Allodemic distribution of plasmids co-harbouring bla CTX-M-15 / aac(6′)-Ib -cr/ qnrB in Klebsiella pneumoniae is the main source of extended-spectrum β-lactamases in Uruguay’s paediatric hospital

Great Plasticity in a Great Pathogen: Capsular Types, Virulence Factors and Biofilm Formation in ESBL-Producing Klebsiella pneumoniae from Pediatric Infections in Uruguay

Klebsiella pneumoniae is widely recognized as an opportunistic hospital and community pathogen. It is one of the priority microorganisms included in the ESKAPE group, and its antibiotic resistance related to extended-spectrum β-lactamases (ESBL) is a global public health concern. The multi-drug resistance (MDR) phenotype, in combination with pathogenicity factors, could enhance the ability of this pathogen to cause clinical infections. The aim of this study was to characterize pathogenicity factors and biofilm formation in ESBL-producing K. pneumoniae from pediatric clinical infections. Capsular types, virulence factors, and sequence types were characterized by PCR. Biofilm formation was determined by a semiquantitative microtiter technique. MDR phenotype and statistical analysis were performed. The K24 capsular type (27%), virulence factors related to iron uptake fyuA (35%) and kfuBC (27%), and sequence types ST14 (18%) and ST45 (18%) were the most frequently detected. Most of the strains were biofilm producers: weak (22%), moderate (22%), or strong (12%). In 62% of the strains, an MDR phenotype was detected. Strains with K24 capsular type showed an association with ST45 and the presence of fyuA; strains with kfuBC showed an association with moderate or strong biofilm production and belonging to ST14. Weak or no biofilm producers were associated with the absence of kfuBC. The MDR phenotype was associated with the main ESBL gene, blaCTX-M-15. The high plasticity of K. pneumoniae to acquire an MDR phenotype, in combination with the factors exposed in this report, could make it even more difficult to achieve a good clinical outcome with the available therapeutics.

Imported One-Day-Old Chicks as Trojan Horses for Multidrug-Resistant Priority Pathogens Harboring mcr-9, rmtG and Extended-Spectrum β-Lactamase Genes

Antimicrobial resistance is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving intensive animal production systems. In this study, we have performed a microbiological and molecular investigation of priority pathogens carrying transferable resistance genes to critical antimicrobials in one-day-old chickens imported from Brazil to Uruguay. Bacterial identification was performed by MALDI-TOF mass spectrometry and antibiotic susceptibility was determined by Sensititre. Antimicrobial resistance genes were sought by polymerase chain reaction and clonality was assessed by PFGE. Four multidrug-resistant (MDR) representative strains were sequenced by Illumina and/or Oxford Nanopore Technologies. Twenty-eight MDR isolates identified as Escherichia coli (n= 14), Enterobacter cloacae (n= 11) and Klebsiella pneumoniae (n= 3). While resistance to oxyiminocephalosporins was due to bla_CTX-M-2, bla_CTX-M-8, bla_CTX-M-15, bla_CTX-M-55 and bla_CMY-2, plasmid-mediated quinolone resistance was associated with qnrB19, qnrE1, and qnrB2 genes. Finally, resistance to aminoglycosides and fosfomycin was due to the presence of 16S rRNA methyltransferase rmtG and fosA-type genes, respectively. Short and long-read genome sequencing of E. cloacae ODC-Eclo3 strain revealed the presence of IncQ/rmtG (pUR-EC3.1, 7400-pb), IncHI2A/mcr-9.1/bla_CTX-M-2 [pUR-EC3.2, ST16 (pMLST), 408,436-bp] and IncN2/qnrB19/aacC3/aph(3'')-Ib (pUR-EC3.3) resistance plasmids. Strikingly, the bla_CTX-M-2 gene was carried by a novel Tn1696-like composite transposon designated Tn7337. In summary, we report that imported one-day-old chicks can act as Trojan horses for the hidden spread of WHO critical priority MDR pathogens harboring mcr-9, rmtG and extended-spectrum β-lactamase genes in poultry farms, which is a critical issue within a One Health perspective. Importance section Antimicrobial resistance is considered a significant problem for global health, including within the concept of "One Health", therefore, the food chain is a link that connects human and animal health directly. In this work, we searched for microorganisms resistant to antibiotics considered critical for human health in intestinal microbiota of one-day-old baby chicks imported to Uruguay from Brazil. We described antibiotic-resistant genes to antibiotics named as to watch or reserve for the WHO, such as rmtG or mcr9.1, which confers resistance to all the aminoglycosides and colistin, respectively, among others genes, and their presence in new mobile genetic elements that favor its dissemination. The sustained entry of these microorganisms evades the sanitary measures implemented by the countries and production establishments to reduce the selection of resistant microorganisms. These silently imported resistant microorganisms could explain a considerable part of the antimicrobial resistance problems found in the production stages of the system.

Antibiotic susceptibility and fosfomycin resistance characterization in a cohort of children older than 6 years of age with urinary tract infection

Fosfomycin tromethamol (FT) was reintroduced as an option for the treatment of low urinary tract infection (UTI) in children. In this study, we described the antibiotic sensitivity and mechanisms of resistance to fosfomycin in isolates from children older than 6 years with UTI. Urine culture and antibiotic susceptibility study were performed. In fosfomycin resistant strains, PCR for fos, bla_CTX-M was performed followed by classification by phylogenetic group and sequencetyping. Escherichia coli was the most frequent etiological agent (89.2%). The susceptibility percentages were: fosfomycin 97.9%; amoxicillin-clavulanate 92.7%; cefuroxime and ceftriaxone 99%; nitrofurantoin 94.4%. An E. coli strain (ST69, phylogenetic group D) was resistant to fosfomycin (MIC 256mg/l) and carried the bla_CTX-M-14 and fosA3 genes in a 45kb IncN-type plasmid. This is the first report of E. coli ST69 with bla_CTX-M-14/fosA3 of human origin.

Description of novel resistance islands harbouring blaCTX-M-2 in IncC type 2 plasmids

OBJECTIVES

We sequenced two IncA/C plasmids harbouring bla_CTX-M-2 in Klebsiella pneumoniae clinical isolates and compared their antibiotic resistance islands.

METHODS

Transconjugants were obtained from two clinical K. pneumoniae isolates harbouring bla_CTX-M-2. Plasmid DNA from transconjugants underwent short-read whole-genome sequencing, reads were assembled, and gaps were closed by PCR and sequencing. Determination of plasmid replicons, antibiotic resistance genes, identification and characterisation of insertion sequence (IS) elements, and comparison with publicly available plasmid sequences were performed.

RESULTS

bla_CTX-M-2 was located in a complex class 1 integron In35::ISCR1::bla_CTX-M-2, inserted in two different transposons designated Tn7057 and Tn7058, that reside in the resistance islands of plasmids pUR-KP0923 and pUR-KP1025, respectively. The general modules of both transposons were In35::ISCR1::bla_CTX-M-2-Tn1000-like-Tn2*-ISKpn11-12-13 variable module-ΔTn21. In Tn7057 there was ΔIS10R-catA2 associated with an additional ISKpn13. Both plasmids belonged to IncC type 2 and ST3. pUR-KP0923 was 167 138 bp in length and had a 37 926-bp resistance island at position 4 (RI-4). Plasmid pUR-KP1025 was 168 128 bp with a RI-4 of 36 222 bp.

CONCLUSION

This report describes the molecular nature of two transposons (Tn7057 and Tn7058) harbouring bla_CTX-M-2 that reside in IncC type 2 ST3 plasmids. These transposons mediate resistance to oxyimino-cephalosporins, gentamicin and, in the case of Tn7057, chloramphenicol. CTX-M-2 is an important extended-spectrum β-lactamase (ESBL) to South American epidemiology. It is remarkable that despite being only two plasmid sequences, the information revealed here could contribute to a better understanding of the resistance islands from IncC type 2 plasmids.

Prevalence and molecular characterisation of carbapenemase-producing Enterobacterales in an outbreak-free setting in a single hospital in Uruguay

OBJECTIVES

This study aimed to characterise all carbapenemase-producing enterobacteria (CPE) isolates obtained from an outbreak-free setting in Uruguay.

METHODS

We studied 12 CPE isolated from Hospital de Clínicas between 2012-2016. Bacterial identification and antibiotic susceptibility testing were performed using VITEK®2 and Sensititre or agar dilution, respectively. Antimicrobial resistance genes and mobile genetic elements were identified by PCR and sequencing. Multilocus sequence typing was performed for Klebsiella pneumoniae. Plasmid conjugation was assessed, plasmid size was estimated by S1-PFGE and plasmid incompatibility groups were sought by PCR.

RESULTS

Among 8364 enterobacteria, 12 CPE were isolated from urine, blood culture, wound, peritoneal fluid and punch samples. NDM-1 was the most prevalent carbapenemase, followed by VIM-2 and KPC-2. All isolates were resistant to gentamicin, cefotaxime, ceftazidime, trimethoprim/sulfamethoxazole, ciprofloxacin and imipenem and were susceptible to fosfomycin. We characterised six class 1 integrons: dfrA12-orfF-aadA2; aacA4-bla_OXA-2-orfD; aadB-aadA2; dfrA1; aadB-bla_OXA-10-aadA1; and bla_VIM-2-dfrA7. An association between various aminoglycoside, β-lactam and fluoroquinolone resistance genes were observed, some of them located in transferable plasmids belonging to incompatibility groups IncC, IncHI1 and IncM1. We described a new composite transposon (assigned Tn6935) including bla_NDM-1 flanked by two directly-oriented copies of a Tn3-like element ISKox2-like family transposase. The sequence types of K. pneumoniae isolates were ST11, ST14 and ST661.

CONCLUSIONS

The presence of CPE is sporadic and could be due to measures taken by the Public Health Committee. Nevertheless, the coexistence of several resistance mechanisms and their presence in conjugative plasmids and high-risk clones is worrisome.

Transferable Resistance to Highest Priority Critically Important Antibiotics for Human Health in Escherichia coli Strains Obtained From Livestock Feces in Uruguay

The aim of this work was to detect Escherichia coli isolates displaying resistance to oxyimino-cephalosporins, quinolones, and colistin in feces from livestock in Uruguay. During 2016–2019, fecal samples from 132 broiler and layer chicken flocks, 100 calves, and 50 pigs, were studied in Uruguay. Samples were cultured on MacConkey Agar plates supplemented with ciprofloxacin, ceftriaxone, or colistin. E. coli isolates were identified by mass spectrometry and antibiotic susceptibility testing was performed by disk diffusion agar method and colistin agar test. Antibiotic resistance genes were detected by polymerase chain reaction and sequencing. The most frequently detected resistance gene was qnrB19, recovered from 87 animals. Regarding plasmid-mediated quinolone resistance genes, qnrS1 was the second in prevalence (23 animals) followed by qnrE1, found in 6 chickens and two calves. Regarding resistance to oxyimino-cephalosporins, 8 different β-lactamase genes were detected: bla_CTX−M−8 and bla_CMY−2 were found in 23 and 19 animals, respectively; next, bla_CTX−M−2 and bla_SHV−12 in 7 animals each, followed by bla_CTX−M−14 in 5, bla_CTX−M−15 and bla_SHV2a in 2, and bla_CTX−M−55 in a single animal. Finally, the mcr-1 gene was detected only in 8 pigs from a single farm, and in a chicken. Isolates carrying bla_CMY−2 and bla_SHV−12 were also found in these animals, including two isolates featuring the bla_CMY−2/mcr-1 genotype. To the best of our knowledge, this is the first work in which the search for transferable resistance to highest priority critically important antibiotics for human health is carried out in chickens and pigs chains of production animals in Uruguay.

First characterization of K. pneumoniae ST11 clinical isolates harboring blaKPC-3 in Latin America

Antimicrobial resistance due to carbapenemase production in Enterobacteriaceae clinical isolates is a global threat. Klebsiellapneumoniae harboring the bla_KPC gene is one of the major concerns in hospital settings in Latin America. The aim of this study was to characterize the antibiotic resistance mechanisms and to typify four carbapenem-resistant K. pneumoniae clinical isolates from the city of Manizales, Colombia. We identified bla_KPC-3 in all four isolates by polymerase chain reaction and subsequent sequencing. The plasmid-mediated quinolone resistance genes qnrB19-like and aac(6')Ib-cr; fosfomycin resistance gene fosA and an insertion sequence IS5-like in mgrB (colistin resistance) were also detected. Sequence types ST11 with capsular type wzi75, and ST258 with wzi154, were characterized. The bla_KPC-3 gene was mobilized in a 100-kb IncFIB conjugative plasmid with vagCD toxin-antitoxin system. This work reports multiple resistance genes in bla_KPC-producing K. pneumoniae and the first occurrence of ST11 clinical isolates harboring bla_KPC-3 in Latin America.

Characterization of a multidrug-resistant Klebsiella pneumoniae ST607-K25 clone responsible for a nosocomial outbreak in a neonatal intensive care unit

PURPOSE

Multidrug-resistant Klebsiella pneumoniae strains are regularly involved in hospital outbreaks. This study describes an ESBL-producing K. pneumoniae clone (ST607-K25) responsible for a nosocomial outbreak in a neonatal intensive care unit.

METHODOLOGY

Fourteen strains isolated from 13 patients were included. Antimicrobial susceptibility testing was performed by the agar diffusion method. A clonal link was first investigated by fingerprinting (ERIC-PCR and REP-PCR) then confirmed by MLST. Characterization was performed by molecular detection and identification of several drug resistance and virulence determinants.

RESULTS

All strains expressed the same antibiotype, combining ESBL production, fluoroquinolones and aminoglycoside resistance, except for one which remained susceptible to fluoroquinolones. Fingerprinting methods confirmed the clonal link and MLST identified a ST607 clone. Molecular investigations revealed: (I) genes encoding for two narrow-spectrum beta-lactamases (SHV-1 and TEM-1) and an ESBL (CTX-M-15); (II) absence of any chromosomal mutation in quinolone resistance-determining- regions (QRDR) of gyrA/gyrB and parC/parE genes; (III) genes encoding for three plasmid-mediated quinolone-resistance (PMQR) determinants: oqxAB (14/14), aac(6')-Ib-cr (14/14) and qnrB (13/14); (IV) production of a K25 capsule; and (V) carriage of three genes encoding for virulence factors: mrkD (type 3 fimbriae) (14/14), ybts (yersiniabactin) (12/14) and entB (enterobactin) (14/14).

CONCLUSION

We described a multidrug-resistant Kp ST607 clone responsible for a nosocomial outbreak in vulnerable and premature newborns. Molecular investigations allowed us to identify several resistance factors responsible for ESBL production (CTX-M-15) and quinolone resistance (three PMQR determinants). The detection of a gene (ybtS) belonging to the high-pathogenicity island yersiniabactin could partly explain its high colonization and diffusion potential.

Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates

The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The bla_NDM-1 and bla_OXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A bla_OXA-48-carrying IncL/M-type plasmid was found in all bla_OXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.

Detection of qnrVC6, within a new genetic context, in an NDM-1-producing Citrobacter freundii clinical isolate from Uruguay

OBJECTIVES

The objective of this study was to characterise the mechanisms underlying quinolone and oxyimino-cephalosporin resistance in a Citrobacter freundii clinical isolate obtained from the ICU in a university hospital in Uruguay.

METHODS

Citrobacter freundii strain CF638 was isolated from a urine culture. Identification was performed using a VITEK^®2 system, and antimicrobial susceptibility was established by MIC determination and disk diffusion assay. Resistance genes and mobile genetic elements were identified by PCR and sequencing. Plasmid transfer was assessed by conjugation and the plasmid size was estimated by S1-PFGE. Plasmid incompatibility (Inc) group and toxin-antitoxin systems were sought by PCR.

RESULTS

Strain CF638 showed a multidrug-resistant profile, including resistance to carbapenems and quinolones. Transconjugant TcCF638, harbouring an ca. 200-kb IncA/C plasmid, also showed resistance to all β-lactams (except aztreonam) and diminished susceptibility to ciprofloxacin. PCR was positive for bla_NDM-1 and qnrVC in CF638 and TcCF638. Two different class 1 integrons were detected (In127 and In907). In127 featured the genetic array aadA2-ltr2. Conversely, complex In907 featured two variable regions (VRs); VR-1 consisted of aadB-bla_OXA-10-aadA1cc, whereas VR-2 featured a qnrVC6 gene 108bp downstream from ISCR1 and 45bp upstream from qacEΔ1. Expression of qnrVC6 was due to a putative promoter region, detected using the Neural Network Promoter Prediction program.

CONCLUSION

To the best of our knowledge, this constitutes the first report of qnrVC within a complex class 1 integron, as well as the first report of the occurrence of such a gene in an NDM-1-producing enterobacterial clinical isolate.

Differences in tetracycline resistance determinant carriage among Shigella flexneri and Shigella sonnei are not related to different plasmid Inc-type carriage

OBJECTIVES

The aim of this study was to establish the prevalence of the most common molecular mechanisms involved in tetracycline resistance as well as their relationship with plasmid incompatibility (Inc) groups in a collection of Shigella spp. causing traveller's diarrhoea.

METHODS

Tetracycline susceptibility was established in 187 Shigella spp. (74 Shigella flexneri and 113 Shigella sonnei), of which 153 isolates were recovered as a confirmed cause of traveller's diarrhoea. The prevalence of the tet(A), tet(B) and tet(G) genes was analysed by PCR. Eighteen plasmid Inc groups was determined in a subset of 59 isolates.

RESULTS

Among 154 tetracycline-resistant isolates, 122 (79.2%) harboured at least tet(A) or tet(B). The tet(B) gene was the most frequently detected, being present in 70 isolates (45.5%), whilst tet(A) was detected in 57 isolates (37.0%). The tet(G) gene was present in only 11 (7.2%) isolates. Moreover, the tet(A) gene was more frequent in S. sonnei (P=0.0007), whilst the tet(B) gene was more frequent in S. flexneri (P<0.0001). Plasmids belonging to Inc group B (P<0.05) were significantly more frequent among S. flexneri, whilst those belonging to groups K, FIC and FIIA (P<0.05) were preferentially detected among S. sonnei.

CONCLUSION

The prevalence of the tet(A) and tet(B) genes differed between S. sonnei and S. flexneri. Moreover, the prevalence of plasmid Inc groups in S. flexneri and S. sonnei differed. However, no relationship was found between the two phenomena.