Prevalence of CTX-M-Type Extended-Spectrum β-Lactamase-Producing Escherichia coli B2-O25-ST131 H30R Among Residents in Nonacute Care Facilities in Japan

Isolation of extended‐spectrum β‐lactamase‐producing Escherichia coli from Japanese red fox ( Vulpes vulpes japonica )

Antimicrobial resistance is a global concern requiring a one‐health approach. Given wild animals can harbor antimicrobial‐resistant bacteria (ARB), we investigated their presence in 11 fecal samples from wild animals using deoxycholate hydrogen sulfide lactose agar with or without cefotaxime (CTX, 1 mg/L). Thus, we isolated CTX‐resistant Escherichia coli from two Japanese red fox fecal samples. One strain was O83:H42‐ST1485‐fimH58 CTX‐M‐55‐producing E. coli carrying the genes aph(3″)‐Ib, aph(3′)‐Ia, aph(6)‐Id, mdf(A), sitABCD, sul2, tet(A), and tet(B), whereas the other was O25:H4‐ST131‐fimH30 CTX‐M‐14‐producing E. coli carrying mdf(A) and sitABCD and showing fluoroquinolone resistance. Thus, the presence of extended‐spectrum β‐lactamase producers in wild foxes suggests a spillover of ARB from human activities to these wild animals.

Identification of a Novel IncHI1B Plasmid in MDR Klebsiella pneumoniae 200 from Swine in China

Multidrug-resistant (MDR) Klebsiella pneumoniae poses a seriously threat to public health. The aim of this study was to better understand the genetic structure of its plasmids and chromosomes. The whole-genome sequence of K. pneumoniae 200 isolated from the liver of a swine with diarrhea in China was determined using PacBio RS II and Illumina MiSeq sequencing. The complete sequences of the chromosomal DNA and the plasmids were analyzed for the presence of resistance genes. The phylogenetic trees revealed that K. pneumoniae 200 displayed the closest relationship to a human-associated K. pneumoniae strain from Thailand. K. pneumoniae 200 contained two plasmids, pYhe2001 and pYhe2002, belonging to the incompatibility groups IncH-HI1B and IncF-FIA. The plasmid pYhe2001 was a novel plasmid containing four types of heavy metal resistance genes and a novel Tn6897 transposon flanked by two copies of IS26 at both ends. Mixed plasmids could be transferred from K. pneumoniae 200 to Escherichia coli DH5α through transformation together. This study reported the first time a novel plasmid pYhe2001 from swine origin K. pneumoniae 200, suggesting that the plasmids may act as reservoirs for various antimicrobial resistance genes and transport multiple resistance genes in K. pneumoniae of both animal and human origin.

Epidemiology and molecular characterization of fecal carriage of third-generation cephalosporin-resistant enterobacterales among elderly residents in Japan

INTRODUCTION

The spread of third-generation cephalosporin-resistant Gram-negative bacteria is a serious concern in acute and post-acute care settings. This study aimed to understand the epidemiology and molecular background of fecal colonization of resistant Enterobacterales in elderly people.

METHODS

In December 2015-December 2017, stool or rectal swab samples were collected from 101 elderly patients receiving home care, using long-term care facilities (LTCF), and living in nursing homes repeatedly at 3-9-month intervals. Patient clinical background data were collected from medical records. After phenotypic screening for extended-spectrum β-lactamase (ESBL), AmpC-type β-lactamase or carbapenemase production, drug resistance genes of isolates were analyzed using polymerase chain reaction (PCR). ESBL-producing Escherichia coli isolates obtained from the same patients in repetitive screenings were analyzed using PCR-based ORF typing. Risk factors for persistent carriage of resistant Enterobacterales were analyzed using multivariate analysis.

RESULTS

Resistant Enterobacterales isolates were detected in 37 of 101 (36.6%) and 29 of 80 (36.3%) residents in first and second screenings, respectively. ESBL-producing E. coli accounted for 80% isolates, the most common being CTX-M-9-group β-lactamase producers. Molecular epidemiological analysis revealed probable transmissions of ESBL-producing E. coli; 58% of ESBL-producing E. coli colonizers were persistent colonizers at least after 3 -month intervals. Age > 87 years and LTCF residence were independent risk factors for persistent carriage of ESBL-producing E. coli.

CONCLUSIONS

We showed, for the first time, high persistent colonization rate of ESBL-producing E. coli among elderly people in post-acute care settings with probable horizontal transmission. We also identified significant risk factors for persistent colonization.

OUP accepted manuscript

Objectives

The widespread intestinal carriage of ESBL-producing Escherichia coli (ESBL E. coli) among both patients and healthy individuals is alarming. However, the global prevalence and trend of this MDR bacterium in healthcare settings remains undetermined. To address this knowledge gap, we performed a comparative meta-analysis of the prevalence in community and healthcare settings.

Methods

Our systematic review included 133 articles published between 1 January 2000 and 22 April 2021 and indexed in PubMed, EMBASE or Google Scholar. A random-effects meta-analysis was performed to obtain the global pooled prevalence (community and healthcare settings). Subgroup meta-analyses were performed by grouping studies using the WHO regions and 5 year intervals of the study period.

Results

We found that 21.1% (95% CI, 19.1%–23.2%) of inpatients in healthcare settings and 17.6% (95% CI, 15.3%–19.8%) of healthy individuals worldwide carried ESBL E. coli in their intestine. The global carriage rate in healthcare settings increased 3-fold from 7% (95% CI, 3.7%–10.3%) in 2001–05 to 25.7% (95% CI, 19.5%–32.0%) in 2016–20, whereas in community settings it increased 10-fold from 2.6% (95% CI, 1.2%–4.0%) to 26.4% (95% CI, 17.0%–35.9%) over the same period.

Conclusions

The global and regional human intestinal ESBL E. coli carriage is increasing in both community and healthcare settings. Carriage rates were generally higher in healthcare than in community settings. Key relevant health organizations should perform surveillance and implement preventive measures to address the spread of ESBL E. coli in both settings.

Distribution of Extended-Spectrum β-Lactamase Genes and Antimicrobial Susceptibility among Residents in Geriatric Long-Term Care Facilities in Japan

A high prevalence of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) may call for monitoring in geriatric long-term care facilities (g-LTCFs). We surveyed the distribution of ESBL-causative gene types and antimicrobial susceptibility in ESBL-PE strains from residents in g-LTCFs, and investigated the association between ESBL-causative gene types and antimicrobial susceptibility. First, we analyzed the types of ESBL-causative genes obtained from 141 ESBL-PE strains collected from the feces of residents in four Japanese g-LTCFs. Next, we determined the minimum inhibitory concentration values for alternative antimicrobial agents against ESBL-PE, including β-lactams and non-β-lactams. Escherichia coli accounted for 96% of the total ESBL-PE strains. Most strains (94%) contained bla_CTX-M group genes. The genes most commonly underlying resistance were of the bla_CTX-M-9 and bla_CTX-M-1 groups. Little difference was found in the distribution of ESBL-causative genes among the facilities; however, antimicrobial susceptibility differed widely among the facilities. No specific difference was found between antimicrobial susceptibility and the number of ESBL-causative genes. Our data showed that ESBL-PEs were susceptible to some antimicrobial agents, but the susceptibility largely differed among facilities. These findings suggest that each g-LTCF may require specific treatment strategies based on their own antibiogram. Investigations into drug resistance should be performed in g-LTCFs as well as acute medical facilities.

The role of potentiating mutations in the evolution of pandemic Escherichia coli clones

The Escherichia coli species exhibits a vast array of variable lifestyles, including environmental, commensal, and pathogenic organisms. Many of these E. coli contribute significantly to the global threat of antimicrobial resistance (AMR). Multidrug-resistant (MDR) clones of E. coli have arisen multiple times over varying timescales. The repeated emergence of successful pandemic clones, including the notorious ST131 lineage, highlights a desperate need to further study the evolutionary processes underlying their emergence and success. Here, we review the evolutionary emergence of E. coli ST131 pandemic clones and draw parallels between their evolutionary trajectories and those of other lineages. From colonization and expansion to the acquisition of multidrug resistance plasmids, potentiating mutations are present at each stage, leading to a proposed sequence of events that may result in the formation of an antimicrobial-resistant pandemic clone.

Characterization of antimicrobial resistance in chicken-source phylogroup F Escherichia coli: similar populations and resistance spectrums between E. coli recovered from chicken colibacillosis tissues and retail raw meats in Eastern China

The extended-spectrum cephalosporin resistant E. coli from food animals transferring to community settings of humans causes a serious threat to public health. Unlike phylogroup B2 E. coli strains, the clinical significance of isolates in phylogroup F is not well revealed. Here, we report on a collection (n = 563) of phylogroup F E. coli isolates recovered from chicken colibacillosis tissues and retail raw chicken meat samples in Eastern China. There was an overlapped distribution of MLST types between chicken colibacillosis-origin and meat-source phylogroup F E. coli, including dominant STs (ST648, ST405, ST457, ST393, ST1158, etc). This study further investigated the presence of extended-spectrum β-lactamase (ESBL/pAmpC) producers in these chicken-source phylogroup F E. coli strains. The prevalence of extended-spectrum cephalosporin resistant strains in phylogroup F E. coli from chicken colibacillosis and raw meat separately accounted for 66.1 and 71.2%. The resistance genotypes and plasmid replicon types of chicken-source phylogroup F E. coli isolates were characterized by multiplex PCR. Our results revealed β-lactamase CTX-M, OXA, CMY and TEM genes were widespread in chicken-source phylogroup F E. coli, and blaCTX-M was the most predominant ESBL gene. Moreover, there was a high prevalence of non-lactamase resistance genes in these β-lactam-resistant isolates. The replicons IncB/O/K/Z, IncI1, IncN, IncFIC, IncQ1, IncX4, IncY, and p0111, associated with antibiotic-resistant large plasmids, were widespread in chicken-source phylogroup F E. coli. There was no obvious difference for the populations, resistance spectrums, and resistance genotypes between phylogroup F E. coli from chicken colibacillosis tissues and retail meats. This detail assessment of the population and resistance genotype showed chicken-source phylogroup F E. coli might hold zoonotic risk and contribute the spread of multidrug-resistant E. coli to humans.

Epidemiology of extended-spectrum β-lactamase and metallo-β-lactamase-producing Escherichia coli in South Asia

Aim: To determine the prevalence of extended-spectrum β-lactamase (ESBL) and metallo-β-lactamase (MBL)-producing Escherichia coli in South Asia. Methodology: A systematic review and meta-analysis of data published in PubMed, EMBASE, Web of Science and Scopus. Results: The pooled prevalence of ESBL and MBL-producing E. coli in South Asia were 33% (95% CI: 27-40%) and 17% (95% CI: 12-24%), respectively. The prevalence of bla_CTX-M type was 58% (95% CI: 49-66%) with bla_CTX-M-15 being the most prevalent (51%, 95% CI: 40-62%) variant. The most prevalent MBL variant was bla_NDM-1 (33%, 95% CI: 20-50%). Conclusion: This study suggests a high prevalence of ESBLs and MBLs among E. coli clinical isolates. Comprehensive resistance surveillance is required to guide clinicians prescribing antibiotics in South Asia.

Characterization of bla CTX-M-27/F1:A2:B20 Plasmids Harbored by Escherichia coli Sequence Type 131 Sublineage C1/H30R Isolates Spreading among Elderly Japanese in Nonacute-Care Settings

We characterized 29 bla _CTX-M-27-harboring plasmids of Escherichia coli sequence type 131 (ST131) sublineage C1/H30R isolates from healthy individuals and long-term-care facility (LTCF) residents. Most (27/29) plasmids were of the FIA, FIB, and FII multireplicon type with the same plasmid multilocus sequence typing (pMLST). Several plasmids (7/23) from LTCF residents harbored only bla _CTX-M-27 as the resistance gene; however, their fundamental structures were very similar to those of previously isolated bla _CTX-M-27/F1:A2:B20 plasmids, suggesting their prevalence as a newly arising public health concern.

Systematic research to overcome newly emerged multidrug-resistant bacteria

In the 1980s, I found that the chromosomal β-lactamase of Klebsiella pneumoniae LEN-1 showed a very high similarity to the R-plasmid-mediated penicillinase TEM-1 on the amino acid sequence level, and this strongly suggested the origination of TEM-1 from the chromosomal penicillinases of K. pneumoniae or related bacteria. Moreover, the chromosomal K1 β-lactamase (KOXY) of Klebsiella oxytoca was found to belong to the class A β-lactamases that include LEN-1 and TEM-1, although KOXY can hydrolyze cefoperazone (CPZ) like the chromosomal AmpC-type cephalosporinases of various Enterobacteriaceae that can hydrolyze several cephalosporins including CPZ. Furthermore, my collaborators and I found plural novel serine-type β-lactamases, such as MOX-1, SHV-24, TEM-91, CTX-M-64, CMY-9, CMY-19, GES-3, GES-4, and TLA-3, mediated by plasmids. Besides these serine-type β-lactamases, we also first identified exogenously acquired metallo-β-lactamases (MBLs), IMP-1 and SMB-1, in imipenem-resistant Serratia marcescens, and the IMP-1-producing S. marcescens TN9106 became the index case for carbapenemase-producing Enterobacteriaceae. I developed the sodium mercaptoacetic acid (SMA)-disk test for the simple identification of MBL-producing bacteria. We were also the first to identify a variety of plasmid-mediated 16S ribosomal RNA methyltransferases, RmtA, RmtB, RmtC, and NpmA, from various Gram-negative bacteria that showed very high levels of resistance to a wide range of aminoglycosides. Furthermore, we first found plasmid-mediated quinolone efflux pump (QepA) and fosfomycin-inactivating enzymes (FosA3 and FosK). We also first characterized penicillin reduced susceptible Streptococcus agalactiae, macrolide-resistant Mycoplasma pneumoniae, as well as Campylobacter jejuni, and Helicobacter pylori, together with carbapenem-resistant Haemophilus influenzae. We constructed a PCR-based open reading frame typing method for rapid identification of Acinetobacter baumannii international clones.

Population structure and antimicrobial resistance traits of avian-origin mcr-1-positive Escherichia coli in Eastern China, 2015 to 2017

Recent emergence of mcr-1-positive Escherichia coli (MCRPEC) is causing serious concern around the world. Due to poultry-origin E. coli holding zoonotic potential, the improved understandings of MCRPEC population structure and antimicrobial resistance are critical to public health purposes. This study provided novel insights into the molecular epidemiology of avian-origin MCRPEC. For the mcr genes prevalence study, we analysed 1,360 E. coli recovered from avian colibacillosis in eastern China from 2015 to 2017. The mcr-1 was present in 172 (12.6%) E. coli isolates. For all of MCRPEC isolates, MICs of colistin were ≥4 mg/L. Avian-origin MCRPEC was widely distributed throughout phylogroups A, B1, B2, D, and F. Moreover, those isolates were assigned to 52 unique STs, such as ST48, ST117, ST131, and ST648, suggesting substantial horizontal dissemination of mcr-1 gene through avian-origin E. coli populations. The susceptibility of MCRPEC isolates was tested with 26 antimicrobial agents from 16 antimicrobial categories. There were high resistance rates of MCRPEC isolates against the clinically used antibiotics. All MCRPEC isolates in this study presented the multidrug-resistant (MDR) trait were even considered as extensively drug-resistant (XDR) strains. Resistance genotypes and plasmid replicon profiling showed that a majority of MCRPEC isolates contained plasmid-mediated resistance genes and exhibited the co-existence of mcr-1 with ESBLs and pAmpCs genes. Furthermore, the overlapped distribution of ST types and resistance gene contents was detected among MCRPEC isolates from humans and poultry. Besides mcr-1, our findings highlighted a significant prevalence of plasmid-mediated resistance genes among avian-origin MCRPEC isolates.