CTX-M-123, a novel hybrid of the CTX-M-1 and CTX-M-9 Group β-lactamases recovered from Escherichia coli isolates in China

Monitoring the Spread of Multidrug-Resistant Escherichia coli Throughout the Broiler Production Cycle

The extensive use of antimicrobials in broiler production is changing the bird microbiota, fostering drug-resistant bacteria, and complicating therapeutic interventions, making the problem of multidrug resistance global. The monitoring of antimicrobial virulence and resistance genes are tools that have come to assist the breeding of these animals, directing possible treatments as already used in human medicine and collecting data to demonstrate possible dissemination of multidrug-resistant strains that may cause damage to industry and public health. This work aimed to monitor broiler farms in southern Brazil, isolating samples of E. coli and classifying them according to the profile of resistance to antimicrobials of interest to human and animal health. We also monitored the profile of virulence genes and conducted an epidemiological survey of possible risk factors that contribute to this selection of multidrug-resistant isolates. Monitoring was carried out on farms in the three southern states of the country, collecting samples of poultry litter, cloacal swabs, and beetles of the species Alphitobius diaperinus, isolating E. coli from each of these samples. These were evaluated by testing their susceptibility to antimicrobials of animal and human interest; detecting whether the samples were extended-spectrum β-lactamase enzyme (ESBL) producers; and when positive, selected for genotypic tests to identify resistant genes (CTX-M, TEM, and SHV) and virulence. Among the antimicrobials tested, enrofloxacin and ciprofloxacin demonstrated some of the highest frequencies of resistance in the isolated strains, with significant statistical results. The use of these antimicrobials increased the likelihood of resistance by over three times and was associated with a 1.5-fold higher probability of multidrug resistance. Of all isolates, 95% were multidrug-resistant, raising concerns for production and public health. Among 231 ESBL-positive samples, the CTX-M1 group predominated.

First Detection of Chimeric β-Lactamase CTX-M-64-Producing Salmonella Typhimurium from a Domestic Source in Japan

Salmonella enterica subsp. enterica serovar Typhimurium has recently emerged worldwide as a producer of extended-spectrum β-lactamase (ESBL). However, drug-resistant clinical isolates are rare in Japan. The common types of ESBLs found are the CTX-M-type β-lactamases, including novel β-lactamases such as CTX-M-64. CTX-M-64 has a chimeric structure comprising a combination of the CTX-M-1 and CTX-M-9 groups. In 2017, S. Typhimurium was isolated from stool, blood, and urine cultures of an 82-year-old man. Herein, we describe the discovery of a clinical isolate of S. Typhimurium in Japan. Antimicrobial susceptibility testing revealed that the isolate was resistant to third- and fourth-generation cephalosporins, including ceftazidime and monobactam. The minimum inhibitory concentrations of ceftazidime and ceftriaxone were restored by administration of clavulanic acid. Whole-genome sequencing analysis revealed that the isolate harbored the blaCTX-M-64 gene on an IncHI2/IncHI2A-type plasmid, with an assembly length of 174,477 bp. The genetic structure of the region surrounding the blaCTX-M-64 gene, ISKpn26-ΔISEcp1-blaCTX-M-64-orf477, was shared only with the chromosome sequence of S. Typhimurium detected in food-producing chickens in Guangdong, China. Although rare, S. Typhimurium can induce bloodstream infections and produce ESBL. To our knowledge, this is the first report of a CTX-M-64-producing Enterobacterales clinical isolate of domestic origin in Japan.

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China

China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.

Extended-spectrum beta-lactamase in Escherichia coli isolated from humans, animals, and environments in Bangladesh: A One Health perspective systematic review and meta-analysis

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-threatening hospital- and community-acquired infections across the globe. Here, we conducted a systematic review and meta-analysis to evaluate the prevalence of ESBL in E. coli isolated from humans, animals, and environments in Bangladesh. Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, the current systematic review and meta-analysis was taken into account for studies published between 2010 and 2021 in peer-reviewed journals. The meta-analysis was performed on "R" version 4.2.2. A total of 36 studies were included in this systematic review and meta-analysis; among them, 22 were human, seven were animal, four were environmental, and three were multidisciplinary studies. The meta-analysis revealed that the pooled prevalence of ESBL-producing E. coli in Bangladesh was 21% (95% CI: 15%-27%). On the sample basis, the pooled prevalence of ESBL-producing E. coli in humans, animals, and environments was 17% (95% CI: 11%-23%), 22% (95% CI: 9%-34%), and 39% (95% CI: 16%-62%), respectively. All the pooled prevalence of ESBL-producing E. coli showed substantial heterogeneity (I2 > 75%; p < 0.05) among the selected studies. This systematic review reported 13 different types of resistance genes encoding ESBL, such as blaTEM-1 (37.5%), blaCMY (34.6%), blaCTX-M-1 (20.7%), blaCTX-M-15 (16.1%), blaTEM (12.3%), blaCTX-M and blaOXA (9.6%), blaOXA-1 (5.8%), blaampC (3.9%), blaSHV (3.8%), blaCMY-2 (2.3%), blaCTX-M-14 (1.3%), and blaCTX-M-9 (0.3%). Moreover, 39 types of epidemiologically important clones (including ST10 and ST131) were detected in ESBL-producing E. coli isolated from humans, animals, and environments in Bangladesh. To the best of our knowledge, this is the first systematic review and meta-analysis of integrated studies on ESBL-producing E. coli using the One Health approach in Bangladesh. The high prevalence of ESBL-producing E. coli, their resistance genes, and epidemiologically important clones in humans, animals, and environments highlights the importance of implementing comprehensive antimicrobial resistance (AMR) surveillance under a One Health perspective to mitigate the AMR consequences in Bangladesh.

Whole genome sequencing and characteristics of extended-spectrum beta-lactamase producing Escherichia coli isolated from poultry farms in Banaskantha, India

Worldwide dissemination of extended-spectrum -lactamase (ESBL)-producing Escherichia coli constitutes an emerging global health issue, with animal food products contributing as potential reservoirs. ESBL E. coli infection is associated with the high mortality and mobility rate in developing countries due to less susceptibility to antibiotics. The present study aimed to elucidate the molecular characteristics and sequence-based analysis of ESBL E. coli in the Gujarat state of India. This study included 108 E. coli strains were isolated from different poultry farms (broiler and layer) in the Banaskantha District. PCR was employed to identify genotypic ESBL-producing antimicrobial resistance genes. Overall, a high occurrence of ESBL genes was found in poultry farms due to the high usage of antimicrobials. The PCR analysis revealed that 79.62% of isolates were detected positive with one or more ESBL genes. Among them, bla_TEM (63.88%) was found to be the predominant genotype, followed by bla_SHV (30.55%) and bla_OXA (28.70%). In the bla_CTX-M group, a higher occurrence was observed in bla_CTX-M-9 (23.14%), followed by bla_CTX-M-2 (24.07%) and bla_CTX-M-1 (22.22%). We used the whole-genome sequencing (WGS) method to evaluate the antimicrobial resistance genes, virulence factors, single nucleotide polymorphisms (SNPs), plasmid replicons, and plasmid-mediated AMR genes of one ESBL E. coli isolated. We examined the genetic relatedness of a human pathogenic E. coli strain by comparing its sequence with the broad geographical reference E. coli sequences. Escherichia coli ST 681 was determined using multi-locus sequence typing. We compared our findings to the reference sequence of Escherichia coli str. K- 12 substr. MG1655. We found 24,937 SNPs with 21,792 in the genic region, 3,145 in the intergenic region, and six InDels across the genome. The WGS analysis revealed 46 antimicrobial resistance genes and seven plasmid-mediated AMR genes viz., tetA, qnrS1, dfrA14, sul2, aph(3”)-lb, aph(6)-ld, and Aph(3’)-la. The ST 681 was found to have Cib, traT, and terC virulence factors and two plasmid replicons, IncFII(pHN7A8) and IncI1-I(Alpha). This study revealed a higher occurrence of ESBL E. coli detected in poultry.

Genomic Characterization of a Uropathogenic Escherichia coli ST405 Isolate Harboring bla CTX-M-15-Encoding IncFIA-FIB Plasmid, bla CTX-M-24-Encoding IncI1 Plasmid, and Phage-Like Plasmid

Escherichia coli sequence type 405 is an emerging antibiotic-resistant clonal group associated with the global dissemination of extended-spectrum β-lactamase-producing E. coli. In this study, we report the genome assembly and characterization of a uropathogenic E. coli ST405 strain, SZESBLEC201, based on long and short reads obtained from the Nanopore and Illumina sequencing platforms, respectively. Whole-genome sequencing revealed that SZESBLEC201 harbors a 5,020,403 bp chromosome and three plasmids, namely, pSZESBLEC201-1, pSZESBLEC201-2, and pSZESBLEC201-3. pSZESBLEC201-1 (111,621 bp) belongs to the IncFIA-FIB type and harbors bla _CTX-M-15. However, this plasmid does not harbor conjugative transfer-associated genes, rendering pSZESBLEC201-1 unable to be conjugatively transferred. pSZESBLEC201-2 (95,138 bp) is a phage-like plasmid that shows a strong genome synteny with Escherichia phage P1 but with the absence of mobile genetic elements and some regulatory genes. pSZESBLEC201-3 (92,865 bp) belongs to the IncI1 type and carries bla _CTX-M-24. In contrast to pSZESBLEC201-1, pSZESBLEC201-3 retains its full active conjugation machinery and can be transferred via conjugation. The genetic features of the genome show that the SZESBLEC201 has a unique virulence pattern compared with genetically similar strains found in the same country (China). The plasmid backbones exhibit a high degree of similarity to those of geographically distant isolates, highlighting the global spread of bla _CTX-M genes and the genome plasticity of this clonal group. The coexistence of two bla _CTX-M variants in the same strain increases the risk of the emergence of new bla _CTX-M variants. Further studies on phage-like plasmids are necessary to provide insights into their biological activities and clinical significance.

Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand

OBJECTIVES

The incidence of infections with ESBL-producing Escherichia coli (ESBL-Ec) in New Zealand is increasing. ESBL-Ec most commonly cause urinary tract infections and are seen in both community and hospitalized patients. The reason for the increasing incidence of ESBL-Ec infections is unknown.

METHODS

In this study, 65 urinary ESBL-Ec isolates from the Otago region in 2015 were fully genetically characterized to understand the mechanisms of transmission. The ESBL gene, E. coli STs, plasmid types and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. The phylogenetic relationships of the isolates were compared with ESBL-Ec isolates sequenced as part of the 2016 nationwide survey.

RESULTS

Significant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. However, there was evidence of common mobile genetic elements in unrelated ESBL-Ec.

CONCLUSIONS

Multiple introductions of ESBL resistance genes or resistant bacterial strains with limited horizontal transmission of mobile genetic elements accounts for the increased incidence of ESBL-Ec in this low prevalence area. Future studies should investigate modes of transmission of ESBL-Ec in the Otago region.

Transmission of plasmid-borne and chromosomal blaCTX-M-64 among Escherichia coli and Salmonella isolates from food-producing animals via ISEcp1-mediated transposition

OBJECTIVES

To clarify the transmission mechanism of the blaCTX-M-64 gene between Escherichia coli and Salmonella isolates from food animals.

METHODS

A total of 329 E. coli and 60 Salmonella isolates collected from food animals in 2016 were screened for the presence of blaCTX-M-64 genes. The blaCTX-M-64-positive isolates were typed and plasmid and chromosome DNA was sequenced to determine the genetic context of blaCTX-M-64 and the plasmid types present.

RESULTS

The blaCTX-M-64 gene was identified in only three E. coli isolates but was the predominant gene in the Salmonella isolates (n = 9). These 12 CTX-M-64-positive isolates were all resistant to ampicillin, cefotaxime, ceftiofur, ceftriaxone, ceftazidime and florfenicol and 9 were resistant to ciprofloxacin. The blaCTX-M-64 gene was located on transferable IncI2 plasmids and an IncHI2 plasmid in three E. coli and one Salmonella isolate, respectively. The remaining eight Salmonella isolates contained blaCTX-M-64 integrated into the chromosome. Different genetic contexts of blaCTX-M-64 genes were found among the 12 isolates: ISEcp1-blaCTX-M-64-orf477-A/C on IncI2 plasmids of 3 E. coli isolates; ΔISEcp1-blaCTX-M-64-orf477-A/C in the chromosome of 1 Salmonella isolate; and ISEcp1-blaCTX-M-64-orf477 on the IncHI2 plasmid and chromosome of 8 Salmonella isolates.

CONCLUSIONS

To the best of our knowledge, this is the first report of chromosomally encoded CTX-M-64 in Salmonella isolates. ISEcp1-mediated transposition is likely to be responsible for the spread of blaCTX-M-64 between different plasmids and chromosomes in Enterobacteriaceae especially E. coli and Salmonella.

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

Salmonella enterica remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of S. enterica isolates from retail meat from different sources in China are lacking. A total of 341 S. enterica strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was S. Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the Salmonella In Silico Typing Resource (SISTR) (96.5%). The pangenome of the 341 S. enterica isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher Salmonella phage 118970 sal3 (219/341, 64.2%) and Gifsy-2 (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates. Three beta-lactamases, namely, bla_CTX–M–55 (n = 15), bla_CTX–M–14 (n = 11), and bla_CTX–M–65 (n = 11), were more prevalent in retail meats. The emergence of qnrE1 and bla_{CTX–M–123} indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes mcr-1.1 and mcr-9, respectively. Thus, we explored the evolution and genomic features of S. enterica isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.

Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum β-Lactamase and Its Inhibition by Avibactam

The diazabicyclooctane (DBO) inhibitor avibactam (AVI) reversibly inactivates most serine β-lactamases, including the CTX-M β-lactamases. Currently, more than 230 unique CTX-M members distributed in five clusters with less than 5% amino acid sequence divergence within each group have been described. Recently, a variant named CTX-M-151 was isolated from a Salmonella enterica subsp. enterica serovar Choleraesuis strain in Japan. This variant possesses a low degree of amino acid identity with the other CTX-Ms (63.2% to 69.7% with respect to the mature proteins), and thus it may represent a new subgroup within the family. CTX-M-151 hydrolyzes ceftriaxone better than ceftazidime (k _cat/K _m values 6,000-fold higher), as observed with CTX-Ms. CTX-M-151 is well inhibited by mechanism-based inhibitors like clavulanic acid (inactivation rate [k _inact]/inhibition constant [K_i ] = 0.15 μM^-1 · s^-1). For AVI, the apparent inhibition constant (K_{i app}), 0.4 μM, was comparable to that of KPC-2; the acylation rate (k₂/K) (37,000 M^-1 · s^-1) was lower than that for CTX-M-15, while the deacylation rate (k _off) (0.0015 s^-1) was 2- to 14-fold higher than those of other class A β-lactamases. The structure of the CTX-M-151/AVI complex (1.32 Å) reveals that AVI adopts a chair conformation with hydrogen bonds between the AVI carbamate and Ser70 and Ser237 at the oxyanion hole. Upon acylation, the side chain of Lys73 points toward Ser130, which is associated with the protonation of Glu166, supporting the role of Lys73 in the proton relay pathway and Glu166 as the general base in deacylation. To our knowledge, this is the first chromosomally encoded CTX-M in Salmonella Choleraesuis that shows similar hydrolytic preference toward cefotaxime (CTX) and ceftriaxone (CRO) to that toward ceftazidime (CAZ).

Fecal Carriage and Genetic Characterization of CTX-M-1/9/1-Producing Escherichia coli From Healthy Humans in Hangzhou, China

CTX-M-199, a novel chimeric β-lactamase which mediated resistance to sulbactam and tazobactam, was recently identified in Hangzhou, China. This study investigated the prevalence of fecal carriage of bacteria producing CTX-M-199 and other CTX-M-1/9/1-type enzymes among healthy individuals and characterized the genetic features of bla_{CTX–M–1/9/1}-bearing mobile elements. A total of 74 Enterobacterales strains carrying various bla_{CTX–M–1/9/1} genes, including bla_CTX–M–64 (n = 40, carriage rate of 0.74%), bla_{CTX–M–199} (n = 23, 0.40%), bla_{CTX–M–123} (n = 5, 0.10%), novel bla_{CTX–M–153} (n = 5, 0.10%), and bla_{CTX–M–132} (n = 2, 0.04%), were isolated from 68 out of 5,000 (1.36%) fecal samples of healthy adults in Hangzhou City. Phylogenetic analysis based on whole-genome sequencing data showed that 72 bla_{CTX–M–1/9/1}-bearing Escherichia coli isolates were clustered into four major clades, three of which included CTX-M-199 producers. Sixty out of 75 bla_{CTX–M–1/9/1} genes were located on plasmids belonging to four Inc types: IncI2, IncI1, IncFIB, and IncHI2. The bla_{CTX–M–199} genes were harbored by three of the four types of plasmids except for IncHI2. All these bla_{CTX–M–1/9/1} genes were carried on an ISEcp1-mediated transposition unit. In conclusion, human fecal carriage of bla_{CTX–M–1/9/1} was low in healthy populations of China. The ISEcp1 was commonly associated with bla_{CTX–M–1/9/1} and may mediate its transmission on various mobile elements. Our findings provide insights into the dissemination and the development of further measures for the control of pathogens producing CTX-M-1/9/1-type enzymes.

Epidemiological Study on Prevalence, Serovar Diversity, Multidrug Resistance, and CTX-M-Type Extended-Spectrum β-Lactamases of Salmonella spp. from Patients with Diarrhea, Food of Animal Origin, and Pets in Several Provinces of China

A total of 2,283 Salmonella isolates were recovered from 18,334 samples, including samples from patients with diarrhea, food of animal origin, and pets, across 5 provinces of China. The highest prevalence of Salmonella spp. was detected in chicken meats (39.3%, 486/1,237). Fifteen serogroups and 66 serovars were identified, with Salmonella enterica serovars Typhimurium and Enteritidis being the most dominant. Most (85.5%, 1,952/2,283) isolates exhibited resistance to ≥1 antimicrobial, and 56.4% were multidrug resistant (MDR). A total of 222 isolates harbored extended-spectrum β-lactamases (ESBLs), and 200 of these were of the CTX-M type and were mostly detected in isolates from chicken meat and turtle fecal samples. Overall, eight blaCTX-M genes were identified, with blaCTX-M-65, blaCTX-M-123, blaCTX-M-14, blaCTX-M-79, and blaCTX-M-130 being the most prevalent. In total, 166 of the 222 ESBL-producing isolates had amino acid substitutions in GyrA (S83Y, S83F, D87G, D87N, and D87Y) and ParC (S80I), while the plasmid-mediated quinolone resistance (PMQR)-encoding genes oqxA, oqxB, qepA, qnrB, and qnrS were detected in almost all isolates. Of the 15 sequence types (STs) identified in the 222 ESBLs, ST17, ST11, ST34, and ST26 ranked among the top 5 in number of isolates. Our study revealed considerable serovar diversity and a high prevalence of the co-occurrence of MDR determinants, including CTX-M-type ESBLs, quinolone resistance-determining region (QRDR) mutations, and PMQR genes. This is the first report of CTX-M-130 Salmonella spp. from patients with diarrhea and QRDR mutations from turtle fecal samples. Our study emphasizes the importance of actions, both in health care settings and in the veterinary medicine sector, to control the dissemination of MDR, especially the CTX-M-type ESBL-harboring Salmonella isolates.

Wastewater as a Probable Environmental Reservoir of Extended-Spectrum-β-Lactamase Genes: Detection of Chimeric β-Lactamases CTX-M-64 and CTX-M-123

The presence of antimicrobial-resistant bacteria and resistance genes in aquatic environments is a serious public health concern. This study focused on Escherichia coli possessing blaCTX-M genes in wastewater inflows. Twelve crude inflow water samples from wastewater treatment plant (WWTP) A and two samples each from three other WWTPs were collected in 2017 and 2018. A total of 73 E. coli isolates with 31 different sequence types (STs) harboring distinctive blaCTX-M gene repertoires were detected. In WWTP A influents, blaCTX-M-14 (14 isolates) was dominant, followed by blaCTX-M-15 (12 isolates) and blaCTX-M-27 (10 isolates). The chimeric blaCTX-M-64 and blaCTX-M-123 genes were each identified in one of the E. coli isolates from the same WWTP A inflow port. The blaCTX-M-27 gene was associated with five of seven B2-ST131 isolates, including three isolates of the B2-O25b-ST131-H30R/non-Rx lineage. One of the remaining two isolates belonged to the B2-O25b-ST131-H30R/Rx lineage harboring the blaCTX-M-15 gene. As for the B2-O25b-ST131-H30R/non-Rx lineage, two isolates with blaCTX-M-27 were recovered from each of the WWTP B and D influents, and one isolate with blaCTX-M-174 was also recovered from WWTP B influent. Whole-genome sequencing of chimeric blaCTX-M-harboring E. coli isolates revealed that the blaCTX-M-64 gene was integrated into the chromosome of ST10 E. coli B22 via ISEcp1-mediated transposition of a 9,467-bp sequence. The blaCTX-M-123-carrying IncI1 plasmid pB64 was 109,169 bp in length with pST108. The overall findings suggest that wastewater may act as a probable reservoir of clinically significant clonal lineages mediating antimicrobial resistance genes and chimeric genes that have not yet been identified from human isolates of domestic origin in Japan.IMPORTANCE Global spread of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is a critical concern in both clinical and community settings. This dominance of CTX-M-type ESBL producers may be largely due to the successful international spread of epidemic clones, as represented by the extraintestinal pathogenic Escherichia coli (ExPEC) ST131. Our findings highlight the worrisome presence of diverse E. coli clones associated with humans, including ExPEC lineages harboring the most common blaCTX-M variants in untreated wastewater samples. Moreover, the chimeric genes blaCTX-M-64 and blaCTX-M-123, which have not yet been identified from human isolates of domestic origin in Japan, were identified. Exposure to untreated wastewater through combined sewer overflow caused by heavy rains derived from abnormal weather change could pose a risk for human health due to ingesting those antimicrobial-resistant bacteria.

Prevalence, Antibiogram, and Resistance Profile of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates from Pig Farms in Luzon, Philippines

This cross-sectional study was conducted to determine the prevalence, antibiogram, and resistance profile of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) isolates from healthy pigs and pig farms in Luzon, Philippines. A total of 162 rectal samples from healthy finisher and breeder pigs and boot swab samples from pig houses were collected from 54 randomly selected pig farms. Bacteria were isolated and screened using MacConkey agar plate supplemented with 1 mg/L cefotaxime. Identification of bacteria and antimicrobial susceptibility test were carried out through Vitek^® 2 and combined disk test. PCR amplifications were carried out in all isolates targeting bla_CTX-M and its five major groupings, bla_TEM, and bla_SHV. The farm prevalence of ESBL-EC was 57.41% (95% confidence interval [CI] = 43.21-70.77). A total of 48 (29.63%) ESBL-EC isolates were isolated from samples that showed 14 different phenotypic multidrug resistance patterns. The prevalence of bla_CTX-M gene was 91.67% (95% CI = 80.02-97.68). All major bla_CTX-M-groups except bla_{CTX-M-25group} were detected. The bla_CTX-M-1 was the most prevalent bla_CTX-M gene, 75.0% (95% CI = 60.40-86.36). The prevalence of bla_TEM and bla_SHV genes was 91.67% (95% CI = 80.02-97.68) and 60.42% (95% CI = 45.27-74.23), respectively. Coexistence of different bla_CTX-M, bla_TEM, and bla_SHV genes was observed in 44 isolates with 20 different genotypic patterns. High prevalence, diverse antibiogram profile, and genotypic resistance pattern of ESBL-EC isolates from healthy pigs and pig farms were observed in this study that could result in possible transmission to farm workers, susceptible bacteria, and the environment.

Prevalence and distribution of blaCTX-M, blaSHV, blaTEM genes in extended- spectrum β- lactamase- producing E. coli isolates from broiler farms in the Philippines

BACKGROUND

Antimicrobial resistance is a worldwide problem causing serious health threats. Escherichia coli is one of the most important bacteria that causes resistance problem. These bacteria produce an enzyme called extended-spectrum β-lactamase (ESBL) that allows it to become resistant to a wide variety of penicillins and cephalosporins. Currently, no information or published studies on ESBL-producing E.coli in broilers are available in the Philippines. This cross-sectional study was conducted to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)-encoding genes, blaCTX-M, blaSHV, and blaTEM, among E. coli isolates from broiler farms in Luzon, Philippines.

RESULTS

Results showed a farm prevalence of 66. 67%. A total of 69 (44.23%) ESBL-producing E. coli were isolated from boot swabs and cloacal swab samples from broiler farms. All major blaCTX-M groups except blaCTX-M-25 group were identified in the isolates. The most prevalent group was blaCTX-M-1, 72.46% (CI: 60.38-82.54%), followed by blaCTX-M-2, blaCTX-M-9 group and blaCTX-M-8. The blaTEM and blaSHV genes were identified in 57.97 and 27.54% of isolates, respectively. The blaCTX-M and blaTEM were the most common gene combinations (33.33%). Coexistence of blaCTX-M types was observed in 50 (73.53%) isolates.

CONCLUSION

This study shows the high prevalence, diversity of patterns and coexistence of ESBL genes in the E. coli isolates from cloacal and boot swabs from broiler farms which pose risks of possible transmission to the environment, other animals and human.

Molecular Characterization of Extended-Spectrum β-Lactamase-Producing Multidrug Resistant Escherichia coli From Swine in Northwest China

Objectives: The aim of the present study was to explore the prevalence and molecular characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli collected from pig farms in Northwest China.

Methods: Between May 2015 and June 2017, a total of 456 E. coli isolates were collected from fecal samples of healthy and diarrheal pigs in Northwest China to screen the ESBL producers. The β-lactamases, plasmid-mediated quinolone resistance (PMQR) genes and virulence genes among ESBL producers were corroborated by PCR and sequencing. Finally, ESBL producers were further grouped according to phylogenetic background and genetic relatedness.

Results: Forty-four (9.6%) out of the 456 E. coli isolates were identified as ESBL-producing isolates. All ESBL producers exhibited multidrug resistance (MDR) phenotype, and more than 90% of the ESBL producers were resistant to amoxicillin, amoxicillin-clavulanic acid, oxytetracycline, enrofloxacin and sulfamethoxazole/trimethoprim. All ESBL producers harbored at least one type of β-lactamase, with bla_CTX−M, bla_TEM, bla_SHV, bla_OXA−48, and bla_KPC−2 being detected in forty, thirty, seven, four, two and one isolates, respectively. Sequencing revealed the most common bla_CTX−M subtype was bla_CTX−M−14 (n = 24), followed by bla_CTX−M−15 (n = 14), bla_CTX−M−64 (n = 11), bla_CTX−M−9 (n = 10) and bla_{CTX−M−123} (n = 9). qnrS (n = 23) was the predominant PMQR gene, and all PMQR genes were detected in co-existence with β-lactamase genes. estA (n = 18) and F4 (n = 18) were the most prevalent enterotoxin and fimbrial adhesin, respectively, and 27 different virotypes were found with respect to the association of enterotoxins and fimbrial adhesins. Twenty-four different sequence types (STs) were identified among 44 ESBL producers, and clones ST405, ST10 and ST648 were strongly present in more than one-third (34.1%) of ESBL producers.

Conclusion: All ESBL-producing E. coli isolates exhibited MDR phenotype, and showed high prevalence of β-lactamase and PMQR genes. Especially, one isolate harbored ESBL genes bla_TEM, bla_SHV, bla_CTX−M−9, bla_CTX−M−14, bla_CTX−M−64, and carbapenemase gene bla_OXA−48 and bla_KPC−2, as well as PMQR genes qnrS, qnrB, qnrD, qepA and aac(6')-Ib-cr.

Characterization of Extended-Spectrum β-Lactamase Genes of Shigella flexneri Isolates With Fosfomycin Resistance From Patients in China

BACKGROUND

The emergence of fosfomycin resistance and extended-spectrum β-lactamase (ESBL) genes is a serious threat to public health and a new challenge in shigellosis treatment. The purpose of this study was to identify fosfomycin resistance and characterize β-lactamase genes in fos-carrying isolates of Shigella flexneri from patients in China.

METHODS

A total of 263 S. flexneri isolates were collected from 34 hospitals in the Anhui Province of China during September 2012-September 2015 and screened for fosA3, fosA, and fosC2 by PCR amplification and sequencing. The fos-carrying isolates were then screened for β-lactamase genes. The clonal relationships between fosA3-carrying isolates, the transmissibility of fosfomycin resistance, replicon types of plasmids carrying fosfomycin resistance genes and other associated resistance genes were investigated.

RESULTS

Twenty-five of the 263 isolates (9.5%) showed resistance to fosfomycin, and 18 (6.8%) were positive for fosA3. None of the isolates was positive for fosA or fosC2. Seventeen of the isolates carrying fosA3 (94%) were CTX-M producers (seven CTX-M-55, five CTX-M-14, and five CTX-M-123), while three (16.7%) were TEM producers (TEM-1).Sixteen (88.9%) fosA3-carrying isolates exhibited multi-drug resistance. The replicon types of the 13 fosA3-carrying plasmids were IncF (n=13), IncHI2 (n=3), IncIl-Ir (n=2), and IncN (n=1).

CONCLUSIONS

Our results indicated that fosA3 could spread through plasmids in S. flexneri isolates, along with the bla(CTX-M) and bla(TEM), which facilitate its quick dispersal. To the best of our knowledge, this is the first report of CTX-M-123-type ESBLs in S. flexneri isolates from patients in China.

High prevalence of fosfomycin resistance gene fosA3 in bla CTX-M-harbouring Escherichia coli from urine in a Chinese tertiary hospital during 2010-2014

Fosfomycin has become a therapeutic option in urinary tract infections. We identified 57 fosfomycin-resistant Escherichia coli from 465 urine-derived extended-spectrum β-lactamase (ESBL)-producing isolates from a Chinese hospital during 2010-2014. Of the 57 fosfomycin-resistant isolates, 51 (89·5%) carried fosA3, and one carried fosA1. Divergent pulsed-field gel electrophoresis profiles and multi-locus sequence typing results revealed high clonal diversity in the fosA3-positive isolates. Conjugation experiments showed that the fosA3 genes from 50 isolates were transferable, with IncFII or IncI1 being the most prevalent types of plasmids. The high prevalence of fosA3 was closely associated with that of bla CTX-M. Horizontal transfer, rather than clonal expansion, might play a central role in dissemination. Such strains may constitute an important reservoir of fosA3 and bla CTX-M, which may well be readily disseminated to other potential human pathogens. Since most ESBL-producing E. coli have acquired resistance to fluoroquinolones worldwide, further spread of fosA3 in such E. coli isolates should be monitored closely.

Prevalence and quinolone resistance of fecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in 6 communities and 2 physical examination center populations in Shanghai, China

OBJECTIVES

To characterize extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from the community, determine their antibiotic sensitivity profiles and quinolone resistance mechanisms, and identify any horizontal transfer of ESBL genes.

METHODS

One thousand seven hundred thirty-two stool samples were collected from healthy individuals in 6 communities and 2 physical examination centers in Shanghai, China. ESBL-producing E. coli was screened and confirmed by confirmatory test and E. coli-identifying agars. PCR was used to amplify ESBL-encoding genes blaCTX-M, blaTEM, blaSHV genes, and quinolone resistance-relating genes gyrA, gryB, parC, parE, qnrS, aac (6')-Ib-cr, oqxA, and oqxB, followed by sequencing. Antimicrobial susceptibility tests and conjugation assays were also performed.

RESULTS

Overall, 528 isolates were identified as ESBL-producing E. coli, and all were positive for blaCTX-M. CTX-M-14 was found most frequently (48.9%). S83L±D87N in gyrA and S80I in parC were the most common topoisomerase mutations. Plasmid-mediated quinolone resistance (PMQR) determinants were also detected, including qnrS1 (11.7%), qnrS2 (3.7%), aac (6')-Ib-cr(12.8%), oqxA(8.5%), and oqxB(11.0%). The rate of multidrug resistance was very high (92.2%). ESBL genes transferred successfully in 39.4% isolates.

CONCLUSIONS

There is a high prevalence of fecal carriage of ESBL-producing E. coli in the community in Shanghai, with high-level quinolone resistance and CTX-M-14 being the predominant CTX-M enzyme.

Occurrence of OXA-48 Carbapenemase and Other β-Lactamase Genes in ESBL-Producing Multidrug Resistant Escherichia coli from Dogs and Cats in the United States, 2009-2013

OBJECTIVE

The aim of this study was to explore the occurrence and molecular characterization of extended-spectrum β-lactamases (ESBL), plasmid-mediated AmpC β-lactamase (pAmpC) and carbapenemases among ESBL-producing multidrug resistant (MDR) Escherichia coli from dogs and cats in the United States.

METHODS

Of 2443 E.coli isolated from dogs and cats collected between August 2009 and January 2013, 68 isolates were confirmed as ESBL-producing MDR ones. PCR and sequencing were performed to identify β-lactamases and plasmid-mediated quinolone resistance (PMQR) genes, and shed light on the virulence gene profiles, phylogenetic groups and ST types.

RESULTS

Phylogenic group D and B2 accounted for 69.1% of the isolates. 50 (73.5%) isolates carried CTX-M ESBL gene, and the most predominant specific CTX-M subtype identified was bla CTX-M-15 (n = 33), followed by bla CTX-M-1 (n = 32), bla CTX-M-123 (n = 27), bla CTX-M-9 (n = 19) and bla CTX-M-14 (n = 19), and bla CTX-M-123 was firstly reported in E. coli isolates in the United States alone or in association. Other β-lactamase genes bla TEM, bla SHV, bla OXA-48, and bla CMY-2 were detected in 41.2, 29.4, 19.1, and 17.6% of 68 ESBL-producing MDR isolates, respectively. The bla TEM and bla SHV genes were classfied as ESBLs with the exception of the bla TEM-1 gene. Additionally, 42.6% (29/68) of isolates co-expressed bla CTX-M-15 and PMQR gene aac(6')-Ib-c. The overall occurrence of virulence genes ranged from 11.8 (ireA) to 88.2% (malX), and most of virulence genes were less frequent among CTX-M-producing isolates than non-CTX-M isolates with the exception of malX and iutA. The 68 isolates analyzed were assigned to 31 STs with six being novel. Three pandemic clonal lineages ST131 (n = 10), ST648 (n = 9), and ST405 (n = 9) accounted for more than 41% of the investigated isolates, and ST648 and ST405 of phylogenetic D were firstly reported in E. coli from dogs and cats in the United States.

CONCLUSION

bla CTX-M-123 of ESBLs and carbapenemase bla OXA-48 were firstly reported in ESBL-producing MDR E.coli from dogs and cats in the United States, and ST131, ST648, and ST405 were the predominant clonal groups.

Prevalence and Antibiotic Resistance Profiles of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Broilers in Shandong Province, China

Food-producing animals carrying extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have posed a potential threat to human and animal health. However, information regarding ESBL-EC in the intensive broiler breeding areas of Shandong Province, People's Republic of China, is very limited. The goal of our study was to investigate the prevalence and drug resistance characteristics of ESBL-EC in healthy broilers from Shandong Province. A total of 142 ESBL-EC isolates were collected from four prefectures in Shandong Province from October 2014 to February 2015. ESBL-EC isolates were frequently detected (142 of 160 samples, 88.8%) in healthy broilers. Antibiotic susceptibility testing showed that all 142 ESBL-EC isolates were resistant to ampicillin, piperacillin, and cefazolin but were sensitive to imipenem and meropenem. All ESBL-EC isolates carried one or more of the bla genes, in which blaCTX-M, blaTEM-1, and blaSHV-5 genes were identified in 142, 106, and 5 isolates, respectively. The blaCTX-M gene includes blaCTX-M-15 (56), blaCTX-M-65 (42), blaCTX-M-55 (36), blaCTX-M-14 (21), blaCTX-M-79 (1), blaCTX-M-3 (1), blaCTX-M-123 (1), and blaCTX-M-132 (1). In addition, 17 ESBL-EC isolates cocarried the genes of the CTX-M-1 and CTX-M-9 groups. Our findings indicate that healthy broiler flocks in Shandong Province in China are an important reservoir for ESBL-EC, with blaCTX-M and blaTEM-1 being the prevalent resistance genes identified.

Characterization of CTX-M-14-producing Escherichia coli from food-producing animals

Bacterial resistance to the third-generation cephalosporin antibiotics has become a major concern for public health. This study was aimed to determine the characteristics and distribution of bla CTX-M-14, which encodes an extended-spectrum β-lactamase, in Escherichia coli isolated from Guangdong Province, China. A total of 979 E. coli isolates isolated from healthy or diseased food-producing animals including swine and avian were examined for bla CTX-M-14 and then the bla CTX-M-14 -positive isolates were detected by other resistance determinants [extended-spectrum β-lactamase genes, plasmid-mediated quinolone resistance, rmtB, and floR] and analyzed by phylogenetic grouping analysis, PCR-based plasmid replicon typing, multilocus sequence typing, and plasmid analysis. The genetic environments of bla CTX-M-14 were also determined by PCR. The results showed that fourteen CTX-M-14-producing E. coli were identified, belonging to groups A (7/14), B1 (4/14), and D (3/14). The most predominant resistance gene was bla TEM (n = 8), followed by floR (n = 7), oqxA (n = 3), aac(6')-1b-cr (n = 2), and rmtB (n = 1). Plasmids carrying bla CTX-M-14 were classified to IncK, IncHI2, IncHI1, IncN, IncFIB, IncF or IncI1, ranged from about 30 to 200 kb, and with insertion sequence of ISEcp1, IS26, or ORF513 located upstream and IS903 downstream of bla CTX-M-14. The result of multilocus sequence typing showed that 14 isolates had 11 STs, and the 11 STs belonged to five groups. Many of the identified sequence types are reported to be common in E. coli isolates associated with extraintestinal infections in humans, suggesting possible transmission of bla CTX-M-14 between animals and humans. The difference in the flanking sequences of bla CTX-M-14 between the 2009 isolates and the early ones suggests that the resistance gene context continues to evolve in E. coli of food producing animals.

Residues Distal to the Active Site Contribute to Enhanced Catalytic Activity of Variant and Hybrid β-Lactamases Derived from CTX-M-14 and CTX-M-15

A variety of CTX-M-type extended-spectrum β-lactamases (ESBLs), including hybrid ones, have been reported in China that are uncommon elsewhere. To better characterize the substrate profiles and enzymatic mechanisms of these enzymes, we performed comparative kinetic analyses of both parental and hybrid CTX-M enzymes, including CTX-M-15, -132, -123, -64, -14 and -55, that are known to confer variable levels of β-lactam resistance in the host strains. All tested enzymes were susceptible to serine β-lactamase inhibitors, with sulbactam exhibiting the weakest inhibitory effects. CTX-M-55, which differs from CTX-M-15 by one substitution, A(77)V, displayed enhanced catalytic activity (kcat/Km) against expanded-spectrum cephalosporins (ESCs). CTX-M-55 exhibits higher structure stability, most likely by forming hydrophobic interactions between A(77)V and various key residues in different helices, thereby stabilizing the core architecture of the helix cluster, and indirectly contributes to a more stable active site conformation, which in turn shows higher catalytic efficiency and is more tolerant to temperature change. Analyses of the hybrids and their parental prototypes showed that evolution from CTX-M-15 to CTX-M-132, CTX-M-123, and CTX-M-64, characterized by gradual enhancement of catalytic activity to ESCs, was attributed to introduction of different substitutions to amino acids distal to the active site of CTX-M-15. Similarly, the increased hydrolytic activities against cephalosporins and sensitivity to β-lactamase inhibitors, clavulanic acid and sulbactam, of CTX-M-64 were partly due to the amino acids that were different from CTX-M-14 and located at both the C and N termini of CTX-M-64. These data indicate that residues distal to the active site of CTX-Ms contributed to their enhanced catalytic activities to ESCs.

blaCTX-M-1/9/1 Hybrid Genes May Have Been Generated from blaCTX-M-15 on an IncI2 Plasmid

Three hybrid CTX-M β-lactamases, CTX-M-64, CTX-M-123, and CTX-M-132, with N and C termini matching CTX-M-1 group enzymes and centers matching CTX-M-9 group enzymes, have been identified. The hybrid gene sequences suggested recombination between blaCTX-M-15 and blaCTX-M-14, the two most common blaCTX-M variants worldwide. However, blaCTX-M-64 and blaCTX-M-123 are found in an ISEcp1-blaCTX-M transposition unit with a 45-bp "spacer," rather than the 48 bp usually associated with blaCTX-M-15, and 112 bp of IncA/C plasmid backbone. This is closer to the context of blaCTX-M-55, which has one nucleotide difference from blaCTX-M-15, on IncI2 plasmid pHN1122-1. Here, we characterized an IncI2 plasmid carrying blaCTX-M-15 with a 45-bp spacer (pHNY2-1) by complete sequencing and also sequenced IncI2 plasmids carrying blaCTX-M-64 (pHNAH46-1) or blaCTX-M-132 (pHNLDH19) and an IncI1 plasmid carrying blaCTX-M-123 (pHNAH4-1). pHNY2-1 has the same ISEcp1-blaCTX-M-IncA/C insertion as pHN1122-1, pHNAH46-1, and pHNLDH19, and all four plasmid backbones are almost identical. pHNAH4-1 (IncI1 sequence type 108 [ST108]) carries a transposition unit that includes a 2,720-bp fragment of the IncI2 backbone, suggesting ISEcp1-mediated transfer of blaCTX-M-IncA/C-IncI2 to an IncI1 plasmid. All three hybrid blaCTX-M genes may have resulted from recombination between blaCTX-M-14 and blaCTX-M-15 with a 45-bp spacer on an IncI2 plasmid. Five additional Escherichia coli isolates of different sequence types from different provinces, farms, and/or animals had blaCTX-M-64 on a pHNAH46-1-like IncI2 plasmid and 9 had blaCTX-M-123 on a pHNAH4-1-like IncI1 ST108 plasmid. Thus, epidemic IncI plasmids may be responsible for the spread of blaCTX-M-64 and blaCTX-M-123 between different animals and different locations in China.

High Prevalence of CTX-M Beta-Lactamases in Enterobacteriaceae from Healthy Individuals in Guangzhou, China

This study aimed to determine the prevalence of extended-spectrum beta-lactamases (ESBLs) in Enterobacteriaceae and to characterize the genetic composition of ESBL determinants among Enterobacteriaceae isolates from healthy people in Guangzhou, China. A total of 200 rectal swab samples were collected from healthy asymptomatic individuals and tested for ESBL production using ChromID ESBL agar. Phenotypic ESBL producers were screened for blaCTX-M, blaTEM, and blaSHV genes using PCR and DNA sequencing. The prevalence of ESBL-producing Enterobacteriaceae among rectal swab samples was 69.5%. All ESBL-producing isolates harbored blaCTX-M genes (n=138) except for one isolate that harbored blaSHV-2a. Eleven CTX-M ESBL genes were detected. The most predominant CTX-M-type genes were blaCTX-M-14 (n=82), followed by blaCTX-M-55 (n=19), blaCTX-M-65 (n=10), and blaCTX-M-27 (n=9). Isolates carrying blaCTX-M-38,-3,-15,-14b,-98,-121 and -123 were also identified. Molecular homology analysis of the selected isolates was performed by phylogenetic grouping and multilocus sequence typing and indicated that the predominant clone belonged to A-CC10. This study showed a high rate of CTX-M-type ESBL genes among Enterobacteriaceae isolates from healthy individuals in China.

Prevalence and characterization of hybrid blaCTX-M among Escherichia coli isolates from livestock and other animals

This study investigated 248 extended-spectrum β-lactamase-producing Escherichia coli isolates from 2012 to 2013 for hybrid blaCTX-M genes. blaCTX-M genes were detected in 228 isolates of which 14 isolates were hybrid blaCTX-M positive (6 blaCTX-M-123, 6 blaCTX-M-64, and 2 blaCTX-M-132). The 14 hybrid blaCTX-M-carrying isolates (8 from chickens, 2 each from pigs and cattle, 1 each from dog and rodent) were genetically diverse. All but 2 hybrid blaCTX-M were carried on IncI1 (5 blaCTX-M-123) and IncI2 (6 blaCTX-M-64 and one blaCTX-M-132) plasmids. Our IncI1 and IncI2 plasmids had pHNAH4-1-like and pHN1122-1-like restriction fragment length polymorphism patterns, respectively. Genetic relatedness of the plasmids to pHNAH4-1 and pHN1122-1 were confirmed by complete sequencing of 3 plasmids, pCTXM123_C0996, pCTXM64_C0967, and pCTXM132_P0421. Plasmids closely related to pHNAH4-1 and pHN1122-1 and carrying different blaCTX-M alleles have been reported from multiple geographic areas in China previously. The findings highlighted the wide dissemination of hybrid blaCTX-M variants in different parts of China.

F33: A-: B-, IncHI2/ST3, and IncI1/ST71 plasmids drive the dissemination of fosA3 and bla CTX-M-55/-14/-65 in Escherichia coli from chickens in China

The purpose of this study was to examine the occurrence of fosfomycin-resistant Escherichia coli from chickens and to characterize the plasmids carrying fosA3. A total of 661 E. coli isolates of chicken origin collected from 2009 to 2011 were screened for plasmid-mediated fosfomycin resistance determinants by PCR. Plasmids were characterized using PCR-based replicon typing, plasmid multilocus sequence typing, and restriction fragment length polymorphisms. Associated addiction systems and resistance genes were identified by PCR. PCR-mapping was used for analysis of the genetic context of fosA3. Fosfomycin resistance was detected in 58 isolates that also carried the fosA3 gene. Fifty-seven, 17, and 52 FosA3-producers also harbored bla CTX-M, rmtB, and floR genes, respectively. Most of the 58 fosA3-carrying isolates were clonally unrelated, and all fosA3 genes were located on plasmids belonged to F33:A-:B- (n = 18), IncN-F33:A-:B- (n = 7), IncHI2/ST3 (n = 10), IncI1/ST71 (n = 3), IncI1/ST108 (n = 3), and others. The genetic structures, IS26-ISEcp1-bla CTX-M-55-orf477-bla TEM-1-IS26-fosA3-1758bp-IS26 and ISEcp1-bla CTX-M-65-IS903-iroN-IS26-fosA3-536bp-IS26 were located on highly similar F33:A-:B- plasmids. In addition, bla CTX-M-14-fosA3-IS26 was frequently present on similar IncHI2/ST3 plasmids. IncFII plasmids had a significantly higher frequency of addiction systems (mean 3.5) than other plasmids. Our results showed a surprisingly high prevalence of fosA3 gene in E. coli isolates recovered from chicken in China. The spread of fosA3 can be attributed to horizontal dissemination of several epidemic plasmids, especially F33:A-:B- plasmids. Since coselection by other antimicrobials is the major driving force for the diffusion of the fosA3 gene, a strict antibiotic use policy is urgently needed in China.

Novel conjugative plasmid from Escherichia coli of swine origin that coharbors the multiresistance gene cfr and the extended-spectrum-β-lactamase gene blaCTX-M-14b

Two porcine Escherichia coli isolates harbored the cfr gene on conjugative plasmids of 38,405 bp (pGXEC6) and 41,646 bp (pGXEC3). In these two plasmids, the cfr gene was located within a 4,612-bp region containing a tnpA-IS26-cfr-IS26-Δhyp element. Plasmid pGXEC3 was almost identical to pGXEC6 except for a 3,235-bp ISEcp1-blaCTX-M-14b insertion. The colocation of the multiresistance cfr gene with an extended-spectrum-β-lactamase gene on a conjugative plasmid may support the dissemination of these genes by coselection.

Dominance of CTX-M-type extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from patients with community-onset and hospital-onset infection in China

Objective

To investigate CTX-M genotypes among extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) isolated from patients with community-onset and hospital-onset infections in China, their clonality and the distribution of CTX-M variants in different specimens of community-onset and hospital-onset infections.

Methods

ESBL-EC isolates were collected from general hospitals from 2011 to 2012 in China. Broth microdilution method antimicrobial susceptibility testing of 16 antibiotics was performed. Clinical data from community-onset and hospital-onset infections due to ESBL-EC were analyzed. ESBL-encoding genes were amplified by PCR and sequenced, and multilocus sequence typing (MLST) was performed for a random selection of predominant CTX-M type strains identified.

Results

A total of 1,168 ESBL-EC isolates were obtained from various clinical specimens, 41.7% of which were responsible for causing community-onset infections. The presence of urinary calculi was higher in community-onset infections, whereas malignancy, cardiovascular and cerebrovascular diseases, dementia, chronic renal disease, diabetes mellitus and surgical treatment were found to have higher proportions in hospital-onset infections. There was no significant difference in trauma between community-onset and hospital-onset infections. 96.2% of the isolates were detected to harbor bla_CTX-M genes. bla_CTX-M-1 group and bla_CTX-M-9 group were detected at 40.7% and 48.7% respectively, and both positive group accounted for 10.6%. bla_CTX-M-55 (24.8%) and bla_CTX-M-15 (18.2%) were the major genotypes in bla_CTX-M-1 group while bla_CTX-M-14 (46.8%) was predominant in bla_CTX-M-9 group. A comparison of bla_CTX-M distribution in different specimens between ESBL-EC causing community-onset and hospital-onset infection showed no significant difference. A total of 229 isolates were tested for MLST. ST131 (14%) was the predominant type. ST648, ST405 and ST1193 were also detected.

Conclusions

Community-onset ESBL-EC has emerged as a common pathogen in China. CTX-M-14 is the most commonly encountered, CTX-M-55 and CTX-M-15 have spread rapidly. ST131 is the predominant clonal group, and the great diversity of CTX-M-producing isolates of E. coli has emerged in China.

CTX-M-137, a hybrid of CTX-M-14-like and CTX-M-15-like β-lactamases identified in an Escherichia coli clinical isolate

OBJECTIVES

To characterize a novel CTX-M chimera, CTX-M-137, from Escherichia coli clinical isolates in China.

METHODS

Isolates were collected from five hospitals between 22 February 2009 and 20 December 2011. Resistance genes were investigated by PCR. blaCTX-M-137 was cloned and purified for kinetic measurements. Conjugation experiments, S1-PFGE and Southern blotting were performed to study the plasmid harbouring blaCTX-M-137. The genetic environment of blaCTX-M-137 was determined by genomic cloning and sequencing.

RESULTS

A total of 247 cephalosporin-resistant E. coli were identified. blaCTX-M group genes were the most prevalent extended-spectrum β-lactamase (ESBL) genes, with 71 isolates harbouring blaCTX-M-1 group genes and 137 isolates harbouring blaCTX-M-9 group genes. A novel chimera of CTX-M-14-like and CTX-M-15-like ESBLs, designated CTX-M-137, was identified from a 60-year-old man with a urinary tract infection. The N-terminus of CTX-M-137 matched CTX-M-14 and the C-terminus matched CTX-M-15. CTX-M-137 conferred resistance to ceftazidime, cefotaxime and aztreonam. Purified CTX-M-137 showed good hydrolytic activity against ceftazidime and cefotaxime, and was inhibited by clavulanic acid. The blaCTX-M-137 was carried on an ∼83 kb IncI1 plasmid. blaCTX-M-137 was carried on a complete transposition unit ISEcp1-blaCTX-M-137-Δorf477 inserted into yagA, which is part of the IncI1 plasmid backbone.

CONCLUSIONS

We identified a novel CTX-M chimera, CTX-M-137, with a CTX-M-14-like N-terminus and a CTX-M-15-like C-terminus. Our findings suggest an ongoing diversification of CTX-M-type ESBLs through recombination events.