High rates of intestinal colonisation with fluoroquinolone-resistant ESBL-harbouring Enterobacteriaceae in hospitalised patients with antibiotic-associated diarrhoea

Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance

Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.

Association between Clostridioides difficile infection and multidrug-resistant organism colonization or infection among hospitalized adults: A case-control study

Using an ambidirectional case-control study, we found that the odds of Clostridioides difficile infection (CDI) were 3.38 (P = .01) times higher for patients with multidrug-resistant organism (MDRO) colonization compared to those without. MDRO colonization or infection 1-12 months before CDI testing significantly increased risk of positive CDI diagnosis (odds ratio 4.71, P = .02 and odds ratio = 5.03, P = .05, respectively) independent of antibiotic use, age, and comorbidity status. MDRO colonization and infection are associated with CDI, most significantly if they precede CDI.

Effectiveness of oral antibiotics for treating pyelonephritis caused by extended-spectrum beta-lactamase-producing Enterobacteriaceae: A case series

BACKGROUND

Recently, the spread of multidrug-resistant bacteria has become a global problem. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (enterobacteria) is one example. The incidence of urinary tract infections caused by ESBL-producing enterobacteria has been increasing in some Japanese community settings. Currently, there is insufficient evidence on the effectiveness of oral antibiotics used for the treatment of pyelonephritis caused by ESBL-producing enterobacteria. We investigated the effectiveness of oral antibacterial agents against pyelonephritis caused by ESBL-producing Enterobacteriaceae.

METHODS

The records of patients who had been treated for pyelonephritis caused by ESBL-producing enterobacteria with oral antibiotics between April 1, 2014, and March 31, 2019, were reviewed retrospectively to assess the effectiveness of oral antibiotic treatment.

RESULTS

A total of seven cases were identified, including 1 patient with a positive blood culture and one patient with a Pitt bacteremia score of four points, indicating that the infections were severe. The antibiotics used to treat pyelonephritis were amoxicillin-clavulanic acid (n = 3), minocycline (n = 1), levofloxacin (n = 3), and sulfamethoxazole-trimethoprim with amoxicillin-clavulanic acid (n = 1). None of the patients had recurrence of pyelonephritis in the 60 days following oral antibiotic treatment, and there were no deaths during the 60-day follow-up period.

CONCLUSIONS

These antibiotics should be considered for oral treatment of pyelonephritis caused by ESBL-producing enterobacteria. However, as there is insufficient evidence available on the effectiveness of these antibiotics for the management of ESBL-producing enterobacterial infections, further large-scale prospective studies are needed.

Extended-spectrum β-lactamase, plasmid-mediated AmpC β-lactamase, fluoroquinolone resistance, and decreased susceptibility to carbapenems in Enterobacteriaceae: fecal carriage rates and associated risk factors in the community of Northern Cyprus

Background

Antibiotic-resistant Enterobacteriaceae in the gastrointestinal flora can lead to infections with limited therapeutic options. Also, the resistant bacteria can be transferred from colonized persons to others. The present study was conducted to search the fecal carriage rates of (i) Enterobacteriaceae that produce extended-spectrum β-lactamase (ESBL-E) and/or (ii) plasmid-mediated AmpC β-lactamase (pAmpC-E), (iii) ciprofloxacin-resistant Enterobacteriaceae (CIP-RE), and (iv) carbapenem-intermediate or -resistant Enterobacteriaceae (CIRE) in Northern Cyprus.

Methods

A total of 500 community-dwellers were recruited from consecutive admissions to the clinical laboratories of four hospitals. One rectal swab or stool sample was collected from each participant. A questionnaire was applied to evaluate possible risk factors associated with intestinal colonization of resistant bacteria. The samples were cultured on antibiotic containing media to screen for resistant bacteria colonization. The bacterial colonies that grew on the plates were subjected to further phenotypic tests to confirm the resistance.

Results

Of 500 volunteers, ESBL-E, pAmpC-E, CIP-RE and CIRE carriage were detected in 107 (21.4%), 15 (3.0%), 51 (10.2%) and six (1.2%) participants, respectively. Escherichia coli was the most commonly recovered species among Enterobacteriaceae isolates. A significant proportion of ESBL-producing E. coli isolates (n = 22/107; 20.6%) was found to be co-resistant to CIP (p = 0.000, OR 3.21, 95% CI 1.76-5.87). In this study, higher socioeconomic status (CIP-RE: p = 0.024, OR 1.96, 95% CI 1.09-3.53), presence of gastrointestinal symptoms (CIRE: p = 0.033; OR 6.79, 95% CI 1.34-34.39), antibiotic use (ESBL-E: p = 0.031; OR 1.67, 95% CI 1.04-2.67; and CIRE: p = 0.033; OR 6.40, 95% CI 1.16-35.39), and travelling abroad (pAmpC-E: p = 0.010; OR 4.12, 95% CI 1.45-11.66) were indentified as risk factors.

Conclusion

The study indicates that resistant Enterobacteriaceae isolates are carried by humans in the community. To prevent further spread of resistance, rational use of antibiotics should be encouraged, and antibiotic resistance should be carefully monitored in Northern Cyprus.

The co-transfer of plasmid-borne colistin-resistant genes mcr-1 and mcr-3.5, the carbapenemase gene blaNDM-5 and the 16S methylase gene rmtB from Escherichia coli

We found an unusual Escherichia coli strain with resistance to colistin, carbapenem and amikacin from sewage. We therefore characterized the strain and determined the co-transfer of the resistance determinants. Whole genome sequencing was performed using both Illumina HiSeq X10 and MinION sequencers. Short and long reads were subjected to de novo hybrid assembly. Sequence type, antimicrobial resistance genes and plasmid replicons were identified from the genome sequences. Phylogenetic analysis of all IncHI2 plasmids carrying mcr-1 available in GenBank was performed based on core genes. Conjugation experiments were performed. mcr-3.5 was cloned into E. coli DH5α. The strain belonged to ST410, a type with a global distribution. Two colistin-resistant genes, mcr-1.1 and mcr-3.5, a carbapenemase gene bla_NDM-5, and a 16S methylase gene rmtB were identified on different plasmids of IncHI2(ST3)/IncN, IncP, IncX3 and IncFII, respectively. All of the four plasmids were self-transmissible and mcr-1.1, mcr-3.5, bla_NDM-5 and rmtB were transferred together. mcr-1-carrying IncHI2 plasmids belonged to several sequence types with ST3 and ST4 being predominant. MIC of colistin (4 μg/ml) for DH5α containing mcr-3.5 was identical to that containing the original mcr-3 variant. In conclusion, carbapenem resistance, colistin resistance and high-level aminoglycoside resistance can be transferred together even when their encoding genes are not located on the same plasmid. The co-transfer of multiple clinically-important antimicrobial resistance represents a particular challenge for clinical treatment and infection control in healthcare settings. Isolates with resistance to both carbapenem and colistin are not restricted to a given sequence type but rather are diverse in clonal background, which warrants further surveillance. The amino acid substitutions of MCR-3.5 have not altered its activity against colistin.

Does ciprofloxacin prophylaxis during chemotherapy induce intestinal microflora resistance to ceftazidime in children with cancer?

To determine the susceptibility and minimal inhibitory concentrations (MIC) of ceftazidime, the commonly used empirical antibiotic in patients with febrile neutropenia, in Escherichia coli and Klebsiella pneumoniae isolated from the intestinal microflora of pediatric patients with cancer, who received ciprofloxacin prophylaxis during chemotherapy, children younger than 18 years with acute lymphoblastic leukemia or lymphoma scheduled to undergo chemotherapy were randomized to receive oral ciprofloxacin 20 mg/kg/day or placebo from the beginning of their chemotherapy. Rectal swab cultures were taken before (R0) and at 1 (R1), 2 (R2), and 3 (R3) weeks during the intervention. The antimicrobial susceptibilities and MICs of ceftazidime and ciprofloxacin were determined via the E test. Of the total 87 patients enrolled, 44 received ciprofloxacin and 43 placebo. A total of 350 isolates were obtained, 62, 49, 46 and 22 from the ciprofloxacin group and 68, 54, 38 and 11 from the placebo group at R0, R1, R2 and R3, respectively. The percentages of ceftazidime susceptibility did not show significantly greater decreases from R0 to R1-R3 in the ciprofloxacin group compared to the placebo group. The MIC₅₀s of ceftazidime showed significantly greater increases after ciprofloxacin prophylaxis during R1-R3 compared to R0 in the intervention group compared to the placebo group (R0, 0.12 vs. 0.12; R1, 0.19 vs. 0.12; R2, 0.19 vs. 0.12 and R3, 0.38 vs. 0.09 μg/mL, respectively). Due to the increasing MIC₅₀ of ceftazidime over time after ciprofloxacin prophylaxis, the use of ceftazidime in patients who have previously had ciprofloxacin prophylaxis needs to be closely monitored.

Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis

OBJECTIVES

Observational studies have suggested that Escherichia coli sequence type (ST) 131 and Klebsiella pneumoniae ST258 have hyperendemic properties. This would be obvious from continuously high incidence and/or prevalence of carriage or infection with these bacteria in specific patient populations. Hyperendemicity could result from increased transmissibility, longer duration of infectiousness, and/or higher pathogenic potential as compared with other lineages of the same species. The aim of our research is to quantitatively estimate these critical parameters for E. coli ST131 and K. pneumoniae ST258, in order to investigate whether E. coli ST131 and K. pneumoniae ST258 are truly hyperendemic clones.

PRIMARY OUTCOME MEASURES

A systematic literature search was performed to assess the evidence of transmissibility, duration of infectiousness, and pathogenicity for E. coli ST131 and K. pneumoniae ST258. Meta-regression was performed to quantify these characteristics.

RESULTS

The systematic literature search yielded 639 articles, of which 19 data sources provided information on transmissibility (E. coli ST131 n=9; K. pneumoniae ST258 n=10)), 2 on duration of infectiousness (E. coli ST131 n=2), and 324 on pathogenicity (E. coli ST131 n=285; K. pneumoniae ST258 n=39). Available data on duration of carriage and on transmissibility were insufficient for quantitative assessment. In multivariable meta-regression E. coli isolates causing infection were associated with ST131, compared to isolates only causing colonisation, suggesting that E. coli ST131 can be considered more pathogenic than non-ST131 isolates. Date of isolation, location and resistance mechanism also influenced the prevalence of ST131. E. coli ST131 was 3.2 (95% CI 2.0 to 5.0) times more pathogenic than non-ST131. For K. pneumoniae ST258 there were not enough data for meta-regression assessing the influence of colonisation versus infection on ST258 prevalence.

CONCLUSIONS

With the currently available data, it cannot be confirmed nor rejected, that E. coli ST131 or K. pneumoniae ST258 are hyperendemic clones.

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multidrug-resistant (MDR) bacterial pathogens. With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency, and accuracy of information vary considerably across different databases. In this article, we explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions.

SOS response and its regulation on the fluoroquinolone resistance

Bacteria can survive fluoroquinolone antibiotics (FQs) treatment by becoming resistant through a genetic change-mutation or gene acquisition. The SOS response is widespread among bacteria and exhibits considerable variation in its composition and regulation, which is repressed by LexA protein and derepressed by RecA protein. Here, we take a comprehensive review of the SOS gene network and its regulation on the fluoroquinolone resistance. As a unique survival mechanism, SOS may be an important factor influencing the outcome of antibiotic therapy in vivo.

First Report of OXA-181-Producing Escherichia coli in China and Characterization of the Isolate Using Whole-Genome Sequencing

We report the first OXA-181-producing strain in China. blaOXA-181 was found in sequence type 410 (ST410) Escherichia coli strain WCHEC14828 from a Chinese patient without recent travel history. Genome sequencing and conjugation experiments were performed. blaOXA-181 was carried on a 51-kb self-transmissible IncX3 plasmid and was linked with qnrS1, a quinolone resistance gene. blaOXA-181 was introduced onto the IncX3 plasmid from a ColE2-type plasmid, and IncX3 plasmids have the potential to mediate the dissemination of blaOXA-181.