Current status of extended spectrum β-lactamase-producing Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis in Okinawa prefecture, Japan

Rapid discrimination methods for clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using the N-terminal sequence of the flaA gene and investigation of antimicrobial resistance

Although the genus Aeromonas inhabits the natural environment, it has also been isolated from hospital patient specimens as a causative agent of Aeromonas infections. However, it is not known whether clinical strains live in the natural environment, and if these strains have acquired antimicrobial resistance. In this study, we performed the typing of flagellin A gene (flaA) of clinical and environmental strains of Aeromonas hydrophila and A. veronii biovar sobria using Polymerase Chain Reaction (PCR) assay with newly designed primers. Detection rates of the clinical and environmental flaA types of A. hydrophila were 66.7% and 88.2%, and the corresponding rates for A. veronii biovar sobria were 66.7% and 90.9%. The PCR assays could significantly discriminate between clinical and environmental strains of both species in approximately 4 h. Also, among the 63 clinical Aeromonas strains used, only one extended-spectrum β-lactamase-producing bacteria, no plasmid-mediated quinolone resistance bacteria, and only four multidrug-resistant bacteria were detected. Therefore, the PCR assays could be useful for the rapid diagnosis of these Aeromonas infections and the monitoring of clinical strain invasion into water-related facilities and environments. Also, the frequency of drug-resistant Aeromonas in clinical isolates from Okinawa Prefecture, Japan, appeared to be low.

Efficacy of Carbapenems Compared With Noncarbapenem Broad-Spectrum Beta-Lactam Antibiotics as Initial Antibiotic Therapy Against Sepsis: A Nationwide Observational Study

OBJECTIVES

As causative pathogens are not usually identified at the time of initiating antibiotics in sepsis, carbapenems are commonly used as an initial treatment. To reduce indiscriminate use of carbapenems, the efficacy of alternative empiric regimens, such as piperacillin-tazobactam and the fourth-generation cephalosporins, should be elucidated. This study aimed to evaluate survival effect associated with carbapenems as initial therapy for sepsis compared with these antibiotics.

DESIGN

Multicenter retrospective observational study.

SETTING

Tertiary hospitals in Japan.

PATIENTS

Adult patients diagnosed as having sepsis from 2006 to 2019.

INTERVENTIONS

Administration of carbapenems as initial antibiotic therapy.

MEASUREMENTS AND MAIN RESULTS

This study used data of adult patients with sepsis extracted from a large-scale database in Japan. Patients were divided into two groups as follows: patients receiving carbapenems and patients receiving noncarbapenem broad-spectrum beta-lactam antibiotics as initial treatment. In-hospital mortality was compared between the groups by a logistic regression model adjusted by an inverse probability treatment weighting using propensity scores. To evaluate heterogeneity of effects according to patient characteristics, we also fitted logistic models in several subgroups. Among 7,392 patients with sepsis, 3,547 patients received carbapenems, and 3,845 patients received noncarbapenem agents. The logistic model showed no significant association between carbapenem therapy and lower mortality (adjusted OR 0.88, p = 0.108). Subgroup analyses suggested that there were significant survival benefits associated with carbapenem therapy in patients with septic shock, in ICUs, or with mechanical ventilation ( p for effect modifications: < 0.001, 0.014, and 0.105, respectively).

CONCLUSIONS

Compared with the noncarbapenem broad-spectrum antibiotics, carbapenems as an initial therapy for sepsis were not associated with significantly lower mortality.

Analysis of the upstream genetic structures of the ISEcp1-blaCTX-M transposition units in Escherichia coli isolates carrying blaCTX-M obtained from the Indonesian and Vietnamese communities

Extended spectrum β-lactamase (ESBL)-producing Escherichia coli have been found in healthy individuals in Indonesia and Vietnam. The ISEcp1-bla_CTX-M transposition unit of ESBL-producing bacterial isolates has been considered responsible for the production of CTX-M type ESBL and it is important for the dissemination of bla_CTX-M . This study aimed to characterize the upstream genetic structure (UGS) of E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes obtained from healthy individuals in Indonesia and Vietnam. A total of 501 CTX-M type ESBL-producing E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes were obtained from healthy individuals of the two countries in 2018. The UGSs of the ISEcp1-bla_CTX-M transposition unit of the 501 ESBL-producing E. coli isolates were amplified by barcode-adaptor-ligation-mediated PCR and analyzed using the Nanopore sequencer. The obtained sequence information was used to classify the UGSs of the ISEcp1-bla_CTX-M transposition unit. From the 501 ESBL-producing E. coli isolates, 502 UGSs were obtained, which were classified into 85 UGS types based on the sequence. ISEcp1 of 359 (71.5%) of the 502 UGSs was disrupted by gene insertion, and ISEcp1-bla_CTX-M transposition unit of most (87.1%) of the determined UGSs was confirmed as plasmidic. Only 6 (7.1%) of the 85 UGS types were common to both countries. Our results indicated that many different UGSs of ISEcp1-bla_CTX-M transposition units were detected in Indonesia and Vietnam; hence, we suggest that structurally different kinds of plasmids harboring bla_CTX-M were separately distributed in the two countries.

A high-throughput sequencing determination method for upstream genetic structure (UGS) of ISEcp1-blaCTX-M transposition unit and application of the UGS to classification of bacterial isolates possessing blaCTX-M

INTRODUCTION

Because bla_CTX-M is responsible for resistance of bacteria to the third generation cephalosporins, location of bla_CTX-M could be a good indicator for classifying bacterial isolates harboring bla_CTX-M in molecular epidemiology. However, determination of bla_CTX-M location has been difficult when multiple copies of ISEcp1 were found on bacterial genome. We aimed to establish a high-throughput analytical method for upstream genetic structures (UGS) of ISEcp1 to facilitate determination of bla_CTX-M location.

METHODS

Extracted DNA samples obtained from 168 Escherichia coli isolates possessing bla_CTX-M were digested by restriction enzyme, HaeIII, and the digested DNA fragments were ligated with homemade barcode adaptors. Then, DNA fragments containing UGS of ISEcp1 were amplified and subjected to the Nanopore sequencer.

RESULTS

Nucleotide sequences and locations of 168 UGSs obtained from the examined E. coli isolates were determined. Among the 168 determined UGSs, 150 (89.3%) UGS were confirmed on plasmid and classified into eight types. Interestingly, coding sequence of ISEcp1 transposase gene in seven of the eight types were disrupted by IS26 insertion. The remaining 18 (10.7%) UGSs were observed in identical chromosomal region. The obtained nucleotide sequences the locations of UGSs were confirmed by conventional capillary sequencer and Southern blotting, respectively, and any discrepant result was not observed with these confirmation procedures.

CONCLUSIONS

Our results indicated that the established method was efficient for simultaneously determining at least 100 different UGS, and suggested that the determined UGSs of ISEcp1-bla_CTX-M transposition unit was useful for classification of bacterial isolates harboring bla_CTX-M.

A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

In Enterobacterales, the most common carbapenemases are Ambler's class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.

Genetics of Acquired Antibiotic Resistance Genes in Proteus spp

Proteus spp. are commensal Enterobacterales of the human digestive tract. At the same time, P. mirabilis is commonly involved in urinary tract infections (UTI). P. mirabilis is naturally resistant to several antibiotics including colistin and shows reduced susceptibility to imipenem. However higher levels of resistance to imipenem commonly occur in P. mirabilis isolates consecutively to the loss of porins, reduced expression of penicillin binding proteins (PBPs) PBP1a, PBP2, or acquisition of several antibiotic resistance genes, including carbapenemase genes. In addition, resistance to non-β-lactams is also frequently reported including molecules used for treating UTI infections (e.g., fluoroquinolones, nitrofurans). Emergence and spread of multidrug resistant P. mirabilis isolates, including those producing ESBLs, AmpC cephalosporinases and carbapenemases, are being more and more frequently reported. This review covers Proteus spp. with a focus on the different genetic mechanisms involved in the acquisition of resistance genes to multiple antibiotic classes turning P. mirabilis into a dreadful pandrug resistant bacteria and resulting in difficult to treat infections.

A survey of extended-spectrum β-lactamase-producing Enterobacteriaceae in environmental water in Okinawa Prefecture of Japan and relationship with indicator organisms

Surveys of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-pE) in stream water and untreated wastewater were carried out in Okinawa Prefecture, Japan. Thirty-six samples of water were collected from 18 streams in Okinawa Prefecture, as well as ten samples of wastewater flowing into four wastewater treatment plants (WWTPs). We investigated bacterial species, Escherichia coli O antigen, ESBL phenotype, ESBL genotype, and pulsed-field gel electrophoresis (PFGE) type of isolates, and total viable count and fecal coliforms as indicator organisms. The relation between indicator organisms and ESBL-pE was also validated using the same samples. A total of 141 ESBL-pE including 107 E. coli, 15 Klebsiella pneumoniae, 2 Proteus mirabilis, and 17 other species was isolated from stream water and wastewater. Of the 141 ESBL-pE, 14.9% and 54.6% were found to be blaCTX-M-15 and blaCTX-M-14-like types, respectively, which have been found in hospital isolates in Okinawa. Two pairs of possibly related patterns according to PFGE criteria were isolated from stream water and wastewater in two districts. When ESBL-pE was significantly isolated, total viable count and fecal coliform boundaries were ≥ 6.0 × 10³ CFU/ml and ≥ 4.3 × 10² most probable number/100 ml, respectively. These results suggested that ESBL-pE isolated from stream water is human derived, and that total viable count and fecal coliforms will be useful as indicators for confirming the spread of ESBL-pE to the environment by means of simple hygiene surveys.

Characterisation of chromosomally-located blaCTX-M and its surrounding sequence in CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli isolates

OBJECTIVES

Although it has been regarded that the CTX-M-type extended-spectrum β-lactamase (ESBL) gene bla_CTX-M is mainly carried by antimicrobial resistance plasmids, Escherichia coli possessing chromosomally-located bla_CTX-M has been reported in previous studies. This study aimed to characterise the genetic structure of the chromosomally-located bla_CTX-M transposition unit and its surrounding sequence in ESBL-producing E. coli isolated in a Japanese hospital.

METHODS

A total of 81 ESBL-producing E. coli isolates were studied. The existence of chromosomally-located bla_CTX-M was confirmed by S1 nuclease-digested pulsed-field gel electrophoresis (PFGE) and Southern blot hybridisation and by sequencing analysis of the PCR-amplified DNA fragments.

RESULTS

Chromosomally-located bla_CTX-M was confirmed in 22 (27.2%) of the 81 E. coli isolates examined; five and four location types of chromosomally-located bla_CTX-M-14 and bla_CTX-M-15 were determined, respectively. Among the 22 E. coli isolates, 15 (68.2%) possessed single chromosomally-located bla_CTX-M gene, probably due to single transposition of a plasmidic bla_CTX-M to the chromosome. In isolate N0057, the bla_CTX-M-15 transposition unit was transferred from a plasmid into two different chromosomal regions. In addition, 'recurrent' transposition of already existing chromosomally-located bla_CTX-M-14 to another chromosomal region was observed in isolates N0211, N0214, N01127, N1682 and N1753; consequently, these isolates possessed two copies of chromosomally-located bla_CTX-M-14.

CONCLUSION

Considering that isolates N0211, N0214, N01127, N1682 and N1753 in which the 'recurrent' transposition event occurred were genetically related according to PFGE, these data suggest the possibility of accumulation of bla_CTX-M on the chromosome in CTX-M-type ESBL-producing E. coli.

Characterization of CTX-M type ESBL-producing Enterobacteriaceae isolated from asymptomatic healthy individuals who live in a community of the Okinawa prefecture, Japan

This study was performed to characterize CTX-M type extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae carriage in asymptomatic health individuals, which has not been well investigated, in a community of the Okinawa prefecture, Japan. Fecal samples were voluntary collected from asymptomatic healthy individuals who were going to take a routine medical checkup. The collected fecal samples were inoculated on MacConkey agar supplemented with 2 μg/ml of cefotaxime and incubated at 37 °C. Randomly selected three lactose-fermented colonies per each sample were analyzed. Genetic relatedness among the CTX-M type ESBL-producing Enterobacteriaceae isolates were performed by pulsed-field gel electrophoresis (PFGE) after confirmation of ESBL phenotype and determination of bacterial species. Location of bla_CTX-M was confirmed by S1-PFGE, I-CeuI-PFGE and the Southern blotting hybridization. ESBL-producing Enterobacteriaceae was isolated from 32 (12.2%) of the collected 263 fecal samples, and 96 ESBL-producing Enterobacteriaceae isolates were obtained. CTX-M type ESBL-producing Escherichia coli B2 were major (67 isolates, 72.0%) and 40 (59.7%) of the 67 CTX-M type ESBL -producing E. coli B2 were E. coli B2-ST131. Three CTX-M type ESBL-producing E. coli B2-ST131 isolates from asymptomatic healthy individuals showed similar PFGE band patterns as five CTX-M type ESBL -producing E. coli B2-ST131 isolates from a hospital locates in the same area of the target community. Chromosomally-transferred bla_CTX-M was observed in 10.0% of the examined CTX-M type ESBL-producing Enterobacteriaceae isolates. We report current situation CTX-M type ESBL-producing Enterobacteriaceae carriage in asymptomatic healthy individuals of the Okinawa prefecture, Japan. In addition, our results indicated that worldwide distributed CTX-M type ESBL-producing E. coli B2-ST131 has been spread in a community. Therefore monitoring of ESBL-producing Enterobacteriaceae in healthy individuals is important.

Frequent isolation of extended-spectrum beta-lactamase-producing bacteria from fecal samples of individuals with severe motor and intellectual disabilities

Extended-spectrum beta-lactamase (ESBL) producing bacteria spread worldwide and became major concern for antibiotic treatment. Although surveillance reports in general hospitals and long-term care facilities are increasing, their frequencies in individuals with severe motor and intellectual disabilities (SMID) are so far unknown. In this study, we examined the frequency of ESBL in stool samples collected from 146 asymptomatic SMID subjects hospitalized in a single institution. With their clinical information, we evaluated possible risk factors for ESBL colonization. From 146 fecal samples, ESBL-producing bacteria were isolated in 45 cases (31%). Drug sensitivity testing showed that 82% of the isolates were resistant to levofloxacin but were sensitive to tazobactam/piperacillin and cefmetazole. The most frequent genotype was CTX-M-9 detected in 36/45 (80%). A high degree of disability, antibiotic use within three months before sampling and post-tracheostomy were statistically significant risk factors. Tube feeding was also strongly correlated with ESBL colonization (p < 0.001) and associated with lower micro-organismic diversities. Our findings are the first to reveal a high prevalence of ESBL in the fecal samples of SMID individuals and suggest possible relationships between high degree disability, tube feeding and latest histories of antibiotic use.

Proposed breakpoint of piperacillin/tazobactam against extended spectrum β-lactamases producing bacteria in bacteremia

The isolation rate of extended-spectrum β-lactamase (ESBL)-producing bacteria have been increasing in Japan. While the efficacy of piperacillin/tazobactam (PIPC/TAZ) for ESBL-producing bacteria is controversial, carbapenems have generally been shown to be effective. The aim of this study was to determine whether the current Clinical and Laboratory Standards Institute susceptibility breakpoint of ≤16/4 μg/mL PIPC/TAZ predicts the clinical usefulness for bacteremia caused by ESBL-producing Enterobacteriaceae. We retrospectively investigated 35 patients with bacteremia caused by Enterobacteriaceae producing ESBLs treated with PIPC/TAZ monotherapy. The microbiological and clinical efficacy with PIPC/TAZ minimum inhibitory concentrations (MICs) of ≤16/4 μg/mL was better than that with MICs ≥ 32/4 μg/mL. In contrast, MICs ≤8/4 μg/mL showed significantly higher microbiological and clinical efficacy compared to that of MICs ≥16/4 μg/mL (P < 0.05). These results suggest that 8/4 μg/mL PIPC/TAZ MIC is recommended as a breakpoint for bacteremia caused by ESBL-producing Enterobacteriaceae in Japan, although the current CLSI breakpoint is also useful.