HN257 isolated from chicken belonging to ST224 and serotype O88:H23 was characterized. SNP-based phylogenetic analysis revealed two distinct clades among poultry-associated E. coli ST224 in this study and others from Genbank, with strain HN257 closely related to chicken-derived E. coli YH17148 (serotype O78:H23), from China. The E. coli HN257 harbored four plasmids with 16 resistance determinants. Two blaCTX-M-65 genes were located on different plasmids with an IS26-bracketed resistance module IS26-traI-fip-∆ISEcp1-blaCTX-M-65-IS903D-iroN-IS26. The plasmid pHN257-2 belonged to the IncI1 ST71 epidemic lineage and carried blaCTX-M-65, blaTEM-1b, rmtB, fosA3, floR, aac(3)-IV and oqxAB, while plasmid pHN257-4 belonged to the non-conjugative IncX1 and carried blaCTX-M-65 and fosA3. Under experimental conditions, a rmtB-positive conjugative helper IncI1 ST136 plasmid could fuse with the non-conjugative pHN257-4 carrying blaCTX-M-65, resulting in the formation of a cointegrate pHN257-F mediated by IS26. Importantly, both single and fused plasmids in transconjugants showed minimal impact on bacterial growth. This study highlights the first identification of a non-conjugative IncX1 plasmid carrying blaCTX-M-65 and fosA3 in MDR E. coli ST224 from poultry, offering critical insights into the presence and transmission dynamics of blaCTX-M-65.

Antimicrobial Resistance and Molecular Characterization of Escherichia coli from Healthy Chickens in Shandong, China from 2009 to 2014

Antimicrobial resistance (AMR) is a great threat to animal and public health. Here, we conducted a surveillance of Escherichia coli isolated from healthy chickens during 2009-2014 to identify the characteristics of AMR. A total of 351 (95.64%) E. coli isolates were obtained from 367 healthy chicken fecal samples collected from 6 farms located in Shandong Province, China. The susceptibility to 10 antimicrobials, the prevalence of antibiotic resistance genes (ARGs), phylogenetic clustering, and multilocus sequence typing were evaluated. The isolates exhibited high resistant rates (>95%) to ampicillin, cefotaxime, ciprofloxacin, ceftiofur, and enrofloxacin. The most prevalent ARGs were blaCTX-M (36.36%), aac(6')-Ib-cr (30.79%), qnrS (29.62%), oqxAB (27%), mcr-1 (15.83%), blaTEM (9.09%), qnrC (3.52%), qnrD (0.88%), and qepA (0.29%). Phylogenetic clustering analysis indicated that the most prevalent group was group D (37.89%), followed by group B1 (34.76%), A (24.22%), and B2 (3.13%). Fifty-seven sequence types (STs) were identified among the 124 blaCTX-M-positive strains, and the dominant STs were ST354 (13.71%), ST117 (5.65%), ST155, ST2309, and ST2505 (4.84% each). There was a significant association between 17 pairs of AMR phenotypes, 14 pairs of ARGs, and 11 pairs of AMR-ARGs. The strongest association was found between ST602 and qnrC (odds ratios: 22.2). This study implied that E. coli isolated from healthy chickens could potentially serve as a reservoir of AMR and ARGs, and significant associations exist among AMR, ARGs, phylogenetic groups, and STs. Our study highlighted the need for routine surveillance of AMR in healthy chickens, and promoting appropriate antibiotic use and implementing regular monitoring of resistance in broilers are crucial for fostering the development of the poultry industry and safeguarding public health.

Traveller studies in low- and middle-income countries: a critical gap in global antibiotic resistance surveillance

A substantial proportion of global travel occurs between low- and middle-income countries (LMICs) for the purposes of migration, medical tourism, trade and employment, and this is likely to accelerate due to climate-change-related migration. Traveller studies based in LMICs are needed to better monitor the global spread of antibiotic resistance.

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)). The plasmid and chromosome phylogeny of these isolates was inferred from single nucleotide polymorphisms (SNPs). Our search resolved six Salmonella clusters carrying the pESI plasmid. Four were emergent Salmonella Infantis clusters, and one each belonged to serovar Senftenberg and Alachua. The Infantis cluster with a pESI plasmid carrying blaCTX-M-65 gene was the biggest of the four emergent Infantis clusters, with over 10,000 isolates. This cluster was first detected in South America and has since spread widely in United States. Over time the composition of pESI in United States has changed with the average number of resistance genes showing a decrease from 9 in 2014 to 5 in 2022, resulting from changes in gene content in two integrons present in the plasmid. A recent and emerging cluster of Senftenberg, which carries the blaCTX-M-65 gene and is primarily associated with turkey sources, was the second largest in the United States. SNP analysis showed that this cluster likely originated in North Carolina with the recent acquisition of the pESI plasmid. A single Alachua isolate from turkey was also found to carry the pESI plasmid containing blaCTX-M-65 gene. The study of the pESI plasmid, its evolution and mechanism of spread can help us in developing appropriate strategies for the prevention and further spread of this multi-drug resistant plasmid in Salmonella in poultry and humans.

CTX-M-producing Escherichia coli ST602 carrying a wide resistome in South American wild birds: Another pandemic clone of One Health concern

Wild birds have emerged as novel reservoirs and potential spreaders of antibiotic-resistant priority pathogens, being proposed as sentinels of anthropogenic activities related to the use of antimicrobial compounds. The aim of this study was to investigate the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-producing bacteria in wild birds in South America. In this regard, we have identified two ESBL (CTX-M-55 and CTX-M-65)-positive Escherichia coli (UNB7 and GP188 strains) colonizing Creamy-bellied Thrush (Turdus amaurochalinus) and Variable Hawk (Geranoaetus polyosoma) inhabiting synanthropic and wildlife environments from Brazil and Chile, respectively. Whole-genome sequence (WGS) analysis revealed that E. coli UNB7 and GP188 belonged to the globally disseminated clone ST602, carrying a wide resistome against antibiotics (β-lactams), heavy metals (arsenic, copper, mercury), disinfectants (quaternary ammonium compounds), and pesticides (glyphosate). Additionally, E. coli UNB7 and GP188 strains harbored virulence genes encoding hemolysin E, type II and III secretion systems, increased serum survival, adhesins and siderophores. SNP-based phylogenomic analysis, using an international genome database, revealed genomic relatedness (19-363 SNP differences) of GP188 with livestock and poultry strains, and genomic relatedness (61-318 differences) of UNB7 with environmental, human and livestock strains (Table S1), whereas phylogeographical analysis confirmed successful expansion of ST602 as a global clone of One Health concern. In summary, our results support that ESBL-producing E. coli ST602 harboring a wide resistome and virulome have begun colonizing wild birds in South America, highlighting a potential new reservoir of critical priority pathogens.

Characterization of ESBL-producing Escherichia spp. and report of an mcr-1 colistin-resistance Escherichia fergusonni strain from minced meat in Pamplona, Colombia

Foods of animal origin are increasingly considered a source of extended spectrum β-lactamase (ESBL) producing bacteria which can disseminate throughout the food chain and become a health concern for humans. This work aimed to evaluate the occurrence of ESBL-producing Escherichia coli in 100 retail minced meat samples taken in markets in Pamplona, Colombia. A total of 19 ESBL-producing isolates were obtained, 18 identified as E. coli and one as E. fergusonii. Fifteen isolates (78.9 %) carried bla_CTX-M and bla_TEM genes, one (5.2 %) bla_SHV and bla_TEM genes, one isolate (5.2 %) carried bla_CTX-M and one (5.2 %) bla_SHV alone. The majority of CTX-M-positive E. coli isolates carried the bla_CTX-M-15 gene (13 isolates), being the bla_CTX-M-9, bla_CTX-M-2, and bla_CTX-M-8 (one isolate each) also detected. Two SHV-positive isolates presented the bla_SHV-5 and bla_SHV-12 allele. The isolate identified as E. fergusonii was positive for bla_CTX-M-65 gene and mcr-1 gene. Sixteen isolates (84.2 %) belonged to phylogroups A and B1 and grouped together in the phylogenetic tree obtained by MLST; phylogroups E and F were also detected. Transfer of ESBL resistance was demonstrated for the E. fergusonii isolate. Whole genome sequencing of this isolate revealed the presence of plasmids carrying additional resistance genes. This investigation showed the high prevalence of ESBL-producing E. coli in retail samples of minced meat. Also, the isolation of a strain of E. fergusonii is an additional concern, as some resistance genes are located in mobile elements, which can be transmitted to other bacteria. These evidences support the increasing public health concern considering the spreading of resistance genes through the food chain.

Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

Background

The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.

Methods

To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n = 72) and after (n = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.

Results

A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n = 24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.

Conclusion

Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.

Characterization of IncI1/ST71 and IncF18:A-:B1 multidrug-resistance plasmids from an avian Escherichia coli isolate

To characterize IncI1 and IncF18:A-:B1 multidrug-resistance plasmids from an avian Escherichia coli isolate, antibiotic susceptibility testing, conjugation assays, transformation assays, S1-PFGE, and WGS analysis were performed. The 119,457-bp plasmid pEC014-1 with a multidrug-resistance region (MRR) containing four different segments interspersed with six IS26 elements, belonged to incompatibility group I1 and sequence type 71. The 154,516-bp plasmid pEC014-2 with two replicons, typed as FII-18 and FIB-1, carried 14 resistance determinants including bla_TEM-1b, bla_OXA-1, oqxAB, dfrA17, aac(6')-Ib-cr, sul1, sul2, tet(A), floR, catB3, hph(aph(4)-Ia), aacC4(aac(3)-IV), aadA5, arr-3, and a merEDACPTR loci in MRR, and additionally encoded three virulence loci: iroNEDCB, sitABCD, and iucABCD-iutA. Plasmid stability assays showed that pEC014-1 and pEC014-2 were stable in recipient E. coli C600 for at least 15 days of passage. Competition assays were carried out to evaluate the fitness impact of pEC014-2 carriage in vitro, revealing a decrease in host fitness. Growth kinetics showed that the growth rate for pEC014-1 or/and pEC014-2 bearing cells was significantly slower than that of the E. coli C600 host strain in the exponential stage (p < 0.01), with only cells carrying pEC014-1 sustaining rapid growth after 6 h of exponential growth. Our findings highlight the mosaic structures of epidemic plasmid IncI1/ST71 and F18:A-:B1 lineages and contribute to a better understanding of the evolution and dissemination of these multidrug resistance and virulence plasmids.

Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales

Salmonella enterica serovar Infantis is the fifth most common Salmonella serovar isolated in England and Wales. Epidemiological, genotyping and antimicrobial-resistance data for S . enterica Infantis isolates were used to analyse English and Welsh demographics over a 5 year period. Travel cases associated with S . enterica Infantis were mainly from Asia, followed by cases from Europe and North America. Since 2000, increasing numbers of S . enterica Infantis had multidrug resistance determinants harboured on a large plasmid termed ‘plasmid of emerging S . enterica Infantis’ (pESI). Between 2013 and 2018, 42 S . enterica Infantis isolates were isolated from humans and food that harboured resistance determinants to multiple antimicrobial classes present on a pESI-like plasmid, including extended-spectrum β-lactamases (ESBLs; bla CTX-M-65). Nanopore sequencing of an ESBL-producing human S . enterica Infantis isolate indicated the presence of two regions on an IncFIB pESI-like plasmid harbouring multiple resistance genes. Phylogenetic analysis of the English and Welsh S . enterica Infantis population indicated that the majority of multidrug-resistant isolates harbouring the pESI-like plasmid belonged to a single clade maintained within the population. The bla CTX-M-65 ESBL isolates first isolated in 2013 comprise a lineage within this clade, which was mainly associated with South America. Our data, therefore, show the emergence of a stable resistant clone that has been in circulation for some time in the human population in England and Wales, highlighting the necessity of monitoring resistance in this serovar.

Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans

OBJECTIVES

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on isolation and screening of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a cohort of healthy individuals in Singapore.

METHODS

MinION and Illumina sequencing was performed to obtain the complete genome sequences of Escherichia coli 2EC1-1 and 94EC. Subsequently, 109 human faecal samples were screened retrospectively for eravacycline-resistant Enterobacteriaceae strains, which were further tested for tet(X4) by PCR. The taxonomy of the isolated strains was determined by 16S rRNA gene PCR and Sanger sequencing.

RESULTS

Comparative genomic analysis of E. coli 2EC1-1 and 94EC revealed that both carry tet(X4), which is encoded by IncI1-type plasmids p2EC1-1 and p94EC-2, respectively. Retrospective screening of faecal samples collected from 109 healthy individuals showed that the faecal carriage rate of Tet(X4)-producing Enterobacteriaceae is 10.1% (95% CI = 5.1%-17.3%), suggesting that tet(X4) is widely distributed in the gut microbiota of healthy individuals in Singapore.

CONCLUSIONS

To the best of our knowledge, this is the first report on the prevalence of tet(X4) in the gut microbiota of a healthy human cohort, as well as the first description of this resistance mechanism outside of China. Our findings suggest that surveillance of tet(X4) in community settings is vital to monitor the spread of this resistance mechanism.

Dissemination of IncFII plasmids carrying fosA3 and blaCTX-M-55 in clinical isolates of Salmonella enteritidis

Multidrug-resistant Salmonella Enteritidis (S. Enteritidis) isolates have become a significant threat to public health, and fosfomycin has been proposed as one of the therapeutic antibiotics for serious infections by resistant pathogens. In this study, a total of 501 clinical S. Enteritidis isolates were screened and 14 (2.8%) isolates exhibited resistance to fosfomycin (MIC ≥ 1,024 μg/mL) as well as ceftriaxone (MIC ≥ 128 μg/mL). The fosA3 gene was identified in these 14 isolates. The fosA3 gene that co-transferred with bla_CTX-M-55 was observed on the IncFII plasmids with sizes of ~ 78 (n = 7) or ~ 111 (n = 2) kbp in 9 transconjugants. The fosA3-bearing plasmid p12367A is 111,764 bp in length and possessed a typical IncFII backbone. A 7.6-kbp multidrug resistance region (MRR) was identified in p12367A, which was comprised of fosA3 and bla_CTX-M-55 genes interspersed with ΔISEcp1 and three copies of IS26. Two typical antibiotic resistance determinants (IS26-orf3-orf2-orf1-fosA3-IS26 and IS26-orf477-bla_CTX-M-55 -ΔISEcp1-IS26) shared one IS26 in the MRR. The genetic arrangement of the MRR may have resulted from the stepwise integration of IS26 mobile elements via homologous recombination. Horizontal transfer of IncFII plasmids might contribute to the dissemination of fosA3 and bla_CTX-M-55 resistance genes in S. Enteritidis interspecies. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by epidemic IncFII plasmids bearing fosA3-bla_CTX-M-55 .

A Multidrug-Resistant Salmonella Infantis Clone is Spreading and Recombining in the United States

Recently, there have been reports worldwide of a multidrug-resistant, emergent Salmonella Infantis (ESI) clone with a large megaplasmid (pESI), often containing the extended-spectrum beta-lactamase gene blaCTX-M-65. This clone also has a gyrA mutation conferring fluoroquinolone resistance, further limiting treatment options. In the United States, this clone has also been found in poultry sources, indicating a likely source of human illnesses. We conducted short-read sequencing of Salmonella enterica isolated from retail meats as part of routine surveillance by the National Antimicrobial Resistance Monitoring System (NARMS). We analyzed the resulting data temporally and geographically to determine when and where the ESI clone has spread in the United States. We found the ESI clone was first found in retail meats in Tennessee in 2014, but by 2019 was throughout the United States and comprised 29% of all Salmonella isolated from retail chickens, and 7% from retail turkey. Of these isolates, 85.0% were within 20 single nucleotide polymorphisms (SNPs) of those causing human illnesses. Long-read sequencing data indicated substantial recombination in the pESI plasmid resulting in the presence of 0-10 resistance genes, despite all their chromosomes being within 31 SNPs of one another. This work demonstrates the rapid spread of this clone of Salmonella Infantis in poultry in the United States, with the potential for increased burden of human illness attributed to this multidrug-resistant pathogen.

Compared with Cotrimoxazole Nitroxoline Seems to Be a Better Option for the Treatment and Prophylaxis of Urinary Tract Infections Caused by Multidrug-Resistant Uropathogens: An In Vitro Study

The resistance of uropathogens to various antibiotics is increasing, but nitroxoline remains active in vitro against some relevant multidrug resistant uropathogenic bacteria. E. coli strains, which are among the most common uropathogens, are unanimously susceptible. Thus, nitroxoline is an option for the therapy of urinary tract infections caused by multiresistant bacteria. Since nitroxoline is active against bacteria in biofilms, it will also be effective in patients with indwelling catheters or foreign bodies in the urinary tract. Cotrimoxazole, on the other hand, which, in principle, can also act on bacteria in biofilms, is frequently inactive against multiresistant uropathogens. Based on phenotypic resistance data from a large number of urine isolates, structural characterisation of an MDR plasmid of a recent ST131 uropathogenic E. coli isolate, and publicly available genomic data of resistant enterobacteria, we show that nitroxoline could be used instead of cotrimoxazole for intervention against MDR uropathogens. Particularly in uropathogenic E. coli, but also in other enterobacterial uropathogens, the frequent parallel resistance to different antibiotics due to the accumulation of multiple antibiotic resistance determinants on mobile genetic elements argues for greater consideration of nitroxoline in the treatment of uncomplicated urinary tract infections.

Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance

Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.

Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children

The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (bla_CTX-M-65) and i-pAmpC (bla_DHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with bla_CTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a bla_SHV gene. All isolates presented D₈₇Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR bla_CTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR bla_CTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level.

Characterization of blaCMY-2-carrying IncC and rmtB-carrying IncI1/ST136 plasmids in an avian Escherichia coli ST224 strain

To analyze characteristics and underlying evolutionary processes of IncC and IncI1 plasmids in a multidrug-resistant avian E. coli strain, antibiotic susceptibility testing, PCR, conjugation assays, and next-generation sequencing were performed. The type 1 IncC plasmid pEC009.1 harbored three antimicrobial resistance regions including ISEcp1-bla_CMY-2-blc-sugE, ARI-B resistance island, and ARI-A island that was a mosaic multidrug resistance region (MRR) comprised of a class 1 integron with cassette array |aac(6')-II(aacA7)|qacE∆1|sul1|, IS26-mphR(A)-mrx-mph(A)-IS26, IS26-fosA3-IS26, and mercury resistance cluster merRTPABDE. It is the first report of three different size circular forms derived from IS26-mphR(A)-mrx-mph(A)-IS26-fosA3-IS26 in ARI-A of type 1 IncC plasmid. In IncI1/ST136 pEC009.2, the truncated transposon Tn1722 carrying bla_TEM-1b, rmtB, aac(3)-IId(aacC2d), and a class 1 integron with cassette array |dfrA12|orfF|aadA2|, inserted into the plasmid backbone generating 5-bp direct repeats (DRs, TATAA) at the boundaries of the region, which was highly similar to that of other IncI1 plasmids, and differed by the arrangements of resistance determinants. Comparison among two epidemic plasmid lineages showed complex MRRs respectively located in the specific position in type 1 IncC and IncI1/ST136 plasmids with conserved backbones, and these have evolved via multiple events involved in mobile elements-mediated loss and gain of resistance genes and accessory genes. Strains harboring these plasmids may serve as a reservoir for antibiotic resistance genes, thereby contributing to the rapid spread of resistance genes and posing a public health threat.

Detection of Tn7-Like Transposons and Antibiotic Resistance in Enterobacterales From Animals Used for Food Production With Identification of Three Novel Transposons Tn6813, Tn6814, and Tn6765

Enterobacterales are widely distributed in the gastro-intestinal system of animals and may cause opportunistic infections. Worse still, multidrug-resistant Enterobacterales also poses a serious threat to public health. Tn7-like transposons have been found in several species of the Enterobacterales order and play an important role in dissemination of antibiotic resistance. This study aimed to investigate the distribution and genetic characterization of Tn7-like transposons in Enterobacterales isolates from food animals and their association with antibiotic resistance. Enterobacterales isolated from the samples were identified and classified according to the 16S rDNA sequence. Tn7-like transposons and associated integrons were detected by polymerase chain reaction (PCR) and sequencing. The antibiotic resistance of each Tn7-like transposon positive isolate was detected according to the Kirby-Bauer disk diffusion method. Then, six representative strains were selected to study the genetic environment by whole-genome sequencing (WGS). In total, we isolated 377 Tn7-like transposons positive strains of Enterobacterales. Class 2 integrons were detected in 99.5% of the isolates, and there were high frequency mutation sites especially in base 535, a stop mutation. Many isolates (54.9%) were multidrug-resistant and observed high resistance rates to trimethoprim/sulfamethoxazole and streptomycin. Among these strains, we found three new types of Tn7-like transposons, named Tn6813, Tn6814, and Tn6765. This is the first comprehensive survey that shows Tn7-like transposons in Enterobacterales from animals used for food production in different regions of China. This study also provides an insight into the horizontal transfer of resistance genes associated with Tn7-like transposons.

Antimicrobial resistance-encoding plasmid clusters with heterogeneous MDR regions driven by IS26 in a single Escherichia coli isolate

BACKGROUND

IS26-flanked transposons played an increasingly important part in the mobilization and development of resistance determinants. Heterogeneous resistance-encoding plasmid clusters with polymorphic MDR regions (MRRs) conferred by IS26 in an individual Escherichia coli isolate have not yet been detected.

OBJECTIVES

To characterize the complete sequence of a novel blaCTX-M-65- and fosA3-carrying IncZ-7 plasmid with dynamic MRRs from an E. coli isolate, and to depict the mechanism underlying the spread of resistance determinants and genetic polymorphisms.

METHODS

The molecular characterization of a strain carrying blaCTX-M-65 and fosA3 was analysed by antimicrobial susceptibility testing and MLST. The transferability of a plasmid bearing blaCTX-M-65 and fosA3 was determined by conjugation assays, and the complete structure of the plasmid was obtained by Illumina, PacBio and conventional PCR mapping, respectively. The circular forms derived from IS26-flanked transposons were detected by reverse PCR and sequencing.

RESULTS

A novel IncZ-7 plasmid pEC013 (∼118kb) harbouring the blaCTX-M-65 and fosA3 genes was recovered from E. coli isolate EC013 belonging to D-ST117. The plasmid was found to have heterogeneous and dynamic MRRs in an individual strain and the IS26-flanked composite transposon-derived circular intermediates were identified and characterized in pEC013.

CONCLUSIONS

The heterogeneous MRRs suggested that a single plasmid may actually be a cluster of plasmids with the same backbone but varied MRRs, reflecting the plasmid's heterogeneity and the survival benefits of having a response to antimicrobial-related threatening conditions in an individual strain.

Experimental support for multidrug resistance transfer potential in the preterm infant gut microbiota

BACKGROUND

There is currently a lack of experimental evidence for horizontal gene transfer (HGT) mechanisms in the human gut microbiota. The aim of this study was therefore to experimentally determine the HGT potential in the microbiota of a healthy preterm infant twin pair and to evaluate the global occurrence of the mobilized elements.

METHODS

Stool samples were collected. Both shotgun metagenome sequencing and bacterial culturing were done for the same samples. A range of experimental conditions were used to test DNA transfer for the cultured isolates. Searches for global distribution of transferable elements were done for the ~120,000 metagenomic samples in the Sequence Read Archive (SRA) database.

RESULTS

DNA transfer experiments demonstrated frequent transmission of an ESBL encoding IncI1 plasmid, a high copy number ColEI plasmid, and bacteriophage P1. Both IncI1 and ColE1 were abundant in the stool samples. In vitro competition experiments showed that transconjugants containing IncI1 plasmids outcompeted the recipient strain in the absence of antibiotic selection. The SRA searches indicated a global distribution of the mobilizable elements, with chicken identified as a possible reservoir for the IncI1 ESBL encoding plasmid.

CONCLUSION

Our results experimentally support a major horizontal transmission and persistence potential of the preterm infant gut microbiota mobilome involving genes encoding ESBL.

Antibacterial potential of Forsythia suspensa polysaccharide against resistant Enterobacter cloacae with SHV-12 extended-spectrum β-lactamase (ESBL)

In this study, a homogenous polysaccharide (FSP), with an average molecular weight of 9.08 × 10⁴ Da, was isolated from Forsythia suspense and its antibacterial potential against Enterobacter cloacae producing SHV‐12 ESBL was investigated. Growth kinetics, in vitro competition and biofilm formation experiments demonstrated that SHV‐12 ESBL contributed to a fitness benefit to E cloacae strain. The antibacterial activity of FSP (2.5, 5.0 and 10.0 μg/mL) was tested against E cloacae bearing SHV‐12 ESBL gene using bacterial sensitivity, agar bioassay and agar well diffusion assays. It was found that the addition of FSP demonstrated potent antibacterial activities against this bacterial as showed by the decrease of bacterial growth and the increase of the inhibition zone diameter. Furthermore, SHV‐12 ESBL gene expression was decreased in E cloacae strain following different FSP treatment in a concentration‐dependent manner. In conclusion, these data showed that FSP exhibited potent good antibacterial activity against E cloacae producing SHV‐12 ESBL via inhibition of SHV‐12 ESBL gene expression, which may promote the development of novel natural antibacterial agents to treat infections caused by this drug‐resistant bacterial pathogen.

Comparative analysis of multidrug resistance plasmids and genetic background of CTX-M-producing Escherichia coli recovered from captive wild animals

Multiple interlinked factors are associated with the global resistome, whereas multidrug-resistant (MDR) pathogens have been related to increased mortality rates in humans and animals. CTX-M-type is the most prevalent extended-spectrum β-lactamase (ESBL) among Enterobacteriaceae, which raises concern worldwide. Zoological gardens have a high density of animals that live very close to each other and to humans. Therefore, this study aimed to investigate through the whole-genome sequencing (WGS) MDR Escherichia coli lineages obtained from captivity wild animals in a zoo. Genetic background showed a wide resistome for antimicrobials (e.g., bla_CTX-M-65, bla_CTX-M-8, bla_CMY-2, qnrB19), metals (e.g., pcoABCDERS, silABCEP, merACDEPRT), and antibacterial biocides (e.g., sugE, mdfA) among MDR CTX-M-producing E. coli belonging to CC155 and CC156. Mobilome analysis revealed several plasmids, and eight of them were completely characterized, which showed different backbone-encoding genes. Comparative analysis of plasmids bla_CTX-M-65/IncHI2-ST3, bla_CTX-M-8/IncI1-ST113, and IncQ1 showed a high identity among plasmids obtained from humans and animals worldwide distributed. Besides, several virulence genes, CRISPR, and prophage-related sequences were also detected. The occurrence of MDR E. coli belonging to CCs closely related to humans and food-producing animals and the high similarity among the plasmids from MDR E. coli carrying clinically significant antimicrobial resistance genes may indicate intercontinental dissemination of these lineages and plasmids. Therefore, these findings contribute to the monitoring of antimicrobial resistance and the human-animal-environment interface worldwide. Key Points • Wide resistome for antimicrobials, metals, and antibacterial biocides. • Multidrug resistance plasmids (bla_CTX-M-65/IncHI2-ST3, bla_CTX-M-8/IncI1-ST113). • Co-occurrence of plasmid-mediated resistance and virulence genes.

Ceftazidime-Avibactam Resistance Associated with Increased bla KPC-3 Gene Copy Number Mediated by pKpQIL Plasmid Derivatives in Sequence Type 258 Klebsiella pneumoniae

This study reports on the characterization of two ceftazidime-avibactam (CZA)-resistant KPC-producing Klebsiella pneumoniae strains (KP-14159 and KP-8788) sequentially isolated from infections occurred in a patient never treated with CZA. Whole-genome sequencing characterization using a combined short- and long-read sequencing approach showed that both isolates belonged to the same ST258 strain, had altered outer membrane porins (a truncated OmpK35 and an Asp137Thr138 duplication in the L3 loop of OmpK36), and carried novel pKpQIL plasmid derivatives (pIT-14159 and pIT-8788, respectively) harboring two copies of the Tn4401a KPC-3-encoding transposon. Plasmid pIT-8788 was a cointegrate of pIT-14159 with a ColE replicon (that was also present in KP-14159) apparently evolved in vivo during infection. pIT-8788 was maintained at a higher copy number than pIT-14159 and, upon transfer to Escherichia coli DH10B, was able to increase the CZA MIC by 32-fold. The present findings provide novel insights about the mechanisms of acquired resistance to CZA, underscoring the role that the evolution of broadly disseminated pKpQIL plasmid derivatives may have in increasing the bla _KPC gene copy number and KPC-3 expression in bacterial hosts. Although not self-transferable, similar elements, with multiple copies of Tn4401 and maintained at a high copy number, could mediate transferable CZA resistance upon mobilization.

Genomic surveillance detects Salmonella enterica serovar Paratyphi A harbouring blaCTX-M-15 from a traveller returning from Bangladesh

Whole genome sequencing (WGS) has been used routinely by Public Health England (PHE) for identification, surveillance and monitoring of resistance determinants in referred Salmonella isolates since 2015. We report the first identified case of extended-spectrum-β-lactamase (ESBL) Salmonella enterica serovar Paratyphi A (S. Paratyphi A) isolated from a traveller returning to England from Bangladesh in November 2017. The isolate (440915) was resistant to ciprofloxacin and harboured both the mobile element ISEcp9 –bla_CTX-M-15-hp-tnpA and bla_TEM-191, associated with ESBL production. Phenotypic resistance was subsequently confirmed by Antimicrobial Susceptibility Testing (AST). S. Paratyphi A 440915 harboured an IncI1 plasmid previously reported to encode ESBL elements in Enterobacteriaceae and recently described in a S. Typhi isolate from Bangladesh. Results from this study indicate the importance of monitoring imported drug resistance for typhoidal salmonellae as ceftriaxone is the first line antibiotic treatment for complicated enteric fever in England. We conclude that WGS provides a rapid, accurate method for surveillance of drug resistance genes in Salmonella, leading to the first reported case of ESBL producing S. Paratyphi A and continues to inform the national treatment guidelines for management of enteric fever.

Wild owls colonized by international clones of extended-spectrum β-lactamase (CTX-M)-producing Escherichia coli and Salmonella Infantis in the Southern Cone of America

Extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae have been classified as critical priority pathogens by the World Health Organization (WHO). We have conducted a microbiological and genomic surveillance study, in order to investigate the occurrence and features of antibiotic-resistant bacteria in wild birds admitted to a wildlife rescue and rehabilitation centre in Chile. This study reports for the first time the occurrence of highly virulent ESBL-producing Escherichia coli and Salmonella enterica serovar Infantis in wild owls inhabiting the Southern Cone of America. Genomic analysis revealed a wide resistome (for antibiotics, heavy metals and disinfectants) among international lineages of E. coli belonging to ST345 and ST2705, and S. Infantis ST32, producing CTX-M-8 or CTX-M-65 ESBLs. On the other hand, wide virulome was associated with a highly virulent behaviour in the Galleria mellonella infection model. Worryingly, all these lineages have been previously reported in humans, supporting that wide resistome and virulome could be contributing to rapid adaptation and dissemination of these clones at the human-animal-environment interface. In summary, wild owls can constitute environmental reservoirs of international clones of ESBL (CTX-M)-producing E. coli and S. Infantis carrying a wide resistome and virulome, in the Southern Cone of America, with potential risks to human, animal and environmental health.

Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location

Escherichia coli ST405 is an emerging urosepsis pathogen, noted for carriage of bla_CTX-M, bla_NDM, and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant E. coli ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant E. coli ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing. The genome of strain 2009-27 assembled into two unitigs; a chromosome comprising 5,287,472 bp and an IncB/O plasmid, pSDJ2009-27, of 89,176 bp. In silico and phenotypic analyses showed that strain 2009-27 is a serotype O102:H6, phylogroup D ST405 resistant to ampicillin, azithromycin, kanamycin, streptomycin, trimethoprim, and sulphafurazole. The genes encoding resistance to these antibiotics reside within a novel, mobile IS26-flanked transposon, identified here as Tn6242, in the chromosomal gene yjdA. Tn6242 comprises four modules that each carries resistance genes flanked by IS26, including a class 1 integron with dfrA17 and aadA5 gene cassettes, a variant of Tn6029, and mphA. We exploited unique genetic signatures located within Tn6242 to identify strains of ST405 from Danish patients that also carry the transposon in the same chromosomal location. The acquisition of Tn6242 into yjdA in ST405 is significant because it (i) is vertically inheritable; (ii) represents a reservoir of resistance genes that can transpose onto resident/circulating plasmids; and (iii) is a site for the capture of further IS26-associated resistance gene cargo.

Multidrug resistance and multivirulence plasmids in enterotoxigenic and hybrid Shiga toxin-producing/enterotoxigenic Escherichia coli isolated from diarrheic pigs in Switzerland

Enterovirulent Escherichia coli infections cause significant losses in the pig industry. However, information about the structures of the virulence and multidrug resistance (MDR) plasmids harboured by these strains is sparse. In this study, we used whole-genome sequencing with PacBio and Illumina platforms to analyse the molecular features of the multidrug-resistant enterotoxigenic E. coli (ETEC) strain 14OD0056 and the multidrug-resistant hybrid Shiga toxin-producing/enterotoxigenic E. coli (STEC/ETEC) strain 15OD0495 isolated from diarrheic pigs in Switzerland. Strain 14OD0056 possessed three virulence plasmids similar to others previously found in ETEC strains, while 15OD0495 harboured a 119-kb multivirulence IncFII/IncX1 hybrid STEC/ETEC plasmid (p15ODTXV) that co-carried virulence genes of both ETEC and STEC pathotypes, confirming the key role of plasmids in the emergence of hybrid pathotypes. All resistance genes of 14OD0056 that conferred resistance to ampicillin (bla_TEM-1b), gentamicin (aac(3)-IIa), kanamycin (aph(3')-Ia), sulfonamide (sul1 and sul2), streptomycin (aph(3″)-Ib, aph(6)-Id), tetracycline (tet(B)) and trimethoprim (dfrA1) were identified on a single 207-kb conjugative MDR plasmid of incompatibility group (Inc) IncHI1/IncFIA (p14ODMR). Strain 15OD0495 carried two antimicrobial resistance plasmids (p15ODAR and p15ODMR). The 99-kb IncI1 plasmid p15ODAR harboured only aminoglycoside resistance genes (aac(3)-IIa, aph(3″)-Ib, aph(6)-Id, aph(4)-Ia), whilst the 49-kb IncN MDR plasmid p15ODMR carried genes conferring resistance to ampicillin (bla_TEM-1b), sulfonamide (sul2), streptomycin (aph(6)-Id), tetracycline (tet(A)) and trimethoprim (dfrA14). Filter mating assays showed that p14ODMR, p15ODMR and p15ODAR were conjugative at room temperature and 37°C. The co-localization of multiple resistance genes on MDR conjugative plasmids such as p14ODMR and p15ODMR poses the risk of simultaneous selection of several resistance traits during empirical treatment. Thus, preventive strategies and targeted therapy following antibiotic susceptibility testing should be encouraged to avoid further dissemination of such plasmids.

CTX-M-65 Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Infantis, United States1

Extended-spectrum β-lactamases (ESBLs) confer resistance to clinically important third-generation cephalosporins, which are often used to treat invasive salmonellosis. In the United States, ESBLs are rarely found in Salmonella. However, in 2014, the US Food and Drug Administration found blaCTX-M-65 ESBL-producing Salmonella enterica serotype Infantis in retail chicken meat. The isolate had a rare pulsed-field gel electrophoresis pattern. To clarify the sources and potential effects on human health, we examined isolates with this pattern obtained from human surveillance and associated metadata. Using broth microdilution for antimicrobial susceptibility testing and whole-genome sequencing, we characterized the isolates. Of 34 isolates, 29 carried the blaCTX-M-65 gene with <9 additional resistance genes on 1 plasmid. Of 19 patients with travel information available, 12 (63%) reported recent travel to South America. Genetically, isolates from travelers, nontravelers, and retail chicken meat were similar. Expanded surveillance is needed to determine domestic sources and potentially prevent spread of this ESBL-containing plasmid.

Co-location of the blaKPC-2, blaCTX-M-65, rmtB and virulence relevant factors in an IncFII plasmid from a hypermucoviscous Klebsiella pneumoniae isolate

Hypervirulent variants of klebsiella pneumoniae (hvKP), which cause serious infections not only healthy individuals, but also the immunocompromised patients, have been increasingly reported recently. One conjugation of a hypermucoviscous strian SWU01 co-carried the resistance gene bla_KPC-2 and virulence gene iroN by the PCR detection from three carbapenem-resistance hvKP. To know the genetic context of this plasmid. The whole genome of this strain was sequenced. We got a 162,552-bp plasmid (pSWU01) which co-carried the resistance gene bla_KPC-2 and virulence gene iroN. It is composed of a typical IncFII-type backbone, five resistance genes including bla_CTX-M-65, bla_KPC-2, bla_SHV-12, bla_TEM-1 and rmtB, and several virulence relevant factors including iroN, traT and toxin-antitoxin systems. The plasmid pSWU01 co-carrying the multidrug resistance determinants and virulence relevant factors from the hypermucoviscous K. pneumoniae represents a novel therapeutic challenge.

Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples

Background

Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains.

Results

In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene.

Conclusions

Until this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0238-9) contains supplementary material, which is available to authorized users.

Comparative Analysis of Extended-Spectrum-β-Lactamase CTX-M-65-Producing Salmonella enterica Serovar Infantis Isolates from Humans, Food Animals, and Retail Chickens in the United States

We sequenced the genomes of 10 Salmonella enterica serovar Infantis isolates containing bla_CTX-M-65 obtained from chicken, cattle, and human sources collected between 2012 and 2015 in the United States through routine National Antimicrobial Resistance Monitoring System (NARMS) surveillance and product sampling programs. We also completely assembled the plasmids from four of the isolates. All isolates had a D87Y mutation in the gyrA gene and harbored between 7 and 10 resistance genes [aph(4)-Ia, aac(3)-IVa, aph(3')-Ic, bla_CTX-M-65, fosA3, floR, dfrA14, sul1, tetA, aadA1] located in two distinct sites of a megaplasmid (∼316 to 323 kb) similar to that described in a bla_CTX-M-65-positive S Infantis isolate from a patient in Italy. High-quality single nucleotide polymorphism (hqSNP) analysis revealed that all U.S. isolates were closely related, separated by only 1 to 38 pairwise high-quality SNPs, indicating a high likelihood that strains from humans, chickens, and cattle recently evolved from a common ancestor. The U.S. isolates were genetically similar to the bla_CTX-M-65-positive S Infantis isolate from Italy, with a separation of 34 to 47 SNPs. This is the first report of the bla_CTX-M-65 gene and the pESI (plasmid for emerging S Infantis)-like megaplasmid from S Infantis in the United States, and it illustrates the importance of applying a global One Health human and animal perspective to combat antimicrobial resistance.

Characteristics of extended-spectrum β-lactamase-producing Escherichia coli isolated from fecal samples of piglets with diarrhea in central and southern Taiwan in 2015

Background

The production of extended-spectrum β-lactamases (ESBLs) confer resistance to the commonly used beta-lactam antimicrobials and ESBL–producing bacteria render treatment difficulty in human and veterinary medicine. ESBL–producing bacteria have emerged in livestock in recent years, which may raise concerns regarding possible transfer of such bacteria through the food chain. The swine industry is important in Taiwan, but investigations regarding the status of ESBL in swine are limited.

Results

We collected 275 fecal swab samples from piglets with diarrhea in 16 swine farms located in central and southern Taiwan from January to December 2015 and screened them for ESBL–producing Escherichia coli. ESBL producers were confirmed phenotypically by combination disc test and genotypically by polymerase chain reaction and DNA sequencing. The occurrence rate of ESBL–producing E. coli was 19.7% (54 of 275), and all were obtained in swine farms located in southern Taiwan. bla_{CTX-M-1-group} and bla_{CTX-M-9-group} were the two bla_CTX-M groups found. bla_CTX-M-55 (34 of 54; 63.0%) and bla_CTX-M-15 (16 of 54; 29.6%), which belong to the bla_{CTX-M-1-group}, were the two major bla gene types, whereas bla_CTX-M-65 was the only type found in the bla_{CTX-M-9 group}. Twenty-seven strains contained bla_TEM-1, and the other 27 strains contained bla_TEM-116. One strain found in Pingtung harbored three bla genes: bla_TEM-116, bla_CTX-M-55, and bla_CTX-M-65. ESBL–producing E. coli exhibited a multidrug-resistant phenotype, and multilocus sequence typing revealed that the ST10 clonal complexes, including ST10, 167, 44, and 617 accounted for 35% (19 of 54) of these strains.

Conclusions

ESBL-producing E. coli from piglets with diarrhea were isolated from swine farms located in southern Taiwan. The most commonly detected bla were bla_CTX-M-15 and bla_CTX-M-55. The ST10 clonal complexes comprised most of our ESBL-producing E. coli strains. Fecal shedding from swine may contaminate the environment, resulting in public health concerns; thus, continued surveillance of ESBL is essential in swine and in other food animals.

Complete Sequence of pEC012, a Multidrug-Resistant IncI1 ST71 Plasmid Carrying bla CTX-M-65, rmtB, fosA3, floR, and oqxAB in an Avian Escherichia coli ST117 Strain

A 139,622-bp IncI1 ST71 conjugative plasmid pEC012 from an avian Escherichia coli D-ST117 strain was sequenced, which carried five IS26-bracketed resistance modules: IS26-fosA3-orf1-orf2-Δorf3-IS26, IS26-fip-ΔISEcp1-bla_CTX-M-65-IS903D-iroN-IS26, IS26-ΔtnpR-bla_TEM-1-rmtB-IS26, IS26-oqxAB-IS26, and IS26-floR-aac(3)-IV-IS26. The backbone of pEC012 was similar to that of several other IncI1 ST71 plasmids: pV408, pM105, and pC271, but these plasmids had different arrangements of multidrug resistance region. In addition, the novel ISEc57 element was identified, which is in the IS21 family. The stepwise emergence of multi-resistance regions demonstrated the accumulation of different resistance determinants through homologous recombination. To the best of our knowledge, this is the first study to identify a multidrug-resistant IncI1 ST71 plasmid carrying bla_CTX-M-65, rmtB, fosA3, floR, and oqxAB in an avian E. coli ST117 strain.