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Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 6211

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Dr. Kwang Won Seo

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College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
Interests: antimicrobial resistance; virulence factors; multiple drug resistance; transmission
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Enterobacteriaceae are important zoonotic foodborne bacteria capable of endangering human health and useful indicator of hygiene. In particular, antimicrobial resistance in Enterobacteriaceae is more important than any bacteria due to the spread of antibiotic resistance factors and pathogenic factors. Antimicrobial resistance (AMR) is one of biggest challenges for public health this century. This threat is recognized as a global problem that broke up human settings barriers a long time ago. AMR is reported in all compartments of the whole ecosystem, and, accordingly with the WHO, CDC and ECDC, continuous surveillance continues to be a powerful tool in the fight to break AMR. This Special Issue proposes to build upon one more piece of the molecular characteristics, pathogenicity and antimicrobial resistance in Enterobacteriaceae, through attracting and agglutinating the new data, updates, opinions, points of view and scientific perspectives of Enterobacteriaceae.

Dr. Kwang Won Seo
Guest Editor

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Keywords

antimicrobial resistance
virulence gene
multiple drug resistance
transmission
ESBL
beta-lactamases
PMQR
carbapenemases
MRSA

Published Papers (6 papers)

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Research

13 pages, 538 KiB

Open AccessArticle

Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

by Jessica N. Uwanibe, Idowu B. Olawoye, Christian T. Happi and Onikepe A. Folarin

Microorganisms 2024, 12(3), 505; https://doi.org/10.3390/microorganisms12030505 - 01 Mar 2024

Cited by 1 | Viewed by 1061

Abstract

Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant Citrobacter spp., Enterobacter spp., Klebsiella pneumoniae, and Escherichia coli isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the pmrB_Y358N gene responsible for colistin resistance detected in E. coli ST219, virulence genes such as senB, and ybtP&Q, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated tetA gene, a toxin production caa gene in two E. coli isolates, and a cusC gene in K. quasivariicola ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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11 pages, 1131 KiB

Open AccessArticle

Effect of Temperature on Carbapenemase-Encoding Plasmid Transfer in Klebsiella pneumoniae

by Ji Woo Yang, Ji-Hyun Nam, Kwang Jun Lee and Jung Sik Yoo

Microorganisms 2024, 12(3), 454; https://doi.org/10.3390/microorganisms12030454 - 23 Feb 2024

Viewed by 577

Abstract

Bacteria causing human infections can develop antibiotic resistance due to various factors. Temperature affects bacterial growth and gene transfer; however, studies exploring the association between the changes in local temperature and antibiotic resistance are limited. Here, we investigated the effects of local temperatures on the distribution of antibiotic resistance and transmission of carbapenemase-producing Enterobacterales using the data on Klebsiella pneumoniae from sentinel hospitals in eight regions included in the Korea Global Antimicrobial Resistance Surveillance System between 2017 and 2021. The resistance rates to most antibiotics, including carbapenems, varied significantly according to local temperature (p < 0.047), except for aminoglycosides. Conjugation experiments at various temperatures for strains encoding the carbapenemase gene on a plasmid revealed significant variation in the optimal conjugation temperatures for plasmids carrying bla_KPC and bla_NDM genes. The optimal conjugation temperatures demonstrating the highest stability for bla_KPC- and bla_NDM-carrying plasmids were 25 °C (p = 0.030) and 30 °C (p = 0.007), respectively. The stability of bla_KPC-IncF was higher at 25 °C than that at 30 °C (p = 0.032) or 37 °C (p = 0.047), while bla_KPC-IncX3 exhibited the lowest stability at 37 °C (p = 0.047). bla_NDM-IncX3 was more stable at 30 °C than at 37 °C (p = 0.049). These findings suggest that the optimal temperature for carbapenemase gene transmission varied between 25 °C and 30 °C, indicating that warmer seasons promote the transfer of more antibiotic resistance-related genes and highlighting the importance of local temperature in the spread and transmission of plasmids carrying carbapenemases. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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14 pages, 651 KiB

Open AccessArticle

Antimicrobial Susceptibility Patterns and Genetic Diversity of Campylobacter spp. Isolates from Patients with Diarrhea in South Korea

by So Yeon Kim, Dongheui An, Hyemi Jeong and Jonghyun Kim

Microorganisms 2024, 12(1), 94; https://doi.org/10.3390/microorganisms12010094 - 02 Jan 2024

Viewed by 964

Abstract

This study aimed to characterize the latest antimicrobial resistance patterns and genetic diversity of Campylobacter spp. isolated from patients with acute diarrhea in Korea. In total, 371 clinical isolates (361 Campylobacter jejuni and 10 Campylobacter coli) were collected from patients with diarrhea in 106 medical institutions of six provinces during the seasonal peak (April–September 2022) in South Korea. We then assessed their antimicrobial susceptibility to eight antimicrobial agents and performed multilocus sequence typing (MLST). This study investigated the antimicrobial resistance (AMR) profiles to tetracycline (32.3%), nalidixic acid (64.9%), and ciprofloxacin (83.3%), confirming high levels of the latter even after its Korean ban in 2010. However, tetracycline resistance displayed a decreasing trend. Alternatively, significantly lower resistance rates to clindamycin (0.8%), azithromycin (0.53%), erythromycin (0.53%), and gentamicin (0.53%) as well as absolute susceptibility to florfenicol (0%) were observed. Four C. jejuni and three C. coli isolates (7/371, 1.88%) were classified as multidrug-resistant (MDR) to at least three antimicrobial classes. MLST identified a high genetic diversity with 21 clonal complexes (CCs) and sixty-six sequence types (STs), including eight novel STs. The high CC frequency of C. jejuni comprised CC21 (37.7%), CC22 (13.8%), and CC206 (9.4%), while C. coli was predominated by CC828 (90%). The high CC21 and CC828 strain prevalence in this study was consistent with their worldwide distribution. This study highlights that quinolone- and tetracycline-resistant Campylobacter circulate in Korea with diverse genotypes, providing important information that could contribute to controlling and preventing increasing antimicrobial resistance in patients. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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13 pages, 638 KiB

Open AccessArticle

Exploring Antimicrobial Resistance Profiles of E. coli Isolates in Dairy Cattle: A Baseline Study across Dairy Farms with Varied Husbandry Practices in Puerto Rico

by Yadira Malavez, Sharon M. Nieves-Miranda, Paola N. Loperena Gonzalez, Adrian F. Padin-Lopez, Lingzi Xiaoli and Edward G. Dudley

Microorganisms 2023, 11(12), 2879; https://doi.org/10.3390/microorganisms11122879 - 28 Nov 2023

Viewed by 976

Abstract

Antimicrobial treatment in livestock can contribute to the emergence and spread of antimicrobial-resistant (AMR) microorganisms. Despite substantial surveillance of AMR bacteria in the continental United States, the prevalence of these AMR organisms in U.S. territories, such as Puerto Rico, remains understudied. The goals of this research included obtaining baseline data on the antimicrobial profile of E. coli isolates from Puerto Rico dairy farms with different husbandry practices. Seventy-nine fecal samples were collected from two types of conventional dairy farms: those that fed calves with tank milk and those that fed calves with waste milk. These samples were collected from the animals’ rectums, culture, and subsequently confirmed through biochemical tests. Out of these samples, 32 isolates were analyzed phenotypically and genotypically to elucidate their AMR profiles. The results underscore a discrepancy in the occurrence of antimicrobial resistance genes between calves and adult cattle. Notably, waste milk-fed calves exhibited a significantly higher prevalence of antibiotic-resistant E. coli when compared to their tank milk-fed counterparts. These disparities emphasize the need for more comprehensive investigations to determine causative factors. These results underscore the urgency of comprehensive strategies to raise awareness about how management practices influence antimicrobial resistance, shifting the focus from treatment to prevention. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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16 pages, 2191 KiB

Open AccessArticle

Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing

by Zeinab Ebrahimzadeh Mousavi, Leonard Koolman, Guerrino Macori, Séamus Fanning and Francis Butler

Microorganisms 2023, 11(11), 2749; https://doi.org/10.3390/microorganisms11112749 - 11 Nov 2023

Viewed by 1136

Abstract

Cronobacter sakazakii is an opportunistic pathogen linked to outbreaks in powdered infant formula (PIF), primarily causing meningitis and necrotizing enterocolitis. Whole-genome sequencing (WGS) was used to characterize 18 C. sakazakii strains isolated from PIF (powdered infant formula) manufacturing plants (2011–2015). Sequence Type (ST) 1 was identified as the dominant sequence type, and all isolates carried virulence genes for chemotaxis, flagellar motion, and heat shock proteins. Multiple antibiotic resistance genes were detected, with all isolates exhibiting resistance to Cephalosporins and Tetracycline. A significant correlation existed between genotypic and phenotypic antibiotic resistance. The plasmid Col(pHAD28) was identified in the isolates recovered from the same PIF environment. All isolates harbored at least one intact phage. All the study isolates were compared with a collection of 96 publicly available C. sakazakii genomes to place these isolates within a global context. This comprehensive study, integrating phylogenetic, genomic, and epidemiological data, contributes to a deeper understanding of Cronobacter outbreaks. It provides valuable insights to enhance surveillance, prevention, and control strategies in food processing and public health contexts. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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7 pages, 770 KiB

Open AccessCommunication

Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing

by Kwang-Won Seo, Kyung-Hyo Do and Wan-Kyu Lee

Microorganisms 2023, 11(8), 1922; https://doi.org/10.3390/microorganisms11081922 - 28 Jul 2023

Cited by 2 | Viewed by 845

Abstract

Pathogenic E. coli causes intra- and extraintestinal diseases in humans and pigs and third-generation cephalosporins are the primary option for the treatment of these diseases. The objective of this study was to investigate the characteristics and correlation between CTX-M-producing E. coli from humans and pigs regarding CTX-M-producing E. coli using next-generation sequencing and bioinformatic tools. Among the 24 CTX-M–producing E. coli, three types of CTX-M genes (CTX-M-12, CTX-M-14, and CTX-M-15) were detected in humans and four types of CTX-M genes (CTX-M-14, CTX-M-15, CTX-M-55, and CTX-M-101) were detected in pigs. A total of 24 CTX-M–producing E. coli isolates also showed the following antimicrobial resistance genes: other B-Lactam resistance gene (75.0%); aminoglycoside resistance genes (75.0%); phenicol resistance genes (70.8%); tetracycline resistance genes (70.8%); sulfonamide resistance genes (66.7%); quinolone resistance genes (62.5%); trimethoprim resistance genes (54.2%); and fosfomycin resistance genes (8.3%). FII (92.3%) and FIB (90.9%) were the most common plasmid replicon in humans and pigs, respectively. A total of thirty-eight different genes associated with virulence 24 CTX-M–producing E. coli and all isolates contained at least more than one virulence gene. A total of 24 CTX-M–producing E. coli isolates showed 15 diverse sequence types (STs): thirteen isolates from human belonged to 6 different STs, and 11 isolates from pig belonged to 9 different STs. The presence of virulence genes in E. coli together with antimicrobial resistance genes (including CTX-M genes) emphasizes the necessity of comprehensive surveillance and persistent monitoring of the food chain to avoid all types of bacterial contamination, regardless of human or pig origin. Full article

(This article belongs to the Special Issue Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae)

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Molecular Characteristics, Pathogenicity and Antimicrobial Resistance of Enterobacteriaceae

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