Comparative epidemiology of CTX-M-14 and CTX-M-15 producing Escherichia coli: association with distinct demographic groups in the community in New Zealand

Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis

BACKGROUND

International travel increases the risk of acquisition of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Previous studies have characterized the changes in the gut microbiome and resistome of Western travellers; however, information on non-Western populations and the effects of travel-related risk factors on the gut microbiome and resistome remains limited.

METHODS

We conducted a prospective observational study on a cohort of 90 healthy Chinese adult residents of Hong Kong. We characterized the microbiome and resistome in stools collected from the subjects before and after travelling to diverse international locations using shotgun metagenomic sequencing and examined their associations with travel-related variables.

RESULTS

Our results showed that travel neither significantly changed the taxonomic composition of the faecal microbiota nor altered the alpha (Shannon) or beta diversity of the faecal microbiome or resistome. However, travel significantly increased the number of ARGs. Ten ARGs, including aadA, TEM, mgrB, mphA, qnrS9 and tetR, were significantly enriched in relative abundance after travel, eight of which were detected in metagenomic bins belonging to Escherichia/Shigella flexneri in the post-trip samples. In sum, 30 ARGs significantly increased in prevalence after travel, with the largest changes observed in tetD and a few qnrS variants (qnrS9, qnrS and qnrS8). We found that travel to low- or middle-income countries, or Africa or Southeast Asia, increased the number of ARG subtypes, whereas travel to low- or middle-income countries and the use of alcohol-based hand sanitizer (ABHS) or doxycycline as antimalarial prophylaxis during travel resulted in increased changes in the beta diversity of the faecal resistome.

CONCLUSIONS

Our study highlights travel to low- or middle-income countries, Africa or Southeast Asia, a long travel duration, or the use of ABHS or doxycycline as antimalarial prophylaxis as important risk factors for the acquisition/enrichment of ARGs during international travel.

Genomic Characterization of ESBL/AmpC-Producing Escherichia coli in Stray Dogs Sheltered in Yangzhou, China

Purpose

Limited data are available on the prevalence and antimicrobial resistance of extended spectrum β-lactamase- (ESBL) and AmpC β-lactamase-producing Escherichia coli in stray dogs. We aimed to investigate the genomic characteristics of ESBL/AmpC-producing E. coli isolated from stray dogs sheltered in Yangzhou, China.

Methods

We collected 156 samples including 115 fecal swabs, 35 kennel floor swabs, two breeder hand and shoe sole swabs, and four feed samples. The isolates were tested for resistance by antimicrobial susceptibility testing and further analyzed for cefotaxime-resistant E. coli isolates by whole genome sequencing.

Results

We identified 80 cefotaxime-resistant E. coli isolates (51.3%), 59 isolates (73.8%) from feces and 21 (26.2%) from the environment. Whole-genome sequencing analysis showed that bla _CTX-M-15 (n=30) and bla _CTX-M-55 (n=29) were the most prevalent genotypes. Two isolates only carried the AmpC β-lactamase gene bla _CMY-2; one isolate had a combination of AmpC β-lactamase gene bla _DHA-1 and ESBL β-lactamase gene bla _CTX-M-14. Other important resistance genes such as bla _OXA-10, bla _TEM-1B, bla _TEM-135, bla _TEM-106, tet(A), qnrS1, qnrB4, and oqxAB were also detected. The serotype combination was highly abundant, with O10:H25 predominating (n=12). Most cefotaxime-resistant E. coli isolates belonged to phylogroup A (62.5%, n=50), followed by phylogroup B1 (26.3%, n=21). Thirty different sequence types (STs) and 27 distinct plasmid replicons were identified, among which ST2325 (n=12) and IncFII (n=38) was the most frequent ST and plasmid, respectively. ESBL/AmpC-producing isolates were divided into four major clades; clade IV was the primary lineage containing 37 isolates from feces and 13 from the environment. Three high-risk E. coli clone ST23 strains and one ST10 strain belonged to clades III and IV, respectively.

Conclusion

Our study provides a comprehensive overview of resistance profiles and genomic characteristics in ESBL/AmpC-producing E. coli and highlights the possible role of stray dogs as an antibiotic resistance gene reservoir.

Pan-genome and resistome analysis of extended-spectrum ß-lactamase-producing Escherichia coli: A multi-setting epidemiological surveillance study from Malaysia

Objectives

This study profiled the prevalence of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-EC) in the community and compared their resistome and genomic profiles with isolates from clinical patients through whole-genome sequencing.

Methods

Fecal samples from 233 community dwellers from Segamat, a town in southern Malaysia, were obtained between May through August 2018. Putative ESBL strains were screened and tested using antibiotic susceptibility tests. Additionally, eight clinical ESBL-EC were obtained from a hospital in the same district between June through October 2020. Whole-genome sequencing was then conducted on selected ESBL-EC from both settings (n = 40) for pan-genome comparison, cluster analysis, and resistome profiling.

Results

A mean ESBL-EC carriage rate of 17.82% (95% CI: 10.48%– 24.11%) was observed in the community and was consistent across demographic factors. Whole-genome sequences of the ESBL-EC (n = 40) enabled the detection of multiple plasmid replicon groups (n = 28), resistance genes (n = 34) and virulence factors (n = 335), with no significant difference in the number of genes carried between the community and clinical isolates (plasmid replicon groups, p = 0.13; resistance genes, p = 0.47; virulence factors, p = 0.94). Virulence gene marker analysis detected the presence of extraintestinal pathogenic E. coli (ExPEC), uropathogenic E. coli (UPEC), and enteroaggregative E. coli (EAEC) in both the community and clinical isolates. Multiple blaCTX-M variants were observed, dominated by blaCTX-M-27 (n = 12), blaCTX-M-65 (n = 10), and blaCTX-M-15 (n = 9). The clinical and community isolates did not cluster together based on the pan-genome comparison, suggesting isolates from the two settings were clonally unrelated. However, cluster analysis based on carried plasmids, resistance genes and phenotypic susceptibility profiles identified four distinct clusters, with similar patterns between the community and clinical isolates.

Conclusion

ESBL-EC from the clinical and community settings shared similar resistome profiles, suggesting the frequent exchange of genetic materials through horizontal gene transfer.

Prevalence of third-generation cephalosporin-resistant Enterobacterales colonization on hospital admission and ESBL genotype-specific risk factors: a cross-sectional study in six German university hospitals

OBJECTIVES

To assess the admission prevalence of third-generation cephalosporin-resistant Enterobacterales (3GCREB) and to assess whether risk factors vary by β-lactamase genotype.

METHODS

Adult patients were recruited within 72 h of admission to general wards of six university hospitals in 2014 and 2015. Rectal swabs were screened for 3GCREB and isolates were analysed phenotypically and genotypically. Patients were questioned on potential risk factors. Multivariable analyses were performed to identify risk factors for 3GCREB colonization and for specific β-lactamases.

RESULTS

Of 8753 patients screened, 828 were 3GCREB positive (9.5%). Eight hundred and thirteen isolates were available for genotyping. CTX-M-15 was the most common ESBL (38.0%), followed by CTX-M-1 (22.5%), CTX-M-14 (8.7%), CTX-M-27 (7.5%) and SHV-ESBL (4.4%). AmpC was found in 11.9%. Interestingly, 18 Escherichia coli isolates were AmpC positive, 12 of which (67%) contained AmpC on a gene of plasmid origin [CMY (n = 10), DHA (n = 2)]. Risk factors for 3GCREB colonization varied by genotype. Recent antibiotic exposure and prior colonization by antibiotic-resistant bacteria were risk factors for all β-lactamases except CTX-M-14 and CTX-M-27. Travel outside Europe was a risk factor for CTX-M-15 and CTX-M-27 [adjusted OR (aOR) 3.49, 95% CI 2.88-4.24 and aOR 2.73, 95% CI 1.68-4.43]. A previous stay in a long-term care facility was associated with CTX-M-14 (aOR 3.01, 95% CI 1.98-4.59). A preceding hospital stay in Germany increased the risk of CTX-M-15 (aOR 1.27, 95% CI 1.14-1.41), while a prior hospital stay in other European countries increased the risk of SHV-ESBL colonization (aOR 3.85, 95% CI 1.67-8.92).

CONCLUSIONS

The detection of different ESBL types is associated with specific risk factor sets that might represent distinct sources of colonization and ESBL-specific dissemination routes.

The Continuing Plague of Extended-Spectrum β-Lactamase Producing Enterbacterales Infections: An Update

Antimicrobial resistance is a common iatrogenic complication of modern life and medical care. One of the most demonstrative examples is the exponential increase in the incidence of extended-spectrum β-lactamases (ESBLs) production among Enterobacteriaceae, that is, the most common human pathogens outside of the hospital setting. Infections resulting from ESBL-producing bacteria are associated with devastating outcomes, now affecting even previously healthy individuals. This poses an enormous burden and threat to public health. This article aims to narrate the evolving epidemiology of ESBL infections and highlights current challenges in terms of management and prevention of these common infections.

Extended-spectrum β-lactamase-producing Escherichia coli bacteremia: Comparison of pediatric and adult populations

BACKGROUND/PURPOSE

The prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is increasing worldwide. This study investigated the clinical features and bacteriology of pediatric patients with ESBL-producing E. coli bacteremia and compared their characteristics with those of adult patients.

METHODS

Clinical and laboratory data from all of the 41 patients aged ≤18 years diagnosed with E. coli bacteremia were collected over 5 years. Patients aged >18 years diagnosed with E. coli bacteremia, matched 1:1 for calendar time, were enrolled as the adult group. All E. coli isolates were tested for their blaCTX-M group and sequence type 131 (ST131). A novel seven-single nucleotide polymorphism-based clonotyping test was applied to detect the septatypes of each isolate.

RESULTS

In the adult group, patients with ESBL-producing E. coli bacteremia had more previous hospitalizations and antimicrobial agent use than did those with non-ESBL-producing E. coli bacteremia, but these differences were not found in pediatric group. In the pediatric group, the proportion of isolates producing CTX-M group 9 was higher than that in the adult group (85.7% vs. 42.9%; p < 0.05). Among both groups, there were more E. coli ST131 in ESBL isolates in than there were non-ESBL isolates. The distribution of septatypes was more homogenous in ESBL-producing E. coli among the pediatric patients than among the adult patients.

CONCLUSION

ST131 was the major clone causing E. coli bacteremia in both pediatric and adult populations. The pediatric population demonstrated a higher number of isolates producing CTX-M group 9 with more homogenous septatypes compared with the adult population.

The Continuing Plague of Extended-spectrum β-lactamase-producing Enterobacteriaceae Infections

Antimicrobial resistance is a common iatrogenic complication of modern life and medical care. One of the most demonstrative examples is the exponential increase in the incidence of extended-spectrum β-lactamases (ESBLs) production among Enterobacteriaceae, which is the most common human pathogens outside of the hospital settings. Infections resulting from ESBL-producing bacteria are associated with devastating outcomes, now affecting even previously healthy individuals. This development poses an enormous burden and threat to public health. This paper aims to narrate the evolving epidemiology of ESBL infections, and highlight current challenges in terms of management and prevention of these common infections.

Escherichia coli β-Lactamases: What Really Matters

Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes.

Resistance mechanisms in Enterobacteriaceae

Enterobacteriaceae are responsible for a large proportion of serious, life-threatening infections and resistance to multiple antibiotics in these organisms is an increasing global public health problem. Mutations in chromosomal genes contribute to antibiotic resistance, but Enterobacteriaceae are adapted to sharing genetic material and much important resistance is due to 'mobile' resistance genes. Different mobile genetic elements, which have different characteristics, are responsible for capturing these genes from the chromosomes of a variety of bacterial species and moving them between DNA molecules. If transferred to plasmids, these resistance genes are then able to be transferred 'horizontally' between different bacterial cells, including different species, and well as being transferred 'vertically' during cell division. Carriage of several resistance genes on the same plasmid enables a bacterial cell to acquire multi-resistance in a single step and means that spread of one resistance gene may be co-selected for by use of antibiotics other than those to which it confers resistance. Many different mobile genes conferring resistance to each class of antibiotic have been identified, complicating detection of the factors responsible for a particular resistance phenotype, especially when changes in chromosomal genes may also confer or contribute to resistance. Understanding the mechanisms of antibiotic resistance, and the means by which these mechanisms can evolve and disseminate, is important for developing ways to efficiently track the spread of resistance and to optimise treatment.

The complex epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae

ABSTRACT 

Antimicrobial resistance is a growing worldwide iatrogenic complication of modern medical care. Extended-spectrum β-lactamases have emerged as one of the most successful resistance mechanisms, limiting our therapeutic options to treat various human infections. The dissemination of these enzymes to the community probably signifies an irreversible step. This paper will review the evolution of human infections associated with extended-spectrum β-lactamase-producing organisms in the past 20 years, and will present and discuss the current challenges, controversies, debates and knowledge gaps in this research field.

CTX-M-27- and CTX-M-14-producing, ciprofloxacin-resistant Escherichia coli of the H30 subclonal group within ST131 drive a Japanese regional ESBL epidemic

OBJECTIVES

The global increase in ESBL-producing Escherichia coli is associated with the ST131 clonal group, especially its CTX-M-15-producing H30Rx subset. To understand the rapid spread of ESBL-producing E. coli in Japan, we investigated the molecular epidemiology and ESBL-associated genetic environments of Japanese ST131 isolates.

METHODS

Between 2001 and 2012, 1079 ESBL-producing E. coli isolates were collected at 10 Japanese acute-care hospitals. ESBL types, ST131 status, fimH allele, H30Rx-defining sequences and ESBL-associated genetic environments were defined using PCR and sequencing. Subclonal groups were defined based on fimH allele and H30Rx status.

RESULTS

Overall, 461 (43%) of the 1079 ESBL-producing E. coli isolates represented ST131. According to fimH-based subclonal typing, the ST131 isolates included 398 fimH allele 30 (H30) isolates, 49 H41 isolates, 10 H22 isolates and 4 other fimH-type isolates. The 398 H30 isolates included 396 ciprofloxacin-resistant H30R isolates, of which 64 (16%) represented the H30Rx subset. Between 2001 and 2007, the CTX-M-14-producing H30R subgroup predominated, accounting for 46% of ST131 isolates, whereas the CTX-M-27-producing H30R and CTX-M-15-producing H30Rx subgroups were rarely detected. In contrast, from 2008 onward the latter two subgroups rose to dominance, accounting for 45% and 24% of ST131 isolates, respectively, versus only 15% for the (formerly dominant) CTX-M-14-producing H30R subgroup. The emergent CTX-M-27-H30R subgroup frequently had an IS26-ΔISEcp1-blaCTX-M-27-ΔIS903D-IS26-like structure, whereas the older CTX-M-14-H30R subgroup frequently had an ISEcp1-blaCTX-M-14-IS903D-like structure.

CONCLUSIONS

This Japanese regional ESBL-producing E. coli epidemic is closely associated with newly identified CTX-M-27- and CTX-M-14-producing ST131 H30R subclonal groups and with mobile elements IS26, ISEcp1 and IS903D.

Differences in risk-factor profiles between patients with ESBL-producing Escherichia coli and Klebsiella pneumoniae: a multicentre case-case comparison study

Background

Generic epidemiological differences between extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) and Klebsiella pneumoniae (ESBL-KP), are poorly defined. Nonetheless, defining such differences and understanding their basis could have strategic implications for infection control policy and practice.

Methods

Between 2009 and 2011 patients with bacteraemia due to ESBL-EC or ESBL-KP across all three acute hospitals in the city of Auckland, New Zealand, were eligible for inclusion. Recognised risk factors for ESBL bacteraemia were compared between species in a retrospective case-case study design using multivariate logistic regression. Representative isolates underwent ESBL gene characterisation and molecular typing.

Results

170 patients and 176 isolates were included in the study (92 patients with ESBL-EC, 78 with ESBL-KP). 92.6% had CTX-Ms. 39% of EC were ST131 while 51% of KP belonged to 3 different STs (i.e. ST20, ST48 & ST1087). Specific sequence types were associated with specific hospitals for ESBL-KP but not ESBL-EC. Variables positively associated with ESBL-EC on multivariate analysis were: community acquired infection (odds ratio [OR] 7.9; 95% CI: 2.6-23.9); chronic pulmonary disease (OR 5.5; 95% CI: 1.5-20.1); and high prevalence country of origin (OR 4.3; 95% CI: 1.6-11.6). Variables negatively associated with ESBL-EC were previous transplant (OR 0.06; 95% CI: 0.007-0.6); Hospital 2 (OR 0.3; 95% CI: 0.1-0.7) and recent ICU admission (OR 0.3; 95% CI: 0.07-0.9).

Conclusions

Differences in risk profiles between patients with ESBL-EC and ESBL-KP suggest fundamental differences in transmission dynamics. Understanding the biological basis for these differences could have implications for infection control practice. Tailoring of infection control measures according to ESBL species may be indicated in some instances.

Community-onset Escherichia coli infection resistant to expanded-spectrum cephalosporins in low-prevalence countries

By global standards, the prevalence of community-onset expanded-spectrum-cephalosporin-resistant (ESC-R) Escherichia coli remains low in Australia and New Zealand. Of concern, our countries are in a unique position, with high extramural resistance pressure from close population and trade links to Asia-Pacific neighbors with high ESC-R E. coli rates. We aimed to characterize the risks and dynamics of community-onset ESC-R E. coli infection in our low-prevalence region. A case-control methodology was used. Patients with ESC-R E. coli or ESC-susceptible E. coli isolated from blood or urine were recruited at six geographically dispersed tertiary care hospitals in Australia and New Zealand. Epidemiological data were prospectively collected, and bacteria were retained for analysis. In total, 182 patients (91 cases and 91 controls) were recruited. Multivariate logistic regression identified risk factors for ESC-R among E. coli strains, including birth on the Indian subcontinent (odds ratio [OR]=11.13, 95% confidence interval [95% CI]=2.17 to 56.98, P=0.003), urinary tract infection in the past year (per-infection OR=1.430, 95% CI=1.13 to 1.82, P=0.003), travel to southeast Asia, China, the Indian subcontinent, Africa, and the Middle East (OR=3.089, 95% CI=1.29 to 7.38, P=0.011), prior exposure to trimethoprim with or without sulfamethoxazole and with or without an expanded-spectrum cephalosporin (OR=3.665, 95% CI=1.30 to 10.35, P=0.014), and health care exposure in the previous 6 months (OR=3.16, 95% CI=1.54 to 6.46, P=0.02). Among our ESC-R E. coli strains, the blaCTX-M ESBLs were dominant (83% of ESC-R E. coli strains), and the worldwide pandemic ST-131 clone was frequent (45% of ESC-R E. coli strains). In our low-prevalence setting, ESC-R among community-onset E. coli strains may be associated with both "export" from health care facilities into the community and direct "import" into the community from high-prevalence regions.