ABSTRACT
Two novel variants of
Klebsiella pneumoniae
carbapenemase (KPC) associated with resistance to ceftazidime-avibactam (CZA) and designated as KPC-113 and KPC-114 by NCBI were identified in ...2020, in clinical isolates of
Klebsiella pneumoniae
in Brazil. While
K. pneumoniae
of ST16 harbored the
bla
KPC-113
variant on an IncFII-IncFIB plasmid,
K. pneumoniae
of ST11 carried the
bla
KPC-114
variant on an IncN plasmid. Both isolates displayed resistance to broad-spectrum cephalosporins, β-lactam inhibitors, and ertapenem and doripenem, whereas
K. pneumoniae
producing KPC-114 showed susceptibility to imipenem and meropenem. Whole-genome sequencing and
in silico
analysis revealed that KPC-113 presented a Gly insertion between Ambler positions 264 and 265 (R264_A265insG), whereas KPC-114 displayed two amino acid insertions (Ser-Ser) between Ambler positions 181 and 182 (S181_P182insSS) in KPC-2, responsible for CZA resistance profiles. Our results confirm the emergence of novel KPC variants associated with resistance to CZA in international clones of
K. pneumoniae
circulating in South America.
IMPORTANCE
KPC-2 carbapenemases are endemic in Latin America. In this regard, in 2018, ceftazidime-avibactam (CZA) was authorized for clinical use in Brazil due to its significant activity against KPC-2 producers. In recent years, reports of resistance to CZA have increased in this country, limiting its clinical application. In this study, we report the emergence of two novel KPC-2 variants, named KPC-113 and KPC-114, associated with CZA resistance in
Klebsiella pneumoniae
strains belonging to high-risk clones ST11 and ST16. Our finding suggests that novel mutations in KPC-2 are increasing in South America, which is a critical issue deserving active surveillance.
KPC-2 carbapenemases are endemic in Latin America. In this regard, in 2018, ceftazidime-avibactam (CZA) was authorized for clinical use in Brazil due to its significant activity against KPC-2 producers. In recent years, reports of resistance to CZA have increased in this country, limiting its clinical application. In this study, we report the emergence of two novel KPC-2 variants, named KPC-113 and KPC-114, associated with CZA resistance in
Klebsiella pneumoniae
strains belonging to high-risk clones ST11 and ST16. Our finding suggests that novel mutations in KPC-2 are increasing in South America, which is a critical issue deserving active surveillance.
The spread of carbapenemase-producing Klebsiella pneumoniae beyond hospital settings is a global critical issue within a public health and One Health perspective. Another worrisome concern is the ...convergence of virulence and resistance in healthcare-associated lineages of K. pneumoniae leading to unfavorable clinical outcomes. During a surveillance study of WHO critical priority pathogens circulating in an impacted urban river in São Paulo, Brazil, we isolate two hypermucoviscous and multidrug-resistant K. pneumoniae strains (PINH-4250 and PINH-4900) from two different locations near to medical centers. Genomic investigation revealed that both strains belonged to the global high-risk sequence type (ST) ST11, carrying the blaKPC-2 carbapenemase gene, besides other medically important antimicrobial resistance determinants. A broad virulome was predicted and associated with hypervirulent behavior in the Galleria mellonella infection model. Comparative phylogenomic analysis of PINH-4250 and PINH-4900 along to an international collection of publicly available genomes of K. pneumoniae ST11 revealed that both environmental strains were closely related to hospital-associated K. pneumoniae strains recovered from clinical samples between 2006 and 2018, in São Paulo city. Our findings support that healthcare-associated KPC-2-positive K. pneumoniae of ST11 clone has successfully expanded beyond hospital settings. In summary, aquatic environments can become potential sources of international clones of K. pneumoniae displaying carbapenem resistance and hypervirulent behaviors, which is a critical issue within a One Health perspective.
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•WHO critical-priority K. pneumoniae strains were recovered from urban rivers.•Genomic data revealed presence of global hospital-associated clones KPC-2/ST11.•Environmental hypermucoviscous KPC-2/ST11 carried broad resistomes/virulomes.•Phylogenomics revealed clonal relatedness with human and environmental lineages.•Expansion of KPC-2/ST11 clones beyond hospital walls is a critical One Health issue.
Extended spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a medically important pathogen that commonly causes human nosocomial infections. Since veterinary emergency and critical care ...services have also significantly progressed over the last decades, there are increasing reports of ESBL-producing K. pneumoniae causing hospital-associated infections in companion animals. We present microbiological and genomic analysis of a multidrug-resistant ESBL-positive K. pneumoniae (LCKp01) isolated from a fatal infection in a dog admitted to a veterinary intensive care unit. LCKp01 strain belonged to the sequence type ST392 and displays a KL27 (wzi-187) and O-locus 4 (O4). A broad resistome and presence of the blaCTX-M-15 ESBL gene were predicted. SNP-based phylogenomic analysis, using an international genome database, clustered LCKp01 (60–80 SNPs differences) with K. pneumoniae ST392 from human and animal infections, isolated at 4-year interval, whereas phylogeographical analysis confirmed successful expansion of ST392 as a global clone of One Health concern.
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•A fatal infection by a multidrug-resistant K. pneumoniae in dog was investigated.•Identification of human pandemic K. pneumoniae ST392/CTX-M-15 clone is highlighted.•Phylogenomic analysis revealed clonal relatedness with nosocomial lineages.•Phylogeographical analysis confirmed expansion of ST392 as global One Health clone.•Dissemination of K. pneumoniae ST392 at the human-animal interface is discussed.
Wild birds have emerged as novel reservoirs and potential spreaders of antibiotic-resistant priority pathogens, being proposed as sentinels of anthropogenic activities related to the use of ...antimicrobial compounds. The aim of this study was to investigate the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-producing bacteria in wild birds in South America. In this regard, we have identified two ESBL (CTX-M-55 and CTX-M-65)-positive Escherichia coli (UNB7 and GP188 strains) colonizing Creamy-bellied Thrush (Turdus amaurochalinus) and Variable Hawk (Geranoaetus polyosoma) inhabiting synanthropic and wildlife environments from Brazil and Chile, respectively. Whole-genome sequence (WGS) analysis revealed that E. coli UNB7 and GP188 belonged to the globally disseminated clone ST602, carrying a wide resistome against antibiotics (β-lactams), heavy metals (arsenic, copper, mercury), disinfectants (quaternary ammonium compounds), and pesticides (glyphosate). Additionally, E. coli UNB7 and GP188 strains harbored virulence genes encoding hemolysin E, type II and III secretion systems, increased serum survival, adhesins and siderophores. SNP-based phylogenomic analysis, using an international genome database, revealed genomic relatedness (19–363 SNP differences) of GP188 with livestock and poultry strains, and genomic relatedness (61–318 differences) of UNB7 with environmental, human and livestock strains (Table S1), whereas phylogeographical analysis confirmed successful expansion of ST602 as a global clone of One Health concern. In summary, our results support that ESBL-producing E. coli ST602 harboring a wide resistome and virulome have begun colonizing wild birds in South America, highlighting a potential new reservoir of critical priority pathogens.
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•ESBL-producing bacteria in wild birds from South America have been investigated.•Colonization of wild birds by CTX-M-producing E. coli is highlighted.•Global E. coli ST602 clone carrying wide resistome and virulome was identified.•Phylogenomics revealed relatedness with animal, environmental and human strains.•Phylogeographical analysis confirmed ST602 as a global clone of One Health concern.
The aim of this study was to perform a genomic investigation of a multiple fluoroquinolone-resistant Leclercia adecarboxylata strain isolated from a synanthropic pigeon in São Paulo, Brazil.
...Whole-genome sequencing was performed using an Illumina platform, and in silico deep analyses of the resistome were performed. Comparative phylogenomics was conducted using a global collection of publicly available genomes of L. adecarboxylata strains isolated from human and animal hosts.
L. adecarboxylata strain P62P1 displayed resistance to human (norfloxacin, ofloxacin, ciprofloxacin, and levofloxacin) and veterinary (enrofloxacin) fluoroquinolones. This multiple quinolone-resistant profile was associated with mutations in the gyrA (S83I) and parC (S80I) genes and the presence of the qnrS gene within an ISKpn19-orf-qnrS1-ΔIS3-blaLAP-2 module, previously identified in L. adecarboxylata strains isolated from pig feed and faeces in China. Genes associated with arsenic, silver, copper, and mercury resistance were also predicted. Phylogenomic analysis revealed clustering (378–496 single nucleotide polymorphism differences) with two L. adecarboxylata strains isolated from human and fish sources in China and Portugal, respectively.
L. adecarboxylata is a Gram-negative bacterium of the Enterobacterales order and is considered an emergent opportunistic pathogen. Since L. adecarboxylata has adapted to human and animal hosts, genomic surveillance is highly recommended, in order to identify the emergence and spread of resistant lineages and high-risk clones. In this regard, this study provides genomic data that can help clarify the role of synanthropic animals in the dissemination of clinically relevant L. adecarboxylata within a One Health context.
WHO priority pathogens have disseminated beyond hospital settings and are now being detected in urban and wild animals worldwide. In this regard, synanthropic animals such as urban pigeons (Columba ...livia) and rodents (Rattus rattus, Rattus norvegicus and Mus musculus) are of interest to public health due to their role as reservoirs of pathogens that can cause severe diseases. These animals usually live in highly contaminated environments and have frequent interactions with humans, domestic animals, and food chain, becoming sentinels of anthropogenic activities. In this study, we report genomic data of Escherichia coli strains selected for ceftriaxone and ciprofloxacin resistance, isolated from pigeons and black rats. Genomic analysis revealed the occurrence of international clones belonging to ST10, ST155, ST224 and ST457, carrying a broad resistome to beta-lactams, aminoglycosides, trimethoprim/sulfamethoxazole, fluoroquinolones, tetracyclines and/or phenicols. SNP-based phylogenomic investigation confirmed clonal relatedness with high-risk lineages circulating at the human-animal-environmental interface globally. Our results confirm the dissemination of WHO priority CTX-M-positive E. coli in urban rodents and pigeons in Brazil, highlighting potential of these animals as infection sources and hotspot for dissemination of clinically relevant pathogens and their resistance genes, which is a critical issue within a One Health perspective.
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•Synanthropic pigeons and rodents as source of AMR bacteria were investigated.•Identification of One Health global clones of CTX-M-positive E.coli is highlighted.•Phylogenomic analysis revealed clonal relatedness with hospital-associated lineages.•Phylogeographical analysis confirmed expansion of ST392 as global One Health clone.•Synanthropic animals could be indicators of AMR burden in anthropized environments.
•Extended-spectrum β-lactamase–positive Enterobacter cloacae complex members are critical priority pathogens.•E. hormaechei belonging to sequence type (ST) ST78 is an emergent high-risk ...clone.•Phylogenomic data of an E. hormaechei ST78/CTX-M-15 infecting a calf is presented.•E. hormaechei carried a broad resistome and phylogenomic relatedness to human ST78.•The success of E. hormaechei ST78 as a One Health clone is discussed.
Extended-spectrum β-lactamase (ESBL)–producing Enterobacter cloacae complex (ECC) members have been a leading cause of severe infections in hospital setting and have lately been recognized as important pathogens for animals. In this article, we report phylogenomic data of a multidrug-resistant and CTX-M-15–positive E. hormaechei belonging to ST78 isolated from a calf with omphalitis.
Genomic DNA was extracted and sequenced using the Illumina NextSeq platform. De novo assembly was performed by Unicycler and in silico prediction accomplished by curated bioinformatics tools. Single nucleotide polymorphism (SNP)-based comparative phylogenomic analysis was conducted by using publicly available ECC genomes belonging to ST78.
The genome size was calculated at 3 8465 40 bp, comprising 4717 total genes, 3 rRNAs, 43 tRNAs, 7 ncRNAs, and 74 pseudogenes. The animal-associated E. hormaechei (ECBEZ strain) ST78 harboured the blaCTX-M-15 ESBL gene in addition to other critically important resistance genes conferring resistance to β-lactams, aminoglycosides, fosfomycin, phenicol, quinolones, sulphonamides, tetracyclines, and trimethoprim. Phylogenetic analysis revealed that ECBEZ is closely related to human-isolated strains from Asian and African countries.
Phylogenomic analysis of CTX-M-15-producing E. hormaechei from animal infection reveals that ST78 is a successful One Health clone among ECC members. Furthermore, data presented in this study reinforce the urgent need to monitor ESBL-producing ECC members in veterinary settings.
The aim of this study was to investigate the genomic features of an extensively drug-resistant (XDR) Pseudomonas aeruginosa isolate (P-469) emerging in Chile. Antibiotic susceptibility was determined ...by disk diffusion and "colistin agar" test. Whole-genome sequencing (WGS) was performed by the Illumina NextSeq 2000 platform, and epidemiologically and clinically relevant data (i.e., sequence-type, serotype, mobile genetic elements, virulome, resistome, plasmidome, prophages, and CRISPR-Cas systems) were retrieved using multiple bioinformatic tools. The P-469 strain displayed an XDR profile, remaining susceptible to colistin. Genomic analysis revealed that this isolate belonged to the "high-risk" clone ST654 (CC654), serotype O4, and genotype
. Strikingly, two CRISPR-Cas systems, five intact prophages sequences, and a broad resistome that included
and the novel
carbapenemase genes were predicted. Our results revealed the genomic characteristics of P. aeruginosa belonging to the high-risk clone ST654/O4 coproducing NDM-1 and VIM-80 in Chile, supporting that genomic surveillance is necessary to track the emergence and spread of epidemiologically successful WHO's critical priority pathogens in order to prevent their rapid dissemination.
Untreated wastewater is a reservoir for multidrug-resistant bacteria, but its role in the spread of antibiotic resistance in the human population remains poorly investigated. In this study, we ...isolated a KPC-2-producing ST2787
Klebsiella quasipneumoniae
subsp.
quasipneumoniae
(WW14A), recovered from raw sewage at a wastewater treatment plant in Argentina in 2018 and determined its complete genome sequence. Strain WW14A was resistant to all β-lactams, ciprofloxacin and amikacin. A core genome phylogenetic analysis indicated that WW14A was closely related to a GES-5-producing Taiwanese strain isolated from hospital wastewater in 2015 and it was clearly distinct from strains isolated recently in Argentina and Brazil. Interestingly,
bla
KPC-2
was harbored by a recently described IncP-6 broad-spectrum plasmid which was sporadically reported worldwide and had never been reported before in Argentina. We investigated the presence of the IncP-6 replicon in isolates obtained from the same sampling and found a novel non-typable/IncP-6 hybrid plasmid in a newly assigned ST1407
Enterobacter asburiae
(WW19C) also harboring
bla
KPC-2
. Nanopore sequencing and hybrid assembly of strains WW14A and WW19C revealed that both IncP-6 plasmids shared 72% of coverage (~20 kb), with 99.99% of sequence similarity and each one also presented uniquely combined regions that were derived from other plasmids recently reported in different countries of South America, Asia, and Europe. The region harboring the carbapenem resistance gene (~11 kb) in both plasmids contained a Tn
3
transposon disrupted by a Tn
3
-IS
Apu
-flanked element and the core sequence was composed by ΔIS
Kpn6
/
bla
KPC-2
/Δ
bla
TEM-1
/IS
Kpn27
. Both strains also carried genes conferring resistance to heavy metals (e.g., arsenic, mercury, lead, cadmium, copper), pesticides (e.g., glyphosate), disinfectants, and several virulence-related genes, posing a potential pathogenic risk in the case of infections. This is the first study documenting
bla
KPC-2
associated with IncP-6 plasmids in
K. quasipneumoniae
and
Enterobacter cloacae
complex from wastewater in Argentina and highlights the circulation of IncP-6 plasmids as potential reservoirs of
bla
KPC-2
in the environment.
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