Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli Causing Bloodstream Infections in Three Hospitals in Shanghai, China

First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh

Colistin resistance is a global concern warning for a one health approach to combat the challenge. Colistin resistant E. coli and their resistance determinants are widely distributed in the environment, and rats could be a potential source of these isolates and resistant determinants to a diverse environmental setting. This study was aimed to determine the presence of colistin resistant E. coli (CREC) in wild rats, their antimicrobial resistance (AMR) phenotypes, and genotypic analysis of mcr-1 CREC through whole genome sequencing (WGS). A total of 39 rats were examined and CREC was isolated from their fecal pellets onto MacConkey agar containing colistin sulfate (1 μg/ mL). AMR of the CREC was determined by disc diffusion and broth microdilution was employed to determine MIC to colistin sulfate. CREC were screened for mcr genes (mcr-1 to mcr-8) and phylogenetic grouping by PCR. Finally, WGS of one mcr-1 CREC was performed to explore its genetic characteristics especially resistomes and virulence determinants. 43.59% of the rats carried CREC with one (2.56%) of them carrying CREC with mcr-1 gene among the mcr genes examined. Examination of seventeen (17) isolates from the CREC positive rats (n = 17) revealed that majority of them belonging to the pathogenic phylogroup D (52.94%) and B2 (11.76%). 58.82% of the CREC were MDR on disc diffusion test. Shockingly, the mcr-1 CREC showed phenotypic resistance to 16 antimicrobials of 8 different classes and carried the ARGs in its genome. The mcr-1 gene was located on a 60 kb IncI2 plasmid. On the other hand, ARGs related to aminoglycosides, phenicols, sulfonamides, tetracyclines and trimethoprims were located on a 288 kb mega-plasmid separately. The mcr-1 CREC carried 58 virulence genes including genes related to adhesion, colonization, biofilm formation, hemolysis and immune-evasion. The isolate belonged to ST224 and closely related to E. coli from different sources including UPEC clinical isolates from human based on cgMLST analysis. The current research indicates that rats might be a possible source of CREC, and the presence of mcr-1 and other ARGs on plasmid increases the risk of ARGs spreading and endangering human health and other environmental components through this infamous pest.

Integron distribution and relationship to antimicrobial resistance in E. coli isolated from blood culture

PURPOSE

The aim of this study was to evaluate the distribution of integrons in strains of E. coli isolated from blood culture and the relationship between integrons and antimicrobial resistance.

METHODS

The study included 100 E. coli strains sent to the Medical Microbiology Laboratory from different clinics between September 2022 and June 2023. Antibiotic susceptibility was evaluated according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST). The presence of integrons was determined by the inhouse polymerase chain reaction (PCR).

RESULTS

Integron positivity was detected in 45 (45%) of isolates, and class 1 integrons were found in 41 (41%), class 2 integrons in 2 (2%), and both class 1 integrons and class 2 integrons in 2 (2%). Class 3 integron positivity was not detected. In total, 63 cases of community origin and 37 cases of hospital origin were identified. When antibiotic resistance was evaluated, the highest sensitivity was noted for amikacin (1%), meropenem (5%), imipenem (6%), and the highest resistant antibiotics were ampicillin (82%), cepfuroxime sodium (65%), and amoxicillin/clavulanate (62%), respectively. Of the 16 antimicrobial substances evaluated, 10 had an antibiotic resistance rate of over 45%. In class 1 integron-positive samples, ampicillin resistance and trimethoprim/sulfamethoxazole resistance were higher than in negative samples (p = 0.02, p = 0.0001, respectively). Fifty-one (51%) samples were found to have multiple drug resistance (MDR). In total, 59.5% of hospital-acquired isolates and 46% of community-acquired isolates were considered to be MDR. The class 1 integron positivity in MDR samples was high (p = 0.038).

CONCLUSION

The high MDR rates in both hospital-acquired and community-acquired isolates are alarming. In particular, class 1 integron monitoring is very important to prevent the spread of MDR isolates.

Whole genome-based genetic insights of blaNDM producing clinical E. coli isolates in hospital settings of Pakistan

Carbapenem resistance among Enterobacterales has become a global health concern. Clinical Escherichia coli isolates producing the metallo β-lactamase NDM have been isolated from two hospitals in Faisalabad, Pakistan. These E. coli strains were characterized by MALDI-TOF, PCR, antimicrobial susceptibility testing, XbaI and S1 nuclease pulsed-field gel electrophoresis (PFGE), conjugation assay, DNA hybridization, whole genome sequencing, bioinformatic analysis, and Galleria mellonella experiments. Thirty-four blaNDM producing E. coli strains were identified among 52 nonduplicate carbapenem-resistant strains. More than 90% of the isolates were found to be multidrug resistant by antimicrobial susceptibility testing. S1 PFGE confirmed the presence of blaNDM gene on plasmids ranging from 40 kbps to 250 kbps, and conjugation assays demonstrated transfer frequencies of blaNDM harboring plasmids ranging from 1.59 × 10-1 to 6.46 × 10-8 per donor. Whole genome sequencing analysis revealed blaNDM-5 as the prominent NDM subtype with the highest prevalence of blaOXA-1, blaCTX-M-15, aadA2, aac(6')-Ib-cr, and tet(A) associated resistant determinants. E. coli sequence types: ST405, ST361, and ST167 were prominent, and plasmid Inc types: FII, FIA, FIB, FIC, X3, R, and Y, were observed among all isolates. The genetic environment of blaNDM region on IncF plasmids included partial ISAba125, the bleomycin ble gene, and a class I integron. The virulence genes terC, traT, gad, fyuA, irp2, capU, and sitA were frequently observed, and G. mellonella experiments showed that virulence correlated with the number of virulence determinants. A strong infection control management in the hospital is necessary to check the emergence of carbapenem resistance in Gram-negative bacteria.IMPORTANCEWe describe a detailed analysis of highly resistant clinical E. coli isolates from two tertiary care centers in Pakistan including carbapenem resistance as well as common co-resistance mechanisms. South Asia has a huge problem with highly resistant E. coli. However, we find that though these isolates are very difficult to treat they are of low virulence. Thus the Western world has an increasing problem with virulent E. coli that are mostly of low antibiotic resistance, whereas, South Asia has an increasing problem with highly resistant E. coli that are of low virulence potential. These observations allow us to start to devise methodologies to limit both virulence and resistance and combat problems in developing nations as well as the Western world.

Molecular Characteristics and Genetic Analysis of Extensively Drug-Resistant Isolates with different Tn3 Mobile Genetic Elements

Extensively drug-resistant (XDR) bacteria are the main caues for causing clinical infectious diseases. Our aim was to distinguish the present molecular epidemiological situation of XDR Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli isolates recovered from local hospitals in Changzhou. Antibiotic susceptibility and phenotypic analysis, multilocus sequence typing and Pulsed Field Gel Electrophoresis were performed to trace these isolates. Resistant phenotype and gene analysis from 29 XDR strains demonstrated that they mainly included TEM, CTX-M-1/2, OXA-48, and KPC products. A. baumannii strains belonged to sequence type (ST) ST224, and carrying the bla_CTX-M-2/TEM gene. The quinolone genes aac(6')-ib-cr and qnrB were carrying only in A. baumannii and E.coli. Three (2.3%) of these strains were found to contain the bla_NDM-1 or bla_NDM-5 gene. A new genotype of K. pneumoniae was found as ST2639. Epidemic characteristics of the XDR clones showed that antibiotic resistance genes distributed unevenly in different wards in Changzhou's local hospitals. With the sequencing of bla_NDM carrying isolates, the plasmids often carrying a highly conservative Tn3-relavent mobile genetic element. The especially coupled insert sequence ISKox3 may be a distinctive resistance gene transfer loci. The genotypic diversity variation of XDRs suggested that tracking and isolating the sources of antibiotic resistance especially MBL-encoding genes such as bla_NDM-will help manage the risk of infection by these XDRs.

Safety of megadose meropenem in the empirical treatment of nosocomial sepsis: a pilot randomized clinical trial

Objective: To evaluate the safety of megadose meropenem as empirical treatment of nosocomial sepsis. Materials & methods: Critically ill patients diagnosed with sepsis received either high-dose (2 g every 8 h) or megadose (4 g every 8 h) meropenem as an intravenous infusion over 3 h. Results: A total of 23 patients with nosocomial sepsis were eligible and included in the megadose (n = 11) or high-dose (n = 12) group. No treatment-related adverse events were observed during a 14-day follow-up. Clinical response was also comparable between the groups. Conclusion: Megadose meropenem may be considered for empirical treatment of nosocomial sepsis without serious concern regarding its safety.

The Characteristics of Extended-Spectrum β-Lactamases (ESBLs)-Producing Escherichia coli in Bloodstream Infection

Background

Bloodstream infection (BSI) is a common type of infection frequently diagnosed in clinics. The emergence and spread of ESBLs-producing Escherichia coli (E. coli) has emerged as one of the biggest challenges in global community health.

Methods

The production of ESBLs was determined by the composite disk diffusion method. The expression of the various resistance and virulence genes were detected by PCR and sequencing. Multi-locus sequence typing (MLST) and phylogenetic groups were used for the classification. The transfer of resistant plasmids was determined by conjugation assay. The statistical differences were analyzed using Statistical Product and Service Solutions (SPSS) version 23.0.

Results

A total of 60 strains of ESBLs-producing E. coli were collected. The resistance genes that were identified included bla _CTX-M, bla _TEM, bla _SHV, bla _OXA-1 and mcr-1. The most common one was the bla _CTX-M including bla _CTX-M-27 (n = 16), bla _CTX-M-14 (n = 15), bla _CTX-M-15 (n = 11), bla _CTX-M-55 (n = 14) and bla _CTX-M-65 (n = 5). A total of 31 STs were detected, and the most abundant among which was ST131 (n = 16, 26.7%). Most of the E. coli (n = 46, 76.7%) belonged to the groups B2 and D. And some virulence genes were related to the classification of the E. coli. Among them, the detection rates of hek/hra, kpsMII and papGII-III in groups B2 and D were higher than those in groups A and B1. The detection rates of cnf1, iucC and papGII-III in ST131 were higher than those in non-ST131. And the distributions of hek/hra, iroN, iucC, kpsMII and papGII-III were related to the bla _CTX-M subtypes. Finally, most bacterial (n = 32, 53.3%) resistance genes could be transferred between the bacteria by plasmids, especially IncFIB.

Conclusion

ESBLs-producing E. coli in BSI exhibited had high resistance rates and carried a variety of virulence factors (VFs). This is necessary to strengthen the monitoring of ESBLs-producing isolates in the medical environment.

Characterization of NDM-5-Producing Escherichia coli Strains Isolated from Pediatric Patients with Bloodstream Infections in a Chinese Hospital

Escherichia coli (E. coli) bloodstream infections (BSIs) are among the most predominant causes of death in infants and children worldwide. NDM-5 (New Delhi Metallo-lactamase-5) is responsible for one of the main mechanisms of carbapenem resistance in E. coli. To analyze the phenotypic and genomic characteristics of NDM-5-producing E. coli from bloodstream infections (BSIs), a total of 114 E. coli strains was collected from a children's hospital in Jiangsu province, China. Eight blaNDM-5-carrying E. coli strains were identified which were all carbapenem-resistant and carried diverse antimicrobial resistance genes apart from blaNDM-5. They belonged to six distinct sequence types (STs) and serotypes including one each for ST38/O7:H8, ST58/O?:H37, ST131/O25:H4, ST156/O11:H25 and ST361/O9:H30 and three strains are originating from a single clone belonging to ST410/O?:H9. Apart from blaNDM-5, the E. coli strains isolated from BSIs also carried other β-lactamase genes, including blaCMY-2 (n = 4), blaCTX-M-14 (n = 2), blaCTX-M-15 (n = 3), blaCTX-M-65 (n = 1), blaOXA-1 (n = 4) and blaTEM-1B (n = 5). The blaNDM-5 genes were located on three different types of plasmids, which were IncFII/I1 (n = 1), IncX3 (n = 4) and IncFIA/FIB/FII/Q1 (n = 3). The former two types were conjugatively transferable at frequencies of 10-3 and 10-6, respectively. The dissemination of NDM-producing strains, which exhibit resistance to the last-line antibiotics, carbapenems, may increase the muti-antimicrobial resistance burden among E. coli BSIs and further threaten public health.

The Dynamics of Antimicrobial Resistance among Enterobacteriaceae Isolates in Russia: Results of the 2012-2018 INFORM and ATLAS International Program Studies

Background: The increasing prevalence of multidrug-resistant Enterobacteriaceae limits the range of active antimicrobial agents, thus worsening clinical outcomes. The objective of this study was to identify the trends in antimicrobial resistance for Enterobacteriaceae in Russia using the databases for the International Network for Optimal Resistance Monitoring (INFORM) and Antimicrobial Testing Leadership and Surveillance (ATLAS) studies between 2012 and 2018. Methods: This subanalysis was performed for 3811 non-duplicate clinical isolates of Enterobacteriaceae to evaluate the in vitro activity of the main classes of antibiotics against relevant clinical isolates from hospitalized patients with complicated infections of different anatomical locations. Results: The lowest susceptibility was observed for colistin (0%), ampicillin (16.4%), and ampicillin/sulbactam (31.1%), whereas the best susceptibility was observed for all combinations containing avibactam (>96%). Among individual antimicrobials, doripenem (3.2%), tigecycline (1.6%), and meropenem (5.9%) exhibited the lowest resistance. Important trends included the decreasing resistance of Enterobacteriaceae to glycylcyclines and the increasing resistance to aminoglycosides and carbapenems. K. pneumoniae strains were most aggressive in terms of the percentage of strains having multidrug resistance (8.3−18.3%, depending on location) and the percentage of ESBL-positive strains (44.8−86.8%). Conclusions: The current patterns and trends of antimicrobial resistance in different bacterial species should be taken into consideration for timely updating of clinical guidelines and local treatment protocols to ensure effective antimicrobial therapy.

Antibiotic resistance, virulence, and phylogenetic analysis of Escherichia coli strains isolated from free-living birds in human habitats

Wild birds can be colonized by bacteria, which are often resistant to antibiotics and have various virulence profiles. The aim of this study was to analyze antibiotic resistance mechanisms and virulence profiles in relation to the phylogenetic group of E. coli strains that were isolated from the GI tract of wildfowl. Out of 241 faecal samples, presence of E. coli resistant to a cephalosporin (ESBL/AmpC) was estimated for 33 isolates (13,7%). Based on the analysis of the coexistence of 4 genes encoding ESBLs/AmpC (bla_CTX-M, bla_TEM,bla_SHV, bla_AmpC) and class 1 and 2 integrons genes (intI1, intI2) a subset of two resistance profiles was observed among the investigated E. coli isolates carrying bla_AmpC, bla_SHV, and bla_CTX-M, bla_TEM, class 1 and 2 integrons, respectively. The E. coli isolates were categorized into 4 phylogenetic groups A (39.4%), B2 (24.25%), D (24.25%) and B1 (12.1%). The pathogenic B2 and D groups were mainly typical for the Laridae family. Among the 28 virulence factors (Vfs) detected in pathogenic phylogenetic groups B2 and D, 7 were exclusively found in those groups (sfa, vat, tosA, tosB, hly, usp, cnf), while 4 VFs (fecA, fyuA, irp2, kspMTII) showed a statistically significant association (P≤0.05) with phylogroups A and B1. Our results indicated that strains belonging to commensal phylogroups A/B1 possess extensive iron acquisition systems (93,9%) and autotransporters (60,6%), typical for pathogens, hence we suggest that these strains evolve towards higher levels of virulence. This study, which is a point assessment of the virulence and drug resistance potential of wild birds, confirms the importance of taking wild birds as a reservoir of strains that pose a growing threat to humans. The E. coli analyzed in our study derive from different phylogenetic groups and possess an arsenal of antibiotic resistance genes and virulence factors that contribute to their ability to cause diseases.

Clinical Impact of Colistin Banning in Food Animal on mcr-1-Positive Enterobacteriaceae in Patients From Beijing, China, 2009-2019: A Long-Term Longitudinal Observational Study

The colistin resistance gene mcr-1 is emerging as a global public health concern, altering the regulation of colistin usage globally since 2017, especially in China. However, few studies have revealed the impact of policy change on the epidemiology of mcr-positive Enterobacteriaceae (MCRPE) in patients. Here, we describe a molecular epidemiological study to investigate the MCRPE in patients in China from 2009-2019. During the surveillance period, 26,080 non-duplicated Enterobacteriaceae isolates were collected in Beijing. Colistin-resistant isolates were screened by enrichment culture supplemented with colistin, and the presence of the mcr gene was determined by PCR amplification. MCRPE isolates were then analyzed by susceptibility testing, genotyping, and risk factor analysis. Of the 26,080 isolates, mcr-1 was detected in 171 (1.1%) of 15,742 Escherichia coli isolates and 7 (0.1%) of 10,338 Klebsiella pneumoniae isolates. The prevalence of mcr-1-positive E. coli (MCRPEC) showed an increasing trend from 2009 to 2016, while a decreasing trend was observed since 2017. Multi-locus sequence typing analysis showed that MCRPEC isolates had extremely diverse genetic backgrounds, and most of these isolates were non-clonal. The prevalence of MCRPE in China remained at a low level, and even showed a declining trend over the last 3 years after the banning of colistin usage as feed additive in food animal in 2017. However, colistin permission in clinical therapy could still increase the risk of MCRPE transmission and intractable infections, active surveillance and monitoring strategies of MCRPE are recommended to prolong the clinical longevity of colistin.

A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58

Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.

Antimicrobial Resistance and Molecular Epidemiology of Escherichia coli From Bloodstream Infection in Shanghai, China, 2016-2019

Background: Bloodstream infections are recognized as important nosocomial infections. Escherichia coli (E. coli) is the most prevalent Gram-negative bacillary pathogen causing bloodstream infections (BSIs). This retrospective study investigated drug susceptibility and molecular epidemiology of E. coli isolated from patients with BSI in Shanghai, China.

Methods: We collected E. coli isolated from the blood cultures of patients with BSI between January 2016 and December 2019. We randomly selected 20 strains each year to investigate antimicrobial resistance, resistance genes, and molecular epidemiological characteristics. Antimicrobial susceptibility testing was performed by the disk diffusion method. PCR was performed to detect extended-spectrum β-lactamases (ESBLs), carbapenemase genes, and housekeeping genes, and phyloviz was applied to analyze multilocus sequence typing (MLST).

Results: Penicillins, first- and second-generation cephalosporins and fluoroquinolones have high resistance rates (>60%). Among the 80 randomly selected strains, 47 (58.8%) produced ESBLs, and one produced carbapenemase. Sequencing of resistance genes identified bla_CTX−M−14 (34%, 16/47), bla_CTX−M−15 (23.4%, 11/47) and bla_CTX−M−27 (14.8%, 7/47) as the most prevalent genotypes of ESBLs. ST131 (14/80) was the most prevalent sequence type (ST), followed by ST1193 (10/80), ST648 (7/80).

Conclusions: Our findings suggest that amikacin, carbapenems, and piperacillin-tazobactam have relatively low resistance rates and may be the preferred antibiotic regimens for empiric therapy. ST131 and bla_CTX−M−14 are still the main prevalent in Shanghai with a rapid increase in the occurrence of ST1193 is rapidly increasing and more diverse bla_CTX genes.

Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China

Objectives

We carried out a retrospective study to investigate the drug susceptibility and genetic relationship of clinical Escherichia coli isolates from patients with BSIs in Shanxi, China.

Methods

E. coli isolates causing BSIs were consecutively collected from June 2019 to March 2020. Antimicrobial susceptibility testing was performed by broth microdilution method. PCR was used to detect antimicrobial resistance genes coding for extended-spectrum β-lactamases (ESBLs), phylogenetic groups and seven housekeeping genes of E. coli.

Results

A total of 76 E. coli were collected. Antimicrobial susceptibility testing revealed that the top six E. coli resistant antibiotics were ampicillin (90.7%), ciprofloxacin (69.7%), cefazolin (65.7%), levofloxacin (63.1%), ceftriaxone and cefotaxime (56.5%). Among the 76 isolates, 43 produced ESBLs. Molecular analysis showed that CTX-M-14 was the most common ESBLs, followed by CTX-M-15 and CTX-M-55. Phylogenetic group D (42.2%) predominated, followed by group B2 (34.2%), group A (18.4%) and group B1 (5.2%). The most prevalent sequence types (STs) were ST131 (15/76), ST69 (12/76) and ST38 (6/76).

Conclusions

This study is the first to report the phenotypic and molecular characteristics of E. coli isolated from BSIs in Shanxi, China. Our results indicated a high prevalence of MDR in E. coli strains isolated from BSIs and a serious spread of ESBL genes in Shanxi, especially the epidemiological bla _CTX-M. Phylogenetic analysis indicated genetic diversity among E. coli BSIs isolates.

Antimicrobial Resistance and Molecular Epidemiology of Uropathogenic Escherichia coli Isolated From Female Patients in Shanghai, China

Urinary tract infection (UTI) is one of the most common bacterial infections and UTI is the most common extraintestinal infectious disease entity in women worldwide. Uropathogenic Escherichia coli (UPEC) is the leading cause of UTI. While antimicrobial resistance has emerged as one of the principal problems of UTI, little is known about the epidemiology of UPEC isolated from female patients in Shanghai. This study aimed to describe the antimicrobial resistance and molecular epidemiology of UPEC isolated from female patients in Shanghai, China. UPEC isolates were collected from female patients from July 2019 to June 2020 in Shanghai and a total of 151 isolates were obtained randomly. Antimicrobial susceptibility testing was performed using the disk diffusion method. Multilocus sequencing type, phylogenetic groups, antimicrobial resistance genes, and virulence genes were detected by polymerase chain reaction. In our study, no carbapenem-resistant isolates were found, but fluoroquinolone-resistant and multi-drug resistant UPEC accounted for 62.25% and 42.38%, respectively. The phylogenetic group B2 (58.94%) predominated, followed by phylogenetic group D (26.49%). The most prevalent sequence type was ST1193 (25.83%), which was first reported in Shanghai. The rate of extended-spectrum β-lactamase (ESBL)-positive isolates was 39.74% and the dominant ESBL genotype was bla_CTX-M-14 (21/60), followed by bla_CTX-M-55 (12/60). Mutations in gyrA were detected in the majority of fluoroquinolone-resistant isolates (90/94), followed by parC (85/94) and parE (71/94). The aac (3) -IIa was also found in 85% of aminoglycoside resistance isolates. Among 151 UPEC isolates, the common virulence genes were csgA (97.35%), fimH (92.72%), sitA (82.12%), and malX (65.56%). In conclusion, the high antimicrobial resistance of UPEC isolated from female patients, harboring a series of virulence genes, are troublesome for medical practitioners in Shanghai. At present, the prevalent ST1193 and emerging bla_CTX-M-55 make UTI therapy more challenging.

Antimicrobial Resistance Profiling and Molecular Epidemiological Analysis of Extended Spectrum β-Lactamases Produced by Extraintestinal Invasive Escherichia coli Isolates From Ethiopia: The Presence of International High-Risk Clones ST131 and ST410 Revealed

The treatment of invasive Escherichia coli infections is a challenge because of the emergence and rapid spread of multidrug resistant strains. Particular problems are those strains that produce extended spectrum β-lactamases (ESBL’s). Although the global characterization of these enzymes is advanced, knowledge of their molecular basis among clinical E. coli isolates in Ethiopia is extremely limited. This study intends to address this knowledge gap. The study combines antimicrobial resistance profiling and molecular epidemiology of ESBL genes among 204 E. coli clinical isolates collected from patient urine, blood, and pus at four geographically distinct health facilities in Ethiopia. All isolates exhibited multidrug resistance, with extensive resistance to ampicillin and first to fourth line generation cephalosporins and sulfamethoxazole-trimethoprim and ciprofloxacin. Extended spectrum β-lactamase genes were detected in 189 strains, and all but one were positive for CTX-Ms β-lactamases. Genes encoding for the group-1 CTX-Ms enzymes were most prolific, and CTX-M-15 was the most common ESBL identified. Group-9 CTX-Ms including CTX-M-14 and CTX-27 were detected only in 12 isolates and SHV ESBL types were identified in just 8 isolates. Bacterial typing revealed a high amount of strains associated with the B2 phylogenetic group. Crucially, the international high risk clones ST131 and ST410 were among the sequence types identified. This first time study revealed a high prevalence of CTX-M type ESBL’s circulating among E. coli clinical isolates in Ethiopia. Critically, they are associated with multidrug resistance phenotypes and high-risk clones first characterized in other parts of the world.

Antimicrobial Resistance Conferred by OXA-48 β-Lactamases: Towards a Detailed Mechanistic Understanding

OXA-48-type β-lactamases are now routinely encountered in bacterial infections caused by carbapenem-resistant Enterobacterales These enzymes are of high and growing clinical significance due to the importance of carbapenems in treatment of health care-associated infections by Gram-negative bacteria, the wide and increasing dissemination of OXA-48 enzymes on plasmids, and the challenges posed by their detection. OXA-48 confers resistance to penicillin (which is efficiently hydrolyzed) and carbapenem antibiotics (which is more slowly broken down). In addition to the parent enzyme, a growing array of variants of OXA-48 is now emerging. The spectrum of activity of these variants varies, with some hydrolyzing expanded-spectrum oxyimino-cephalosporins. The growth in importance and diversity of the OXA-48 group has motivated increasing numbers of studies that aim to elucidate the relationship between structure and specificity and establish the mechanistic basis for β-lactam turnover in this enzyme family. In this review, we collate recently published structural, kinetic, and mechanistic information on the interactions between clinically relevant β-lactam antibiotics and inhibitors and OXA-48 β-lactamases. Collectively, these studies are starting to form a detailed picture of the underlying bases for the differences in β-lactam specificity between OXA-48 variants and the consequent differences in resistance phenotype. We focus specifically on aspects of carbapenemase and cephalosporinase activities of OXA-48 β-lactamases and discuss β-lactamase inhibitor development in this context. Throughout the review, we also outline key open research questions for future investigation.

Drug resistance phenotypes and genotypes in Mexico in representative gram-negative species: Results from the infivar network

Aim

This report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum β-lactamases (ESBLs) and representative carbapenemases-producing Gram-negative species in Mexico.

Material and methods

A total of 52 centers participated, 43 hospital-based laboratories and 9 external laboratories. The distribution of antimicrobial resistance data for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, Acinetobacter baumannii complex, and Pseudomonas aeruginosa in selected clinical specimens from January 1 to March 31, 2020 was analyzed using the WHONET 5.6 platform. The following clinical isolates recovered from selected specimens were included: carbapenem-resistant Enterobacteriaceae, ESBL or carbapenem-resistant E. coli, and K. pneumoniae, carbapenem-resistant A. baumannii complex, and P. aeruginosa. Strains were genotyped to detect ESBL and/or carbapenemase-encoding genes.

Results

Among blood isolates, A. baumannii complex showed more than 68% resistance for all antibiotics tested, and among Enterobacteria, E. cloacae complex showed higher resistance to carbapenems. A. baumannii complex showed a higher resistance pattern for respiratory specimens, with only amikacin having a resistance lower than 70%. Among K. pneumoniae isolates, bla_TEM, bla_SHV, and bla_CTX were detected in 68.79%, 72.3%, and 91.9% of isolates, respectively. Among E. coli isolates, bla_TEM, bla_SHV, and bla_CTX were detected in 20.8%, 4.53%, and 85.7% isolates, respectively. For both species, the most frequent genotype was bla_CTX-M-15. Among Enterobacteriaceae, the most frequently detected carbapenemase-encoding gene was bla_NDM-1 (81.5%), followed by bla_OXA-232 (14.8%) and bla_oxa-181(7.4%), in A. baumannii was bla_OXA-24 (76%) and in P. aeruginosa, was bla_IMP (25.3%), followed by bla_GES and bla_VIM (13.1% each).

Conclusion

Our study reports that NDM-1 is the most frequent carbapenemase-encoding gene in Mexico in Enterobacteriaceae with the circulation of the oxacillinase genes 181 and 232. KPC, in contrast to other countries in Latin America and the USA, is a rare occurrence. Additionally, a high circulation of ESBL bla_CTX-M-15 exists in both E. coli and K. pneumoniae.

Bloodstream Infection Etiology among Children and Adults

Every year in the world, sepsis occurs in 31.5 million people, and the number of deaths reaches 5.3 million per year. There are not enough studies that describe etiological structure of sepsis pathogens in different groups of population of the Republic of Kazakhstan. In this study, we have investigated difference of local sepsis etiology and antibiotic susceptibility among children and adults. A total 200 blood samples were examined using the standard and express method of identification of bloodstream pathogens. The determination of antimicrobial sensitivity was carried out by the disc-diffusion method according to CLSI guidelines. Overall, 23/90 (25.5%) positive blood cultures were isolated from adult patients and 43/110 (39%) from pediatric patients. It was found that children are statistically more often affected with bacterial bloodstream infection than adults (p < 0.05). The Gram-positive bacteria are the leading cause of sepsis in both groups: S. epidermidis (35.5%) in pediatric patients and S. aureus (21.7%) in adults. However, statistical significance was detected in pediatric patients (p < 0.05). The number of resistant strains of S. epidermidis (MRSE) in the group of children was 66.7%, while in adults, all S. epidermidis was resistant to azithromycin and cefoxitin (MRSE). S. aureus strains from adult patients and children had a similar picture of antibiotic patterns. The proportion of MRSA in pediatric patients was 16, 6%, and in adult patients, 20%. Enterobacterales (39%) were the second cause of sepsis in adult patients. 62.5% of Enterobacterales strains isolated from adults were phenotypically identified as ESBL, while in pediatric patients, 25% of ESBL producers were isolated. We have noted the resistance to antibiotics that are prescribed according to protocols of treatment of the Republic of Kazakhstan in the strains isolated from the patient's blood.

Distinguishing Pathovars from Nonpathovars: Escherichia coli

Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.

Risk factors and diagnostic markers for Escherichia coli bloodstream infection in older patients

OBJECTIVE

To investigate risk factors for Escherichia coli (E. coli) bloodstream infection (BSI) in older patients and the diagnostic accuracy of laboratory parameters.

METHODS

The electronic medical records of patients aged 60 years and above who were admitted with a serious condition were extracted. Propensity score matching (PSM) was used to ensure that the included patients had similar baseline clinical features. Multiple regression analysis was used to identify risk factors for E. coli BSI and extended-spectrum β-lactamase (ESBL)-producing E. coli BSI. Receiver operating characteristic (ROC) curve analysis was performed to determine the diagnostic utility of relevant laboratory indicators.

RESULTS

After PSM, 508 patients were included: 254 patients with E. coli BSI and 254 control patients. Bile duct stone (adjusted odds ratio [aOR] 5.131), kidney stone (aOR 3.678), and urinary system infection (aOR 3.173) were independent risk factors for E. coli BSI. Prior exposure to cephems (aOR 3.782) and drainage tube placement (aOR 2.572) were independent risk factors for ESBL-producing E. coli BSI. Serum procalcitonin (PCT) yielded the highest area under the curve (0.783) and the best cut-off value (1.3 ng/ml).

CONCLUSION

Bile duct stone, kidney stone, and urinary system infection must be detected and treated early, in order to prevent E. coli BSI in older patients. Further, administration of cephems and invasive procedures must be undertaken with caution, in order to reduce the risk of BSI with ESBL-producing E. coli. Finally, serum PCT level has potential as diagnostic marker for E. coli BSI in older individuals.

Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy

Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, bla_CTX-M1,15,55, bla_CMY-2, gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified.

Genetic diversity, antimicrobial resistance and extended-spectrum β-lactamase type of Escherichia coli isolates from chicken, dog, pig and yak in Gansu and Qinghai Provinces, China

OBJECTIVES

In this study, the genetic diversity, phylogenetic grouping, antimicrobial resistance and extended-spectrum β-lactamase (ESBL) types of Escherichia coli isolates from chickens, dogs, pigs and yaks in six prefectures of Gansu and Qinghai Provinces, China, were investigated.

METHODS

E. coli was isolated from diarrhoeic and healthy faecal samples. Multilocus sequence typing (MLST), phylogenetic grouping, antimicrobial resistance and ESBL profiles were investigated.

RESULTS

A total of 142 MLST sequence types (STs) were identified from 400 E. coli isolates. eBURST clustering analysis resolved the 142 STs into 19 clonal complexes (CCs) and 67 singletons. PCR phylogenetic typing determined the isolation rate of potentially pathogenic B2/D group isolates among all E. coli to be 12.5% from healthy animal samples and 17.5% from diarrhoeic samples. Antimicrobial susceptibility testing revealed 78 antimicrobial resistance patterns. E. coli resistance rates were highest to doxycycline, ampicillin and tetracycline, whereas polymyxin B and meropenem had the lowest resistance rates. All polymyxin B-resistant E. coli isolates were positive for the mcr-1 gene. A total of 62 ESBL-producing isolates were identified. The ESBL prevalence was 55.0% in diarrhoeic samplings and 5.6% in healthy animals. TEM (82.3%) was the predominant ESBL type, followed by CTM (43.5%) and SHV (19.4%).

CONCLUSION

E. coli isolates in the study area have a high diversity of genetic and antimicrobial resistance patterns but a relatively low isolation rate of potentially pathogenic phylogroups. However, the somewhat high isolation rate of multidrug-resistant E. coli, particularly ESBL-producing isolates, requires continual surveillance of E. coli from animals in these areas.

Prognostic roles of time to positivity of blood cultures in patients with Escherichia coli bacteremia

The time to positivity (TTP) of blood cultures has been considered a predictor of clinical outcomes for bacteremia. This retrospective study aimed to determine the clinical value of TTP for the prognostic assessment of patients with Escherichia coli bacteremia. A total of 167 adult patients with E.coli bacteremia identified over a 22-month period in a 3500-bed university teaching hospital in China were studied. The standard cut-off TTP was 11 h in the patient cohort. The septic shock occurred in 27.9% of patients with early TTP (⩽11 h) and in 7.1% of those with a prolonged TTP (>11 h) (P = 0.003). The mortality rate was significantly higher for patients in the early than in the late group (17.7% vs. 4.0%, P < 0.001). Multivariate analysis showed that an early TTP (OR 4.50, 95% CI 1.70–11.93), intensive care unit admission (OR 8.39, 95% CI 2.01–35.14) and neutropenia (OR 4.20, 95% CI 1.55–11.40) were independently associated with septic shock. Likewise, the independent risk factors for mortality of patients were an early TTP (OR 3.80, 95% CI 1.04–12.90), intensive care unit admission (OR 6.45; 95% CI 1.14–36.53), a Pittsburgh bacteremia score ⩾2 (OR 4.34, 95% CI 1.22–15.47) and a Charlson Comorbidity Index ⩾3 (OR 11.29, 95% CI 2.81–45.39). Overall, a TTP for blood cultures within 11 h appears to be associated with worse outcomes for patients with E.coli bacteremia.

Epidemiology of Febrile Neutropenia Episodes with Gram-Negative Bacteria Infection in Patients Who Have Undergone Chemotherapy for Hematologic Malignancies: A Retrospective Study of 10 Years' Data from a Single Center

Background

The epidemiology of Gram-negative bacteria in patients with febrile neutropenia (FN) and their susceptibility to initial empirical antibiotic therapy is key to successful treatment during the treatment of hematologic malignancies.

Methods

A retrospective study was conducted. Patients with FN and confirmed laboratory results of Gram-negative bacteria infections were included. If no direct sensitivity of the identified pathogen to the initially prescribed antibiotic regimen was confirmed, it was defined as inappropriate initial antibiotic treatment (IIAT).

Results

A total of 247 patients with FN were proven to be infected with Gram-negative bacteria, and 200 were diagnosed with acute leukemia. The most commonly detected bacteria were Escherichia coli (40%), Klebsiella pneumoniae (20%), and Pseudomonas aeruginosa (11%). In sum, 176 patients were classified as IIAT. The mortality rate in the IIAT group was significantly higher (37.7% vs 23.9%, P=0.038). With monotherapy as empirical treatment, high possibility of IIAT with fluoroquinolones (52%) and cephalosporins (35%) was detected, while more sensitivity to carbapenems (16%) and glycopeptides antibiotics (19%) was noticed. With combined treatment, cephalosporins/carbapenems had with the lowest percentage of IIAT (18%).

Conclusion

In conclusion, inappropriate initial empirical antibiotic treatments were associated with higher mortality in patients with hematologic malignancies. The current empirical antibiotic regimen needs to be further optimized.

Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae: Update on Molecular Epidemiology and Treatment Options

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are a major global public health concern. Presently, Escherichia coli with CTX-Ms are the most common species associated with global ESBLs; CTX-M-15 is the most frequent CTX-M worldwide and is followed by CTX-M-14, which is often found in South-East Asia. Recent surveillance studies showed that CTX-M-27 is emerging in certain parts of the world especially in Japan and Europe. The population structure of ESBL-producing E. coli is dominated globally by an high-risk clone named ST131. Escherichia coli ST131 belongs to three clades (A, B, and C) and three different subclades (C1, C1-M27, and C2). Clade C1-M27 is associated with bla_CTX-M-27, and C2 with bla_CTX-M-15. Recent whole genome sequencing studies have shown that clade C has evolved from clade B in a stepwise fashion, resulting in one of the most influential global antimicrobial resistance clones that has emerged during the 2000's. Other important E. coli clones that have been detected among ESBL producers include ST405, ST38, ST648, ST410, and ST1193. The INCREMENT project has shown that ertapenem is as effective as other carbapenems for treating serious infections due to ESBL-producing Enterobacteriaceae. The results of the MERINO open-label randomized controlled study has provided clear evidence that piperacillin-tazobactam should be avoided for targeted therapy of blood-stream infections due to ESBL-producing E. coli and K. pneumoniae, regardless of the patient population, source of infection, bacterial species, and susceptibility result of piperacillin-tazobactam. Research is still warranted to define the optimal therapy of less severe infections due to ESBL-producing Enterobactericeae.

Spreading of extended-spectrum β-lactamase-producing Escherichia coli ST131 and Klebsiella pneumoniae ST11 in patients with pneumonia: a molecular epidemiological study

Supplemental Digital Content is available in the text

Background:

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) are the important pathogens causing pneumonia. This study aimed to investigate the clinical characteristics and molecular epidemiology of ESBL-producing E. coli and K. pneumoniae causing pneumonia at a large teaching hospital in China.

Methods:

We collected patient's clinical data and ESBL-producing E. coli and K. pneumoniae strains causing pneumonia (from December 2015 to June 2016) at a hospital in Wuhan. The susceptibilities, multi-locus sequence typing, homologous analysis, ESBL genes by polymerase chain reaction and sequencing were determined.

Results:

A total of 59 ESBL-producing strains (31 E. coli and 28 K. pneumoniae) isolated from patients with pneumonia were analyzed. The majority of strains were isolated from patients were with hospital-acquired pneumonia (37/59, 62.7%), followed by community-acquired pneumonia (13/59, 22.0%), and ventilator-related pneumonia (9/59, 15.3%). The E. coli ST131 (9 isolates, 29.0%) and K. pneumoniae ST11 (5 isolates, 17.9%) were the predominant sub-types. The most prevalent ESBL gene was CTX-M-14, followed by SHV-77, CTX-M-3, SHV-11, and CTX-M-27. At least 33 (55.9%) of the ESBL-producing strains carried two or more ESBL genes. The ISEcp1 and IS26 were found upstream of all blaCTX-M (CTX-Ms) and of most blaSHV (SHVs) (57.6%), respectively. Moreover, three ESBL-producing K. pneumoniae ST11 strains which were resistant to carbapenems carried the bla_NDM-1 and bla_KPC-2, two of which also bearing bla_OXA-48 were resistant to all antibiotics (including Tigecycline).

Conclusions:

Hospital-acquired pneumonia is more likely correlated with ESBL-producing E. coli and K. pneumoniae. ESBL-producing E. coli ST131 and multi-drug resistance ESBL-producing, as well as New Delhi metallo-β-lactamase-1 (NDM-1) and Klebsiella pneumoniae carbapenemases-2 (KPC-2) bearing K. pneumoniae ST11 are spreading in patients with pneumonia in hospital.

Sequence Types, Clonotypes, Serotypes, and Virotypes of Extended-Spectrum β-Lactamase-Producing Escherichia coli Causing Bacteraemia in a Spanish Hospital Over a 12-Year Period (2000 to 2011)

The aim of the present study was to examine the prevalence and determine the molecular characteristics of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) causing bacteraemia in a Spanish Hospital over a 12-year period (2000 to 2011). As far as we know, this is the first study which has investigated and compared the serotypes, phylogroups, clonotypes, virotypes, and PFGE profiles of ST131 and non-ST131 clones of bacteraemia ESBL-EC isolates. Of the 2,427 E. coli bloodstream isolates, 96 (4.0%) were positive for ESBL production: 40 for CTX-M-15, 36 for CTX-M-14, eight for CTX-M-1, four for CTX-M-9, CTX-M-32, and SHV-12. The number of ESBL-EC increased from 1.0% during 2000 to 2005 to 5.5% during 2006-2011 (P < 0.001). The 96 ESBL-EC isolates belonged to 36 different STs. The commonest was ST131 (41 isolates), followed by ST58, ST354, ST393 and ST405 (four isolates each). Most CTX-M-15 isolates (87.5%, 35/40) were ST131, whereas the 36 CTX-M-14 isolates belonged to 23 different STs and only 3 (8.3%) of them were ST131. The 35 ST131 CTX-M-15-producing isolates belonged to the H30Rx subclone and 29 of them showed the virotype A. A drastic change in ST131 virotypes happened in 2011 due to the emergence of the virotypes E (sat, papGII, cnf1, hlyA, and kpsMII-K5) and F (sat, papGII, and kpsMII-K5) which displaced virotype A (afa/draBC, afa operon FM955459, sat, and kpsMII-K2). Although the 96 ESBL-EC isolates showed 21 O serogroups and 17 H flagellar antigens, 39 belonged to serotype O25b:H4 (ST131 isolates). The second most prevalent serotype (O15:H1) was found to be associated with another important high-risk clone (ST393). In conclusion, the ST131 was the most frequent sequence type, being the H30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H30Rx subclone emerged in 2011. Future molecular studies are needed to understand the dynamics of expansion of this successful high-risk subclone in order to prevent its spread and establish the importance of the two new virotypes.

Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages

Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.

Dissemination of genetically diverse NDM-1, -5, -7 producing-Gram-negative pathogens isolated from pediatric patients in Pakistan

Aim: To determine the prevalence of New Delhi metallo-β-lactamase (NDM)-producing Gram-negative pathogens isolated from children's samples. Materials & methods: Carbapenem-resistant clinical isolates (n = 117) were confirmed by VITEK^® 2 compact system, matrix-assisted laser desorption ionization-time of flight and multilocus sequence typing. MIC (μg/ml) of various antibiotics was determined by VITEK 2 compact system. Molecular characterization of the isolates was performed by PCR, DNA sequencing, PFGE and DNA hybridization. Results: Out of 117 carbapenemase producers, 37 (31.6%) and 29 (24.7%) were Klebsiella pneumoniae and Acinetobacter baumannii, respectively. 72 (61.5%) isolates were NDM positive and among these 60, 9 and 3 were NDM-1, -5 and -7, respectively. Majority of the NDM-producing K. pneumoniae belonged to ST11 and ST273 while most of the Escherichia coli belonged to ST405 and ST101. bla_NDM were mainly located on 150kb plasmids. MIC displayed high resistance against β-lactams drugs including carbapenems, and the most sensitive drugs were tigecycline and colistin. Conclusion: Dissemination of bla_NDM-producing pathogens, particularly in children clinical settings, is a matter of great public health concern.

Phenotypic and genotypic characterization of multi-drug-resistant Escherichia coli isolates harboring blaCTX-M group extended-spectrum β-lactamases recovered from pediatric patients in Shenzhen, southern China

Aims and Objectives: The emergence and spread of extended-spectrum β-lactamases (ESBLs) particularly CTX-M producing multi-drug-resistant (MDR) Escherichia coli (E. coli) is one of the greatest challenges for community health globally. The study investigated the phenotypic and genotypic characteristics of ESBLs-producing E. coli recovered from pediatric patients from Shenzhen Children’s Hospital, China.

Materials and methods: Present study, a total of 2,670 isolates of E. coli were collected from Shenzhen Children’s Hospital, China of which 950 were ESBLs producer. ESBLs production was confirmed by using the combination disc diffusion method, and antimicrobial susceptibility test was detected. In addition, β-lactamase-producing genes and co-existence of carbapenem/colistin resistance genes were determined by PCR assay and sequencing. The diversity and phylogenetic relationship were determined by multi-locus sequence typing method.

Results: Thirty-five percent (n=950) prevalence of ESBLs-producing E. coli we reported in Shenzhen, China of which 50 ESBLs producing E. coli were randomly selected for a further characterization. All 50 ESBLs- producing E. coli isolates revealed MDR phenotype and 100% were resistant to Ampicillin/sulbactam, Ampicillin, Cefazolin, and Ceftriaxone. All 50 ESBLs producers harbored at least one type of β-lactamase gene particular bla_CTX-M. The PCR and sequencing revealed the most common CTX-M subtype was bla_CTX-M-15 (n=18), followed by bla_CTX-M-14 (n=16), bla_CTX-M-90 (n=9), bla_CTX-M-55 (n=3), bla_CTX-M-27, bla_CTX-M-101, and bla_CTX-M-211 each (n=1). Co-existence of bla_CTX-M with bla_TEM, bla_SHV, bla_GES, and bla_VEB was detected in few isolates. Among identified sequence types, ST131 (12%) was more dominant in ESBLs-producing E. coli. Phylogenetic group A was the most prominent group among the ESBLs-producing E. coli based on multiplex PCR.

Conclusion: Our study shows the prevalence of bla_CTX-M gene in ESBLs-producing E. coli in pediatric patients in Shenzhen, China. We highlight the importance to monitor the emergence and trends of ESBLs-producing isolates in a pediatric healthcare setting.

Genotypic and Phenotypic Characterization of Clinical Escherichia coli Sequence Type 405 Carrying IncN2 Plasmid Harboring bla NDM-1

We report a bla NDM-carrying ST405 Escherichia coli recovered from the abdominal fluid of a patient in Shandong, China. This strain belonged to the high-risk phylogenetic group D and carried the virulence genes, papG II, papG III, papC, and iroN. In addition to bla NDM-1, this isolate carried the quinolone resistance gene acc(6')-Ib and extended-spectrum β-lactamase (ESBL) genes bla CTX-M-15 and bla CTX-M-14. bla NDM-1 was located on a 41 Kb IncN2 self-transmissible plasmid. The IncN2 plasmid named as pJN24NDM1 was fully sequenced and analyzed. Genome comparative analysis showed that IncN2 plasmids harboring carbapenem-resistance genes possessed conserved backbones and variable accessory regions. Phylogenetic analysis of 87 IncN plasmids based on orthologous genes indicated that 9 IncN2 plasmids fell into one phylogenetic clade, while 4 IncN3 plasmids were in two phylogenetic clades of the 74 IncN1 plasmids. The presence of IncN2 plasmids harboring bla NDM in the high-risk clone ST405 E. coli raises serious concerns for its potential of dissemination.

The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

Future Challenges in Pediatric and Neonatal Sepsis: Emerging Pathogens and Antimicrobial Resistance

The incidence of severe infections caused by multidrug-resistant (MDR) pathogens is currently rising worldwide, and increasing numbers of neonates and children with serious bloodstream infections due to resistant bacteria are being reported. Severe sepsis and septic shock due to gram-negative bacteria represent a significant cause of morbidity and mortality, and contribute to high health care costs. Antimicrobial resistance among Enterobacteriaceae represents a major problem in both health care-associated and community-acquired infections, with extended-spectrum β-lactamases (ESBLs) and carbapenem-resistant Enterobacteriaceae (CRE) now presenting the main threat. These infections in adult populations have been associated with poor clinical outcomes, but very limited data have been published so far about risk factors and clinical outcome of ESBL-associated and CRE sepsis in the pediatric population. The treatment of these infections in neonates and children is particularly challenging due to the limited number of available effective antimicrobials. Evidence-based use of new and older antibiotics based on both strategic and regulatory clinical trials is paramount to improve management of these severe infections in neonates and children.

Clinical features and microbiological characteristics of hospital- and community-onset Escherichia coli bloodstream infection

PURPOSE

Escherichia coli is a leading cause of bloodstream infection (BSI) in hospitals and communities.

METHODOLOGY

We conducted a retrospective study in 2015 to evaluate the clinical features and microbiological characteristics of E. coli BSI acquired in the hospital and community.

RESULTS

A total of 100 patients with E. coli BSI were enrolled, among whom 60 % had hospital-onset (HO) BSI while 40 % had community-onset (CO) BSI. Patients with HO BSI had higher percentages of haematological disorders, immunosuppression conditions, underwent surgery within 2 weeks and had a higher 30-day mortality. The prevalences of multidrug-resistant and extended-spectrum β-lactamase-producing strains were 81 and 60 %, respectively. Resistance percentages to ampicillin, ampicillin-sulbactam, cefazolin, ceftriaxone, ciprofloxacin and levofloxacin were greater than 50 %. Of the 43 different sequence types (STs) identified, ST131 (15.3 %) was the most common. The serum agglutination rate was 52 % in which 13 O and 11 H serogroups were observed. Among the 36 detected virulence factor (VF) genes, IutA (66 %) and traT (61 %) were the most predominant. papA, papC and papEF were different between the CO and HO BSI groups. VF scores were high (mean >7) in the frequently detected ST95, ST1193 and ST131.

CONCLUSION

This study revealed that the clinical features of HO and CO E. coli BSI were different. STs and serotypes showed a great diversity in this region while VF genes of the isolates varied between clones.

[Bloodstream infections with Escherichia coli O16-ST131 and O25b-ST131: molecular epidemiology, phylogenetic analysis and antimicrobial resistance]

OBJECTIVE

To investigate the phylogenetics and prevalence of bloodstream infections with Escherichia coli ST131, the antimicrobial resistance profiles of the pathogens, and the clinical features.

METHODS

Non-duplicate Escherichia coli isolates were collected from 144 patients with bloodstream infections in our hospital between January and December, 2016.The phylogenetic groups of the isolates were analyzed using multiplex PCR, and O serotyping of ST131 strains was performed by allele-specific PCR.The clinical characteristics of the 144 patients were analyzed to define the differences in the clinical features between patients with ST131 infection and those with non-ST131 infection.Antibiotic susceptibility of the isolates was determined using the Vitek 2 compact system.

RESULTS

The phylogenetic group analysis showed a domination by group B2 (41.0%[59/144]), followed by group F, group B1 and group E, which accounted for 16.7%(24/144), 13.9%(20/144), and 13.2% (19/144), respectively.Nine strains (6.3%) of Escherichia coli were identified to be ST131 strains, among which 8 were O25b-B2-ST131 strains and 1 was O16-B2-ST131 strain.Of the 9 cases of ST131 infection, 7(77.8%) were found to occur in a nosocomial setting.The demographic characteristics and clinical features of the ST131-infected patients were similar to those of non-ST131-infected patients.ST131 strains were sensitive to piperacillin/tazobactam, imipenem, ertapenem, and amikacin, but showed high resistance rates to cefazolin, ceftriaxone, ciprofloxacin, levofloxacin, gentamicin, and trimethoprim/ sulfamethoxazole (all over 50%).The positivity rate of ESBLs in the ST131 strains was 77.8%, and the multidrug resistance rate reached 88.9%, which was higher than that of non-ST131 isolates, but the difference was not statistically significant.

CONCLUSIONS

The most common phylogenetic groups of Escherichia coli isolates from patients with bloodstream infections are group B2 and F, and the positivity rate of ST131 is low.We for the first time detected O16-ST131 in patients with blood-borne infections in China.The clinical features of ST131-infected patients are similar to those of non-ST131-infected patients.The positivity rate of ESBLs and the multidrug resistance rate are high in ST131 strains, which may raise concerns in the future.

High Prevalence of bla NDM Variants Among Carbapenem-Resistant Escherichia coli in Northern Jiangsu Province, China

The continuous emergence of carbapenem-resistant Escherichia coli (CRECO) presents a great challenge to public health. New Delhi metallo-lactamase (NDM) variants are widely disseminated in China, so the research on the prevalence and transmission of diverse bla_NDM variants is urgently needed. In the present study, 54 CRECO isolates were collected from 1,185 Escherichia coli isolates in five hospitals in Northern Jiangsu Province, China from September 2015 to August 2016. Antimicrobial susceptibility tests, PCR detection of resistance determinants, multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to characterize these strains. Plasmid conjugation experiments were carried out to determine the transferability of resistant genes from selected isolates. PCR-based replicon typing (PBRT), S1 nuclease-PFGE, and Southern blotting were conducted for plasmid profiling. Carbapenemase genes were detectable in all CRECO isolates, among which thirty-one CRECO isolates were found to carry bla_NDM−5 (54.7%), while, bla_NDM−1, bla_NDM−7, bla_NDM−4, bla_NDM−9, and bla_KPC−2 were identified in 14, five, two, one, and one isolates, respectively. MLST results revealed 15 different STs and four new STs were first reported to be linked with NDM-producing isolates. PFGE typing showed that no more than two isolates with the same ST appeared to the same band pattern except three ST410 isolates. Twenty-six selected NDM-producing isolates were successfully transferred to E. coli J53 by conjugation experiments. Notably, 50.0% (13/26) of bla_NDM variants were found to be carried by ~55 kb IncX3 plasmid. Our study reported a high prevalence of bla_NDM variants, especially bla_NDM−5, in Northern Jiangsu province, China. Diverse bla_NDM variants were mainly carried by ~55 kb IncX3 plasmids, suggesting that the fast evolution and high transferability of this kind of plasmid promote the high prevalence of bla_NDM variants. Therefore, large-scale surveillance and effective infection control measures are also urgently needed to prevent diverse bla_NDM variants from becoming epidemic in the future.

Molecular characterization and antimicrobial susceptibility profile of New Delhi metallo-beta-lactamase-1-producing Escherichia coli among hospitalized patients

BACKGROUND

Carbapenemase-producing microorganisms are becoming a major concern among hospital-acquired infections. There is also increased multidrug resistance seen among these isolates.

AIMS

We have conducted this study to determine the prevalence of New Delhi metallo-beta-lactamase-1 (NDM-1) gene-producing Escherichia coli among hospitalized patients in a tertiary care hospital in Northern India.

SETTINGS AND DESIGN

The study was conducted in the Department of Microbiology with the tertiary care hospital settings. It was a prospective cross-sectional observational study conducted during January 2014-August 2014.

MATERIALS AND METHODS

A total of 500 nonduplicate E. coli samples were processed. The isolates with reduced susceptibility to ertapenem, i.e., zone diameter between 19 and 21 mm, were considered carbapenemase producers. These isolates were subjected to modified Hodge test for phenotypic confirmation. Polymerase chain reaction was performed on all the screened isolates for molecular detection of NDM-1 gene.

STATISTICAL ANALYSIS USED

Chi-square test was used to analyze the data and P < 0.05 was considered statistically significant.

RESULTS

Out of 500 E. coli isolates, 61 (12.2%) were screened for carbapenemase production. 47 (9.4%) isolates were positive by modified Hodge test and 36 (7.2%) isolates showed the presence of blaNDM-1 gene (P < 0.05).

CONCLUSION

There is an increased prevalence of NDM-1 gene-producing E. coli isolates. These carbapenemase-producing isolates are more resistant to other group of antibiotics (aminoglycosides, fluoroquinolones along with β-lactam group). Early detection of blaNDM-1 gene can help in choosing the effective treatment options for hospitalized patients in time, thereby reducing the risk of mortality.

Genetic contexts related to the diffusion of plasmid-mediated CTX-M-55 extended-spectrum beta-lactamase isolated from Enterobacteriaceae in China

Background

CTX-M-55 extended-spectrum beta-lactamases are being rapidly disseminated and transmitted in clinical practices around the world. The genetic contexts of the transferable plasmid-mediated bla_CTX-M-55 gene in Enterobacteriaceae were detected and characterized in this study.

Methods

Isolates were obtained from the First Affiliated Hospital of Zhengzhou University between September 2015 and March 2016. Based on polymerase chain reaction and BLAST analysis, resistance genes and genetic context of the bla_CTX-M-55 gene were investigated. Conjugation experiments and multilocus sequence typing were performed to demonstrate plasmid-mediated bla_CTX-M-55 transmission.

Results

Thirteen bla_CTX-M-55-positive isolates of Enterobacteriaceae were obtained. Seven isolates were Escherichia coli, 3 were Klebsiella pneumoniae, 1 was Citrobacter freundii, 1 was Morganella morganii and 1 was Serratia marcescens. The bla_CTX-M-55 gene has not previously been identified from C. freundii and M. morganii. Four different bla_CTX-M-55 genetic contexts were identified, and all of them harbored ISEcp1 in the region upstream of bla_CTX-M-55 (in two cases, ISEcp1 was truncated by IS26, and in one case, it was truncated by IS1294), whereas ORF477 was detected downstream of the bla_CTX-M-55 gene from 12 of 13 strains. The novel genetic context of ISEcp1∆-bla_CTX-M-55-∆IS903 was firstly detected the IS903 element which was identified downstream of bla_CTX-M-55. A conjugation assay revealed that all bla_CTX-M-55 plasmids were quickly and easily transferable to recipient E. coli, which then presented resistance to multiple antibiotics.

Conclusions

Numerous bla_CTX-M-55-positive strains were isolated in a short period of 7 months. The findings indicate that bla_CTX-M-55 was rapidly disseminated. The genetic context and conjugative transfer found in this study demonstrate that there is active transmission of bla_CTX-M-55 among strains of Enterobacteriaceae in China, which could give rise to an urgent global public health threat.

Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil

Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.

Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype

Globally, rates of ESBL-producing Enterobacteriaceae are rising. We undertook a literature review, and present the temporal trends in blaCTX-M epidemiology, showing that blaCTX-M-15 and blaCTX-M-14 have displaced other genotypes in many parts of the world. Explanations for these changes can be attributed to: (i) horizontal gene transfer (HGT) of plasmids; (ii) successful Escherichia coli clones; (iii) ESBLs in food animals; (iv) the natural environment; and (v) human migration and access to basic sanitation. We also provide explanations for the changing epidemiology of blaCTX-M-2 and blaCTX-M-27. Modifiable anthropogenic factors, such as poor access to basic sanitary facilities, encourage the spread of blaCTX-M and other antimicrobial resistance (AMR) genes, such as blaNDM, blaKPC and mcr-1. We provide further justification for novel preventative and interventional strategies to reduce transmission of these AMR genes.

Antimicrobial susceptibility and molecular epidemiology of clinical Enterobacter cloacae bloodstream isolates in Shanghai, China

BACKGROUND

Enterobacter cloacae is a major nosocomial pathogen causing bloodstream infections. We retrospectively conducted a study to assess antimicrobial susceptibility and phylogenetic relationships of E. cloacae bloodstream isolates in two tertiary university-affiliated hospitals in Shanghai, in order to facilitate managements of E. cloacae bloodstream infections and highlight some unknowns for future prevention.

METHODS

Fifty-three non-duplicate E. cloacae bloodstream isolates were consecutively collected from 2013 to 2016. Antimicrobial susceptibility was determined by disk diffusion. PCR was performed to detect extended-spectrum β-lactamase (ESBL), carbapenemase and colistin resistance (MCR-1) gene. Plasmid-mediated AmpC β-lactamase (pAmpC) genes were detected using a multiplex PCR assay targeting MIR/ACT gene (closely related to chromosomal EBC family gene) and other plasmid-mediated genes, including DHA, MOX, CMY, ACC, and FOX. eBURST was applied to analyze multi-locus sequence typing (MLST).

RESULTS

The rates of resistance to all tested antibiotics were <40%. Among 53 E. cloacae isolates, 8(15.1%) were ESBL producers, 3(5.7%) were carbapenemase producers and 18(34.0%) were pAmpC producers. ESBL producers bear significantly higher resistance to cefotaxime (100.0%), ceftazidime (100.0%), aztreonam (100.0%), piperacillin (87.5%), tetracycline (75.0%), and trimethoprim-sulfamethoxazole (62.5%) than non-producers (p<0.05). PAmpC- and non-producers both presented low resistance rates (<40%) to all antibiotics (p>0.05). SHV (6/8, 75.0%) and MIR/ACT (15/18, 83.3%) predominated in ESBL and pAmpC producers respectively. Moreover, 2 isolates co-carried TEM-1, SHV-12, IMP-26 and DHA-1. MLST analysis distinguished the 53 isolates into 51 STs and only ST414 and ST520 were assigned two isolates of each (2/53).

CONCLUSION

The antimicrobial resistance rates were low among 53 E. cloacae bloodstream isolates in the two hospitals. Multiclonality disclosed no evidence on spread of these isolates in Shanghai. The simultaneous presence of ESBL, carbapenemase and pAmpC detected in 2 isolates was firstly reported in Shanghai, which necessitated active ongoing surveillances and consistent prevention and control of E. cloacae.

Prevalence and characteristics of ST131 clone among unselected clinical Escherichia coli in a Chinese university hospital

Background

Escherichia coli clinical sequence type 131 (ST131) has emerged as an extensively antimicrobial resistant E. coli clonal group in recent years throughout the world. The aim of this study was to investigate the prevalence and molecular characteristics of ST131 among unselected E. coli clinical isolates in a Chinese university hospital.

Methods

Seven hundred consecutive E. coli isolates were collected at a Chinese university hospital between 2014 and 2015. Isolates belonging to ST131 were identified by PCR and multilocus sequence typing (MLST), and then characterized for antibiotic resistance, CTX-M-type extended-spectrum β-lactamase genes, fluoroquinolone resistance genes, O types, phylogenetic groups, virulence factors and PFGE patterns.

Results

Overall, 83 (11.6%) isolates were identified as ST131 group. The H30 lineage accounted for 53 (63.9%) of the ST131 isolates, including 13 H30-Rx and 40 H30 non-Rx. The remaining 30 isolates belonged to H41 lineage. Two O types were identified in this study: O25b (66.3%) and O16 (33.7%). Compared with O25b-B2-ST131 isolates, O16-B2-ST131 isolates harbored less virulence factors of adhesins. ST131 H30 Rx isolates had significantly higher virulence score than those of other isolates. O16-B2-ST131 isolates were shown to have a lower resistance to quinolones than O25b-B2-ST131 isolates. 5 nonsynonymous mutations (GyrA S83 L, D87N, ParC S80I, E84V and ParE I529L) were strongly associated with ST131 H30 and O25b isolates. Results of PFGE demonstrated that these isolates were classified into 68 pulsotypes and these subtypes were grouped into 23 different PFGE clusters using 70% similarity cut-off value.

Conclusions

This is the first study to reveal the prevalence and molecular characteristic of ST131 clonal group among consecutive clinical E. coli isolates in China. Our findings demonstrated that ST131 lineage accounts for a small proportion of clinical E. coli isolates in China, which included two major groups: O25b-B2-ST131 and O16-B2-ST131. Our results implies that O16-B2-ST131 subclone may be an important type of E. coli ST 131 in China, which suggests that future studies should not ignore such clone in this country.

Treatment of sepsis: What is the antibiotic choice in bacteremia due to carbapenem resistant Enterobacteriaceae?

Sepsis is one of the major challenges of today. Although gram-positive bacteria related infections are more prevalent in hospital setting, the highest mortality rate is associated with gram-negative microorganisms especially Enterobacteriaceae. Enterobacteriaceae, including Escherichia coli, Klebsiella spp., Proteus spp., Enterobacter spp. and Serratia spp. Resistance to β-lactams in Enterobacteriaceae is primarily attributed to the production of B-lactamase enzymes with subsequent antibiotic hydrolysis and to a lesser extent by alteration of efflux pump or porins expression. Carbapenem resistant Enterobacteriaceae (CRE) and Acinetobacter baumannii are the most notorious pathogens due to the high incidence of morbidity and mortality especially in the immunocompromised patients in the intensive care unit. The most appropriate antimicrobial therapy to treat CRE is still controversial. Combination therapy is preferred over monotherapy due to its broad-spectrum coverage of micro-organisms, due to its synergetic effect and to prevent development of further resistance. Current suggested therapies for CRE resistance as well as promising antibiotics that are currently under investigation for winning the war against the emerging CRE resistance are reviewed and discussed.

Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection

The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCEEscherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time. Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.

Prevalence of ST1193 clone and IncI1/ST16 plasmid in E-coli isolates carrying blaCTX-M-55 gene from urinary tract infections patients in China

To study molecular epidemiology of CTX-M-55-carrying Escherichia coli isolates from urinary tract infections (UTIs) in China. 111 bla_CTX-M-55-positive E.coli isolates from UTIs patients in China were studied. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analyze the homologies among the strains. Conjugation experiments, S1nuclease PFGE and PCR analysis were performed to characterize plasmids harboring bla_CTX-M-55 and their genetic environment. 111 isolates were clustered into 86 individual pulsotypes and three clusters by PFGE. Fifty-five (49.5%) of the isolates belonged to 8 STs. Most of the ST1193 isolates belonged to one PFGE cluster. Transconjugants (n = 45) derived from randomly selected bla_CTX-M-55 donors (n = 58), were found to contain a single 90-kb conjugative plasmid, which mainly belonged to the IncI1 groups (34, 76%). Among the IncI1 plasmids, the bla_CTX-M-55/IncI1/ST16 predominated (23/34, 68%). The bla_TEM-1 and aac (3′)-II genes were frequently detected on the IncI1 plasmids, and the insertion of ISEcp1 or IS26 was observed at the 48 bp or 45 bp upstream of the start codon of bla_CTX-M-55 gene. The dissemination of bla_CTX-M-55 gene among E. coli UTI isolates, appeared to be due to both the major clonal lineage of ST1193 and the horizontal transfer of epidemic plasmid IncI1/ST16.

The Resistance Phenotype and Molecular Epidemiology of Klebsiella pneumoniae in Bloodstream Infections in Shanghai, China, 2012-2015

Klebsiella pneumoniae (K.pneumoniae) is a common nosocomial pathogen causing bloodstream infections. Antibiotic susceptibility surveillance and molecular characterization will facilitate prevention and management of K. pneumoniae bloodstream infections. K. pneumoniae isolates causing bloodstream infections were consecutively collected between January 2012 and December 2015 in Shanghai. Eighty isolates (20 per year) were randomly selected and enrolled in this study. Drug susceptibility were determined by the disk diffusion method. Polymerase chain reaction (PCR) was employed to detect extended-spectrum β-lactamases (ESBLs), carbapenemases, and seven housekeeping genes of K. pneumoniae. eBURST was used for multi-locus sequence typing (MLST). More than 50% isolates were resistant to cefuroxime, ampicillin-sulbactam, and piperacillin, while carbapenems had lower resistant rates than other antibiotics. Of the 80 isolates, 22 produced ESBLs, and 14 were carbapenemase producers. In the ESBL-producing K. pneumoniae isolates, the most common ESBL genes were bla_SHV and bla_CTX-M. Thirteen carbapenemase producers harbored bla_KPC-2 and one other carried bla_NDM-5. ST11 (14/80) was the most frequent sequence type (ST), followed by ST15 (7/80) and ST29 (4/80). Our data revealed high prevalence of antibiotic resistant K. pneumoniae isolates from bloodstream infections but their genetic diversity suggested no clonal dissemination in the region. Also, one K. pneumoniae isolate harbored bla_NDM-5 in this study, which was firstly reported in Shanghai.

Prevalence and Molecular Characteristics of Extended-Spectrum β-Lactamase Genes in Escherichia coli Isolated from Diarrheic Patients in China

Background: The emergence and spread of antimicrobial resistance has become a major global public health concern. A component element of this is the spread of the plasmid-encoded extended-spectrum b-lactamase (ESBL) genes, conferring resistance to third-generation cephalosporins. The purpose of this study was to investigate the molecular characteristics of ESBL-encoding genes identified in Escherichia coli cultured from diarrheic patients in China from 2013 to 2014.

Materials and Methods: A total of 51 E. coli were confirmed as ESBL producers by double-disk synergy testing of 912 E. coli isolates studied. Polymerase chain reaction (PCR) and DNA sequencing were performed to identify the corresponding ESBL genes. Susceptibility testing was tested by the disk diffusion method. Plasmids were typed by PCR-based replicon typing and their sizes were determined by S1-nuclease pulsed-field gel electrophoresis. Multi-locus sequence typing (MLST) and phylogrouping were also performed. Broth mating assays were carried out for all isolates to determine whether the ESBL marker could be transferred by conjugation.

Results: Of the 51 ESBL-positive isolates identified, bla_CTX-M, bla_TEM, bla_OXA, and bla_SHV were detected in 51, 26, 3, 1 of these isolates, respectively. Sequencing revealed that 7 bla_CTX-M subtypes were detected, with bla_CTX-M-14 being the most common, followed by bla_CTX-M-79 and bla_CTX-M-28. Of the 26 TEM-positive isolates identified, all of these were bla_TEM-1 genotypes. All isolates contained one to three large plasmids and 10 replicon types were detected. Of these, IncFrep (n = 50), IncK/B (n = 31), IncFIB (n = 26), IncB/O (n = 14), and IncI1-Ir (n = 8) replicon types were the predominating incompatibility groups. Twenty-six isolates demonstrated the ability to transfer their cefotaxime resistance marker at high transfer rates. MLST typing identified 31 sequence types and phylogenetic grouping showed that 12 of the 51 donor strains belonged to phylogroup B2.

Conclusion: This study highlights the diversity of the ESBL producing E. coli and also the diversity of ESBL genes and plasmids carrying these genes in China, which poses a threat to public health.

Antimicrobial Resistance and Molecular Epidemiology of ESBL-Producing Escherichia coli Isolated from Outpatients in Town Hospitals of Shandong Province, China

This study aimed to investigate antimicrobial resistance and molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from outpatients in town hospitals of Shandong province, China. Antimicrobial susceptibility of ESBL-producing E. coli was tested using the disk diffusion and resistance genes encoding for β-lactamases (bla_TEM, bla_CTXM, and bla_SHV) were detected by polymerase chain reaction (PCR). Multilocus sequence typing (ST) of ESBL-producing E. coli was analyzed in this study. Our results showed that of 320 E. coli isolates, 201 carried ESBL genes (201/320, 62.8%), and these isolates all carried bla_CTX-M genes, the most common being bla_CTX-M-14 (116/201, 57.7%), followed by bla_CTX-M-55 (47/201, 23.4%) and bla_CTX-M-15 (31/201, 15.4%). ESBL-producing E. coli exhibited highly resistant to penicillin derivatives, fluoroquinolones, folate pathway inhibitors, and third-generation cephalosporins, but no carbapenem-resistant isolates were found in this study. Forty-two STs were found among the 201 ESBL-producing E. coli, and the most common ST was ST131 (27/201, 13.4%), followed by ST405 (19/201, 9.5%) and ST69 (15/201, 7.5%). Taken together, a high isolation rate of ESBL-producing E. coli (62.8%) was found among outpatients in town hospitals. bla_CTX-M gene was most dominant and was composed of a variety of subtypes. No dominant ST was detected among ESBL-producing E. coli, indicating that these ESBL-producing E. coli isolates derive from different clones.

The global epidemiology of carbapenemase-producing Enterobacteriaceae

Carbapenemase-producing Enterobacteriaceae (CPE) are an important and increasing threat to global health. Both clonal spread and plasmid-mediated transmission contribute to the ongoing rise in incidence of these bacteria. Among the 4 classes of β-lactamases defined by the Ambler classification system, the carbapenemases that confer carbapenem resistance in Enterobacteriaceae belong to 3 of them: Class A (K. pneumoniae carbapenemases, KPC), Class B (metallo-β-lactamases, MBL including New Delhi metallo-β-lactamases, NDM) and Class D (OXA-48-like carbapenemases). KPC-producing CPE are the most commonly occurring CPE in the United States. MBL-producing CPE have been most commonly associated with the Indian Subcontinent as well as with specific countries in Europe, including Romania, Denmark, Spain, and Hungary. The epicenter of OXA-48-like-producing is in Turkey and surrounding countries. Detailed knowledge of the epidemiology and molecular characteristics of CPE is essential to stem the spread of these pathogens.