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Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria

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A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Mechanism and Evolution of Antibiotic Resistance".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 24682

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Dr. Andrey Shelenkov

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Central Research Institute of Epidemiology, Rospotrebnadzor, 111123 Moscow, Russia
Interests: genomic epidemiology; ESKAPE pathogens; antimicrobial resistance; whole genome sequencing; bioinformatics; healthcare-associated infections
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Dear Colleagues,

In recent years, the infections caused by antibiotic-resistant bacteria have become a major challenge worldwide, and this problem is expected to worsen in the next few years, in particular due to the extensive use of antimicrobial drugs during the COVID-19 pandemic. The rapid detection of specific bacterial species causing infections and their antibiotic resistance determinants could provide the crucial tools for coping with this global problem. Currently, molecular detection tools and whole-genome sequencing have become the gold standard for the detection and characterization of various pathogens. The combination of molecular, genomic, and bioinformatics tools has already given rise to genomic epidemiology approaches, which are currently attracting increasing attention in different fields of pathogen investigation.

For this Special Issue, we invite you to contribute original research, case reports, and review papers describing the application of current molecular techniques to the detection, characterization, antimicrobial resistance determination, and epidemiological surveillance of various bacterial pathogens, including the ones causing co-infections in COVID-19 patients. Reports based on whole-genome sequencing and genomic epidemiology analysis are particularly welcome. Novel computational approaches for antimicrobial resistance determination and genomic characterization will also be considered.

Dr. Andrey Shelenkov
Guest Editor

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Keywords

pathogenic bacteria
molecular detection
antibiotic resistance
whole genome sequencing
genomic epidemiology
antimicrobial resistance prediction
ESKAPE pathogens
COVID-19 co-infections

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Editorial

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4 pages, 154 KiB

Open AccessEditorial

Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria

by Andrey Shelenkov

Antibiotics 2024, 13(6), 494; https://doi.org/10.3390/antibiotics13060494 - 27 May 2024

Viewed by 1586

Abstract

In recent decades, growing attention has been directed worldwide toward antimicrobial-resistant (AMR) bacterial pathogens causing infections in clinical, environmental, and food chain production settings [...] Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

Research

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17 pages, 3804 KiB

Open AccessArticle

First Report of Colistin-Resistant Escherichia coli Carrying mcr-1 IncI2(delta) and IncX4 Plasmids from Camels (Camelus dromedarius) in the Gulf Region

by Akela Ghazawi, Nikolaos Strepis, Febin Anes, Dana Yaaqeib, Amal Ahmed, Aysha AlHosani, Mirah AlShehhi, Ashrat Manzoor, Ihab Habib, Nisar A. Wani, John P. Hays and Mushtaq Khan

Antibiotics 2024, 13(3), 227; https://doi.org/10.3390/antibiotics13030227 - 28 Feb 2024

Cited by 1 | Viewed by 2178

Abstract

Addressing the emergence of antimicrobial resistance (AMR) poses a significant challenge in veterinary and public health. In this study, we focused on determining the presence, phenotypic background, and genetic epidemiology of plasmid-mediated colistin resistance (mcr) in Escherichia coli bacteria isolated from camels farmed in the United Arab Emirates (UAE). Fecal samples were collected from 50 camels at a Dubai-based farm in the UAE and colistin-resistant Gram-negative bacilli were isolated using selective culture. Subsequently, a multiplex PCR targeting a range of mcr-genes, plasmid profiling, and whole-genome sequencing (WGS) were conducted. Eleven of fifty camel fecal samples (22%) yielded colonies positive for E. coli isolates carrying the mcr-1 gene on mobile genetic elements. No other mcr-gene variants and no chromosomally located colistin resistance genes were detected. Following plasmid profiling and WGS, nine E. coli isolates from eight camels were selected for in-depth analysis. E. coli sequence types (STs) identified included ST7, ST21, ST24, ST399, ST649, ST999, and STdaa2. Seven IncI2(delta) and two IncX4 plasmids were found to be associated with mcr-1 carriage in these isolates. These findings represent the first identification of mcr-1-carrying plasmids associated with camels in the Gulf region. The presence of mcr-1 in camels from this region was previously unreported and serves as a novel finding in the field of AMR surveillance. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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15 pages, 1628 KiB

Open AccessArticle

Acinetobacter Non-baumannii Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance

by Eugene Sheck, Andrey Romanov, Valeria Shapovalova, Elvira Shaidullina, Alexey Martinovich, Natali Ivanchik, Anna Mikotina, Elena Skleenova, Vladimir Oloviannikov, Ilya Azizov, Vera Vityazeva, Alyona Lavrinenko, Roman Kozlov and Mikhail Edelstein

Antibiotics 2023, 12(8), 1301; https://doi.org/10.3390/antibiotics12081301 - 9 Aug 2023

Cited by 9 | Viewed by 3176

Abstract

Background: Acinetobacter species other than A. baumannii are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical Acinetobacter non-baumannii (Anb) isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of Anb isolates. Methods: Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016–2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific bla_OXA-51-like gene was used as a means of differentiating A. baumannii from Anb species, and the partial sequencing of the rpoB gene was used as a reference method for Anb species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim–sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in Acinetobacter-acquired carbapenemase genes (bla_OXA-23-like, bla_{OXA-24/40-like}, bla_OXA-58-like, bla_NDM, bla_IMP, and bla_VIM) was assessed using real-time PCR. Results: In total, 234 isolates were identified as belonging to 14 Anb species. These comprised 6.2% of Acinetobacter spp. and 0.7% of all bacterial isolates from the observations. Among the Anb species, the most abundant were A. pittii (42.7%), A. nosocomialis (13.7%), the A. calcoaceticus/oleivorans group (9.0%), A. bereziniae (7.7%), and A. geminorum (6.0%). Notably, two environmental species, A. oleivorans and A. courvalinii, were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in Anb species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of A. bereziniae, A. johnsonii, A. nosocomialis, A. oleivorans, A. pittii, and A. ursingii were resistant to carbapenems. A. bereziniae was more frequently resistant to sulbactam, aminoglycosides, trimethoprim–sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of A. bereziniae, A. johnsonii, A. pittii were found to carry carbapenemase genes (bla_OXA-58-like and bla_NDM, either alone or in combination). The overall accuracy rates of the species-level identification of Anb isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively. Conclusions: This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical Anb isolates. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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14 pages, 1326 KiB

Open AccessArticle

Cracking the Code: Unveiling the Diversity of Carbapenem-Resistant Klebsiella pneumoniae Clones in the Arabian Peninsula through Genomic Surveillance

by Amani H Al Fadhli, Shaimaa F. Mouftah, Wafaa Y. Jamal, Vincent O. Rotimi and Akela Ghazawi

Antibiotics 2023, 12(7), 1081; https://doi.org/10.3390/antibiotics12071081 - 21 Jun 2023

Cited by 3 | Viewed by 1658

Abstract

The rise of antimicrobial resistance is a global challenge that requires a coordinated effort to address. In this study, we examined the genetic similarity of carbapenem-resistant Klebsiella pneumoniae (CRKP) in countries belonging to the Gulf Cooperation Council (GCC) to gain a better understanding of how these bacteria are spreading and evolving in the region. We used in silico genomic tools to investigate the occurrence and prevalence of different types of carbapenemases and their relationship to specific sequence types (STs) of CRKP commonly found in the region. We analyzed 720 publicly available genomes of multi-drug resistant K. pneumoniae isolates collected from six GCC countries between 2011 and 2020. Our findings showed that ST-14 and ST-231 were the most common STs, and 51.7% of the isolates carried bla_OXA-48-like genes. Additionally, we identified rare carbapenemase genes in a small number of isolates. We observed a clonal outbreak of ST-231 in Oman, and four Saudi isolates were found to have colistin resistance genes. Our study offers a comprehensive overview of the genetic diversity and resistance mechanisms of CRKP isolates in the GCC region that could aid in developing targeted interventions to combat this pressing global issue. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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11 pages, 1160 KiB

Open AccessArticle

Molecular Characterization and Epidemiology of Antibiotic Resistance Genes of β-Lactamase Producing Bacterial Pathogens Causing Septicemia from Tertiary Care Hospitals

by Mohammad Riaz Khan, Sadiq Azam, Sajjad Ahmad, Qaisar Ali, Zainab Liaqat, Noor Rehman, Ibrar Khan, Metab Alharbi and Abdulrahman Alshammari

Antibiotics 2023, 12(3), 617; https://doi.org/10.3390/antibiotics12030617 - 20 Mar 2023

Cited by 1 | Viewed by 2117

Abstract

Septicemia is a systematic inflammatory response and can be a consequence of abdominal, urinary tract and lung infections. Keeping in view the importance of Gram-negative bacteria as one of the leading causes of septicemia, the current study was designed with the aim to determine the antibiotic susceptibility pattern, the molecular basis for antibiotic resistance and the mutations in selected genes of bacterial isolates. In this study, clinical samples (n = 3389) were collected from potentially infected male (n = 1898) and female (n = 1491) patients. A total of 443 (13.07%) patients were found to be positive for bacterial growth, of whom 181 (40.8%) were Gram-positive and 262 (59.1%) were Gram-negative. The infected patients included 238 males, who made up 12.5% of the total number tested, and 205 females, who made up 13.7%. The identification of bacterial isolates revealed that 184 patients (41.5%) were infected with Escherichia coli and 78 (17.6%) with Pseudomonas aeruginosa. The clinical isolates were identified using Gram staining biochemical tests and were confirmed using polymerase chain reaction (PCR), with specific primers for E. coli (USP) and P. aeruginosa (oprL). Most of the isolates were resistant to aztreonam (ATM), cefotaxime (CTX), ampicillin (AMP) and trimethoprim/sulfamethoxazole (SXT), and were sensitive to tigecycline (TGC), meropenem (MEM) and imipenem (IPM), as revealed by high minimum inhibitory concentration (MIC) values. Among the antibiotic-resistant bacteria, 126 (28.4%) samples were positive for ESBL, 105 (23.7%) for AmpC β-lactamases and 45 (10.1%) for MBL. The sequencing and mutational analysis of antibiotic resistance genes revealed mutations in TEM, SHV and AAC genes. We conclude that antibiotic resistance is increasing; this requires the attention of health authorities and clinicians for proper management of the disease burden. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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12 pages, 1066 KiB

Open AccessArticle

The Diversity, Resistance Profiles and Plasmid Content of Klebsiella spp. Recovered from Dairy Farms Located around Three Cities in Pakistan

by Samia Habib, Marjorie J. Gibbon, Natacha Couto, Khadija Kakar, Safia Habib, Abdul Samad, Asim Munir, Fariha Fatima, Mashkoor Mohsin and Edward J. Feil

Antibiotics 2023, 12(3), 539; https://doi.org/10.3390/antibiotics12030539 - 8 Mar 2023

Cited by 2 | Viewed by 2758

Abstract

The rise of antimicrobial resistance (AMR) in bacterial pathogens such as Klebsiella pneumoniae (Kp) is a pressing public health and economic concern. The ‘One-Health’ framework recognizes that effective management of AMR requires surveillance in agricultural as well as clinical settings, particularly in low-resource regions such as Pakistan. Here, we use whole-genome sequencing to characterise 49 isolates of Klebisella spp. (including 43 Kp) and 2 presumptive Providencia rettgeri isolates recovered from dairy farms located near 3 cities in Pakistan—Quetta (n = 29), Faisalabad (n = 19), and Sargodha (n = 3). The 43 Kp isolates corresponded to 38 sequence types (STs), and 35 of these STs were only observed once. This high diversity indicates frequent admixture and limited clonal spread on local scales. Of the 49 Klebsiella spp. isolates, 41 (84%) did not contain any clinically relevant antimicrobial resistance genes (ARGs), and we did not detect any ARGs predicted to encode resistance to carbapenems or colistin. However, four Kp lineages contained multiple ARGs: ST11 (n = 2), ST1391-1LV (n = 1), ST995 (n = 1) and ST985 (n = 1). STs 11, 1391-1LV and 995 shared a core set of five ARGs, including bla_CTX-M-15, harboured on different AMR plasmids. ST985 carried a different set of 16 resistance genes, including bla_CTX-M-55. The two presumptive P. rettgeri isolates also contained multiple ARGs. Finally, the four most common plasmids which did not harbour ARGs in our dataset were non-randomly distributed between regions, suggesting that local expansion of the plasmids occurs independently of the host bacterial lineage. Evidence regarding how dairy farms contribute to the emergence and spread of AMR in Pakistan is valuable for public authorities and organizations responsible for health, agriculture and the environment, as well as for industrial development. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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12 pages, 1254 KiB

Open AccessArticle

Induction of Viable but Non-Culturable State in Clinically Relevant Staphylococci and Their Detection with Bacteriophage K

by Katja Šuster and Andrej Cör

Antibiotics 2023, 12(2), 311; https://doi.org/10.3390/antibiotics12020311 - 2 Feb 2023

Cited by 2 | Viewed by 1713

Abstract

Prosthetic joint infections are frequently associated with biofilm formation and the presence of viable but non-culturable (VBNC) bacteria. Conventional sample culturing remains the gold standard for microbiological diagnosis. However, VBNC bacteria lack the ability to grow on routine culture medium, leading to culture-negative results. Bacteriophages are viruses that specifically recognize and infect bacteria. In this study, we wanted to determine if bacteriophages could be used to detect VBNC bacteria. Four staphylococcal strains were cultured for biofilm formation and transferred to low-nutrient media with different gentamycin concentrations for VBNC state induction. VBNC bacteria were confirmed with the BacLight^TM viability kit staining. Suspensions of live, dead, and VBNC bacteria were incubated with bacteriophage K and assessed in a qPCR for their detection. The VBNC state was successfully induced 8 to 19 days after incubation under stressful conditions. In total, 6.1 to 23.9% of bacteria were confirmed alive while not growing on conventional culturing media. During the qPCR assay, live bacterial suspensions showed a substantial increase in phage DNA. No detection was observed in dead bacteria or phage non-susceptible E. coli suspensions. However, a reduction in phage DNA in VBNC bacterial suspensions was observed, which confirmed the detection was successful based on the adsorption of phages. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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11 pages, 4601 KiB

Open AccessArticle

Biocide-Resistant Escherichia coli ST540 Co-Harboring ESBL, dfrA14 Confers QnrS-Dependent Plasmid-Mediated Quinolone Resistance

by Srinivasan Vijaya Bharathi and Govindan Rajamohan

Antibiotics 2022, 11(12), 1724; https://doi.org/10.3390/antibiotics11121724 - 30 Nov 2022

Viewed by 1592

Abstract

Emerging sequence types of pathogenic bacteria have a dual ability to acquire resistance islands/determinants, and remain renitent towards disinfection practices; therefore, they are considered “critical risk factors” that contribute significantly to the global problem of antimicrobial resistance. Multidrug-resistant Escherichia coli was isolated, its genome sequenced, and its susceptibilities characterized, in order to understand the genetic basis of its antimicrobial resistance.The draft genome sequencing of E. coli ECU32, was performed with Illumina NextSeq 500, and annotated using a RAST server. The antibiotic resistome, genomic island, insertion sequences, and prophages were analyzed using bioinformatics tools. Subsequently, analyses including antibiotic susceptibility testing, E-test, bacterial growth, survival, and efflux inhibition assays were performed.The draft genome of E. coli ECU32 was 4.7 Mb in size, the contigs were 107, and the G+C content was 50.8%. The genome comprised 4658 genes, 4543 CDS, 4384 coding genes, 115 RNA genes, 88 tRNAs, and 3 CRISPR arrays. The resistome characterization of ST540 E. coli ECU32 revealed the presence of ESBL, APH(6)-Id, APH(3′)-IIa, dfrA14, and QnrS1, with broad-spectrum multidrug and biocide resistance. Comparative genome sequence analysis revealed the presence of transporter and several virulence genes. Efflux activity and growth inhibition assays, which were performed with efflux substrates in the presence of inhibitor PAβN, exhibited significant reduced growth relative to its control.This study discusses the genotypic and phenotypic characterization of the biocide-tolerant multidrug-resistant E. coli O9:H30 strain, highlighting the contributory role of qnrS-dependent plasmid-mediated quinolone resistance, in addition to innate enzymatic modes of multidrug resistance mechanisms. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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16 pages, 2290 KiB

Open AccessArticle

Genomic Analysis of a Hybrid Enteroaggregative Hemorrhagic Escherichia coli O181:H4 Strain Causing Colitis with Hemolytic-Uremic Syndrome

by Angelina A. Kislichkina, Nikolay N. Kartsev, Yury P. Skryabin, Angelika A. Sizova, Maria E. Kanashenko, Marat G. Teymurazov, Ekaterina S. Kuzina, Alexander G. Bogun, Nadezhda K. Fursova, Edward A. Svetoch and Ivan A. Dyatlov

Antibiotics 2022, 11(10), 1416; https://doi.org/10.3390/antibiotics11101416 - 14 Oct 2022

Cited by 5 | Viewed by 1931

Abstract

Hybrid diarrheagenic E. coli strains combining genetic markers belonging to different pathotypes have emerged worldwide and have been reported as a public health concern. The most well-known hybrid strain of enteroaggregative hemorrhagic E. coli is E. coli O104:H4 strain, which was an agent of a serious outbreak of acute gastroenteritis and hemolytic uremic syndrome (HUS) in Germany in 2011. A case of intestinal infection with HUS in St. Petersburg (Russian Federation) occurred in July 2018. E. coli strain SCPM-O-B-9427 was obtained from the rectal swab of the patient with HUS. It was determined as O181:H4-, stx2-, and aggR-positive and belonged to the phylogenetic group B2. The complete genome assembly of the strain SCPM-O-B-9427 contained one chromosome and five plasmids, including the plasmid coding an aggregative adherence fimbriae I. MLST analysis showed that the strain SCPM-O-B-9427 belonged to ST678, and like E. coli O104:H4 strains, 2011C-3493 caused the German outbreak in 2011, and 2009EL-2050 was isolated in the Republic of Georgia in 2009. Comparison of three strains showed almost the same structure of their chromosomes: the plasmids pAA and the stx2a phages are very similar, but they have distinct sets of the plasmids and some unique regions in the chromosomes. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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11 pages, 979 KiB

Open AccessArticle

Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients

by Andrey Shelenkov, Lyudmila Petrova, Anna Mironova, Mikhail Zamyatin, Vasiliy Akimkin and Yulia Mikhaylova

Antibiotics 2022, 11(10), 1364; https://doi.org/10.3390/antibiotics11101364 - 6 Oct 2022

Cited by 3 | Viewed by 2185

Abstract

Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3′)-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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19 pages, 5251 KiB

Open AccessArticle

The Detection of Potential Native Probiotics Lactobacillus spp. against Salmonella Enteritidis, Salmonella Infantis and Salmonella Kentucky ST198 of Lebanese Chicken Origin

by Rima El Hage, Jeanne El Hage, Selma P. Snini, Imad Ammoun, Joseph Touma, Rami Rachid, Florence Mathieu, Jean-Marc Sabatier, Ziad Abi Khattar and Youssef El Rayess

Antibiotics 2022, 11(9), 1147; https://doi.org/10.3390/antibiotics11091147 - 24 Aug 2022

Cited by 11 | Viewed by 2736

Abstract

Salmonella continues to be a major threat to public health, especially with respect to strains from a poultry origin. In recent years, an increasing trend of antimicrobial resistance (AMR) in Salmonella spp. was observed due to the misuse of antibiotics. Among the approaches advised for overcoming AMR, probiotics from the Lactobacillus genus have increasingly been considered for use as effective prophylactic and therapeutic agents belonging to the indigenous microbiota. In this study, we isolated lactobacilli from the ilea and ceca of hens and broilers in order to evaluate their potential probiotic properties. Four species were identified as Limosilactobacillusreuteri (n = 22, 45.8%), Ligilactobacillussalivarius (n = 20, 41.6%), Limosilactobacillus fermentum (n = 2, 4.2%) and Lactobacillus crispatus (n = 1, 2%), while three other isolates (n = 3, 6.25%) were non-typable. Eight isolates, including Ligilactobacillussalivarius (n = 4), Limosilactobacillusreuteri (n = 2), L. crispatus (n = 1) and Lactobacillus spp. (n = 1) were chosen on the basis of their cell surface hydrophobicity and auto/co-aggregation ability for further adhesion assays using the adenocarcinoma cell line Caco-2. The adhesion rate of these strains varied from 0.53 to 10.78%. Ligilactobacillussalivarius A30/i26 and 16/c6 and Limosilactobacillus reuteri 1/c24 showed the highest adhesion capacity, and were assessed for their ability to compete in and exclude the adhesion of Salmonella to the Caco-2 cells. Interestingly, Ligilactobacillussalivarius 16/c6 was shown to significantly exclude the adhesion of the three Salmonella serotypes, S. Enteritidis, S. Infantis and S. Kentucky ST 198, to Caco-2 cells. The results of the liquid co-culture assays revealed a complete inhibition of the growth of Salmonella after 24 h. Consequently, the indigenous Ligilactobacillussalivarius 16/c6 strain shows promising potential for use as a preventive probiotic added directly to the diet for the control of the colonization of Salmonella spp. in poultry. Full article

(This article belongs to the Special Issue Molecular Detection, Characterization, Antimicrobial Resistance and Genomic Epidemiology of Pathogenic Bacteria)

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