Rapid and simple detection of blaCTX-M genes by multiplex PCR assay

Plasmid-mediated acquisition and chromosomal integration of blaCTX-M-14 in a subclade of Escherichia coli ST131-H30 clade C1

Escherichia coli ST131 is a multidrug-resistant lineage associated with the global spread of extended-spectrum β-lactamase-producing organisms. Particularly, ST131 clade C1 is the most predominant clade in Japan, harboring blaCTX-M-14 at a high frequency. However, the process of resistance gene acquisition and spread remains unclear. Here, we performed whole-genome sequencing of 19 E. coli strains belonging to 12 STs and 12 fimH types collected between 1997 and 2016. Additionally, we analyzed the full-length genome sequences of 96 ST131-H30 clade C0 and C1 strains, including those obtained from this study and those registered in public databases, to understand how ST131 clade C1 acquired and spread blaCTX-M-14. We detected conjugative IncFII plasmids and IncB/O/K/Z plasmids carrying blaCTX-M-14 in diverse genetic lineages of E. coli strains from the 1990s to the 2010s, suggesting that these plasmids played an important role in the spread of blaCTX-M-14. Molecular phylogenetic and molecular clock analyses of the 96 ST131-H30 clade C0 and C1 strains identified 8 subclades. Strains harboring blaCTX-M-14 were clustered in subclades 4 and 5, and it was inferred that clade C1 acquired blaCTX-M-14 around 1993. All 34 strains belonging to subclade 5 possessed blaCTX-M-14 with ISEcp1 upstream at the same chromosomal position, indicating their common ancestor acquired blaCTX-M-14 in a single ISEcp1-mediated transposition event during the early formation of the subclade around 1999. Therefore, both the horizontal transfer of plasmids carrying blaCTX-M-14 to diverse genetic lineages and chromosomal integration in the predominant genetic lineage have contributed to the spread of blaCTX-M-14.

Epidemiological analysis and antimicrobial susceptibility profile of Gram-negative bacilli that cause bacteremia in Japan

We investigated the epidemiology and antimicrobial susceptibility profiles of seven major Gram-negative bacilli (Escherichia coli, Klebsiella spp., Enterobacter spp., Pseudomonas aeruginosa, Acinetobacter spp., Stenotrophomonas maltophilia, and Bacteroides spp.) that caused bacteremia in Japan. We collected clinical information and isolates from patients aged 20 years or older who developed bacteremia during a year at three Japanese university hospitals and performed microbiological examination. In total, 628 cases were included, half of which were caused by E. coli (315 isolates). P. aeruginosa (56 isolates) was isolated most frequently among non-fermenting bacteria and 33 Bacteroides spp. were isolated. Mortality rates were the highest for P. aeruginosa (7-day, 16.1%; 30-day, 26.8%). The 7- and 30-day mortality rates ranged 3.8-9.0% and 8.3-17.6%, respectively, for Enterobacterales, and they were 15.2% each for Bacteroides spp. Regarding antimicrobial resistance, Enterobacterales and Acinetobacter spp. showed susceptibility to carbapenems and amikacin (98.0-100.0%). The susceptibility rates to ceftolozane/tazobactam ranged 82.4-99.0% for Enterobacterales and 92.9% for P. aeruginosa. More than 30.0% of E. coli isolates were resistant to fluoroquinolone. Extended-spectrum β-lactamase (ESBL) producers were found in 21.0% of E. coli and approximately 80% of those were resistant to fluoroquinolones. The susceptibility of the 33 Bacteroides spp. to carbapenems, ampicillin/sulbactam, and piperacillin/tazobactam was 100.0%. Among the ESBL producers, blaCTX-M group 9 was the major subgroup in E. coli (77.3%), and blaCTX-M group 1 was detected in 18.2% of E. coli and 50.0% of Klebsiella spp. Continuous surveillance is needed to understand the epidemiology and consider appropriate therapeutic strategies.

Prevalence, clonal diversity, and antimicrobial resistance of hypervirulent Klebsiella pneumoniae and Klebsiella variicola clinical isolates in northern Japan

OBJECTIVES

Hypervirulent Klebsiella pneumoniae (hvKp) and Klebsiella variicola (hvKv) cause hospital/community-acquired infections, often associated with antimicrobial resistance (AMR). This study aimed to investigate the molecular epidemiology of hvKp and hvKv in northern Japan.

METHODS

A total of 500 K. pneumoniae and 421 K. variicola clinical isolates collected from August to December 2021 were studied. Prevalence of virulence factor-encoding genes, wzi sequence and associated K/KL type, sequence type (ST), and beta-lactamases and their types were characterized.

RESULTS

Any virulence gene (rmpA, rmpA2, peg-344, iucA, iutA, and iroB) and/or magA was detected in 25% (n = 125) of K. pneumoniae and 1% (n = 5) of K. variicola. Among these hvKp/hvKv, 22 wzi types (18 and 4 types, respectively) and 24 STs (20 and 4 STs, respectively) were identified. Sequence types of hvKp were classified into some clonal groups (CGs), among which CG35, including six STs, was the most common (n = 59; 47%), followed by CG23, and CG65. ST268 (CG35) associated with wzi95-K20 or wzi720 was the dominant lineage (n = 43, 34%), while K1:ST23/ST249 and K2:ST65/ST86 accounted for 26% and 13% of hvKp, respectively. Extended-spectrum beta-lactamase (ESBL) genes (blaCTX-M-2, blaCTX-M-3, blaCTX-M-15, and blaCTX-M-27) were detected in only ST23 and CG35 (ST268 and ST412) hvKp. No isolate was resistant to carbapenems, without detection of the ESBL gene in K. variicola. Phylogenetically, wzi was differentiated into two main clusters of K. pneumoniae and K. variicola. A major clonal group CG347 was identified in K. variicola.

CONCLUSION

Clonal structures were revealed for hvKp and hvKv clinical isolates with their AMR status in northern Japan.

Antimicrobial resistance of Salmonella Indiana from retail chickens in China and emergence of an mcr-1-harboring isolate with concurrent resistance to ciprofloxacin, cefotaxime, and colistin

Salmonella enterica serotype Indiana (S. Indiana) in Chinese poultry meat has aroused widespread concern because of its high prevalence and strong antimicrobial resistance. In consideration of the relationship in our previous study between S. Indiana and co-resistance to ciprofloxacin and cefotaxime (CIP-CTX), which were the first-line drug which were used in Salmonella infection in clinical, the antimicrobial resistance (AMR) of 224 CIP-CTX co-resistant S. Indiana isolated from retail chicken samples in China were investigated, with the aim of characterizing the AMR profiles and related resistance mechanisms to ciprofloxacin and cefotaxime among these CIP-CTX co-resistant S. Indiana isolates, all of which showed multi-drug-resistant (MDR) phenotypes. GyrA (S83F and D87N/G) with ParC (T57S and S80R) were the dominant amino acid substitution types, with oqxA, oqxB, and aac (6′)-Ib-cr identified as common plasmid-mediated quinolone resistance (PMQR)-encoding genes. Five bla_CTX-M gene subtypes were identified with bla_CTX-M-65 ranking at the top. Equally important, we obtained one isolate CFSA664 harboring the mcr-1 gene was ESBL producer with co-resistance to nine in ten classes of tested drugs inclduing colistin. A single circular chromosome and 3 circular plasmids were found in its genome. Among the 26 AMR genes identified, 24 were located on plasmid pCFSA664-1, including three ESBL genes, while plasmid pCFSA664-3 owning only the mcr-1 gene and sharing the same backbone structure with plasmids from Enterobacteriaceae. No insertion sequences were found near the mcr-1 gene but a relaxase-encoding gene in the flank, which could transfer into E. coli J53 at a relatively high frequency. S. Indiana in this study exhibited highly drug-resistant phenotypes, contributing to the acceleration of the dissemination and emergence of this pathogen among different sources. Surveillance and a One Health strategy are needed to limit the emergence of S. Indiana along the food chain.

Dissemination of Multiple Drug-Resistant Shigella flexneri 2a Isolates Among Pediatric Outpatients in Urumqi, China

Multiple drug-resistant (MDR) Shigella isolates have been reported worldwide. Between May 2017 and September 2018, 55 Shigella flexneri 2a isolates were collected from 3322 stool samples of 0-10-year-old outpatients with diarrhea at the Children's Hospital of Urumqi, China. All isolates were characterized using serotyping, antimicrobial susceptibility testing, and whole-genome sequencing. A total of 54 of 55 (98.2%) isolates exhibited MDR phenotypes and had accumulated multiple resistance determinants, particularly of fluoroquinolones and cephalosporins preferred for shigellosis treatment: point mutations in quinolone resistance-determining regions (QRDRs) of topoisomerases (GyrA (S83L, D87N) and ParC (S80I) [n = 9]; GyrA (S83L) and ParC (S80I) [n = 45]) and acquisition of qnrS1 (n = 3) and bla_CTX-M (n = 8). Over 70% of isolates acquired two point mutations of GyrA (S83L) and ParC (S80I) in QRDRs and 11 highly resistant isolates accumulated three point mutations in QRDRs or acquired qnrS1. Four S. flexneri 2a isolates from three single-nucleotide polymorphism clusters exhibited coresistance to ciprofloxacin, cefotaxime, or azithromycin (AZM), which are used as first- and second-line shigellosis treatment antimicrobials in clinics. Our data indicated that fluoroquinolones should be terminated in shigellosis treatment for outpatients in Urumqi. The transferable antimicrobial resistance determinants have been identified for third-generation cephalosporins and AZM. Novel strategies are urgently required for developing empirical medication to reduce the antimicrobial selective pressure and prevent dissemination of MDR S. flexneri 2a isolates.

Prevalence and Profiles of Antibiotic Resistance Genes mph(A) and qnrB in Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli Isolated from Dairy Calf Feces

The use of antibiotics to treat dairy calves may result in multidrug-resistant extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. This study investigated fluoroquinolone and macrolide resistance genes among ESBL-producing E. coli isolated from dairy calves. Fresh fecal samples from 147 dairy calves across three age groups were enriched to select for ESBL-producing E. coli. Plasmid-mediated fluoroquinolone (qnrB), macrolide (mph(A)), and beta-lactam (bla_CTX-M groups 1 and 9) resistance genes were identified by PCR and gel electrophoresis in ESBL-producing E. coli. Beta-lactamase variants and antibiotic resistance genes were characterized for eight isolates by whole-genome sequencing. Seventy-one (48.3%) samples were positive for ESBL-producing E. coli, with 159 (70.4%) isolates identified as bla_CTX-M variant group 1 and 67 (29.6%) isolates as bla_CTX-M variant group 9. Resistance gene mph(A) was more commonly associated with bla_CTX-M variant group 1, while resistance gene qnrB was more commonly associated with variant group 9. E. coli growth was quantified on antibiotic media for 30 samples: 10 from each age group. Significantly higher quantities of ceftriaxone-resistant E. coli were present in the youngest calves. Results indicate the dominant bla_CTX-M groups present in ESBL-producing E. coli may be associated with additional qnrB or mph(A) resistance genes and ESBL-producing E. coli is found in higher abundance in younger calves.

Case report of enterobacter hormaechei in sheep with respiratory disease and death

Background

Enterobacter hormaechei is typically a opportunistic pathogenic bacterium in humans, and no pathological change of of Enterobacter hormaechei in diseased sheep has previously been documented.

Case presentation

Three free-range, four-month-old female sheep were ill with respiratory disease and died three days after receiving treatment with ceftiofur sodium. A frozen lung sample of one sheep was studied using bacterium isolation, and lung samples of the other two sheep were collected and analyzed by histopathological examination and bacterium isolation. The 16S rRNA gene sequences and biochemical characteristics of the isolates were analyzed. All results showed the isolated strain to be Enterobacter hormaechei. Phylogenetic analysis of the 16S rRNA sequence showed three representative strains were most closely related to the strains isolated from calf. Antimicrobial sensitivity tests indicated that no sensitivity to the β-lactam antimicrobials involved in treatment of sheep respiratory disease in China. Detection of the genes responsible for β-lactam resistance showed that all three isolates from sheep harbor bla_SHV and bla_KPC. Interstitial pneumonia, bronchial epithelial cells shedding, and massive mucous secretion were observed in the lung histopathological sections. Immunohistochemical staining showed that specific staining was mainly limited to the alveoli and alveolar septum.

Conclusions

This appears to be the first report of pathological changes in lungs of sheep with respiratory disease and death associated with Enterobacter hormaechei.

Studies on molecular epidemiology of ESβL-producing Klebsiella pneumoniae isolated from patients hospitalized in a specialist hospital in southern Poland

Introduction. Extended-spectrum β-lactamase (ESβL)-producing Klebsiella pneumoniae is currently one of the most common causes of nosocomial infections worldwide. The study aimed to characterize antibiotic resistance profile, the prevalence of selected genes encoding ESβLs, virulence, and the genetic relationship in 139 K. pneumoniae isolates identified in John Paul II Specialist Hospital in Southern Poland, collected in 2016.

Materials/Methods. Bacterial identification and the preliminary antibiotic susceptibilities was performed using the VI-TEK® 2 Compact automated system. Genes encoding ESβLs were amplified by CTX-Mplex PCR and PCR reactions. The presence of nine genes encoding virulence factors was studied by multiplex PCR. Clonality was investigated by PFGE after digestion with SpeI endonuclease.

Results. K. pneumoniae were mostly recovered from the respiratory tract (40.3%), urine (32.4%), wound swabs (19.4%) and blood (5%). In summary, 82.7% of strains were classified as multidrug resistant (MDR). All isolates were confirmed as ESβL producers and carried bla CTX-M-type (85.6%), bla SHV (82%), bla TEM (77.7%), bla CTX-M-9 (75.6%) and bla CTX-M-1 (1.4%) in various combinations. Moreover, triple bla genes were observed in 72% of isolates. The most common virulence-as-sociated genes found among the isolates were entB (91.4%), ybtS (55.4%), iutA (55.4%), magA (53.2%), kfu (14.4%), K2 (11.5%), mrkD (10.1%), rmpA (7.9%) and allS (5%). The PFGE analysis identified 4 major clusters (A–D) comprising 61% of the entire collection.

Conclusions. Our results indicate that the presence of a wide variety of MDR K. pneumoniae harbor ESβLs and virulence genes. Studies on molecular epidemiology of ESβL-producing K. pneumoniae isolates are needed, particularly for epidemiological surveillance in the hospital environment.

Biofilm Formation of Clinical Klebsiella pneumoniae Strains Isolated from Tracheostomy Tubes and Their Association with Antimicrobial Resistance, Virulence and Genetic Diversity

(1) Background: Due to the commonness of tracheotomy procedures and the wide use of biomaterials in the form of tracheostomy tubes (TTs), the problem of biomaterial-associated infections (BAIs) is growing. Bacterial colonization of TTs results in the development of biofilms on the surface of biomaterials, which may contribute to the development of invasive infections in tracheostomized patients. (2) Methods: Clinical strains of K. pneumoniae, isolated from TTs, were characterized according to their ability to form biofilms, as well as their resistance to antibiotics, whether they harbored ESβL genes, the presence of selected virulence factors and genetic diversity. (3) Results: From 53 patients, K. pneumoniae were detected in 18 of the TTs examined, which constituted 34% of all analyzed biomaterials. Three of the strains (11%) were ESβL producers and all had genes encoding CTX-M-1, SHV and TEM enzymes. 44.4% of isolates were biofilm formers, SEM demonstrating that K. pneumoniae formed differential biofilms on the surface of polyethylene (PE) and polyvinyl chloride (PVC) TTs in vitro. A large range of variation in the share of fimbrial genes was observed. PFGE revealed sixteen genetically distinct profiles. (4) Conclusions: Proven susceptibility of TT biomaterials to colonization by K. pneumoniae means that the attention of research groups should be focused on achieving a better understanding of the bacterial pathogens that form biofilms on the surfaces of TTs. In addition, research efforts should be directed at the development of new biomaterials or the modification of existing materials, in order to prevent bacterial adhesion to their surfaces.

High β-Lactam and Quinolone Resistance of Enterobacteriaceae from the Respiratory Tract of Sheep and Goat with Respiratory Disease

During the last decade's increase of antimicrobial resistance (AMR) in animals, animal-human transmission has become a major threat. Therefore, the present study aimed to evaluate the genetic basis of AMR in Gram-negative bacteria recovered from sheep and goats with respiratory disease. Nasal and ocular swabs were collected from 69 diseased animals, and 76 Gram-negative bacterial isolates were identified from 59 animals. All isolates were checked phenotypically for resistance and genotypically for different resistance mechanisms, including β-lactam, quinolone, and aminoglycoside resistance. Our results demonstrated that 9.2% (95% CI 4.5-17.8%) of the isolates were multidrug-resistant, with high resistance rates to β-lactams and quinolones, and 11.8% (95% CI 6.4-21%) and 6.6% (95% CI 2.8-14.5%) of the isolates were phenotypically positive for AmpC and ESBL, respectively. Genotypically, blaTEM was the most identified β-lactamase encoding gene in 29% (95% CI 20-40%) of the isolates, followed by blaSHV (14.5%, 95% CI 8.3-24.1%) and blaCTX-M (4%, 95% CI 1.4-11%). Furthermore, 7.9% (95% CI 3.7-16.2%) of the isolates harbored plasmid-mediated quinolone resistance gene qnrS. Our study revealed for the first time to our knowledge high β-lactam and quinolone resistance associated with the bacteria recovered from sheep and one goat with respiratory disease. Furthermore, different antimicrobial resistant determinants were identified for the first time from animals in Africa, such as blaLEN-13/55, blaTEM-176 and blaTEM-198/214. This study highlights the potential role of sheep and goats in disseminating AMR determinants and/or resistant bacteria to humans. The study regenerates interest for the development of a One Health approach to combat this formidable problem.

Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand

Nontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005–2007 to 11.2% (18/161) during 2014–2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and bla_CTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with bla_CTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.

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

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

Clonal Dissemination of KPC-2, VIM-1, OXA-48-Producing Klebsiella pneumoniae ST147 in Katowice, Poland

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important bacterium of nosocomial infections. In this study, CRKP strains, which were mainly isolated from fecal samples of 14 patients in three wards of the hospital in the Silesia Voivodship, rapidly increased from February to August 2018. Therefore, we conducted microbiological and molecular studies of the CRKP isolates analyzed. Colonized patients had critical underlying diseases and comorbidities; one developed bloodstream infection, and five died (33.3%). Antibiotic susceptibilities were determined by the E-test method. A disc synergy test confirmed carbapenemase production. CTX-Mplex PCR evaluated the presence of resistance genes bla_CTX-M-type, bla_CTX-M-1, bla_CTX-M-9, and the genes bla_SHV, bla_TEM, bla_KPC-2, bla_NDM-1, bla_OXA-48, bla_IMP, and bla_VIM-1 was detected with the PCR method. Clonality was evaluated by Multi Locus Sequence Typing (MLST) and Pulsed Field Gel Electrophoresis (PFGE). Six (40%) strains were of XDR (Extensively Drug-Resistant) phenotype, and nine (60%) of the isolates exhibited MDR (Multidrug-Resistant) phenotype. The range of carbapenem minimal inhibitory concentrations (MICs, μg/mL) was as follows doripenem (16 to >32), ertapenem (> 32), imipenem (4 to > 32), and meropenem (> 32). PCR and sequencing confirmed the bla_CTX-M-15, bla_KPC-2, bla_OXA-48, and bla_VIM-1 genes in all strains. The isolates formed one large PFGE cluster (clone A). MLST assigned them to the emerging high-risk clone of ST147 (CC147) pandemic lineage harboring the bla_OXA-48 gene. This study showed that the K. pneumoniae isolates detected in the multi-profile medical centre in Katowice represented a single strain of the microorganism spreading in the hospital environment.

High β-lactam resistance in Gram-negative bacteria associated with kennel cough and cat flu in Egypt

Antimicrobial resistance within pets has gained worldwide attention due to pets close contact with humans. This report examined at the molecular level, the antimicrobial resistance mechanisms associated with kennel cough and cat flu. 1378 pets in total were assessed for signs of respiratory infection, and nasal and conjunctival swabs were collected across 76 diseased animals. Phenotypically, 27% of the isolates were characterized by multidrug resistance and possessed high levels of resistance rates to β-lactams. Phenotypic ESBLs/AmpCs production were identified within 40.5% and 24.3% of the isolates, respectively. Genotypically, ESBL- and AmpC-encoding genes were detected in 33.8% and 10.8% of the isolates, respectively, with bla_SHV comprising the most identified ESBL, and bla_CMY and bla_ACT present as the AmpC with the highest levels. qnr genes were identified in 64.9% of the isolates, with qnrS being the most prevalent (44.6%). Several antimicrobial resistance determinants were detected for the first time within pets from Africa, including bla_CTX-M-37, bla_CTX-M-156, bla_SHV-11, bla_ACT-23, bla_ACT25/31, bla_DHA-1, and bla_CMY-169. Our results revealed that pets displaying symptoms of respiratory illness are potential sources for pathogenic microbes possessing unique resistance mechanisms which could be disseminated to humans, thus leading to the development of severe untreatable infections in these hosts.

Molecular Characterization of Cephalosporin-Resistant Salmonella Enteritidis ST11 Isolates Carrying blaCTX-M from Children with Diarrhea

Salmonella Enteritidis is an important foodborne pathogen with high prevalence of resistance to cephalosporins, imposing a serious threat to public health. Therefore, a total of 162 Salmonella Enteritidis isolates collected from child patients in China from 2007 to 2017 were characterized for their resistance to cephalosporins and investigated the transmission characteristics of cephalosporin resistance gene. We found that 15 (9.26%) isolates were all resistant to cefalotin (minimum inhibitory concentration [MIC] ≥512 μg/mL), ceftazidime (MIC 16-128 μg/mL), ceftriaxone (MIC 64 to ≥512 μg/mL), ceftiofur (MIC 64-256 μg/mL), and cefotaxime (MIC 64 to ≥512 μg/mL) with the possession of cephalosporin resistance genes bla_CTX-M-55 (n = 13), bla_CTX-M-101 (n = 1), and bla_CTX-M-153 (n = 1). Molecular typing further revealed that these 15 isolates belonged to sequence type ST11 and shared close pulsed-field gel electrophoresis patterns, suggesting the possibility of clonal spread in Salmonella Enteritidis interspecies. Furthermore, conjugation experiments were successfully performed in 13 of 15 isolates, and bla_CTX-M-55 was present on conjugative plasmids with sizes ranging from 54.7 to 173.4 kb. Compared with recipient Escherichia coli C600, transconjugants conferred elevated MICs for cephalosporins ranging from 2- to 2048-fold. The genetic structure surrounding of bla_CTX-M-55 gene in transconjugants were ΔISEcp1-bla_CTX-M-55-orf477 (n = 8) and ISEcp1-bla_CTX-M-55-orf477 (n = 3), respectively. Taken together, bla_CTX-M on the plasmids might contribute to cephalosporin resistance in Salmonella Enteritidis, and conjugative transfer of bla_CTX-M-55 might facilitate the spread of cephalosporin resistance in Salmonella Enteritidis. Hence, effective mitigation measurements are needed to reduce the threat caused by cephalosporin-resistant Salmonella Enteritidis to public health.

Genetic characterization of coliform bacterial isolates from environmental water in Thailand

INTRODUCTION

In contrast to the study in other part of the world, information about characteristics of plasmids carrying antimicrobial resistance genes (ARGs) in Enterobacteriaceae derived from environmental water in tropical Asian countries including Thailand is limited. This study, therefore, aimed to gain insight into genetic information of antimicrobial resistance in environmental water in Thailand.

METHODS

Coliform bacteria were isolated from environmental water collected at 20 locations in Thailand and identified. Then, susceptibility profiles to ampicillin, cefazoline, cefotaxime, kanamycin, ciprofloxacin, sulfamethoxazole, tetracycline, and nalidixic acid were assessed. In addition, antimicrobial resistant genes integrons, and replicon types were analyzed. And furthermore, plasmids carrying bla_TEM and tetM were identified by S1-PFGE analysis and confirmed transmissibility by transconjugation experiments.

RESULTS

In 130 coliform bacteria isolated, 89 were resistant to cefazoline while 41 isolates were susceptible. Cefazoline-resistant coliform bacteria were found to be significantly resistant to cefotaxime and tetracycline as compared to susceptible isolates. Hence, bla_TEM and tetM correlating with β-lactam antibiotics and tetracycline, respectively, were analyzed found to co-localize on the IncFrepB plasmids in isolates from pig farms' wastewater by S1-PFGE analysis. And furthermore, transmissibility of the plasmids was confirmed.

CONCLUSIONS

Results obtained in this study suggested that ARGs in coliform bacteria may have been spreading on the farm via IncFrepB plasmids. Hence, appropriate use of antimicrobials and good hygiene management on the farm are required to prevent the emergence and spread of resistant bacteria.

Therapeutic Effect and Mechanisms of the Novel Monosulfactam 0073

This study aimed to evaluate the antimicrobial activity of the novel monosulfactam 0073 against multidrug-resistant Gram-negative bacteria in vitro and in vivo and to characterize the mechanisms underlying 0073 activity. The in vitro activities of 0073, aztreonam, and the combination with avibactam were assessed by MIC and time-kill assays. The safety of 0073 was evaluated using 3-(4,5-dimethylthizol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and acute toxicity assays. Murine thigh infection and pneumonia models were employed to define in vivo efficacy. A penicillin-binding protein (PBP) competition assay and confocal microscopy were conducted. The inhibitory action of 0073 against β-lactamases was evaluated by the half-maximal inhibitory concentration (IC₅₀), and resistance development was evaluated via serial passage. The monosulfactam 0073 showed promising antimicrobial activity against Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii isolates producing metallo-β-lactamases (MBLs) and serine β-lactamases. In preliminary experiments, compound 0073 exhibited safety both in vitro and in vivo In the murine thigh infection model and the pneumonia models in which infection was induced by P. aeruginosa and Klebsiella pneumoniae, 0073 significantly reduced the bacterial burden. Compound 0073 targeted several PBPs and exerted inhibitory effects against some serine β-lactamases. Finally, 0073 showed a reduced propensity for resistance selection compared with that of aztreonam. The novel monosulfactam 0073 exhibited increased activity against β-lactamase-producing Gram-negative organisms compared with the activity of aztreonam and showed good safety profiles both in vitro and in vivo The underlying mechanisms may be attributed to the affinity of 0073 for several PBPs and its inhibitory activity against some serine β-lactamases. These data indicate that 0073 represents a potential treatment for infections caused by β-lactamase-producing multidrug-resistant bacteria.

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

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

CTX-M group gene distribution of extended spectrum beta-lactamase-producing Enterobacteriaceae at a Japanese Children's hospital

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae have spread globally as one of the most common multidrug resistant organisms. Although a wide variety of ESBL genes were known in each geographical region, few reports existed on the distribution of ESBL genes in Japanese children. To clarify the distribution of ESBL genes, we investigated the CTX-M type of the ESBL-producing Enterobacteriaceae and patient characteristics among hospital-acquired and community-acquired cases. Total of 253 isolates of ESBL-producing Enterobacteriaceae were recovered from 238 pediatric patients. ESBL-producing Enterobacteriaceae were mostly recovered from children with underlying diseases (76.5%). Ratio of community-acquired and hospital-acquired cases was 58.8% and 41.2%, respectively. Compared to the hospital-acquired cases, community-acquired cases had younger age, fewer underlying diseases, and the dominant detection of Escherichia coli. The most common ESBL-producing Enterobacteriaceae was E. coli (79.8%), followed by Klebsiella pneumoniae (9.1%). CTX-M9 group was the most prevalent CTX-M group gene (63.2%), which was dominantly detected in E. coli (72.7%). This was the largest descriptive study to find CTX-M9 group as the most prevalent ESBL genotype among Enterobacteriaceae isolated from Japanese children in line with adult's epidemiology.

High Prevalence of CTX-M Type Extended-Spectrum Beta-Lactamase Genes and Detection of NDM-1 Carbapenemase Gene in Extraintestinal Pathogenic Escherichia coli in Cuba

Increase of extraintestinal pathogenic Escherichia coli (ExPEC) showing resistance to beta-lactams is a major public health concern. This study was conducted as a first molecular epidemiological study on ExPEC in Cuba, regarding prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenemase genes. A total of 306 ExPEC isolates collected in medical institutions in 16 regions in Cuba (2014–2018) were analyzed for their genotypes and presence of genes encoding ESBL, carbapenemase, plasmid-mediated quinolone resistance (PMQR) determinants by PCR and sequencing. The most common phylogenetic group of ExPEC was B2 (49%), followed by D (23%), A (21%), and B1 (7%). Among ESBL genes detected, bla_CTX-M was the most common and detected in 61% of ExPEC, with bla_CTX-M-15 being dominant and distributed to all the phylogenetic groups. NDM-1 type carbapenemase gene was identified in two isolates of phylogenetic group B1-ST448. Phylogenetic group B2 ExPEC belonged to mostly ST131 (or its single-locus variant) with O25b allele, harboring bla_CTX-M-27, and included an isolate of emerging type ST1193. aac (6’)-Ib-cr was the most prevalent PMQR gene (40.5%), being present in 54.5% of CTX-M-positive isolates. These results indicated high prevalence of CTX-M genes and the emergence of NDM-1 gene among recent ExPEC in Cuba, depicting an alarming situation.

Prevalence and antimicrobial resistance of Shiga toxin-producing Escherichia coli in milk and dairy products in Egypt

Food contaminated with Shiga toxin-producing Escherichia coli (STEC) represents a hazardous public health problem worldwide. Therefore, the present study was performed to elucidate the virulent and antimicrobial resistance characteristics of STEC isolated from milk and dairy products marketed in Egypt. A total of 125 samples (raw market milk, bulk tank milk, Kareish cheese, white soft cheese, and small scale-produced ice cream, 25 each) were collected for determination the prevalence and antimicrobial resistance profiling of STEC. Thirty-six STEC isolates were recovered from milk and dairy products. Serological analysis illustrated that three isolates were E. coli O157:H7 and 33 isolates belonged to different serotypes. Molecular examination indicated that all isolates harboured stx1 and/or stx2 genes, 14 isolates expressed eaeA gene and 3 isolates possessed rfbE gene. Antimicrobial resistance profiling of the isolates was both phenotypically and genetically examined. Interestingly, 31 out of 36 (86.11%) isolates were multidrug-resistant and harboured the extended-spectrum β-lactamase encoding genes, namely, bla_CTX-M-15, bla_SHV-12 and bla_CTX-M-14. Moreover, 12 isolates (33.33%) harboured plasmid-mediated quinolone resistant gene, qnrS. The overall conclusion of the current investigation indicated insufficient hygienic measures adopted during milking, handling, and processing leading to development of pathogenic and multidrug-resistant STEC.

Host-specific differences in the contribution of an ESBL IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4

Objectives

To assess stability and contribution of a large ESBL-encoding IncI1 plasmid to intestinal colonization by Escherichia coli O104:H4 in two different mammalian hosts.

Methods

Specific-pathogen-free 3-4-day-old New Zealand White rabbits and conventionally reared 6-week-old weaned lambs were orally infected with WT E. coli O104:H4 or the ESBL-plasmid-cured derivative, and the recovery of bacteria in intestinal homogenates and faeces monitored over time.

Results

Carriage of the ESBL plasmid had differing impacts on E. coli O104:H4 colonization of the two experimental hosts. The plasmid-cured strain was recovered at significantly higher levels than WT during late-stage colonization of rabbits, but at lower levels than WT in sheep. Regardless of the animal host, the ESBL plasmid was stably maintained in virtually all in vivo passaged bacteria that were examined.

Conclusions

These findings suggest that carriage of ESBL plasmids has distinct effects on the host bacterium depending upon the animal species it encounters and demonstrates that, as for E. coli O157:H7, ruminants could represent a potential transmission reservoir.

CTX-M ESBL-producing Enterobacteriaceae: estimated prevalence in adults in England in 2014

Background

ESBL-producing Enterobacteriaceae (ESBLPE) are increasing in prevalence worldwide and are more difficult to treat than non-ESBLPE. Their prevalence in the UK general population is unknown, as the only previous UK ESBLPE faecal colonization study involved patients with diarrhoea.

Objectives

To estimate the prevalence of CTX-M ESBLPE faecal colonization in the general adult population of England in 2014, and investigate risk factors.

Methods

A stratified random sample of 58 337 registered patients from 16 general practices within four areas of England were invited to participate by returning faeces specimens and self-completed questionnaires. Specimens were tested for ESBLPE and carbapenemase-producing Enterobacteriaceae (CPE).

Results

2430 individuals participated (4% of those invited). The estimated prevalence of colonization with CTX-M ESBLPE in England was 7.3% (95% CI 5.6%–9.4%) (Shropshire 774 participants, 4.9% colonization; Southampton City 740 participants, 9.2%; Newham 612 participants, 12.7%; Heart of Birmingham 234 individuals, 16.0%) and was particularly high in: those born in Afghanistan (10 participants, 60.0% colonization, 95% CI 29.7%–84.2%); those born on the Indian subcontinent (India, Pakistan, Bangladesh or Sri Lanka) (259 participants, 25.0% colonization, 95% CI 18.5%–32.9%); travellers to South Asia (India, Pakistan, Bangladesh, Sri Lanka or Nepal) in the last year (140 participants, 38.5% colonization, 95% CI 27.8%–50.5%); and healthcare domestics (8 participants, unweighted 37.5% colonization, 95% CI 8.5%–75.5%). Risk factors identified included: being born in the Indian subcontinent (aOR 5.4, 95% CI 3.0–9.7); travel to South Asia (aOR 2.9, 95% CI 1.8–4.8) or to Africa, China, South or Central America, South East or Pacific Asia or Afghanistan (aOR 2.6, 95% CI 1.7–4.1) in the last year; and working as a healthcare domestic (aOR 6.2, 95% CI 1.3–31). None of the 48 participants who took co-amoxiclav in the last year was colonized with CTX-M ESBLPE. bla_CTX-M-15 accounted for 66% of CTX-M ESBLPE positives. 0.1% (two participants) were colonized with CPE.

Conclusions

CTX-M ESBLPE are established in the general population in England and prevalence is particularly high in people from certain countries of birth or with recent travel. We recommend that these findings be taken into account in guidance on the empirical management of patients presenting with a likely Enterobacteriaceae infection.

Evaluating Dissemination Mechanisms of Antibiotic-Resistant Bacteria in Rural Environments in China by Using CTX-M-Producing Escherichia coli as an Indicator

It is becoming increasingly recognized that the environment plays an important role both in the emergence and in dissemination of antibiotic-resistant bacteria (ARB), Mechanisms and factors facilitating this development are, however, not yet well understood. The high detection rate of CTX-M genes in environmental sources provides an opportunity to explore this issue. In this study, 88 CTX-M-producing Escherichia coli were isolated from 30 pig feces samples from 30 pig farms and 201 environmental samples. CTX-M-producing E. coli was detected with the following frequencies in the different types of samples: pig feces, 73%; river water, 64%; river sediment, 52%; wastewater, 31%; drinking water, 23%; outlet sediment, 21%; soil, 17%; and vegetables, 4.4%. Dissemination of CTX-M-producing E. coli to different environmental matrices was evaluated by analyzing the genetic relatedness of isolates from different environmental sources, and putative transmission routes through bird feces, pig feces, drinking water, river sediment, river water, and wastewater were hypothesized. Dissemination through these routes is likely facilitated by anthropogenic activities and environmental factors. Wild birds as potential vectors for dissemination of CTX-M-producing E. coli have the capacity to spread ARB across long distances. Regional dissemination between different environmental matrices of CTX-M-producing E. coli increases the exposure risk of humans and animals in the area.

Prevalence of 16S rRNA methylases in Gram-negative bacteria derived from companion animals and livestock in Japan

The emergence and spread of aminoglycoside-resistant bacteria are a public health concern. The acquisition of the genes encoding 16S rRNA methylases, such as armA, rmtA, and rmtB, confers high-level resistance to aminoglycosides. However, the prevalence has not been well investigated in Japanese veterinary fields. To determine the prevalence of 16S rRNA methylases in animals, we detected 16S rRNA methylases genes in Gram-negative bacteria from animals. Here, we report the isolation of rmtB and armA from two of the 446 Escherichia coli (0.5%) and one of the 103 Klebsiella spp. isolates (1.0%) from companion animals, respectively. However, none of the isolations were observed from 2445 E. coli isolates derived from livestock in Japan. The prevalence of 16S rRNA methylases in animals, especially in companion animals, should be carefully monitored in Japanese veterinary fields to avoid the spreading of the genes.

High rates of CTX-M group-1 extended-spectrum β-lactamases producing Escherichia coli from pets and their owners in Faisalabad, Pakistan

PURPOSE

Pet animals have been considered a potential carrier of clinically important multi-drug-resistant Escherichia coli. However, little is known about the role of pets as reservoirs of extended-spectrum β-lactamase (ESBL) producing E. coli in Pakistan. This study was designed to determine the prevalence and genetic relatedness of ESBL-producing multidrug-resistant E. coli in pets, their owners, and veterinary professionals.

METHODS

A total of 105 fecal samples were collected from dogs, cats, their owners, and veterinary professionals from veterinary clinics. Isolates of ESBL-producing E. coli were subjected to antimicrobial susceptibility testing. The presence of bla CTX-M genes and CTX-M groups I and II in multidrug-resistant E. coli was detected using PCR. Clonal diversity was checked using BOX-PCR.

RESULTS

Of the 105 fecal samples screened, 73 (69.5%) were found to contain ESBL-producing E. coli. The percentage of ESBL-producing E. coli isolates in dogs and dog owners was found to be 81.8% (18/22) and 59% (13/22), respectively. In cats, this percentage was 73.9% (17/23) and in cat owners, 56.5% (13/23). Furthermore, 80% (12/15) of E. coli isolates in veterinary professionals were ESBL producers. Of these 73 ESBL-producing E. coli isolates, 23 isolates exhibited a multidrug-resistant phenotype. The most prevalent multidrug-resistant pattern (17.4%) identified was resistant to ampicillin, cefotaxime, ciprofloxacin, and nitrofurantoin. In the multidrug-resistant E. coli, bla CTX-M was identified as the most common ESBL-producing genotype (19/23), with bla CTX-M-1 dominating in all 19 isolates. Furthermore, BOX-PCR analysis exhibited genetically diverse clonal groups among isolates of the CTX-M-1 group.

CONCLUSION

Our results provide important baseline information on the potential burden of multidrug-resistant E. coli among companion animals in Pakistan. Further studies are needed to understand the drivers of antimicrobial resistance at human-animal-environmental intersections.

Characterization of Antimicrobial Resistance in Serratia spp. and Citrobacter spp. Isolates from Companion Animals in Japan: Nosocomial Dissemination of Extended-Spectrum Cephalosporin-Resistant Citrobacter freundii

In many countries including Japan, the status of emerging antimicrobial resistance among Serratia spp. and Citrobacter spp. in companion animals remains unknown because these genera are rarely isolated from animals. In this study, 30 Serratia spp. and 23 Citrobacter spp. isolates from companion animals underwent susceptibility testing for 10 antimicrobials. Phenotypic and genetic approaches were used to identify the mechanisms of extended-spectrum cephalosporins (ESC). Subsequently, ESC-resistant Citrobacter spp. strains underwent multilocus sequence typing and pulsed-field gel electrophoresis (PFGE). A significantly higher rate (34.8%) of ESC resistance was observed in Citrobacter spp. isolates than in Serratia spp. isolates (0%). ESC resistance was detected in five C. freundii strains, two C. portucalensis strains, and one C. koseri strain. All of the ESC-resistant Citrobacter spp. strains harbored CMY-type and/or DHA-type AmpC β-lactamases. Three C. freundii strains harbored the CTX-M-3-type extended-spectrum β-lactamases. Notably, the three blaCTX-3-producing and two blaCMY-117-bearing C. freundii strains (obtained from different patients in one hospital) had the same sequence type (ST156 and ST18, respectively) and similar PFGE profiles. We believe that ESC-resistant Citrobacter spp. are important nosocomial pathogens in veterinary medicine. Therefore, infection control in animal hospitals is essential to prevent dissemination of these resistant pathogens.

Role of TEM-1 β-Lactamase in the Predominance of Ampicillin-Sulbactam-Nonsusceptible Escherichia coli in Japan

We investigated the epidemiology and resistance mechanisms of ampicillin-sulbactam-nonsusceptible Escherichia coli, focusing on the role of the TEM-1 β-lactamase. We collected all nonduplicate E. coli clinical isolates at 10 Japanese hospitals during December 2014 and examined their antimicrobial susceptibility, β-lactamases, TEM-1 transferability, TEM-1 β-lactamase activity, outer membrane protein profile, membrane permeability, and clonal genotypes. Among the 329 isolates collected, 95 were ampicillin-sulbactam nonsusceptible. Of these ampicillin-sulbactam-nonsusceptible isolates, β-lactamases conferring resistance to sulbactam, such as AmpC, were present in 33%. Hyperproduction of sulbactam-susceptible β-lactamases, TEMs with a strong promoter, were rare (5%). The remaining 59 isolates (62%) had only sulbactam-susceptible β-lactamases, including TEM-1 with a wild-type promoter (n = 28), CTX-Ms (n = 13), or both (n = 17). All 45 transconjugants from 96 donors with TEM-1 had higher ampicillin-sulbactam MICs (4 to 96 mg/liter) than the recipient (2 mg/liter). In donors with only TEM-1, TEM-1 activity correlated with the 50% inhibitory concentration of sulbactam and ampicillin-sulbactam MICs. The decreased membrane permeation of sulbactam was associated with an increased ampicillin-sulbactam MIC. The reduced permeation was partly attributable to deficient outer membrane proteins, which were observed in 57% of the ampicillin-sulbactam-nonsusceptible isolates with only TEM-1 and a wild-type promoter. Sequence type 131 (ST131) was the most common clonal type (52%). TEM-1 with a wild-type promoter primarily contributed to ampicillin-sulbactam nonsusceptibility in E. coli, with the partial support of other mechanisms, such as reduced permeation. Conjugative TEM-1 and the clonal spread of ST131 may contribute to the prevalence of Japanese ampicillin-sulbactam-nonsusceptible isolates.

Antimicrobial Resistance in Commensal Escherichia coli Isolated from Pigs and Pork Derived from Farms Either Routinely Using or Not Using In-Feed Antimicrobials

The aims of this study were (i) to evaluate whether routine in-feed antimicrobial use in pigs or not resulted in differences in antimicrobial resistance (AMR) E. coli at different pig producing stages, and (ii) to determine whether resistant strains were presented in pig meat postslaughter. A total of 300 commensal E. coli isolates were obtained and examined for antibiograms, AMR genes, plasmid replicons, and molecular types. The isolates were from two farms either using (A) or not using in-feed antimicrobials (NA), sampled four times during the production cycle and once postslaughter. E. coli resistant to aminoglycosides containing aadA1, aadA2, and aadB and extended-spectrum beta-lactamase-producing (ESBLP) E. coli containing bla_CTX-M-1 were significantly increased in the nursery and growing periods in farm A compared to farm NA. IncI1-Iγ and IncHI2 were common in the nursery period and were shown to transfer bla_CTX-M genes by conjugation. ST10 was the most common type only found in live pigs. ST604, ST877, ST1209, and ST2798 ESBLP were found only in live pigs, whereas ST72, ST302, and ST402 ESBLP were found in pig meat.

Clinical and Molecular Correlates of Escherichia coli Bloodstream Infection from Two Geographically Diverse Centers in Rochester, Minnesota, and Singapore

Escherichia coli bacteremia is caused mainly by sequence type complex 131 (STc131) and two clades within its fluoroquinolone-resistance-associated H30 subclone, H30R1 and H30Rx. We examined clinical and molecular correlates of E. coli bacteremia in two geographically distinct centers. We retrospectively studied 251 unique E. coli bloodstream isolates from 246 patients (48 from the Mayo Clinic, Rochester, MN [MN], and 198 from Tan Tock Seng Hospital, Singapore [SG]), from October 2013 through March 2014. Isolates underwent PCR for phylogroup, STc, bla_CTX-M type, and virulence gene profiles, and medical records were reviewed. Although STc131 accounted for 25 to 27% of all E. coli bacteremia isolates at each site, its extended-spectrum-β-lactamase (ESBL)-associated H30Rx clade was more prominent in SG than in MN (15% versus 4%; P = 0.04). In SG only, patients with STc131 (versus other E. coli STc isolates) were more likely to receive inactive initial antibiotics (odds ratio, 2.8; P = 0.005); this was true specifically for patients with H30Rx (odds ratio, 7.0; P = 0.005). H30Rx comprised 16% of community-onset bacteremia episodes in SG but none in MN. In SG, virulence scores were higher for H30Rx than for H30R1, non-H30 STc131, and non-STc131 isolates (P < 0.02 for all comparisons). At neither site did mortality differ by clonal status. The ESBL-associated H30Rx clade was more prevalent and more often of community onset in SG, where it predicted inactive empirical treatment. The clonal distribution varies geographically and has potentially important clinical implications. Rapid susceptibility testing and clonal diagnostics for H30/H30Rx might facilitate earlier prescribing of active therapy.

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases of Escherichia coli and Klebsiella spp. Isolates from Urinary Tract Infections in Southern Brazil

The objective of this study was to evaluate the frequency of different extended-spectrum β-lactamases (ESBL) as well as to associate these ESBL with antimicrobial (ATM) resistance in Escherichia coli and Klebsiella spp. isolates from outpatients and inpatients with urinary tract infections. The study included 435 consecutive nonduplicate clinical isolates, including 362 E. coli isolates, 62 Klebsiella pneumoniae isolates, and 11 K. oxytoca isolates. Isolates were obtained from patients who were treated in a University Hospital between August 2012 and July 2013. Three multiplex PCR were performed to identify the ESBL groups. A total of 48 (11%) ESBL-producing isolates were found. The risk for the ESBL presence was significantly higher in males (26.4%) than females (8%), from hospital-acquired infections (29.1%) than community-acquired infections (7.0%) and in Klebsiella spp. (27.4%) than in E. coli (7.7%). ESBL-producing isolates presented a significantly higher percentage of resistance in 21 of the 23 ATMs analyzed. The CTX-M-1 group was the most predominant ESBL identified. The bla_{CTX-M-1-group} gene was found in 56% of the total ESBL producers from community and in 42.4% from hospital origins; it was followed in frequency by the bla_{CTX-M-8/25-group}, also found in both environments. Klebsiella spp. presented the largest variety of β-lactamase enzyme combinations and a higher level of resistance to cefotaxime. These findings contribute to better knowledge of the epidemiology of ESBL enzymes and are alarming for the reduced therapeutic options available for the risk groups identified in the studied populations.

Multi-drug resistant Escherichia coli in diarrhoeagenic foals: Pulsotyping, phylotyping, serotyping, antibiotic resistance and virulence profiling

Extraintestinal pathogenic E. coli (ExPEC) possess the ability to cause extraintestinal infections such as urinary tract infections, neonatal meningitis and sepsis. While information is readily available describing pathogenic E. coli populations in food-producing animals, studies in companion/sports animals such as horses are limited. In addition, many antimicrobial agents used in the treatment of equine infections are also utilised in human medicine, potentially contributing to the spread of antibiotic resistance determinants among pathogenic strains. The aim of this study was to phenotypically and genotypically characterise the multidrug resistance and virulence associated with 83 equine E. coli isolates recovered from foals with diarrhoeal disease. Serotyping was performed by both PCR and sequencing. Antibiotic resistance was assessed by disc diffusion. Phylogenetic groups, virulence genes, antibiotic resistance genes and integrons were determined by PCR. Thirty-nine (46%) of the isolates were classified as ExPEC and hence considered to be potentially pathogenic to humans and animals. Identified serogroups O1, O19a, O40, O101 and O153 are among previously reported human clinical ExPEC isolates. Over a quarter of the E. coli were assigned to pathogenic phylogroups B2 (6%) and D (23%). Class 1 and class 2 integrons were detected in 85% of E. coli, revealing their potential to transfer MDR to other pathogenic and non-pathogenic bacteria. With 65% of potentially pathogenic isolates harbouring one or more TEM, SHV and CTX-M-2 group β-lactamases, in addition to the high levels of resistance to fluoroquinolones observed, our findings signal the need for increased attention to companion/sport animal reservoirs as public health threats.

High prevalence of ceftriaxone resistance among invasive Salmonella enterica serotype Choleraesuis isolates in Thailand: The emergence and increase of CTX-M-55 in ciprofloxacin-resistant S. Choleraesuis isolates

S. Choleraesuis is a highly invasive zoonotic pathogen that causes a serious systemic infection in humans. The emergence and increase of resistance to ceftriaxone and ciprofloxacin among S. Choleraesuis has become a serious therapeutic problem. The present study demonstrated high frequency of antimicrobial resistance in Salmonella Choleraesuis among 414 nontyphoidal Salmonella isolates from bacteremic patients in Thailand. High rates of ceftriaxone (58.3%) and ciprofloxacin (19.6%) resistances were observed in S. Choleraesuis isolates. The dissemination of the self-transferable bla_CTX-M-14-carrying IncFII_s, IncFII, and IncI1 plasmids and bla_CMY-2-carrying IncA/C plasmid along with the clonal spread of bla_CMY-2-harbouring S. Choleraesuis isolates contributed to the high frequency of resistance to extended-spectrum cephalosporins (ESCs; third- and fourth-generation cephalosporins) during 2005-2007. We reported the first occurrence of ceftazidime-hydrolysing CTX-M-55 in S. Choleraesuis isolates which dramatically increased and became the most abundant CTX-M variant among ESC-resistant S. Choleraesuis isolates during 2012-2016. The spread of clone pulsotype B3 was due to the dissemination of IncA/C plasmids carrying both bla_CTX-M-55 and qnrS1 among ciprofloxacin-resistant S. Choleraesuis isolates harbouring D87G in GyrA. These isolates were apparently responsible for the high rates of co-resistance to ESCs and ciprofloxacin (51.3%) during 2012-2016. This study emphasizes the importance to have an action plan to control the dissemination of antimicrobial resistance in S. Choleraesuis since this poses a threat to global health due to travel and trade in animal food products.

Prevalence of Extended-Spectrum Beta-Lactamase and Carbapenemase Genes in Clinical Isolates of Escherichia coli in Myanmar: Dominance of blaNDM-5 and Emergence of blaOXA-181

The increasing trend of Escherichia coli producing extended-spectrum beta-lactamases (ESBLs) and carbapenemases is a global public health concern. In this study, prevalence and molecular characteristics of E. coli harboring ESBL and carbapenemase genes were investigated for 426 isolates derived from various clinical specimens in a teaching hospital in Yangon, Myanmar, for the 1-year period beginning January 2016. A total of 157 isolates (36.9%) were ESBL producers and harbored CTX-M-1 group genes (146 isolates; bla_CTX-M-15, bla_CTX-M55) or CTX-M-9 group genes (11 isolates; bla_CTX-M-14, bla_CTX-M-27). Carbapenem resistance was detected in 35 isolates (8.2%), among which 26 isolates had carbapenemase genes encoding NDM-1 (2 isolates), NDM-4 (6 isolates), NDM-5 (14 isolates), NDM-7 (3 isolates), and OXA-181 (2 isolates). bla_NDM-5 was identified in phylogenetic groups A, B1, and D isolates belonging to various genotypes (ST101, ST354, ST405, ST410, ST1196) associated with bla_TEM-1, bla_CTX-M-15, bla_OXA-181, bla_CMY-2, bla_CMY-6, bla_CMY-42, qnrB, qnrS, or aac6'-Ib-cr. While two isolates with bla_OXA-181 belonged to phylogenetic group A-ST410, one isolate had also bla_NDM-5, as well as bla_CTX-M-15 and bla_CMY-2, and the other harbored bla_CMY-42 and aac6'-Ib-cr, showing different resistance patterns. Phylogenetic group B2 isolates examined were classified into mostly ST131 and had solely bla_CTX-M-15 or bla_CTX-M-27, harboring more virulence factors than other phylogenetic groups. The present study revealed high prevalence of ESBL genes represented by bla_CTX-M-15 and dominance of bla_NDM-5 among NDM genes, disseminating to various E. coli clones. Notably, carbapenemase gene encoding OXA-181 was first identified in Myanmar, suggesting its spread together with NDM genes.

Occurrence of multidrug-resistant and ESBL-producing atypical enteropathogenic Escherichia coli in China

Background

Atypical enteropathogenic Escherichia coli (aEPEC) is regarded as a globally emerging enteropathogen. aEPECs exhibit various level of resistance to a range of antibiotics, which is increasing alarmingly. The present study investigated the antimicrobial resistance of aEPEC isolates recovered from diarrheal patients, healthy carriers, animals, and raw meats.

Results

Among 267 aEPEC isolates, 146 (54.7%) were resistant to tetracycline, followed by ampicillin (49.4%), streptomycin (46.1%), and piperacillin (41.2%). Multidrug resistance (MDR) was detected in 128 (47.9%) isolates, and 40 MDR isolates were resistant to ≥ 10 antimicrobial agents. A total of 47 (17.6%) aEPEC isolates were identified as extended-spectrum β-lactamase (ESBL)-producers. The bla_CTX-M-14 and bla_CTX-M-15 genes were predominant among ESBL-producing isolates.

Conclusions

This investigation depicted the occurrence of multidrug-resistant and ESBL-producing aEPEC isolates in China. The results suggested that it is necessary to continuously monitor the emergence and spread of MDR aEPEC.

Electronic supplementary material

The online version of this article (10.1186/s13099-018-0234-0) contains supplementary material, which is available to authorized users.

Phenotypic and Molecular Characterization of Multidrug Resistant Klebsiella pneumoniae Isolated from Different Clinical Sources in Al-Najaf Province-Iraq

BACKGROUND AND OBJECTIVE

Burns infections and urinary tract infections are the most important prevalent diseases in Asian countries, such as Iraq. Klebsiella pneumoniae is one of the most important bacteria cause this type of infections especially in hospitals. Therefore, the aim of this study was to investigate the prevalence of multi-drug resistance K. pneumoniae and extended-spectrum beta-lactamases producing K. pneumoniae isolates from inpatients with urinary tract infection and burns infections in Al-Kufa hospital in Al-Najaf province, Iraq.

MATERIALS AND METHODS

A total of 285 clinical samples were collected from in-patients infected with urinary tract infection (141 urine samples) and burns infections (144 burns swabs). Fourteen different antibiotics were used by disc diffusion method and 13 antimicrobials resistance genes were used by PCR technique.

RESULTS

A total of 43 K. pneumoniae strains were isolated. The highest resistance rate was observed for amoxicillin 25 μg and amoxicillin+clavulanic acid 20+10 μg (97.67%) while the lowest resistance rate was observed for imipenem 10 μg (9.30%). The most common resistance associated-genes were blaSHV (86.04%) and at lower prevalence were IMP (9.30%).

CONCLUSION

Klebsiella pneumoniae strains isolated from burns infections were more virulent than those isolated from urinary tract infections.

Population structure of Japanese extraintestinal pathogenic Escherichia coli and its relationship with antimicrobial resistance

Objectives

To define the population structure of extraintestinal pathogenic Escherichia coli (ExPEC) in Japan and its relationship with antimicrobial resistance and the major resistance mechanisms for fluoroquinolones and β-lactams, we designed a multicentre prospective study.

Methods

A total of 329 ExPEC isolates were collected at 10 Japanese acute-care hospitals during December 2014. We defined the clonal groups of ExPEC by fumC and fimH sequencing (CH typing). Antimicrobial susceptibility testing of 18 agents and the detection of mutations in quinolone resistance-determining regions (QRDRs) and β-lactamases were performed.

Results

Among the study isolates, 103 CH types were found, and CH40-30 (25%) and another 10 CH types (35% in total) constituted the major ExPEC population. Ciprofloxacin non-susceptibility, ESBLs and MDR phenotypes were found in 34%, 22% and 33%, respectively. CH40-30, corresponding to the C/H30 clade of the global pandemic ST131 clone, was associated with four QRDR mutations (100%) and bla CTX-M (60%) and was the most frequent type in 15 antimicrobial-non-susceptible populations (dominating 39%-75% of each population, the highest prevalence for ciprofloxacin), the ESBL producers (70%) and the MDR isolates (59%). Isolates that were non-susceptible to nalidixic acid and low-level resistant to ciprofloxacin with one or two QRDR mutations represented 16% of the study isolates and were distributed among the eight major and non-major CH types.

Conclusions

More than half of the ExPEC population in Japan consisted of 11 major clones. Of these clones, the CH40-30-ST131-C/H30 clone was the predominant antimicrobial-resistant population. The presence of major clones with low-level ciprofloxacin resistance supports the potential future success of a non-ST131 fluoroquinolone-resistant clone.

In vitro efficacy of 16 antimicrobial drugs against a large collection of β-lactamase-producing isolates of extraintestinal pathogenic Escherichia coli from dogs and cats

PURPOSE

The aim of this study was to assess the in vitro efficacy of candidate antimicrobials against extended-spectrum β-lactamase (ESBL)-producing isolates of extraintestinal pathogenic Escherichia coli (ExPEC) from companion animals.

METHODOLOGY

A total of 90 ESBL-producing ExPEC isolates from dogs and cats were tested for susceptibility to 16 antimicrobials with the agar dilution method. We also identified the ESBLs and AmpC β-lactamases of these isolates with PCR and DNA sequencing.Results/Key findings. All isolates were susceptible to meropenem, tebipenem and amikacin (AMK), and various proportions were susceptible to latamoxef (LMX, 97.8 %), fosfomycin (FOM, 97.8 %), faropenem (FPM, 96.7 %), nitrofurantoin (NFT, 96.7 %), flomoxef (FMX, 93.3 %), piperacillin/tazobactam (PTZ, 92.2 %), cefmetazole (CMZ, 91.1 %), chloramphenicol (80.0 %), trimethoprim/sulfamethoxazole (64.4 %), amoxicillin/clavulanic acid (63.3 %), ceftibuten (60.0 %), tetracycline (52.2 %) and enrofloxacin (10.0 %). A genetic analysis showed that 83 of the 90 (92.2 %) isolates were positive for CTX-M-type genes: CTX-M-14 (n=26), CTX-M-27 (n=20), CTX-M-55 (n=17), CTX-M-15 (n=12), CTX-M-2 (n=5), CTX-M-24 (n=2), CTX-M-104 (n=2) and CTX-M-3 (n=1). Eight isolates also expressed AmpC β-lactamase phenotypes.

CONCLUSION

This study demonstrates that the susceptibility rates to PTZ, CMZ, LMX, AMK, FOM, FPM, NFT and FMX were similar to those to carbapenems (>90 %), implying that these drugs are available alternatives to carbapenems for the treatment of companion animals infected with ExPEC-producing CTX-M-type ESBLs. Further in vivo studies of the effective use of these antimicrobials are required.

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli

The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to commensal Escherichia coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies.

Routine Prophylactic Antimicrobial Use Is Associated with Increased Phenotypic and Genotypic Resistance in Commensal Escherichia coli Isolates Recovered from Healthy Fattening Pigs on Farms in Thailand

This study examined antimicrobial resistance (AMR) profiles in commensal Escherichia coli derived from healthy fattening pigs in Thai farms that used prophylactic antimicrobials (in-feed tiamulin fumarate and amoxicillin) [PAs], therapeutic antimicrobials (injectable enrofloxacin or gentamicin) [TAs], or no antimicrobials [NAs]. Commensal E. coli were used as a proxy for overall AMR on the farms. There was a high level of multidrug resistance in all three categories of farm, with isolates showing resistance to β-lactams (amoxicillin, ampicillin, and piperacillin) and tetracyclines (tetracycline), and commonly possessing tetA, bla_TEM, and plasmid replicons FIB and F. On the other hand, isolates with an extended-spectrum beta-lactamase phenotype (ESBLP) and with resistance to aminoglycosides, chloramphenicol, fluoroquinolones, nitrofurantoin, tiamulin, and trimethoprim/sulfamethoxazole were significantly more common among the PA farms (p < 0.05) than in the other two farm categories. In the PA farms, ESBLP E. coli commonly contained the bla_CTX-M-1 group, bla_CTX-M-9 group, or both gene groups, and were shown to transfer bla_CTX-M genes in a conjugation experiment. E. coli containing N, FIC and A/C replicons were found only in PA farms. In summary, although E. coli isolates from all farms contained a core set of resistance to β-lactams and tetracyclines, the routine use of PA increased resistance rates to other important antimicrobials.

Air exposure as a possible route for ESBL in pig farmers

Livestock can carry extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, with bla_CTX-M-1 being most prevalent. ESBL carriage in farmers is associated with ESBL carriage in animals, with direct animal-human contact considered as the dominant route of transmission. However, inhalation of stable air might represent another route of transmission. We, therefore, quantified presence of bla_CTX-M group 1 genes (CTX-M-gr1) in dust and the association with CTX-M-gr1 carriage in pig farmers, family members and employees. We included 131 people living and/or working on 32 conventional Dutch pig production farms (farmers, family members and employees) during two sampling moments over a 12-month interval. Human stool samples, rectal swabs from 60 pigs per farm, and 2-5 dust samples collected using an electrostatic dust collector (EDC) (as a proxy for presence of viable CTX-M-gr1 carrying bacteria in air) were obtained per farm. Presence of ESBL-producing Escherichia Coli (E. coli) in stool samples and rectal swabs was determined by selective plating and CTX-M-gr1 was identified by PCR. Dust samples were analyzed directly by PCR for presence of CTX-M-gr1. Questionnaires were used to collect information on nature, intensity and duration of animal contact. Overall human prevalence of CTX-M-gr1 carriage was 3.6%. CTX-M-gr1 was detected in dust on 26% of the farms and in pigs on 35% of the farms, on at least one sampling moment. Human CTX-M-gr1 carriage and presence of CTX-M-gr1 in dust were associated univariately (OR=12.4, 95% CI=2.7-57.1). In multivariate analysis human CTX-M-gr1 carriage was associated with the number of working hours per week (OR=1.03, 95% CI=1.00-1.06), presence of CTX-M-gr1 carrying pigs on the farm (OR=7.4, 95% CI=1.1-49.7) and presence of CTX-M-gr1 in dust (OR=3.5, 95% CI=0.6-20.9). These results leave open the possibility of airborne CTX-M-gr1 transmission from animals to humans next to direct contact.