Fecal carriage and clonal dissemination of blaNDM-1 carrying Klebsiella pneumoniae sequence type 147 at an intensive care unit in Lao PDR

OBJECTIVES

Carbapenemase-producing Enterobacterales (CPE) are high priority targets of global antimicrobial surveillance. Herein, we determined the colonization rate of CPE on admission to intensive care units in Vientiane, Lao PDR in August-September 2019.

METHODS

Data regarding clinical conditions, infection control, and antibiotic usage were collected during admission. Rectal swab samples (n = 137) collected during admission were inoculated to selective chromogenic agars, followed by confirmatory tests for extended-spectrum beta-lactamases and carbapenemases. All CPE isolates were sequenced on Illumina (HiSeq2500), reads assembled using SPAdes 3.13, and the draft genomes used to query a database (https://www.genomicepidemiology.org) for resistome, plasmid replicons, and sequence types (ST). Optical DNA mapping (ODM) was used to characterize plasmids and to determine location of resistance genes. Minimum spanning tree was generated using the Bacterial Isolate Genome Sequence database (BIGSdb) and annotated using iTOL.

RESULT

From 47 Enterobacterales isolated on selective agars, K. pneumoniae (25/47) and E. coli (12/47) were the most prevalent species, followed by K aerogenes (2/47), K. variicola (1/47), and K. oxytoca (1/47). The overall prevalence of ESBLs was 51.0%; E. coli 83.3% (10/12) and Klebsiella spp. 41.3% (12/29). Twenty percent of the K. pneumoniae (5/25) isolates were carbapenem-resistant, and 4/5 contained the blaNDM-1 gene. All blaNDM-1 isolates belonged to ST147 and were indistinguishable with cgMLST. ODM showed that the blaNDM-1 gene was located on identical plasmids in all isolates.

CONCLUSION

The prevalence of ESBL-producing Enterobacterales was high, while carbapenemases were less common. However, the detection of clonal dissemination of blaNDM-1-producing K. pneumoniae isolates in one of the intensive care units calls for vigilance. Stringent infection prevention and antimicrobial stewardship strategies are highly important measures.

High diversity of blaNDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital

OBJECTIVES

The carbapenemase-encoding gene bla_NDM-1 has been reported in Vietnam over the last ten years, and bla_NDM-producing Enterobacteriaceae are now silently and rapidly spreading. A key factor behind dissemination of bla_NDM-1 are plasmids, mobile genetic elements that commonly carry antibiotic resistance genes and spread via conjugation. Here, we characterized the diversity of bla_NDM-1-encoding plasmids from neonates at a large Vietnamese hospital .

METHODS

18 fecal Klebsiella pneumoniae and Klebsiella quasipneumoniae isolates collected from 16 neonates at a large pediatric hospital in Vietnam were studied with optical DNA mapping (ODM) and next-generation sequencing (NGS). We identified the plasmid(s) carrying bla_NDM-1 by combining ODM with Cas9 restriction. By comparing the plasmids between isolates, we could investigate if the same plasmid was present in different patients.

RESULTS

Although the same plasmid was found among some isolates, ODM confirmed that there were at least 10 different plasmids encoding bla_NDM-1 among the 18 isolates collected from 16 neonates, suggesting a large plasmid diversity. The ODM results were in large agreement with the NGS data. Interestingly, some isolates had two distinct plasmids encoding bla_NDM-1, which could be readily detected with ODM. Thus far, the coexistence of different plasmids carrying the same carbapenem resistance gene in an isolate encoding bla_NDM-1 has rarely been reported, likely due to limitations in existing plasmid characterization techniques.

CONCLUSIONS

Our results show that the plasmids encoding bla_NDM-1 in this cohort were very diverse, suggesting a similar picture in the Vietnamese society. The study also highlights important aspects of the usefulness of ODM for plasmid analysis.

Admission screening and cohort care decrease carbapenem resistant enterobacteriaceae in Vietnamese pediatric ICU's

Objectives

To assess if admission screening for Carbapenem Resistant Enterobacteriaceae (CRE) and cohort care can reduce CRE acquisition (CRE colonization during hospital stay), Hospital Acquired Infections (HAI), hospital-stay, mortality, and costs in three Intensive Care Units (ICU’s) at the Vietnamese National Children’s Hospital.

Method

CRE screening using rectal swabs and ChromIDCarbas elective culture at admission and if CRE negative, once weekly. Patients were treated in cohorts based on CRE colonization status.

Results

CRE colonization at baseline point-prevalence screening was 76.9% (103/134). Of 941 CRE screened at admission, 337 (35.8%) were CREpos. 694 patients met inclusion criteria. The 244 patients CRE negative at admission and screened > 2 times were stratified in 8 similar size groups (periods), based on time of admission. CRE acquisition decreased significant (OR − 3.2, p < 0.005) from 90% in period 2 (highest) to 48% in period 8 (last period). Patients with CRE acquisition compared to no CRE acquisition had a significantly higher rate of culture confirmed HAI, n = 20 (14%) vs. n = 2 (2%), longer hospital stays, 3.26 vs. 2.37 weeks, and higher total treatment costs, 2852 vs. 2295 USD.

Conclusion

Admission CRE screening and cohort care in pediatric ICU’s significantly decreased CRE acquisition, cases of HAI and duration of hospital-stay.

Prospective One Health genetic surveillance in Vietnam identifies distinct blaCTX-M-harbouring Escherichia coli in food-chain and human-derived samples

OBJECTIVES

We performed a One Health surveillance in Hanoi-a region with a high-density human population and livestock production, and a recognized hotspot of animal-associated antimicrobial resistance (AMR)-to study the contribution of bla_CTX-M-carrying Escherichia coli and plasmids from food-animal sources in causing human community-acquired urinary tract infections (CA-UTIs).

METHODS

During 2014-2015, 9090 samples were collected from CA-UTI patients (urine, n = 8564), pigs/chickens from farms and slaughterhouses (faeces, carcasses, n = 448), and from the slaughterhouse environment (surface swabs, water, n = 78). E. coli was identified in 2084 samples. Extended-spectrum β-lactamase (ESBL) production was confirmed in 235 and bla_CTX-M in 198 strains by PCR with short-read plasmid sequencing. Fourteen strains were long-read sequenced to enable plasmid reconstruction.

RESULTS

The majority of the ESBL-producing E. coli strains harboured bla_CTX-M (n = 198/235, 84%). High clonal diversity (48 sequence types, STs) and distinct, dominant STs in human sources (ST1193, n = 38/137; ST131, n = 30/137) and non-human sources (ST155, n = 25/61) indicated lack of clonal transmission between habitats. Eight bla_CTX-M variants were identified; five were present in at least two sample sources. Human and food-animal strains did not show similar plasmids carrying shared bla_CTX-M genes. However, IS6 elements flanking ISEcp1-bla_CTX-M-orf477/IS903B structures were common across habitats.

CONCLUSIONS

In this study, animal-associated bla_CTX-ME. coli strains or bla_CTX-M plasmids were not direct sources of CA-UTIs or ESBL resistance in humans, respectively, suggesting evolutionary bottlenecks to their adaptation to a new host species. Presence of common IS6 elements flanking bla_CTX-M variants in different plasmid backbones, however, highlighted the potential of these transposable elements for AMR transmission either within or across habitats.