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Hiding in Plain Sight: Characterization of Aeromonas Species Isolated from a Recreational Estuary Reveals the Carriage and Putative Dissemination of Resistance Genes

by Anna Luiza Bauer Canellas, Bruno Francesco Rodrigues de Oliveira and Marinella Silva Laport

Antibiotics 2023, 12(1), 84; https://doi.org/10.3390/antibiotics12010084 - 04 Jan 2023

Cited by 4 | Viewed by 1584

Abstract

Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations’ Sustainable Development Goals and, due to its multisectoral character, a [...] Read more.

Antimicrobial resistance (AMR) has become one of the greatest challenges worldwide, hampering the treatment of a plethora of infections. Indeed, the AMR crisis poses a threat to the achievement of the United Nations’ Sustainable Development Goals and, due to its multisectoral character, a holistic approach is needed to tackle this issue. Thus, the investigation of environments beyond the clinic is of utmost importance. Here, we investigated thirteen strains of antimicrobial-resistant Aeromonas isolated from an urban estuary in Brazil. Most strains carried at least one antimicrobial resistance gene and 11 carried at least one heavy metal resistance gene. Noteworthy, four (30.7%) strains carried the bla_KPC gene, coding for a carbapenemase. In particular, the whole-genome sequence of Aeromonas hydrophila strain 34SFC-3 was determined, revealing not only the presence of antimicrobial and heavy metal resistance genes but also a versatile virulome repertoire. Mobile genetic elements, including insertion sequences, transposons, integrative conjugative elements, and an IncQ1 plasmid were also detected. Considering the ubiquity of Aeromonas species, their genetic promiscuity, pathogenicity, and intrinsic features to endure environmental stress, our findings reinforce the concept that A. hydrophila truly is a “Jack of all trades’’ that should not be overlooked under the One Health perspective. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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17 pages, 691 KiB

Open AccessArticle

Evaluation of Antimicrobial Resistance of Different Phylogroups of Escherichia coli Isolates from Feces of Breeding and Laying Hens

by Sandra Pais, Mariana Costa, Ana Rita Barata, Lígia Rodrigues, Isabel M. Afonso and Gonçalo Almeida

Antibiotics 2023, 12(1), 20; https://doi.org/10.3390/antibiotics12010020 - 23 Dec 2022

Cited by 3 | Viewed by 2132

Abstract

Animal and food sources are seen as a potential transmission pathway of multi-drug resistance (MDR) micro-organisms to humans. Escherichia. coli is frequently used as an indicator of fecal contamination in the food industry and known as a reservoir of antimicrobial resistance genes (ARGs). [...] Read more.

Animal and food sources are seen as a potential transmission pathway of multi-drug resistance (MDR) micro-organisms to humans. Escherichia. coli is frequently used as an indicator of fecal contamination in the food industry and known as a reservoir of antimicrobial resistance genes (ARGs). Microbial contamination as a major outcome for the poultry and egg industry and is a serious public health problem. In the present study we performed the quantification of β-glucoronidase positive E. coli in 60 fecal samples of breeding and laying hens collected in Portugal in 2019. Phylogenetic and pathotypic characterization, antimicrobial susceptibility, and detection of resistant extended-spectrum β-lactamase (ESBL) genes were assessed. The phylogenetic and pathogenic characterization and detection of ESBL genes were assessed by real-time PCR and antimicrobial susceptibility was evaluated using the disk diffusion method. Overall, E. coli quantification was 6.03 log CFU/g in breeding hens and 6.02 log CFU/g in laying hens. The most frequent phylogroups were B1. None of the isolates was classified as diarrheagenic E. coli (DEC). In total, 57% of the isolates showed MDR and 3.8% were positive for ESBL. Our study highlights that consumers may be exposed to MDR E. coli, presenting a major hazard to food safety and a risk to public health. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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8 pages, 281 KiB

Open AccessArticle

Evaluation of Retail Meat as a Source of ESBL Escherichia coli in Tamaulipas, Mexico

by Ana Verónica Martínez-Vázquez, Antonio Mandujano, Eduardo Cruz-Gonzalez, Abraham Guerrero, Jose Vazquez, Wendy Lizeth Cruz-Pulido, Gildardo Rivera and Virgilio Bocanegra-García

Antibiotics 2022, 11(12), 1795; https://doi.org/10.3390/antibiotics11121795 - 10 Dec 2022

Cited by 5 | Viewed by 1374

Abstract

In recent decades, the appearance of a group of strains resistant to most β-lactam antibiotics, called extended-spectrum β-lactamases (ESBLs), has greatly impacted the public health sector. The present work aimed to identify the prevalence of ESBL-producing Escherichia coli strains in retail meat from [...] Read more.

In recent decades, the appearance of a group of strains resistant to most β-lactam antibiotics, called extended-spectrum β-lactamases (ESBLs), has greatly impacted the public health sector. The present work aimed to identify the prevalence of ESBL-producing Escherichia coli strains in retail meat from northeast Tamaulipas. A total of 228 meat samples were obtained from 76 different stores. A prevalence of E. coli ESBL of 6.5% (15/228) was detected. All (15/15) of the ESBL strains were multiresistant. Altogether, 40% (6/15) of the strains showed the presence of class 1 integrons. The isolates identified with bla_CTX-M (20%) also showed co-resistance with the tet (A and B), str (A and B), and sul (2 and 3) genes. A total of 20% of the strains belonged to the B2 and D phylogroups, which are considered pathogenic groups. None of the ESBL-positive strains contained any of the virulence gene factors tested. The presence of ESBL-producing E. coli strains in meat indicates a potential risk to the consumer. Although most of these strains were classified as commensals, they were found to serve as reservoirs of multiresistance to antimicrobials and, therefore, are potential routes of dispersion of this resistance to other bacteria. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

11 pages, 1948 KiB

Open AccessArticle

Evaluation of a Sequential Antibiotic Treatment Regimen of Ampicillin, Ciprofloxacin and Fosfomycin against Escherichia coli CFT073 in the Hollow Fiber Infection Model Compared with Simultaneous Combination Treatment

by Ashok Krishna, Tesfalem Zere, Sabyasachy Mistry, Omnia Ismaiel, Heather Stone, Leonard V. Sacks and James L. Weaver

Antibiotics 2022, 11(12), 1705; https://doi.org/10.3390/antibiotics11121705 - 26 Nov 2022

Cited by 2 | Viewed by 1634

Abstract

Objective: Employ the hollow fiber infection model (HFIM) to study sequential antibiotic administration (ampicillin, ciprofloxacin and fosfomycin) using human pharmacokinetic profiles to measure changes in the rate of antibiotic resistance development and compare this to simultaneous combination therapy with the same antibiotic combinations. [...] Read more.

Objective: Employ the hollow fiber infection model (HFIM) to study sequential antibiotic administration (ampicillin, ciprofloxacin and fosfomycin) using human pharmacokinetic profiles to measure changes in the rate of antibiotic resistance development and compare this to simultaneous combination therapy with the same antibiotic combinations. Methods: Escherichia coli CFT073, a clinical uropathogenic strain, was exposed individually to clinically relevant pharmacokinetic concentrations of ampicillin on day 1, ciprofloxacin on day 2 and fosfomycin on day 3. This sequence was continued for 10 days in the HFIM. Bacterial samples were collected at different time points to enumerate total and resistant bacterial populations. The results were compared with the simultaneous combination therapy previously studied. Results: Sequential antibiotic treatment (ampicillin-ciprofloxacin-fosfomycin sequence) resulted in the early emergence of single and multi-antibiotic-resistant subpopulations, while the simultaneous treatment regimen significantly delayed or prevented the emergence of resistant subpopulations. Conclusion: Sequential administration of these antibiotic monotherapies did not significantly delay the emergence of resistant subpopulations compared to simultaneous treatment with combinations of the same antibiotics. Further studies are warranted to evaluate different sequences of the same antibiotics in delaying emergent resistance. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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14 pages, 822 KiB

Open AccessArticle

Identification and Characterization of Plasmids and Genes from Carbapenemase-Producing Klebsiella pneumoniae in Makkah Province, Saudi Arabia

by Rayan Y. Booq, Mohammed H. Abutarboush, Mohammed A. Alolayan, Abdulaziz A. Huraysi, Amjad N. Alotaibi, Maha I. Alturki, Maryam K. Alshammari, Abrar A. Bakr, Azzam A. Alquait, Essam A. Tawfik, Nasser B. Alsaleh, Fayez S. Bahwerth, Mohammed S. Alarawi, Essam J. Alyamani and Bandar K. Sendy

Antibiotics 2022, 11(11), 1627; https://doi.org/10.3390/antibiotics11111627 - 15 Nov 2022

Cited by 1 | Viewed by 2421

Abstract

Klebsiella pneumoniae (K. pneumoniae) is involved in several hospital and community-acquired infections. The prevalence of K. pneumoniae-producing-carbapenemase (KPC) resistance genes rapidly increases and threatens public health worldwide. This study aimed to assess the antibiotic resistance level of K. pneumoniae isolates [...] Read more.

Klebsiella pneumoniae (K. pneumoniae) is involved in several hospital and community-acquired infections. The prevalence of K. pneumoniae-producing-carbapenemase (KPC) resistance genes rapidly increases and threatens public health worldwide. This study aimed to assess the antibiotic resistance level of K. pneumoniae isolates from Makkah Province, Saudi Arabia, during the Islamic ‘Umrah’ ritual and to identify the plasmid types, presence of genes associated with carbapenem hydrolyzing enzymes, and virulence factors. The phenotypic and genotypic analyses based on the minimum inhibitory concentration (MIC), biofilm formation, PCR, and characterization of KPC-encoding plasmids based on the replicon typing technique (PBRT) were explored. The results showed that most isolates were resistant to carbapenem antibiotics and other antibiotics classes. This study identified sixteen different replicons of plasmids in the isolates and multiple genes encoding carbapenem factors, with bla_VIM and bla_OXA-48 being the most prevalent genes identified in the isolates. However, none of the isolates exhibited positivity for the KPC production activity. In addition, this study also identified six virulence-related genes, including kfu, wabG, uge, rmpA, fimH, and a capsular polysaccharide (CPS). Together, the data reported in this study indicate that the isolated K. pneumoniae during the pilgrimage in Makkah were all resistant to carbapenem antibiotics. Although the isolates lacked KPC production activity, they carried multiple carbapenem-resistant genes and virulence factors, which could drive their resistant phenotype. The need for specialized methods for KPC detection, monitoring the possibility of nosocomial transmission, and diverse therapeutic alternatives are necessary for controlling the spreading of KPC. This study can serve as a reference for clinicians and researchers on types of K. pneumoniae commonly found during religious gathering seasons in Saudi Arabia. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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14 pages, 1755 KiB

Open AccessArticle

Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal

by Ricardo Oliveira, Joana Castro, Sónia Silva, Hugo Oliveira, Maria José Saavedra, Nuno Filipe Azevedo and Carina Almeida

Antibiotics 2022, 11(11), 1613; https://doi.org/10.3390/antibiotics11111613 - 13 Nov 2022

Cited by 9 | Viewed by 3002

Abstract

While antibiotic resistance is rising to dangerously high levels, resistance mechanisms are spreading globally among diverse bacterial species. The emergence of antibiotic-resistant Klebsiella pneumoniae, mainly due to the production of antibiotic-inactivating enzymes, is currently responsible for most treatment failures, threatening the effectiveness [...] Read more.

While antibiotic resistance is rising to dangerously high levels, resistance mechanisms are spreading globally among diverse bacterial species. The emergence of antibiotic-resistant Klebsiella pneumoniae, mainly due to the production of antibiotic-inactivating enzymes, is currently responsible for most treatment failures, threatening the effectiveness of classes of antibiotics used for decades. This study assessed the presence of genetic determinants of β-lactam resistance in 102 multi-drug resistant (MDR) K. pneumoniae isolates from patients admitted to two central hospitals in northern Portugal from 2010 to 2020. Antimicrobial susceptibility testing revealed a high rate (>90%) of resistance to most β-lactam antibiotics, except for carbapenems and cephamycins, which showed antimicrobial susceptibility rates in the range of 23.5–34.3% and 40.2–68.6%, respectively. A diverse pool of β-lactam resistance genetic determinants, including carbapenemases- (i.e., bla_KPC-like and bla_OXA-48-like), extended-spectrum β-lactamases (ESBL; i.e., bla_TEM-like, bla_CTX-M-like and bla_SHV-like), and AmpC β-lactamases-coding genes (i.e., bla_CMY-2-like and bla_DHA-like) were found in most K. pneumoniae isolates. bla_KPC-like (72.5%) and ESBL genes (37.3–74.5%) were the most detected, with approximately 80% of K. pneumoniae isolates presenting two or more resistance genes. As the optimal treatment of β-lactamase-producing K. pneumoniae infections remains problematic, the high co-occurrence of multiple β-lactam resistance genes must be seen as a serious warning of the problem of antimicrobial resistance. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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14 pages, 2736 KiB

Open AccessArticle

ST11 Carbapenem-Resistant Klebsiella pneumoniae Clone Harboring bla_NDM Replaced a bla_KPC Clone in a Tertiary Hospital in China

by Qiaoyan Duan, Qi Wang, Shijun Sun, Qiaozhen Cui, Qi Ding, Ruobing Wang and Hui Wang

Antibiotics 2022, 11(10), 1373; https://doi.org/10.3390/antibiotics11101373 - 07 Oct 2022

Cited by 3 | Viewed by 1543

Abstract

The nosocomial spread of carbapenem-resistant Enterobacterales (CRE) is extremely common, resulting in severe burdens on healthcare systems. In particular, the high-risk Klebsiella pneumoniae ST11 strain has a wide endemic area in China. The current study describes the results of continuous monitoring of CRE [...] Read more.

The nosocomial spread of carbapenem-resistant Enterobacterales (CRE) is extremely common, resulting in severe burdens on healthcare systems. In particular, the high-risk Klebsiella pneumoniae ST11 strain has a wide endemic area in China. The current study describes the results of continuous monitoring of CRE genotypes and phenotypes in a tertiary hospital in North China from 2012 to 2020. A total of 160 isolates were collected, including 109 Klebsiella. pneumoniae (68.13%), 29 Escherichia coli (26.60%), 12 Enterobacter cloacae (7.50%), and 10 other strains (6.25%). A total of 149 carbapenemase genes were detected, of which bla_KPC_-2 (51.0%) was the most common, followed by bla_NDM_-1 (22.82%), and bla_NDM_-5 (23.49%). Based on multi-locus sequence typing, the ST11 strain (66.1%) dominates K. pneumoniae, followed by ST15 (13.8%). Interestingly, the proportion of bla_NDM (22.2%, 16/72) in ST11 K. pneumoniae was significantly increased in 2018–2019. Hence, whole-genome sequencing was performed on ST11 K. pneumoniae. Growth curves and in vitro competition experiments showed that K. pneumoniae carrying bla_NDM exhibited a stronger growth rate (p < 0.001) and competition index (p < 0.001) than K. pneumoniae carrying bla_KPC. Moreover, K. pneumoniae carrying bla_NDM had a stronger biofilm-forming ability than K. pneumoniae carrying bla_KPC (t = 6.578; p < 0.001). K. pneumoniae carrying bla_KPC exhibited increased defense against bactericidal activity than K. pneumoniae carrying bla_NDM. Thus, ST11 K. pneumoniae carrying bla_NDM has strong adaptability and can locally replace K. pneumoniae carrying bla_KPC to become an epidemic strain. Based on these findings, infection control and preventive measures should focus on the high-risk ST11-K. pneumoniae strain. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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17 pages, 3056 KiB

Open AccessArticle

Genomic Analysis of a mcr-9.1-Harbouring IncHI2-ST1 Plasmid from Enterobacter ludwigii Isolated in Fish Farming

by Vera Manageiro, Vanessa Salgueiro, Tânia Rosado, Narcisa M. Bandarra, Eugénia Ferreira, Terry Smith, Elsa Dias and Manuela Caniça

Antibiotics 2022, 11(9), 1232; https://doi.org/10.3390/antibiotics11091232 - 10 Sep 2022

Cited by 5 | Viewed by 1944

Abstract

This study analyzed the resistome, virulome and mobilome of an MCR-9-producing Enterobacter sp. identified in a muscle sample of seabream (Sparus aurata), collected in a land tank from multitrophic fish farming production. Average Nucleotide Identity analysis identified INSAq77 at [...] Read more.

This study analyzed the resistome, virulome and mobilome of an MCR-9-producing Enterobacter sp. identified in a muscle sample of seabream (Sparus aurata), collected in a land tank from multitrophic fish farming production. Average Nucleotide Identity analysis identified INSAq77 at the species level as an Enterobacter ludwigii INSAq77 strain that was resistant to chloramphenicol, florfenicol and fosfomycin and was susceptible to all other antibiotics tested. In silico antimicrobial resistance analyses revealed genes conferring in silico resistance to β-lactams (bla_ACT-88), chloramphenicol (catA4-type), fosfomycin (fosA2-type) and colistin (mcr-9.1), as well as several efflux pumps (e.g., oqxAB-type and mar operon). Further bioinformatics analysis revealed five plasmid replicon types, including the IncHI2/HI2A, which are linked to the worldwide dissemination of the mcr-9 gene in different antibiotic resistance reservoirs. The conserved nickel/copper operon rcnR-rcnA-pcoE-ISSgsp1-pcoS-IS903-mcr-9-wbuC was present, which may play a key role in copper tolerance under anaerobic growth and nickel homeostasis. These results highlight that antibiotic resistance in aquaculture are spreading through food, the environment and humans, which places this research in a One Health context. In fact, colistin is used as a last resort for the treatment of serious infections in clinical settings, thus mcr genes may represent a serious threat to human health. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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15 pages, 758 KiB

Open AccessArticle

Occurrence, Phenotypic and Molecular Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Healthy Turkeys in Northern Egypt

by Amira A. Moawad, Helmut Hotzel, Hafez M. Hafez, Hazem Ramadan, Herbert Tomaso, Sascha D. Braun, Ralf Ehricht, Celia Diezel, Dominik Gary, Ines Engelmann, Islam M. Zakaria, Reem M. Reda, Samah Eid, Momtaz A. Shahien, Heinrich Neubauer and Stefan Monecke

Antibiotics 2022, 11(8), 1075; https://doi.org/10.3390/antibiotics11081075 - 08 Aug 2022

Cited by 4 | Viewed by 2270

Abstract

Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. [...] Read more.

Poultry is one of the most important reservoirs for zoonotic multidrug-resistant pathogens. The indiscriminate use of antimicrobials in poultry production is a leading factor for development and dissemination of antimicrobial resistance. This study aimed to describe the prevalence and antimicrobial resistance of E. coli isolated from healthy turkey flocks of different ages in Nile delta region, Egypt. In the current investigation, 250 cloacal swabs were collected from 12 turkey farms in five governorates in the northern Egypt. Collected samples were cultivated on Brilliance^TM ESBL agar media supplemented with cefotaxime (100 mg/L). The E. coli isolates were identified using MALDI-TOF-MS and confirmed by a conventional PCR assay targeting 16S rRNA-DNA. The phenotypic antibiogram against 14 antimicrobial agents was determined using the broth micro-dilution method. DNA-microarray-based assay was applied for genotyping and determination of both, virulence and resistance-associated gene markers. Multiplex real-time PCR was additionally applied for all isolates for detection of the actual most relevant Carbapenemase genes. The phenotypic identification of colistin resistance was carried out using E-test. A total of 26 E. coli isolates were recovered from the cloacal samples. All isolates were defined as multidrug-resistant. Interestingly, two different E. coli strains were isolated from one sample. Both strains had different phenotypic and genotypic profiles. All isolates were phenotypically susceptible to imipenem, while resistant to penicillin, rifampicin, streptomycin, and erythromycin. None of the examined carbapenem resistance genes was detected among isolates. At least one beta-lactamase gene was identified in most of isolates, where blaTEM was the most commonly identified determinant (80.8%), in addition to blaCTX-M9 (23.1%), blaSHV (19.2%) and blaOXA-10 (15.4%). Genes associated with chloramphenicol resistance were floR (65.4%) and cmlA1 (46.2%). Tetracycline- and quinolone-resistance-associated genes tetA and qnrS were detected in (57.7%) and (50.0%) of isolates, respectively. The aminoglycoside resistance associated genes aadA1 (65.4%), aadA2 (53.8%), aphA (50.0%), strA (69.2%), and strB (65.4%), were detected among isolates. Macrolide resistance associated genes mph and mrx were also detected in (53.8%) and (34.6%). Moreover, colistin resistance associated gene mcr-9 was identified in one isolate (3.8%). The class 1 integron integrase intI1 (84.6%), transposase for the transposon tnpISEcp1 (34.6%) and OqxB -integral membrane and component of RND-type multidrug efflux pump oqxB (7.7%) were identified among the isolates. The existing high incidence of ESBL/colistin-producing E. coli identified in healthy turkeys is a major concern that demands prompt control; otherwise, such strains and their resistance determinants could be transmitted to other bacteria and, eventually, to people via the food chain. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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8 pages, 1469 KiB

Open AccessBrief Report

Genomic Analysis of Klebsiella pneumoniae ST258 Strain Coproducing KPC-2 and CTX-M-14 Isolated from Poultry in the Brazilian Amazon Region

by Tiago Barcelos Valiatti, Rodrigo Cayô, Fernanda Fernandes Santos, Francisco Ozório Bessa-Neto, Ramon Giovani Brandão Silva, Ruanita Veiga, Márcia de Nazaré Miranda Bahia, Lívia Maria Guimarães Dutra Guerra, Antônio Carlos Campos Pignatari, Cintya de Oliveira Souza, Danielle Murici Brasiliense and Ana Cristina Gales

Antibiotics 2022, 11(12), 1835; https://doi.org/10.3390/antibiotics11121835 - 17 Dec 2022

Viewed by 1997

Abstract

This study aimed to characterize a Klebsiella pneumoniae strain (KP411) recovered from the stool samples of poultry (Gallus gallus) in the Brazilian Amazon Region. The whole-genome sequencing of KP411 revealed the presence of an important arsenal of antimicrobial resistance genes to [...] Read more.

This study aimed to characterize a Klebsiella pneumoniae strain (KP411) recovered from the stool samples of poultry (Gallus gallus) in the Brazilian Amazon Region. The whole-genome sequencing of KP411 revealed the presence of an important arsenal of antimicrobial resistance genes to β-lactams (bla_CTX-M-14, bla_TEM-1B, bla_KPC-2, bla_SVH-11), aminoglycosides [aph(3″)- Ib, aph(6)-Id, aph(3′)-Ia], sulfonamides (sul1, sul2), quinolones (oqxAB), fosfomycin (fosA^KP), and macrolides [mph(A)]. Furthermore, our analyses revealed that the KP411 strain belongs to the ST258 clonal lineage, which is one of the main epidemic clones responsible for the dissemination of KPC-2 worldwide. Our data suggest that food-producing animals may act as reservoirs of multidrug-resistant K. pneumoniae belonging to the ST258 clone, and, consequently, contribute to their dissemination to humans and the environment. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Profiles of Gram-Negative Bacteria)

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