Pattern of Antibiotic Resistance Among Community Derived Isolates of Enterobacteriaceae Using Urine Sample: A Study From Northern India

Clinical and Microbiological Characteristics of Community-Onset Carbapenem-Resistant Enterobacteriaceae Isolates

Objective

The aim of this study was to investigate the clinical and microbiological features of community-onset CRE (CO-CRE) obtained from outpatients at a tertiary hospital in China.

Patients and Methods

We isolated 64 CRE strains from outpatients and divided them into three groups: 36 hospital-acquired CRE (HA-CRE), 28 CO-CRE including 15 community-acquired CRE (CA-CRE) and 13 healthcare-associated CRE (HCA-CRE). Clinical information was collected. The antibiotic susceptibilities of the 28 CO-CRE strains were tested. Whole-genome sequencing (WGS) was conducted, and then drug resistance gene analysis was performed. CgMLST and SNP comparisons were used to analyze the genomic relationship with E. coli and K. pneumoniae strains, respectively.

Results

In this study, the 28 CO-CRE isolates included K. pneumoniae (53.6%), E. coli (28.6%), E. cloacae (7.1%), C. freundii (7.1%) and E. asburiae (3.6%). The CO-CRE isolates were mainly isolated from urine samples (75%). The ceftazidime/avibactam resistance rate of community-onset E. coli was significantly higher than that of community-onset K. pneumoniae, while the aztreonam, ciprofloxacin, levofloxacin, and chloramphenicol resistance rates were significantly lower (P<0.05). Thirteen of the 15 K. pneumoniae strains belonged to ST11 containing bla_KPC-2. Correspondingly, 8 E. coli strains belonged to 7 STs, and they all were NDM producers. K. pneumoniae belonged to two major clusters, while E. coli was sporadic. The number of SNPs separating ST11 K. pneumoniae isolates ranged from 7 to 2154.

Conclusion

Community-onset CRE is not rare, and the dissemination of E. coli was sporadic while K. pneumoniae was clonal spread with similar STs as HA-CRE. Active surveillance of CRE in the community setting is in demand.

Colonization With Multidrug-Resistant Organisms Among Healthy Adults in the Community Setting: Prevalence, Risk Factors, and Composition of Gut Microbiome

BACKGROUND

The prevalence of colonization with multidrug-resistant organisms (MDROs) among healthy adults in the community is largely unknown. This study investigated the colonization rate of multidrug-resistant Enterobacteriaceae, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE) in the community in Taiwan, and compared the gut microbiota between MDRO carriers and non-carriers.

METHODS

This prospective cohort study was conducted from March 2017 to February 2018 at the Hsin-Chu and Jin-Shan branches of National Taiwan University Hospital. Nasal swabs and stool samples were obtained from healthy adults attending a health examination to screen for MDROs. Bacteria isolates of MDROs were tested for antibiotic susceptibility and resistant genes. Relevant data were collected using a standardized questionnaire to evaluate the risk factors for MDROs carriage, and 16S rRNA metagenomics sequencing was performed to analyze gut microbiota.

RESULTS

Among 187 participants, 4.6% (8/174) carried MRSA and 41.4% (77/186) carried third-generation cephalosporin-resistant (3GC-R) Escherichia coli or Klebsiella pneumoniae. The carriage rate of AmpC beta-lactamases and ESBL-producing strains were 16.1 and 27.4%, respectively. No carbapenem-resistant Enterobacteriaceae (CRE) or VRE were detected. The dominant resistant gene of E. coli isolates was CTX-M-type (73%), while that of K. pneumoniae was AmpC beta-lactamases (80%). In the multivariate analysis, the significant risk factors for carrying 3GC-R E. coli or K. pneumoniae were being an employee of technology company A [adjusted odds ratio (aOR) 4.127; 95% confidence interval (CI) 1.824-9.336; p = 0.001], and traveling to Southeast Asia in the past year (aOR 6.545; 95% CI 1.071-40.001; p = 0.042). The gut microbiota analysis showed that the phylum Proteobacteria and the family Enterobacteriaceae were significantly more abundant in 3GC-R E. coli and K. pneumoniae carriers.

CONCLUSION

A high rate of Taiwanese adults in the community carried 3GC-R Enterobacteriaceae, while no CRE or VRE colonization was noted. Compared with non-carriers, an expansion of Enterobacteriaceae in gut microbiota was found among 3GC-R Enterobacteriaceae carriers.

Trends in Resistance to Extended-Spectrum Cephalosporins and Carbapenems among Escherichia coli and Klebsiella spp. Isolates in a District in Western India during 2004-2014

Surveillance data on the level of resistant bacteria is needed to inform strategies to reduce the development and spread of antibiotic resistance. The aim of this study was to determine the non-susceptibility trends to extended-spectrum cephalosporins and carbapenems among Escherichia coli and Klebsiella spp. isolates from the district of Nashik in Western India during the period 2004-2014. Antibacterial susceptibility testing of clinical isolates was performed using Kirby-Bauer disc diffusion method to determine inhibitory zone diameters. The change in proportions of non-susceptible bacteria over calendar time was investigated with spline transformations in a logistic regression model. For the extended-spectrum cephalosporins, the proportions of non-susceptible E. coli and Klebsiella spp. isolates were above 78.4% and 84.9% throughout the study period, respectively. E. coli and Klebsiella spp. isolates exhibited carbapenem non-susceptibility levels as high as 76.9% and 84.1% respectively. The proportions of extended-spectrum betalactamase (ESBL)-producing isolates ranged from 38.3-85.9% in E. coli and from 45.1-93.1% in Klebsiella spp. Significantly higher proportions of non-susceptible and ESBL-producing isolates were found among isolates from inpatients compared to isolates from outpatients for both E. coli and Klebsiella spp. (p < 0.050). The high proportions of non-susceptible isolates observed show that there is great need to focus on optimal use of antibiotics to reduce the development of antibiotic resistance.

Carbapenem-resistant Enterobacteriaceae in the community: a scoping review

Carbapenem antibiotics are used as a last resort to treat serious Gram-negative bacteria (GNB) infections; however, carbapenemase-producing strains of GNB have emerged as a major source of resistance. Owing to the highly transmissible nature of plasmid-borne carbapenemases, numerous reports have warned about the likely spread into the community from healthcare settings. Since the prevalence of carbapenem-resistant Enterobacteriaceae (CRE) in the community is largely unknown, we conducted a scoping review of the literature to assess the percentage of CRE isolates that could be associated with the community. Initially, 361 studies were assessed and 15 met the inclusion criteria. Although 5 studies (33.3%) found no community-associated CRE, the remaining 10 studies identified percentages ranging from 0.04% to 29.5% of either community-associated or community-onset CRE among their samples, with US-based studies alone ranging from 5.6 to 10.8%. The presence of CRE in the community poses an urgent public health threat.

High Prevalence of ESBL-Producing Klebsiella pneumoniae Causing Community-Onset Infections in China

The aim of this work was to investigate the epidemiological and genetic characteristics of ESBL-producing Klebsiella pneumoniae (ESBL-Kp) causing community-onset infections. K. pneumoniae isolates were collected from 31 Chinese secondary hospitals between August 2010 and 2011. Genes encoding ESBL and AmpC beta-lactamases were detected by PCR. The isolates were assigned to sequence types (STs) using multi-locus sequence typing (MLST). Eleven ESBL-Kp strains were selected for whole-genome sequencing (WGS) for investigating the genetic environment and plasmids encoding ESBL genes. A total of 578 K. pneumoniae isolates were collected, and 184 (31.8%) carried ESBL genes. The prevalence of ESBL-Kp varied from different geographical areas of China (10.2–50.3%). The three most prevalent ESBL genes were bla_CTX-M-14 (n = 74), bla_CTX-M-15 (n = 60), and bla_CTX-M-3 (n = 40). MLST assigned 127 CTX-M-14 and CTX-M-15 producers to 54 STs, and CC17 was the most prevalent population (12.6%). STs (23, 37, and 86) that were known frequently associated with hypervirulent K. pneumoniae (hvKP) account for 14.1% (18/127). Phylogenetic analysis by concatenating the seven loci of MLST revealed the existence of ESBL-producing K. quasipneumoniae (two strains) and K. varricola (one strain), which was further confirmed by WGS. This study highlights the challenge of community-onset infections caused by ESBL-Kp in China. The prevalence of STs frequently associating with hvKP should be of concern. Surveillance of ESBL-KP causing community-onset infections now appears imperative.