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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Public Health Microbiology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 18373

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Prof. Dr. Lúcia Martins Teixeira

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Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeirodisabled, Rio de Janeiro, Brazil
Interests: molecular characterization and epidemiology of bacteria antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals

Dr. Cheryl P. Andam

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Department of Biological Sciences, University at Albany, Albany, NY, USA
Interests: molecular characterization; epidemiology of bactéria; antimicrobial resistance; bacterial evolution; genomic epidemiology of infectious diseases
Special Issues, Collections and Topics in MDPI journals

Dr. Stephanie S. R. Souza

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Special Issue Information

Dear Colleagues,

Bacterial infections are a major cause of morbidity and mortality worldwide, posing considerable health, social, and economic burdens. Therefore, rapid detection and accurate identification of the causative agents play a crucial role to optimize treatment and control measures. The need for rapid and precise methods for detection and characterization is of peculiar importance in the case of highly virulent bacteria associated with severe life-threatening diseases and of multidrug-resistant agents associated with difficult to treat infections. For most cases, the gold standard for the laboratory diagnosis of bacterial infections has been based on usually time consuming phenotypic approaches that include the isolation of the etiologic agent by using growth-supporting media, identification by a variety of techniques and antimicrobial susceptibility testing. Additionally, typing methods with high discriminatory power are needed to trace pathogens at the strain level, in order to understand the source and dissemination of bacterial strains, allowing the study of bacterial population dynamics and epidemiological surveillance of bacterial infections. The introduction and increasing improvements and applications of molecular techniques, in conjunction with advances in technologies associated with bioinformatics an artificial intelligence to handle large scale data analysis, resulted in the development of a multitude of tools that have revolutionized the diagnosis and epidemiology of infectious diseases.

In this Special Issue, we aim to address the most recent advances on the use of molecular methods based on genomic and proteomic approaches, mass spectrometry, digital microbiology, machine learning and bioinformatics applied to the detection, characterization and epidemiology of bacteria and bacterial infections.

We welcome the submission of Original Research Articles, Rewiews mainly focused on, but not limited to, the following topics:

Genomics and proteomics applied to the detection and characterization of bacterial agents
Whole-Genome Sequencing and MALDI-TOF MS as bacterial species Identification tools
MALDI-TOF Mass Spectrometry for detection of bacterial agents in clinical specimens
Bacterial molecules as diagnostic markers
Detection of bacterial markers by immunological, genomic and proteomic approaches
PCR-based techniques for detection and characterization of bacterial agents
Genome typing and epidemiology of bacterial pathogens
Bioinformatics analysis of microbial sequence data
Prediction of antimicrobial resistance in bacterial isolates by analysis of whole genome sequences, machine learning or MALDI-TOF MS
New tools to evaluate epidemiology, population structure and evolution of bacterial pathogens
Application and impact of Machine Learning in Bacteriology

Prof. Dr. Lúcia Martins Teixeira
Dr. Cheryl P. Andam
Dr. Stephanie S. R. Souza
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

bacterial pathogens
bacterial infections
molecular detection
molecular identification
molecular epidemiology
strain typing
genomics and proteomics
whole-genome sequencing
MALDI-TOF MS
antimicrobial resistance
bacterial evolution
bioinformatics analysis
machine learning

Published Papers (10 papers)

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Research

14 pages, 1718 KiB

Open AccessArticle

Invasive Disease Due to Neisseria meningitidis: Surveillance and Trends in Israel Prior to and during the COVID-19 Pandemic

by Chen Stein-Zamir, Hanna Shoob, Nitza Abramson, Lea Valinsky, Joseph Jaffe, David Maimoun, Sharon Amit and Maya Davidovich-Cohen

Microorganisms 2023, 11(9), 2212; https://doi.org/10.3390/microorganisms11092212 - 31 Aug 2023

Viewed by 1003

Abstract

Invasive meningococcal disease (IMD) is a devastating disease with significant mortality and long-term morbidity. The COVID-19 pandemic and containment measures have affected the epidemiology of infectious pathogens. This study’s aim was to assess IMD trends in Israel prior to and during the COVID-19 pandemic. The Neisseria meningitidis invasive infection is a notifiable disease in Israel. Laboratory analysis includes serogrouping and molecular characterization. The overall national IMD incidence rate (1998–2022) was 0.8/100,000 population. The IMD incidence rates declined during the pandemic years (0.3/100,000 in 2020–2022 vs. 0.9/100,000 in 1998–2019). The number of notified IMD cases declined by 65% in 2020–2022. The case fatality rate among laboratory-confirmed IMD cases was 9% (47/521, 2007–2022). Mortality risk markers included cases’ age (older) and socio-economic status (lower). Overall, most Neisseria meningitidis isolates were of serogroup B (62.6%), and the most prevalent clonal complex (CC) was CC32 (24.2%). Serogroup B prevailed in cases aged 0–9 years (74.5%) and less in cases aged 10 years and above (39%). Neisseria meningitidis serogroups and CC distribution altered recently with a decline in serogroup B fraction, an increase in serogroup Y, and a decline in CC32. Ongoing IMD surveillance is necessary to assess trends in circulating strains and support decision-making on meningococcal vaccination programs. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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11 pages, 1190 KiB

Open AccessArticle

Proteotyping of Campylobacter jejuni by MALDI-TOF MS and Strain Solution Version 2 Software

by Teruyo Ojima-Kato, Satomi Nagai, Akane Fujita, Junko Sakata and Hiroto Tamura

Microorganisms 2023, 11(1), 202; https://doi.org/10.3390/microorganisms11010202 - 12 Jan 2023

Viewed by 1899

Abstract

Identification of microorganisms by MALDI-TOF MS has become a popular method in the past 20 years. Strain Solution ver. 2 software appended with MALDI-TOF MS enables accurate discrimination of serotypes and strains beyond the genus and species level by creating a theoretical mass-based database. In this study, we constructed a theoretical mass database with the validated biomarkers to proteotype Campylobacter jejuni. Using 10 strains belonging to Campylobacter spp. available from culture collections and 41 Campylobacter jejuni strains isolated from humans and foods, the ribosomal protein subunits L36, L32, S14, L24, L23, L7/L12, and S11 could be selected as the effective biomarkers for the proteotyping of C. jejuni at MALDI-TOF MS. An accurate database of their theoretical mass-based values was constructed by matching these gene DNA sequences and the observed mass peaks. We attempted to automatically classify 41 strains isolated from nature using this database and Strain Solution ver. 2 software, and 38 strains (93%) were correctly classified into the intended group based on the theoretical mass-based values. Thus, the seven biomarkers found in this study and Strain Solution ver. 2 are promising for the proteotyping of C. jejuni by MALDI-TOF MS. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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15 pages, 1267 KiB

Open AccessArticle

Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds

by Malte Herold, Louise Hock, Christian Penny, Cécile Walczak, Fatu Djabi, Henry-Michel Cauchie and Catherine Ragimbeau

Microorganisms 2023, 11(1), 121; https://doi.org/10.3390/microorganisms11010121 - 03 Jan 2023

Cited by 1 | Viewed by 2509

Abstract

As the world’s leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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12 pages, 1408 KiB

Open AccessArticle

Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in bla_NDM Spread

by Rafael D. S. Tavares, Marta Tacão, Elmano Ramalheira, Sónia Ferreira and Isabel Henriques

Microorganisms 2022, 10(11), 2243; https://doi.org/10.3390/microorganisms10112243 - 12 Nov 2022

Viewed by 1486

Abstract

Background: New Delhi metallo-beta-lactamase (NDM) has been spreading across the globe, but the causes of its success are poorly understood. We characterized a bla_NDM-5-positive Escherichia coli strain from a Portuguese hospital and conducted comparative genomic analyses to understand the role of clonal background and horizontal gene transfer in bla_NDM-5 dissemination. Methods: After bla_NDM PCR screening and genome sequencing, Ec355340 was subjected to mating, transformation, and plasmid curing assays and MICs determination for several antibiotics. Comparison with data compiled from public databases was performed. Results: bla_NDM-5 was in a complex integron co-located in a FIB-FII plasmid (pEc355340_NDM-5). The mating assays were unsuccessful, but plasmid transformation into a susceptible host led to resistance to all beta-lactams and to sulfamethoxazole-trimethoprim. The profile of virulence genes (n = 73) was compatible with extraintestinal pathogenesis. An analysis of genomes from public databases suggested that bla_NDM-5 has rarely been associated with ST156 strains (such as Ec355340), while is has frequently been found on strains of the ST10 clonal complex. However, ST156 may play a role in the co-spreading of bla_NDM and mcr genes. Regardless, comparative genomics confirmed the presence of bla_NDM in similar complex integrons in plasmids (48/100 plasmids most similar to pEc355340_NDM-5) and ST156 genomes (20/41 bla_NDM-positive genomes). Conclusions: bla_NDM-5 and other bla_NDM variants were more frequently associated to complex integrons than previously reported and, therefore, these platforms may be important drivers in their dissemination. The identification of bla_NDM-5 for the first time in Portugal could be a game-changer in the current Portuguese antibiotic resistance scenario, as this gene encodes a higher-level resistance phenotype, and its spread may be facilitated due to the association with complex integrons. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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23 pages, 2725 KiB

Open AccessArticle

Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity

by Larissa Murr, Ingrid Huber, Melanie Pavlovic, Patrick Guertler, Ute Messelhaeusser, Manuela Weiss, Matthias Ehrmann, Christian Tuschak, Hans Bauer, Mareike Wenning, Ulrich Busch and Nancy Bretschneider

Microorganisms 2022, 10(11), 2120; https://doi.org/10.3390/microorganisms10112120 - 26 Oct 2022

Viewed by 1698

Abstract

Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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13 pages, 1578 KiB

Open AccessArticle

Molecular Characterization and Antibiotic Susceptibility of Non-PCV13 Pneumococcal Serotypes among Vaccinated Children in Cape Coast, Ghana

by Richael O. Mills, Mohammed R. Abdullah, Samuel A. Akwetey, Dorcas C. Sappor, Johan A. Bolivar, Gustavo Gámez, Mark P. G. van der Linden and Sven Hammerschmidt

Microorganisms 2022, 10(10), 2054; https://doi.org/10.3390/microorganisms10102054 - 18 Oct 2022

Viewed by 1535

Abstract

Preventive strategies involving the use of pneumococcal conjugate vaccines (PCVs) are known to drastically reduce pneumococcal disease. However, PCV vaccination has been plagued with serotype replacement by non-PCV serotypes. In this study, we describe the prevalence and molecular characteristics of non-PCV13 serotypes (non-vaccine serotypes, NVTs) from pneumococcal carriage isolates obtained from children < 5 years old in Cape Coast, Ghana, after PCV introduction. The isolates were subjected to antibiotic susceptibility testing and multilocus sequence typing (MLST), and molecular techniques were used to detect the presence of virulence genes. Serotypes 11A, 13, 15B, 23B, and 34 formed the top five of the 93 NVT isolates. As such, 20 (21.5%), 49 (48.4%), and 70 (74.3%) isolates were non-susceptible to penicillin, tetracycline, and cotrimoxazole, respectively. Sixteen (17.2%) multidrug-resistant isolates were identified. However, non-susceptibility to ceftriaxone and erythromycin was low and all isolates were fully susceptible to levofloxacin, linezolid, and vancomycin. Whereas pcpA, pavB, lytA, and psrP genes were detected in nearly all serotypes, pilus islet genes were limited to serotypes 11A, 13, and 23B. MLST for predominant serotype 23B isolates revealed three known and seven novel sequence types (STs). ST172 and novel ST15111 were the most dominant and both STs were related to PMEN clone Columbia^23F-26 (ST338). In conclusion, non-PCV13 serotype 23B was the most prevalent, with characteristics of rapid clonal expansion of ST172 and ST15111, which are related to international clones of the pneumococcus. Continuous monitoring of NVTs in Ghana is, therefore, essential, as they have the potential to cause invasive disease, show high antibiotic resistance, and attenuate the effects of PCV vaccination. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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17 pages, 2879 KiB

Open AccessArticle

Shiga Toxin Subtypes, Serogroups, Phylogroups, RAPD Genotypic Diversity, and Select Virulence Markers of Shiga-Toxigenic Escherichia coli Strains from Goats in Mid-Atlantic US

by Eunice Ndegwa, Dahlia O’Brien, Kwame Matthew, Zhenping Wang and Jimin Kim

Microorganisms 2022, 10(9), 1842; https://doi.org/10.3390/microorganisms10091842 - 15 Sep 2022

Cited by 3 | Viewed by 1388

Abstract

Understanding Shiga toxin subtypes in E. coli from reservoir hosts may give insight into their significance as human pathogens. The data also serve as an epidemiological tool for source tracking. We characterized Shiga toxin subtypes in 491 goat E. coli isolates (STEC) from the mid-Atlantic US region (stx1 = 278, stx2 = 213, and stx1/stx2 = 95). Their serogroups, phylogroups, M13RAPD genotypes, eae (intimin), and hly (hemolysin) genes were also evaluated. STEC-positive for stx1 harbored Stx1c (79%), stx1a (21%), and stx a/c (4%). Those positive for Stx2 harbored stx2a (55%) and Stx2b (32%), while stx2a/stx2d and stx2a/stx2b were each 2%. Among the 343 STEC that were serogrouped, 46% (n = 158) belonged to O8, 20% (n = 67) to 076, 12% (n = 42) to O91, 5% (n = 17) to O5, and 5% (n = 18) to O26. Less than 5% belonged to O78, O87, O146, and O103. The hly and eae genes were detected in 48% and 14% of STEC, respectively. Most belonged to phylogroup B1 (73%), followed by D (10%), E (8%), A (4%), B2 (4%), and F (1%). M13RAPD genotyping revealed clonality of 091, O5, O87, O103, and O78 but higher diversity in the O8, O76, and O26 serogroups. These results indicate goat STEC belonged to important non-O157 STEC serogroups, were genomically diverse, and harbored Shiga toxin subtypes associated with severe human disease. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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13 pages, 2175 KiB

Open AccessArticle

Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples

by Montserrat Nácher-Vázquez, Ana Barbosa, Inês Armelim, Andreia Sofia Azevedo, Gonçalo Nieto Almeida, Cristina Pizarro, Nuno Filipe Azevedo, Carina Almeida and Laura Cerqueira

Microorganisms 2022, 10(7), 1409; https://doi.org/10.3390/microorganisms10071409 - 13 Jul 2022

Cited by 2 | Viewed by 2074

Abstract

Legionella are opportunistic intracellular pathogens that are found throughout the environment. The Legionella contamination of water systems represents a serious social problem that can lead to severe diseases, which can manifest as both Pontiac fever and Legionnaires’ disease (LD) infections. Fluorescence in situ hybridization using nucleic acid mimic probes (NAM-FISH) is a powerful and versatile technique for bacterial detection. By optimizing a peptide nucleic acid (PNA) sequence based on fluorescently selective binding to specific bacterial rRNA sequences, we established a new PNA-FISH method that has been successfully designed for the specific detection of the genus Legionella. The LEG22 PNA probe has shown great theoretical performance, presenting 99.9% specificity and 96.9% sensitivity. We also demonstrated that the PNA-FISH approach presents a good signal-to-noise ratio when applied in artificially contaminated water samples directly on filtration membranes or after cells elution. For water samples with higher turbidity (from cooling tower water systems), there is still the need for further method optimization in order to detect cellular contents and to overcome interferents’ autofluorescence, which hinders probe signal visualization. Nevertheless, this work shows that the PNA-FISH approach could be a promising alternative for the rapid (3–4 h) and accurate detection of Legionella. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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14 pages, 4784 KiB

Open AccessArticle

Prevalence and Molecular Characterization of Mycobacterium bovis in Slaughtered Cattle Carcasses in Burkina Faso; West Africa

by Estelle Kanyala, Yassir Adam Shuaib, Norbert Georg Schwarz, Sönke Andres, Elvira Richter, Bernard Sawadogo, Mamadou Sawadogo, Minoungou Germaine, Ouattara Lassina, Sven Poppert and Hagen Frickmann

Microorganisms 2022, 10(7), 1378; https://doi.org/10.3390/microorganisms10071378 - 08 Jul 2022

Cited by 2 | Viewed by 1522

Abstract

This cross-sectional study was conducted at the slaughterhouses/slabs of Oudalan and Ouagadougou in Burkina Faso, between August and September 2013. It aimed at determining the prevalence of bovine tuberculosis (bTB) suggestive lesions in slaughtered cattle carcasses and to identify and characterize the mycobacteria isolated from these lesions. A thorough postmortem examination was conducted on carcasses of a total of 2165 randomly selected cattle. The overall prevalence of bTB suggestive lesions was 2.7% (58/2165; 95% CI 2.1–3.5%). Due to the low number of positive samples, data were descriptively presented. The lesions were either observed localized in one or a few organs or generalized (i.e., miliary bTB) in 96.6% (n = 57) and 3.4% (n = 2), respectively. The identified mycobacteria were M. bovis (44.4%, n = 20), M. fortuitum (8.9%, n = 4), M. elephantis (6.7%, n = 3), M. brumae (4.4%, n = 2), M. avium (2.2%, n = 1), M. asiaticum (2.2%, n = 1), M. terrae (2.2%, n = 1), and unknown non-tuberculous mycobacteria (NTM) (11.1%, n = 5). Moreover, eight mixed cultures with more than one Mycobacterium species growing were also observed, of which three were M. bovis and M. fortuitum and three were M. bovis and M. elephantis. In conclusion, M. bovis is the predominant causative agent of mycobacterial infections in the study area. Our study has identified a base to broaden the epidemiological knowledge on zoonotic transmission of mycobacteria in Burkina Faso by future studies investigating further samples from humans and animals, including wild animals employing molecular techniques. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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8 pages, 7006 KiB

Open AccessCommunication

Emergence of Novel Chlamydia trachomatis Sequence Types among Chlamydia Patients in the Republic of Belarus

by Valentina A. Feodorova, Yury V. Saltykov, Anna A. Kolosova, Liudmila V. Rubanik, Nikolay N. Poleshchuk and Vladimir L. Motin

Microorganisms 2022, 10(2), 478; https://doi.org/10.3390/microorganisms10020478 - 21 Feb 2022

Cited by 4 | Viewed by 1896

Abstract

Chlamydia trachomatis (CT) is a major cause of sexually transmitted diseases worldwide. The multilocus sequence typing (MLST) of clinical samples from random heterosexual chlamydia patients who were either asymptomatic or reported clinical manifestations of genital chlamydiosis (n = 63) in each of the seven major regions of the Republic of Belarus in 2017–2018 revealed 12 different CT sequence types (STs). We found seven known STs, ST4, ST6, ST9, ST13, ST38, ST95 and ST110, and five novel variants, namely ST271–ST275, which have not been detected elsewhere thus far. The ST4 variant was predominant (27/63, 42.9%) and detected in six out of seven regions. The two most common STs, ST9 and ST13, were regularly seen in four out of seven regions. In contrast, the remaining STs, ST6, ST38, ST95, ST110, and novel STs271-275, surfaced randomly in different parts of the country. The emergence of novel STs was registered in two regions, namely Minsk (ST271 and ST275) and Brest (ST271, ST272, ST273, and ST274). All the STs of detected CT strains were clustered into two Groups, I and III, which are characteristic of CT urogenital strains. No STs typical for Group II, specific to the LGV strains, were revealed. Our study contributes to better understanding the genetic diversity and molecular evolution of CT, one of the most important pathogens in public health worldwide. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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