Diversity and biofilm-production ability among isolates of Escherichia coli phylogroup D belonging to ST69, ST393 and ST405 clonal groups

Whole-Genome Sequencing of an Escherichia coli ST69 Strain Harboring blaCTX-M-27 on a Hybrid Plasmid

Objective

Escherichia coli is a common Gram-negative human pathogen. The emergence of E. coli with multiple-antibiotic-resistant phenotypes has become a serious health concern. This study reports the whole-genome sequences of third-generation cephalosporin-resistant (3GC-R) and multidrug-resistant (MDR) E. coli EC6868 and explores the acquired antibiotic-resistance genes (ARGs) as well as their genetic contexts.

Methods

E. coli EC6868 was isolated from a vaginal secretion sample of a pregnant patient in China. The antimicrobial susceptibility was assessed, and whole-genome sequencing was conducted. The acquired ARGs, insertion sequence (IS) elements, and integrons within the genome of E. coli EC6868 were identified, and the genetic contexts associated with the ARGs were analyzed systematically.

Results

E. coli EC6868 was determined to belong to ST69 and harbored a 144.9-kb IncF plasmid (pEC6868-1) with three replicons (Col156, IncFIBAP001918, and IncFII). The ESBL gene blaCTX-M-27 was located on the structure "∆ISEcp1-blaCTX-M-27-IS903B", which was widely present in the species of Enterobacteriales. Other ARGs carried by plasmid pEC6868-1 were mainly located on the 18.9-kb IS26-composite transposon (five copies of intact IS26 and one copy of truncated IS26) composing of IS26-mphA-mrx(A)-mphR(A)-IS6100, ∆TnAs3-eamA-tet(A)-tetR(A)-aph(6)-Id-aph(3")-Ib-sul2-IS26, and a class 1 integron, which was widely present on IncF plasmids of E. coli, mainly distributed in ST131, ST38, and ST405. Notably, pEC6868 in our study was the first report on a plasmid harboring the 18.9-kb structure in E. coli ST69 in China.

Conclusion

The 3GC-R E. coli ST69 strain with an MDR IncF plasmid carrying blaCTX-M-27 and other ARGs, conferring resistance to aminoglycosides, macrolides, sulfonamides, tetracycline, and trimethoprim, was identified in a hospital in China. Mobile genetic elements including ISEcp1, IS903B, IS26, Tn3, IS6100 and class 1 integron were found within the MDR region, which could play important roles in the global dissemination of these resistance genes.

An investigation of the presence and antimicrobial susceptibility of Enterobacteriaceae in raw and cooked kibble diets for dogs in the United Kingdom

Raw meat diets (RMD) for dogs are an increasingly popular alternative pet food choice, however studies worldwide have demonstrated them to be contaminated with zoonotic and antimicrobial resistant (AMR) bacteria, including bacteria resistant to critically important antibiotics. Despite this, few data exist surrounding the presence of these bacteria in RMD in the United Kingdom. The present study aimed to identify the most commonly selected RMD and non-raw diets (NRMD) by United Kingdom dog owners. Additionally, it investigated the presence of AMR-Enterobacteriaceae in samples of pre-prepared RMD and cooked commercial kibble dog foods. An online survey investigating diet preferences of United Kingdom dog owners was open for 6 weeks between February-March 2020. From this, the top 10 brands of pre-prepared raw and cooked kibble diets were ascertained and 134 samples purchased (110 RMD, 24 kibble) and subjected to microbiological testing. Bacterial enumeration of E. coli and other Enterobacteriaceae was undertaken, and the presence of Salmonella spp. and AMR-E. coli within samples determined. Whole genome sequencing was undertaken on Salmonella spp. and third-generation cephalosporin-resistant 3GCR-E. coli isolates. Pre-prepared RMD was most commonly selected by dog owners who fed RMD, and cooked commercial complete dry food was most frequently fed by owners who fed NRMD. Damaged and leaking packaging was observed in samples of RMD, alongside variability in information provided surrounding product traceability. Counts of E. coli and other Enterobacteriaceae exceeding >5,000 CFU/g were identified in samples of RMD. AMR-, extended-spectrum beta-lactamase (ESBL)-producing and 3GCR-E. coli was isolated from 39, 14 and 16% of RMD samples, respectively. Multiple antimicrobial resistance genes were identified in 3GCR-E. coli isolates. Of the ESBL encoding genes, blaCTX-M-15 was most commonly identified. S. enterica was isolated from 5% of RMD samples. No Enterobacteriaceae were isolated from any of the cooked kibble samples. The present study suggests that pre-prepared RMD available for dogs in the United Kingdom can be contaminated with zoonotic and AMR-Enterobacteriaceae. RMDs, therefore, are potentially an important One Health concern. Veterinary and medical professionals, pet food retailers and pet owners should be aware of these risks; and stringent hygiene measures should be practiced if owners choose to feed RMD.

Biofilm Formation by Escherichia coli Isolated from Urinary Tract Infections from Aguascalientes, Mexico

Uropathogenic Escherichia coli (UPEC) strains are among the leading causes of urinary tract infections (UTIs) worldwide. They can colonize the urinary tract and form biofilms that allow bacteria to survive and persist, causing relapses of infections and life-threatening sequelae. Here, we analyzed biofilm production, antimicrobial susceptibility, virulence factors, and phylogenetic groups in 74 E. coli isolated from diagnosed patients with UTIs to describe their microbiological features and ascertain their relationship with biofilm capabilities. High levels of ceftazidime resistance are present in hospital-acquired UTIs. Isolates of multidrug resistance strains (p = 0.0017) and the yfcV gene (p = 0.0193) were higher in male patients. All the strains tested were able to form biofilms. Significant differences were found among higher optical densities (ODs) and antibiotic resistance to cefazolin (p = 0.0395), ceftazidime (p = 0.0302), and cefepime (p = 0.0420). Overall, the presence of fimH and papC coincided with strong biofilm formation by UPEC. Type 1 fimbriae (p = 0.0349), curli (p = 0.0477), and cellulose (p = 0.0253) production was significantly higher among strong biofilm formation. Our results indicated that high antibiotic resistance may be related to male infections as well as strong and moderate biofilm production. The ability of E. coli strains to produce biofilm is important for controlling urinary tract infections.

Exploring the Diversity of Biofilm Formation by the Food Spoiler Brochothrix thermosphacta

Brochothrix thermosphacta is considered as a major spoiler of meat and seafood products. This study explores the biofilm formation ability and the biofilm structural diversity of 30 multi-origin B. thermosphacta strains using a set of complementary biofilm assays (biofilm ring test, crystal violet staining, and confocal laser scanning microscopy). Two major groups corresponding to low and high biofilm producers were identified. High biofilm producers presented flat architectures characterized by high surface coverage, high cell biovolume, and high surface area.

From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat

Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.

International high-risk clone of fluoroquinolone-resistant Escherichia coli O15:H1-D-ST393 in remote communities of Brazilian Amazon

The global dissemination of multidrug-resistant Escherichia coli lineages belonging to high- risk clones poses a significant public health threat. Herein we report the identification and genomic profiling of two multidrug-resistant E. coli strains [BL-II-03(2) and BL-II-11(3)] belonging to the O15:H1-D-ST393 (clonal complex 31) worldwide spread clone, isolated from fecal samples of indigenous peoples belonging to two different ethnic groups of remote communities of Brazilian Amazon. Genomic analysis revealed genes and mutations conferring resistance to β-lactams [bla_TEM-1], aminoglycosides [aadA5, aph(3″)-Ib, aph(6)-Id], tetracyclines [tetB], sulfamethoxazole/trimethoprim [sul1, sul2, dfrA17], and fluoroquinolones [gyrA (D87N, S83L), parC (S80I, S57T), parE (L416F)]; and presence of IncQ1, IncFIA, and IncFIB(pB171) plasmids. On the other hand, phylogenomics of globally reported E. coli ST393 assigned E. coli strains BL-II-03(2) and BL-II-11(3) to a cluster comprising human isolates from Australia, Canada, China, Sweden, and United States of America. These results might provide valuable information for understanding dissemination of intercontinental multidrug-resistant clones in remote communities with low levels of antibiotic exposure.

Evaluating the antibiotic resistance and frequency of adhesion markers among Escherichia coli isolated from type 2 diabetes patients with urinary tract infection and its association with common polymorphism of mannose-binding lectin gene

The present paper aims to determine the frequency and antibiotic resistance patterns of pathogenic bacteria, the virulence factor profile of Escherichia coli and mannose-binding lectin (MBL) gene polymorphism in individuals with diabetes mellitus (DM) and urinary tract infection (UTI). The population under study was 130 individuals with type 2 diabetes mellitus (T2DM) and UTI. The patients' clinical characteristics and urine and blood samples (5 mL) were collected. Antibiotic resistance was determined using a disc diffusion method, and the results were interpreted according to CLSI. The presence of virulence genes was detected by multiplex PCR. To detect the MBL gene polymorphism, PCR and restriction fragment length polymorphism methods were applied. The predominant Gram-negative and Gram-positive bacteria included E. coli and Streptococcus spp.viridans group, respectively. Women were more susceptible to the incidence of UTI than men. The E. coli isolates showed a high level of resistance to amoxicillin-clavulanic acid (87.35%), and nitrofurantoin and ceftizoxime were the most effective antimicrobial agents for E. coli. Cefotaxime and ceftizoxime were the most effective antimicrobial agents for Enterobacter spp., norfloxacin and ciprofloxacin were the most effective antimicrobial agents for Staphylococcus epidermidis and Staphylococcus saprophyticus. papGII (52.87%) and papEF (1.14%) had the highest and lowest frequency among examined genes in E. coli isolates, respectively. The GG genotype had the highest frequency among patients with T2DM and UTI. Results showed that the detection of E. coli in individuals with an AA genotype, codon 54 of the MBL gene, can play an important role in the molecular diagnosis and timely treatment of bacterial infections in individuals with diabetes.

Biofilm Formation and Virulence Determinants of Klebsiella oxytoca Clinical Isolates from Patients with Colorectal Cancer

OBJECTIVE

Biofilm formation has made the therapy of bacterial infections more difficult. The objective our study was assessment of pan-drug-resistant (PDR) Klebsiella oxytoca pathogenicity and virulence factors causing AAHC in patients with colorectal cancer (CRC).

MATERIALS AND METHODS

Among a total of 300 healthy and 300 patients with antibiotic-associated hemorrhagic colitis (AAHC) and CRC, 200 K. oxytoca were identified during May 2015-January 2019. The virulence properties and biofilm formation among the isolates were investigated by phenotypic, PCR, and real-time PCR (RT-qPCR) techniques.

RESULTS

The bla_CTX-M1 (20%), bla_SHV (11%), bla_TEM1 (33%), and AmpC encoding CIT (2%) ESBL genes, carbapenemase-encoding genes blaIM (4%) and bla_OXA-48 (2%), and colistin-resistant mcr-1 gene (2.5%) were detected. The virulence-encoding genes including fimA (80%), pilQ (100%), matB (100%), mrkA (80%), and npsB (100%) were amplified. Therefore, PDR K. oxytoca containing adhesins and toxin-encoding genes with ability of biofilm formation causing AAHC and CRC were isolated. There was a significant difference between healthy and patients with CRC regarding the presence of K. oxytoca (p = 00.221).

CONCLUSION

Bacterial enteric pathogens possibly play a role in CRC. Biofilm formation by K. oxytoca strains prevents the efficient infection elimination; therefore, rapid identification and control measure are chief requirements. Additionally, more investigations are necessary with this regard.

Repeated Isolation of Extended-Spectrum-β-Lactamase-Positive Escherichia coli Sequence Types 648 and 131 from Community Wastewater Indicates that Sewage Systems Are Important Sources of Emerging Clones of Antibiotic-Resistant Bacteria

Antibiotic resistance in bacteria is an emerging problem globally. Resistant bacteria are found in human and animal microbiota, as well as in the environment. Wastewater receives bacteria from all these sources and thus can provide a measurement of abundance and diversity of antibiotic-resistant bacteria circulating in communities. In this study, water samples were collected from a wastewater pump station in a Norwegian suburban community over a period of 15 months. A total of 45 daily samples were cultured and analyzed for the presence of Escherichia coli Eighty E. coli-like colonies were collected from each daily sample and then phenotyped and analyzed for antibiotic resistance using the PhenePlate-AREB system. During the sampling period, two unique E. coli phenotypes with resistance to cefotaxime and cefpodoxime indicating carriage of extended-spectrum β-lactamases (ESBL) were observed repeatedly. Whole-genome sequencing of 15 representative isolates from the two phenotypes identified these as two distinct clones belonging to the two globally spread E. coli multilocus sequence types (STs) ST131 and ST648 and carrying blaCTX-M-15 The number of ESBL-positive E. coli strains in the community wastewater pump station was 314 of 3,123 (10%) analyzed E. coli strains. Of the ESBL-positive isolates, 37% belonged to ST648, and 7% belonged to ST131. Repeated findings of CTX-M-15-positive ST648 and ST131 over time indicate that these STs are resident in the analyzed wastewater systems and/or circulate abundantly in the community.

Expression of adhesin genes and biofilm formation among Klebsiella oxytoca clinical isolates from patients with antibiotic-associated haemorrhagic colitis

PURPOSE

Biofilm formation and resistance to last-line antibiotics have restricted chemotherapy options toward infection eradication.

METHODOLOGY

Fifty K. oxytoca isolates were collected from patients with antibiotic-associated haemorrhagic colitis (AAHC). Antibiotic susceptibility tests were conducted and phenotypic biofilm formation was assessed using microtitre tissue plate (MTP) assay. PCR was employed to amplify the adhesins, extended-spectrum β-lactamases (ESBLs), carbapenemase and colistin resistance genes. The expression of adhesin genes was evaluated using quantitative real-time PCR (RT-qPCR).Results/Key findings. The previous antibiotic consumption and hospitalization (P<0.05) and older ages (P=0.0033) were significantly associated with AAHC. None of the isolates produced biofilm strongly, but 70% of them produced moderate-level biofilm. The blaCTX-M (12/14), the blaIMP (8/14 MICIMI =4 µg ml^-1 ) and blaOXA-48-like (5/14) and mcr-1 (4/14) genes were predominant, three of which harbouring all the genes. The expression of matB (0.023) and mrkA (0.011) was significantly different between multidrug-resistant and susceptible isolates. Furthermore, moderately biofilm producer isolates significantly exhibited higher expression of fimA (P=.0117), pilQ (P=0.002) and mrkA (P=0.020) genes compared to biofilm non-producers. No significant difference regarding gene expression was observed among ESBL alleles.

CONCLUSION

Bacterial attachment by adhesins and biofilm formation among extensive drug-resistant K. oxytoca isolates hinder the efficient infection eradication. Hence, control and surveillance studies should be performed and other therapeutic auspicious approaches must be taken into account against AAHC, biofilm formation and drug resistance spread. Furthermore, previous antibiotic consumption and long-term hospitalization should be controlled.

Incorporation of Actinobacillus pleuropneumoniae in Preformed Biofilms by Escherichia coli Isolated From Drinking Water of Swine Farms

Actinobacillus pleuropneumoniae, the etiological agent of porcine pleuropneumonia, represents one of the most important health problems in the swine industry worldwide and it is included in the porcine respiratory disease complex. One of the bacterial survival strategies is biofilm formation, which are bacterial communities embedded in an extracellular matrix that could be attached to a living or an inert surface. Until recently, A. pleuropneumoniae was considered to be an obligate pathogen. However, recent studies have shown that A. pleuropneumoniae is present in farm drinking water. In this study, the drinking water microbial communities of Aguascalientes (Mexico) swine farms were analyzed, where the most frequent isolated bacterium was Escherichia coli. Biofilm formation was tested in vitro; producing E. coli biofilms under optimal growth conditions; subsequently, A. pleuropneumoniae serotype 1 (strains 4074 and 719) was incorporated to these biofilms. Interaction between both bacteria was evidenced, producing an increase in biofilm formation. Extracellular matrix composition of two-species biofilms was also characterized using fluorescent markers and enzyme treatments. In conclusion, results confirm that A. pleuropneumoniae is capable of integrates into biofilms formed by environmental bacteria, indicative of a possible survival strategy in the environment and a mechanism for disease dispersion.

The association of surface adhesin genes and the biofilm formation among Klebsiella oxytoca clinical isolates

Bacterial adhesins mediate the attachment and biofilm production leading to the persistence of colonized strains. The aim of this study was evaluation of the association of surface adhesin genes with the biofilm formation among Klebsiella oxytoca isolates. Among 50 isolates of K. oxytoca from patients with antibiotic-associated diarrhoea, the susceptibility test, MIC (according to CLSI 2016) and phenotypic biofilm formation (with microtitre tissue-plate assay) were performed. The presence of adhesins was investigated using PCR. Thirty-three (66%) isolates produced moderate-level biofilms, but none of them exhibited strong biofilm formation. The presence of adhesins was as follows: fimA, 60% (n = 30), mrkA, 42% (n = 21), matB, 96% (n = 48) and pilQ, 92% (n = 46). The biofilm formation was related to the presence of fimA (odds ratio (OR) 0.8571, 95% CI 1.733–6.267, p <0.0001), mrkA (OR 0.2462, 95% CI 2.723–4.622, p 0.001), matB (OR 0.4521, 95% CI 1.353–5.332, p 0.008) and pilQ (OR 0.1481, 95% CI 1.691–6.117, p <0.0001). The npsB toxin-encoding gene was detected among 46 (92%) isolates. Resistance to non-β-lactam antibiotics was significantly associated with the presence of adhesin-encoding genes. The presence of adhesins and the capsular encoding gene was significantly associated with biofilm formation among K. oxytoca isolates. The presence of surface adhesin-encoding genes was significantly associated with the biofilm formation and also with resistance to non-β-lactam antibiotics among K. oxytoca clinical isolates. In addition, biofilm production was not significantly associated with β-lactam resistance among the isolates.

First Report of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli ST405 Isolated from Wildlife in Bejaia, Algeria

BACKGROUND

The aim of the present study was to screen for the presence of mcr-1 gene in Enterobacteriaceae isolated from Barbary macaques (Macaca sylvanus) in Algeria.

MATERIALS AND METHODS

From January to April 2016, a total of 86 fresh stool samples from Barbary macaques were collected in the Toudja forest (Bejaia, Algeria). After isolation, the isolates were identified by matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. Antibiotic susceptibility was determined by disk diffusion method, and minimum inhibitory concentration (MIC) of colistin was determined by E-test. Polymerase chain reaction (PCR) and sequencing were used to identify mcr-1gene. The sequence type (ST) was done using multilocus sequence typing. Phylogenetic groups of Escherichia coli and the presence of virulence genes were determined by PCR. Transfer of mcr-1 and extended-spectrum β-lactamase genes was assessed by conjugation and transformation experiments.

RESULTS

E. coli M076 isolate was found resistant to colistin with a MIC of 4 mg/L and to other antibiotic families, including β-lactams, aminoglycosides, and fluoroquinolones. PCR and sequencing revealed that this isolate harbored the mcr-1, bla_CTX-M-15, bla_TEM-1, and qnrB19 genes. This isolate was assigned to ST405, belonged to phylogroup D, and contains only one virulence gene fyuA (siderophore uptake receptor). Neither transconjugants nor transformants were obtained for this isolate.

CONCLUSION

In this study, we report the detection of mcr-1 gene producing E. coli from wild animals.

Collaborative Research on Puerperal Infections in Bangladesh

Bangladesh is considered as a high-risk country for emerging infectious diseases because of its high population density, poverty, and unhygienic conditions. Although control efforts have primarily been focused on major infectious diseases such as diarrheal diseases, tuberculosis, malaria, and HIV infection, the prevalence and impact of many local or minor infectious diseases are still unclarified in this country. In this review, we present our recent experience and outcomes of collaborative research on puerperal infection (PI), which is a poorly defined infectious disease in Bangladesh. PI is the most common complication during the perinatal period in developing countries. We investigated the incidence of individual species of aerobic bacteria causing PIs and their drug resistance, and the genetic traits of isolates during the two-year period (2010-2012). The common species of isolates from patients with PIs were Escherichia coli, Enterococcus faecalis, Staphylococcus haemolyticus, Proteus mirabilis, Staphylococcus aureus, and Klebsiella pneumoniae. A remarkable finding was the high rates of resistance to cephalosporins among Gram-negative bacteria harboring extended-spectrum beta-lactamase genes, which were associated with carbapenem resistance in a few isolates. This study defined the importance of control of antimicrobial resistance in Bangladesh, and provided suggestions for the future direction of collaborative research on infectious diseases in Bangladesh.

Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs

Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures—including immune responses and therapeutic interventions—shape bacterial genomes. We carried out genomic and phenotypic analyses of 215 serially collected Burkholderia cenocepacia isolates from 16 cystic fibrosis patients, spanning a period of 2–20 yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest that distinct lineages follow distinct evolutionary trajectories during lung infection. Pan-genome analysis identified 10,110 homologous gene clusters present only in a subset of strains, including genes restricted to different molecular types. Our phylogenetic analysis based on 2148 orthologous gene clusters from all isolates is consistent with patient-specific clades. This suggests that initial colonization of patients was likely by individual strains, followed by subsequent diversification. Evidence of clonal lineages shared by some patients was observed, suggesting inter-patient transmission. We observed recurrent gene losses in multiple independent longitudinal series, including complete loss of Chromosome III and deletions on other chromosomes. Recurrently observed loss-of-function mutations were associated with decreases in motility and biofilm formation. Together, our study provides the first comprehensive genome-phenome analyses of B. cenocepacia infection in cystic fibrosis lungs and serves as a valuable resource for understanding the genomic and phenotypic underpinnings of bacterial evolution.

Colistin- and Carbapenem-Resistant Escherichia coli Harboring mcr-1 and blaNDM-5, Causing a Complicated Urinary Tract Infection in a Patient from the United States

Colistin is increasingly used as an antibiotic of last resort for the treatment of carbapenem-resistant Gram-negative infections. The plasmid-borne colistin resistance gene mcr-1 was initially identified in animal and clinical samples from China and subsequently reported worldwide, including in the United States. Of particular concern is the spread of mcr-1 into carbapenem-resistant bacteria, thereby creating strains that approach pan-resistance. While several reports of mcr-1 have involved carbapenem-resistant strains, no such isolates have been described in the United States. Here, we report the isolation and identification of an Escherichia coli strain harboring both mcr-1 and carbapenemase gene bla_NDM-5 from a urine sample in a patient without recent travel outside the United States. The isolate exhibited resistance to both colistin and carbapenems, but was susceptible to amikacin, aztreonam, gentamicin, nitrofurantoin, tigecycline, and trimethoprim-sulfamethoxazole. The mcr-1- and bla_NDM-5-harboring plasmids were completely sequenced and shown to be highly similar to plasmids previously reported from China. The strain in this report was first isolated in August 2014, highlighting an earlier presence of mcr-1 within the United States than previously recognized.

Colistin has become the last line of defense for the treatment of infections caused by Gram-negative bacteria resistant to multiple classes of antibiotics, in particular carbapenem-resistant Enterobacteriaceae (CRE). Resistance to colistin, encoded by the plasmid-borne gene mcr-1, was first identified in animal and clinical samples from China in November 2015 and has subsequently been reported from numerous other countries. In April 2016, mcr-1 was identified in a carbapenem-susceptible Escherichia coli strain from a clinical sample in the United States, followed by a second report from a carbapenem-susceptible E. coli strain originally isolated in May 2015. We report the isolation and identification of an E. coli strain harboring both colistin (mcr-1) and carbapenem (bla_NDM-5) resistance genes, originally isolated in August 2014 from urine of a patient with recurrent urinary tract infections. To our knowledge, this is the first report in the United States of a clinical bacterial isolate with both colistin and carbapenem resistance, highlighting the importance of active surveillance efforts for colistin- and carbapenem-resistant organisms.

Trends in ExPEC serogroups in the UK and their significance

Extra-intestinal pathogenic Escherichia coli are a significant cause of urinary tract infection and bacteraemia within the UK. We sought to identify the serogroups of 658 E. coli isolates collected in the UK between January 2011 and March 2012, to better understand the ExPEC population and understand the relevance of serogroups in this pathotype. Isolates were typed and serogroup identified using established phenotypic and molecular methods. Sixty-two serogroups were identified; 54 among urinary isolates and 35 among bloodstream isolates. However, serogroups O25, O6, and O2 dominated both infection types. These serogroups were linked to the major ExPEC STs as follows: ST131-O25, ST73-O6, ST127-O6, and ST95-O2. The serogroup data from this study have increased our understanding of the ExPEC population in the UK, but also highlighted key ST–serogroup relationships within the major ExPEC clones. These data can be used to guide vaccine design and in the development of laboratory diagnostic tests targeting the ExPEC population.

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

Escherichia coli (E. coli) is one of the most frequent and lethal causes of bloodstream infections (BSIs). We carried out a retrospective multicenter study on antimicrobial resistance and phylogenetic background of clinical E. coli isolates recovered from bloodstream in three hospitals in Shanghai. E. coli isolates causing BSIs were consecutively collected between Sept 2013 and Sept 2014. Ninety isolates randomly selected (30 from each hospital) were enrolled in the study. Antimicrobial susceptibility testing was performed by disk diffusion. PCR was used to detect antimicrobial resistance genes coding for β-lactamases (TEM, CTX-M, OXA, etc.), carbapenemases (IMP, VIM, KPC, NDM-1 and OXA-48), and phylogenetic groups. eBURST was applied for analysis of multi-locus sequence typing (MLST). The resistance rates for penicillins, second-generation cephalosporins, fluoroquinolone and tetracyclines were high (>60%). Sixty-one of the 90 (67.8%) strains enrolled produced ESBLs and no carbapenemases were found. Molecular analysis showed that CTX-M-15 (25/61), CTX-M-14 (18/61) and CTX-M-55 (9/61) were the most common ESBLs. Phylogenetic group B2 predominated (43.3%) and exhibited the highest rates of ESBLs production. ST131 (20/90) was the most common sequence type and almost assigned to phylogenetic group B2 (19/20). The following sequence types were ST405 (8/90) and ST69 (5/90). Among 61 ESBL-producers isolates, B2 (26, 42.6%) and ST131 (18, 29.5%) were also the most common phylogenetic group and sequence type. Genetic diversity showed no evidence suggesting a spread of these antimicrobial resistant isolates in the three hospitals. In order to provide more comprehensive and reliable epidemiological information for preventing further dissemination, well-designed and continuous surveillance with more hospitals participating was important.

Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanghai, China, 2011-2013

BACKGROUND

Prevention and management of Escherichia coli bloodstream infections (EC-BSIs) have become increasingly complicated by antimicrobial resistance and rapid dissemination. We investigated the antimicrobial epidemiology and phylogenetic background of clinical E. coli isolates from patients with bloodstream infections in Shanghai from 2011 to 2013.

METHODS

Escherichia coli isolates causing bloodstream infections were consecutively collected between June 2011 and June 2013. Antimicrobial susceptibility testing was performed by disk diffusion. Drug resistance genes coding for extended-spectrum β-lactamases (ESBLs) and carbapenemases, and phylogenetic groups were detected by polymerase chain reaction. eBURST was used for multilocus sequence typing.

RESULTS

Of the strains 128 collected, 80 produced ESBLs. No carbapenem-resistant isolates were found. The resistance rates to penicillins, fluoroquinolone, folate pathway inhibitors, tetracyclines and second generation cephalosporins were high. Molecular analysis showed that CTX-M-14 (40/80) was the most common β-lactamase, followed by CTX-M-55 (17/80) and CTX-M-15 (14/80). Phylogenetic group B2 predominated (37.5%), but phylogenetic group D exhibited the highest rates of ESBL production. ST131 (17/128) was the most common sequence type, followed by ST69 (12/128) and ST648 (10/128).

CONCLUSIONS

The antimicrobial resistance rate was high among EC-BSI isolates, but amikacin, piperacillin-tazobactam and carbapenem could be options for empiric therapy. Genetic diversity showed no correlation with the nosocomial origin of the isolates.

Drug resistance and molecular epidemiology of aerobic bacteria isolated from puerperal infections in Bangladesh

Puerperal infection is a common complication during postnatal period in developing countries. Bacterial species, drug resistance, and genetic characteristics were investigated for a total of 470 isolates from puerperal infections in Bangladesh for a 2-year period (2010-2012). The most common species was Escherichia coli (n=98), followed by Enterococcus faecalis (n=54), Staphylococcus haemolyticus (n=33), Proteus mirabilis (n=32), Staphylococcus aureus (n=27), Klebsiella pneumoniae (n=22), and Enterobacter cloacae (n=21). S. aureus and Acinetobacter baumannii were isolated at a higher frequency from wound infections after cesarean section, while E. coli, E. cloacae, and K. pneumoniae were isolated from community-acquired endometritis and urinary tract infections. Resistance to third-generation cephalosporins was frequent for Enterobacteriacae, and was mainly mediated by blaCTX-M-1 group beta-lactamases. The CTX-M gene in E. coli from the four phylogroups was identified as blaCTX-M-15, and phylogroup B2 isolates with blaCTX-M-15 were classified into ST131 with O25b allele, harboring aac(6')-Ib-cr and various virulence factors. Carbapenemase genes blaNDM-1 and blaNDM-7 were identified in one isolate each of phylogroup A E. coli. Methicillin-resistant S. aureus isolates had type IV or V SCCmec, including isolates of ST361 (CC672), which is related to an emerging ST672 clone in the Indian subcontinent. This study revealed the recent epidemiological status of aerobic bacteria causing puerperal infections in Bangladesh, providing useful information to improve clinical practice and infection control.

Biofilm-based infections in long-term care facilities

The recent trend in the early admittance to long-term care facilities (LTCFs) of severely injured patients transferred from general hospitals has given a new dynamic to the incidence of healthcare-associated infections, including biofilm-based infections related to the implant of urinary and intravascular catheters, and the onset of pressure ulcers. Catheter-associated urinary tract infections lead in most of the surveys on LTCFs, approximately 80% of urinary tract infections in these settings being due to the short- or long-term insertion of a urinary catheter. Furthermore, the implantation of intravascular catheters is often responsible for catheter-related bloodstream infections caused by the development of an intraluminal biofilm. Pressure ulcers, frequently occurring in bedridden patients admitted to LTCFs, are also susceptible to infection by biofilm-growing aerobic and anaerobic bacteria, the biofilm formation on the wound being the main reason for its delayed healing.

Identification of a New Delhi metallo-β-lactamase-4 (NDM-4)-producing Escherichia coli in Italy

BACKGROUND

During June-July 2012, six imipenem-resistant Escherichia coli isolates were isolated from two patients hospitalized in a ward of one large tertiary-care hospital in Genoa, Italy. Genetic features associated with blaNDM-4 gene were investigated.

RESULTS

The isolates exhibited the same PFGE profile and a multidrug-resistant (MDR) phenotype to aminoglycosides, fluoroquinolones, and β-lactams. The strains produced the NDM-4 carbapenemase and the blaNDM-4 gene was part of the variable region of a class 1 integron. MLST analysis revealed that all isolates belonged to sequence type 405 (ST405).

CONCLUSIONS

This is the first report on the emergence of an MDR strain of E.coli producing the NDM-4 MBL in Italy.

MALDI-TOF mass spectrometry as a tool for the discrimination of high-risk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393)

Reliable, quick and low-cost methods are needed for the early detection of multidrug-resistant and highly virulent high-risk B2 and D Escherichia coli clones or clonal complexes (HiRCC). Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) seems to have a good discriminatory potential at different subspecies levels, but it was never evaluated for the discrimination of E. coli clones. We assessed the potential of MALDI-TOF MS coupled to multivariate data analysis to discriminate representative E. coli B2 and D HiRCC. Seventy-three E. coli isolates from B2 (including ST131 and B2 non-ST131 clones) and D (ST69, ST393, ST405) with variable pulsed-field gel electrophoresis (PFGE) patterns, origins and dates (1980-2010) were tested. MS spectra were acquired from independent extracts obtained from different plate cultures in two different Microflex LT MALDI-TOF devices (Bruker) after a standard extraction procedure. MALDI-TOF MS fingerprinting analysis revealed a good discriminatory ability between the four HiRCC analysed (ST131, ST69, ST405, ST393) and between B2 ST131 and other B2 non-ST131 isolates. Clusters defined by MALDI-TOF MS were consistent with the clonal complexes assigned by multilocus sequence typing (MLST), although differences were detected regarding the composition of clusters obtained by the comparison of PFGE profiles. We demonstrate, for the first time, that characteristic mass fingerprints of different E. coli HiRCC are sufficiently discriminatory and robust to enable their differentiation by MALDI-TOF MS, which might represent a promising tool for the optimisation of infection control, individual patient management and large-scale epidemiological studies of public health relevance. The good correlation between phenotypic and genotypic features further corroborates phylogenetic relationships delineated by MLST.

Field emission scanning electron microscopy of biofilm-growing bacteria involved in nosocomial infections

Scanning electron microscopy (SEM) provides useful information on the shape, size, and localization within the biofilm of single bacteria as well as on the steps of biofilm formation process, on bacterial interactions, and on production of extracellular polymeric substances.When biofilms are constituted by microbial species involved in health care-associated infections, information provided by SEM can be fruitfully used not only for basic researches but also for diagnostic purposes.The protocols currently used in our laboratory for biofilm investigation by SEM are reported here. Particularly, the procedures to fix, dehydrate, and metalize in vitro-developed biofilms or ex vivo clinical specimens colonized by biofilm-growing microorganisms are described as well as the advantages of the observation of these samples by field emission scanning electron microscopy.

Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy

We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from B2(n = 9) and D(n = 13) phylogenetic groups. Eighty-eight E. coli isolates belonging to phylogenetic groups B2(n = 39) and D(n = 49), including particularly widespread high risk clones or clonal complexes (HiRCC) ST131, ST69, ST393 and ST405 were studied. Spectra were analysed by unsupervised (hierarchical cluster analysis-HCA) and supervised methods (soft independent modelling of class analogy-SIMCA and partial least square discriminant analysis-PLSDA). B2-ST131 isolates were discriminated from B2 non-ST131 and D phylogroup isolates (ST69, ST393, ST405) by HCA, SIMCA and PLSDA. D-ST69, D-ST393 and D-ST405 isolates were also distinguished from each other and from other STs from phylogroup D by the three methods. We demonstrate that FTIR-ATR coupled with chemometrics is a reliable and alternative method to accurately discriminate particular E. coli clones. Its validation towards an application at a routine basis could revolutionize high-throughput bacterial typing.

Microbiological quality of ready-to-eat salads: an underestimated vehicle of bacteria and clinically relevant antibiotic resistance genes

The increase demand for fresh vegetables is causing an expansion of the market for minimally processed vegetables along with new recognized food safety problems. To gain further insight on this topic we analyzed the microbiological quality of Portuguese ready-to-eat salads (RTS) and their role in the spread of bacteria carrying acquired antibiotic resistance genes, food products scarcely considered in surveillance studies. A total of 50 RTS (7 brands; split or mixed leaves, carrot, corn) were collected in 5 national supermarket chains in Porto region (2010). They were tested for aerobic mesophilic counts, coliforms and Escherichia coli counts as well as for the presence of Salmonella and Listeria monocytogenes. Samples were also plated in different selective media with/without antibiotics before and after enrichment. The E. coli, other coliforms and Enterococcus recovered were characterized for antibiotic resistance profiles and clonality with phenotypic and genetic approaches. A high number of RTS presented poor microbiological quality (86%--aerobic mesophilic counts, 74%--coliforms, 4%--E. coli), despite the absence of screened pathogens. In addition, a high diversity of bacteria (species and clones) and antibiotic resistance backgrounds (phenotypes and genotypes) were observed, mostly with enrichment and antibiotic selective media. E. coli was detected in 13 samples (n=78; all types and 4 brands; phylogenetic groups A, B1 and D; none STEC) with resistance to tetracycline [72%; tet(A) and/or tet(B)], streptomycin (58%; aadA and/or strA-strB), sulfamethoxazole (50%; sul1 and/or sul2), trimethoprim (50%; dfrA1 or dfrA12), ampicillin (49%; blaTEM), nalidixic acid (36%), ciprofloxacin (5%) or chloramphenicol (3%; catA). E. coli clones, including the widespread group D/ST69, were detected in different samples from the same brand or different brands pointing out to a potential cross-contamination. Other clinically relevant resistance genes were detected in 2 Raoultella terrigena carrying a bla(SHV-2) and 1 Citrobacter freundii isolate with a qnrB9 gene. Among Enterococcus (n=108; 35 samples; Enterococcus casseliflavus--40, Enterococcus faecalis--20, Enterococcus faecium--18, Enterococcus hirae--9, Enterococcus gallinarum--5, and Enterococcus spp.--16) resistance was detected for tetracyclines [6%; tet(M) and/or tet(L)], erythromycin [3%; erm(B)], nitrofurantoin (1%) or ciprofloxacin (1%). The present study places ready-to-eat salads within the spectrum of ecological niches that may be vehicles for antibiotic resistance bacteria/genes with clinical interest (e.g. E. coli-D-ST69; bla(SHV-2)) and these findings are worthy of attention as their spread to humans by ingestion cannot be dismissed.

Antibiotic resistance shaping multi-level population biology of bacteria

Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.