Biology subjects

Peixe, L. V.

Publications and source records attributed to Peixe, L. V..

5 recordsLinked to original sources

bioRxiv2024

Decoding Klebsiella pneumoniae in Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs

The rise of antibiotic resistance in the food chain is influenced by the use of antimicrobial agents, such as antibiotics, metals, and biocides, throughout the entire farm-to-fork continuum. Besides, non-clinical reservoirs potentially contribute to the transmission of critical pathogens such as multidrug-resistant (MDR) Klebsiella pneumoniae. However, limited knowledge exists about the population structure and genomic diversity of K. pneumoniae circulating in conventional poultry production. We conducted a comprehensive characterization of K. pneumoniae across the whole chicken production chain (flocks/environment/meat, 2019-2022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features of K. pneumoniae were characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive for K. pneumoniae with a significant increase (p < 0.05) from early to pre-slaughter stages, most persisting in chicken meat batches. Colistin-resistant K. pneumoniae rates were low (4%), while most samples carried MDR strains (67%) and copper-tolerant isolates (63%; sil+pco clusters; MICCuSO4[≥]16mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity in K. pneumoniae (MIC/MBC range=4-64mg/L) from diverse and representative strains independently of the presence/absence of genes linked to QACs tolerance. A polyclonal K. pneumoniae population, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chickens lifecycle at the farm (ST29-KL124, ST11-KL106, ST15-KL19, ST1228-KL38), until the meat (ST1-KL19, ST11-KL111, ST6405-KL109, and ST6406-CG147-KL111), or over years (ST631-49 KL109, ST6651-KL107, ST6406-CG147-KL111). Notably, some lineages were identical to those from human clinical isolates. WGS also revealed F-type multireplicon plasmids carrying sil+pco (copper) co-located with qacE{Delta}1{+/-}qacF (QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverse K. pneumoniae clones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencing K. pneumoniae persistence and dissemination within poultry production, contributing to improved food safety risk management. This study underscores the significance of understanding the interplay between antimicrobial control strategies and non-clinical sources to effectively address the spread of antimicrobial resistance.

microbiology↗

bioRxiv2023

From farm to fork: persistence of clinically-relevant multidrug-resistant and copper-tolerant Klebsiella pneumoniae long after colistin withdrawal in poultry production.

The concern of colistin-resistant bacteria in animal-food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae (Kp) in the whole poultry-production chain needs clarification. We assessed colistin-resistant and copper-tolerant Kp occurrence in chicken raised with inorganic and organic copper-formulas from one-day-old chicks to meat (7 farms/2019-2020), after long-term colistin withdrawal (>2-years). Clonal diversity and Kp adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken-flocks (75%) carried Kp at early+pre-slaughter stages, with a significant decrease (p<0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative Kp were observed among faecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant isolates (81%; pco+sil/MICCuSO4 [≥]16mM). WGS revealed accumulation of colistin resistance associated mutations and F-type multireplicon plasmids carrying antibiotic resistance and metal/copper-tolerance genes. The Kp population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146 and ST392-KL27, and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken-production as a reservoir/source of clinically-relevant Kp lineages and genes with potential risk to humans through food and/or environmental exposure. Despite long-term colistin ban limited mcr spread, it was ineffective in controlling colistin-resistant/mcr-negative Kp, regardless of feed. This study provides crucial insights into the persistence of clinically-relevant Kp in the poultry-production chain and highlights the need for continued surveillance and proactive food safety actions within a One-Health perspective. IMPORTANCEThe spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically-relevant Klebsiella pneumoniae (Kp) throughout poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative Kp in chicken flocks, regardless of inorganic and organic copper-formulas and long-term colistin ban. Despite the high Kp diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human Kp exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in food industry and policymakers tasked with regulating food safety.

microbiology↗

bioRxiv2022

Phylogenomics of globally spread Clonal Groups 14 and 15 of Klebsiella pneumoniae

The increasing worldwide spread of multidrug-resistant (MDR) Kp is largely driven by high-risk sublineages, some of them well-characterised such as Clonal Group (CG) 258, CG147 or CG307. MDR Kp Sequence-Type (ST) 14 and ST15 have been described worldwide causing frequent outbreaks of CTX-M-15 and/or carbapenemase producers. However, their phylogeny, population structure and global dynamics remain unclear. Here, we clarify the phylogenetic structure and evolvability of CG14 and CG15 Kp by analysing the CG14 and CG15 genomes available in public databases (n=481, November 2019) and de novo sequences representing main sublineages circulating in Portugal (n=9). Deduplicated genomes (n=235) were used to infer temporal phylogenetic evolution and to compare their capsular locus (KL), resistome, virulome and plasmidome using high-resolution tools. Phylogenetic analysis supported independent evolution of CG14 and CG15 within two distinct clades and 4 main subclades which are mainly defined according to the KL and the accessory genome. Within CG14, two large monophyletic subclades, KL16 (14%) and KL2 (86%), presumptively emerged around 1937 and 1942, respectively. Sixty-five percent of CG14 carried genes encoding ESBL, AmpC and/or carbapenemases and, remarkably, they were mainly observed in the KL2 subclade. The CG15 clade was segregated in two major subclades. One was represented by KL24 (42%) and KL112 (36%), the latter one diverging from KL24 around 1981, and the other comprised KL19 and other KL-types (16%). Of note, most CG15 genomes contained genes encoding ESBL, AmpC and/or carbapenemases (n=148, 87%) and displayed a characteristic set of mutations in regions encoding quinolone resistance (QRDR, GyrA83F/GyrA87A/ParC80I). Plasmidome analysis revealed 2463 plasmids grouped in 27 predominant plasmid groups (PG) with a high degree of recombination, including particularly pervasive F-type (n=10) and Col (n=10) plasmids. Whereas blaCTX-M-15 was linked to a high diversity of mosaic plasmids, other ARGs were confined to particular plasmids (e.g. blaOXA-48-IncL; blaCMY/TEM-24-IncC). This study firstly demonstrates an independent evolutionary trajectory for CG15 and CG14, and suggests how the acquisition of specific KL, QRDR mutations (CG15) and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-KL2, CG15-KL24/KL112). IMPORTANCEKlebsiella pneumoniae (Kp) represents a major threat in the burden of antimicrobial resistance (AMR). Phylogenetic approaches to explain the phylogeny, emergence and evolution of certain multidrug resistant populations have mainly focused on core-genome approaches while variation in the accessory genome and the plasmidome have been long overlooked. In this study, we provide unique insights into the phylogenetic evolution and plasmidome of two intriguing and yet uncharacterized clonal groups (CGs), the CG14 and CG15, which have contributed to the global dissemination of contemporaneous {beta}-lactamases. Our results point-out an independent evolution of these two CGs and highlight the existence of different clades structured by the capsular-type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome, reflect the exposure and adaptation of Kp under different selective pressures.

genomics↗

bioRxiv2019

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers common genetic features and a chromosomal hotspot for optrA acquisition

Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we still lack a comprehensive analysis of human and animal optrA-LREfs strains. We investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 28 publicly available optrA-positive E. faecalis genomes from different hosts in 7 countries. In the genome-level analysis, in house databases with 57 virulence and 391 plasmid replication genes were tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera, mainly but not exclusive from Firmicutes. The content in AMR and virulence genes was highly identical in contrast to the diversity of phages and plasmids observed. Epidemiologically unrelated clones (ST476-like and ST21-like) obtained from human clinical and animal hosts in different continents over 5 years (2012-2017) were phylogenetically related (3-122 SNPs difference). They also exhibited identical AMR and virulence profiles, highlighting a global spread of optrA-positive strains with relevant adaptive traits in livestock and that they might originate from an animal reservoir. optrA was located on the chromosome within a Tn6674-like element (n=9) or on medium-size plasmids (30-60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was identical in chromosomal (Tn6674) and plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted in the same {Delta}radC integration site and embedded in a 32 kb chromosomal platform common to diverse strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012-2018. This platform is conserved among hundreds of E. faecalis genomes and we here propose a conserved chromosomal hotspot for optrA integration. The finding of optrA in strains sharing identical adaptive features and genetic backgrounds across different hosts and countries suggest the occurrence of common and independent genetic events occurring in distant regions, and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact in the efficacy of linezolid for the treatment of Gram-positive infections.

genomics↗

bioRxiv2019

Integrative and conjugative elements, the neglected drivers of carbapenemase-encoding genes

Carbapenemases inactivate most {beta}-lactam antibiotics, including carbapenems and have been frequently reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in-silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182,663). We detected 17,520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically-relevant bacteria as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g., aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally. Author NotesAll supporting data has been provided within the article or through supplementary data files. Supplementary material is available with the online version of this article. Impact StatementCarbapenems are commonly used to treat severe infections in humans. Resistance is often mediated by carbapenemases. These enzymes degrade carbapenems and are frequently present in plasmids. Here, we demonstrate that common carbapenemase-encoding genes (CEGs) found in clinical isolates (e.g. blaKPC, blaGES, blaIMP, blaNDM, blaVIM) can also be located within integrative and conjugative elements (ICEs). CEG-bearing ICEs belong to three mating-pair formation families. These mobile elements may be particularly important in bacteria where plasmids do not seem to play a significant role in the spread of antibiotic resistance genes, as Pseudomonas spp. This study considerably expands the knowledge of the repertoire of CEGs-bearing ICEs among clinically-relevant bacterial pathogens, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli. Data SummaryAll the bacterial genomes scanned in this study have been deposited previously in the National Center for Biotechnology Information genome database and are listed on the supplementary tables. The extracted 66 ICEs in fasta format and the outputs for the profile HMMs scanned on the 386 putative MGEs identified in this study are deposited on figshare at https://figshare.com/projects/_Comprehensive_genome_data_analysis_establishes_a_triple_whammy_of_carbapenemases_ICEs_and_multiple_clinically-relevant_bacteria/78369.

microbiology↗