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Bacteria, Volume 1, Issue 2 (June 2022) – 5 articles

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15 pages, 3200 KiB  
Article
Comparative Analysis and Ancestral Sequence Reconstruction of Bacterial Sortase Family Proteins Generates Functional Ancestral Mutants with Different Sequence Specificities
by Jordan D. Valgardson, Sarah A. Struyvenberg, Zachary R. Sailer, Isabel M. Piper, Justin E. Svendsen, D. Alex Johnson, Brandon A. Vogel, John M. Antos, Michael J. Harms and Jeanine F. Amacher
Bacteria 2022, 1(2), 121-135; https://doi.org/10.3390/bacteria1020011 - 9 Jun 2022
Cited by 5 | Viewed by 3279
Abstract
Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase [...] Read more.
Gram-positive bacteria are some of the earliest known life forms, diverging from gram-negative bacteria 2 billion years ago. These organisms utilize sortase enzymes to attach proteins to their peptidoglycan cell wall, a structural feature that distinguishes the two types of bacteria. The transpeptidase activity of sortases make them an important tool in protein engineering applications, e.g., in sortase-mediated ligations or sortagging. However, due to relatively low catalytic efficiency, there are ongoing efforts to create better sortase variants for these uses. Here, we use bioinformatics tools, principal component analysis and ancestral sequence reconstruction, in combination with protein biochemistry, to analyze natural sequence variation in these enzymes. Principal component analysis on the sortase superfamily distinguishes previously described classes and identifies regions of relatively high sequence variation in structurally-conserved loops within each sortase family, including those near the active site. Using ancestral sequence reconstruction, we determined sequences of ancestral Staphylococcus and Streptococcus Class A sortase proteins. Enzyme assays revealed that the ancestral Streptococcus enzyme is relatively active and shares similar sequence variation with other Class A Streptococcus sortases. Taken together, we highlight how natural sequence variation can be utilized to investigate this important protein family, arguing that these and similar techniques may be used to discover or design sortases with increased catalytic efficiency and/or selectivity for sortase-mediated ligation experiments. Full article
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9 pages, 1297 KiB  
Article
Acinetobacter baumannii and Its Relationship to Carbapenem Resistance: A Meta-Analysis
by Diego Lucas Neres Rodrigues, Francielly Morais Rodrigues da Costa, Wanderson Marques da Silva, Flavia Aburjaile and Vasco Azevedo
Bacteria 2022, 1(2), 112-120; https://doi.org/10.3390/bacteria1020010 - 19 May 2022
Cited by 1 | Viewed by 2849
Abstract
Infections by antibiotic-resistant bacteria are a significant and complex global health issue. In this context, Acinetobacter baumannii is particularly important because of its ability to withstand treatments by β-lactams, such as carbapenem. The objective of this work was to investigate, through systematic analysis [...] Read more.
Infections by antibiotic-resistant bacteria are a significant and complex global health issue. In this context, Acinetobacter baumannii is particularly important because of its ability to withstand treatments by β-lactams, such as carbapenem. The objective of this work was to investigate, through systematic analysis and meta-analysis, the chance of resistance to carbapenem in A. baumannii strains. For this, a search was conducted for the PubMed and Cochrane databases based on the keywords: “Acinetobacter baumannii” AND “beta-lactam” OR “penicillin” OR “cephalosporin” OR “cephamycin” OR “carbapenem” OR “monobactam”. The initial search resulted in a total of 90,475 articles. It was filtered based on eligibility criteria, and eight articles were selected for analysis. An odds ratio value equivalent to 3.55 was obtained, indicating a high chance of resistance to the carbapenem of strains of the species. Therefore, it is supposed that A. baumannii infection cases have a high probability of not responding adequately to treatments based on carbapenem. Full article
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16 pages, 1127 KiB  
Review
Antimicrobial Resistance of Neisseria gonorrhoeae in Sub-Saharan Populations
by Sinethemba H. Yakobi and Ofentse J. Pooe
Bacteria 2022, 1(2), 96-111; https://doi.org/10.3390/bacteria1020009 - 3 May 2022
Cited by 11 | Viewed by 5557
Abstract
Neisseria gonorrhoeae has become a significant global public health problem due to growing infection rates and antibiotic resistance development. In 2012, N. gonorrhoeae positive samples isolated from Southeast Asia were reported to be the first strains showing resistance to all first-line antibiotics. To [...] Read more.
Neisseria gonorrhoeae has become a significant global public health problem due to growing infection rates and antibiotic resistance development. In 2012, N. gonorrhoeae positive samples isolated from Southeast Asia were reported to be the first strains showing resistance to all first-line antibiotics. To date, N. gonorrhoeae’s antimicrobial resistance has since been identified against a wide range of antimicrobial drugs globally. Hence, the World Health Organization (WHO) listed N. gonorrhoeae’s drug resistance as high-priority, necessitating novel therapy development. The persistence of N. gonorrhoeae infections globally underlines the need to better understand the molecular basis of N. gonorrhoeae infection, growing antibiotic resistance, and treatment difficulties in underdeveloped countries. Historically, Africa has had minimal or rudimentary N. gonorrhoeae monitoring systems, and while antimicrobial-resistant N. gonorrhoeae is known to exist, the degree of resistance is unknown. This review looks at the gender-related symptomatic gonorrhoeae disease and provides an overview of the essential bacterial factors for the different stages of pathogenesis, including transmission, immune evasion, and antibiotic resistance. Finally, we deliberate on how molecular epidemiological studies have informed our current understanding of sexual networks in the Sub-Saharan region. Full article
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8 pages, 1883 KiB  
Communication
Environmental and Anthropogenic Influence on the Core Beneficial Honeybee Gut Microbiota—A Short Communication from Bulgaria
by Svetoslav G. Dimov
Bacteria 2022, 1(2), 88-95; https://doi.org/10.3390/bacteria1020008 - 4 Apr 2022
Viewed by 2544
Abstract
Bees’ and beehives’ health are strongly influenced by the honeybees’ gut microbiota which in turn is strongly dependent on many different factors, including environmental factors as well as anthropogenic pressure. In this study, in four locations in Bulgaria differing strongly in environmental conditions [...] Read more.
Bees’ and beehives’ health are strongly influenced by the honeybees’ gut microbiota which in turn is strongly dependent on many different factors, including environmental factors as well as anthropogenic pressure. In this study, in four locations in Bulgaria differing strongly in environmental conditions and anthropogenic pressure, an assessment was made using several obligatory core symbiont species and genera for reference, such as Lactobacillus sp., Bifidobacterium sp., Snodgrassiella alvi, Gilliamella apicola, Frishella perrara, and Commensalibacter sp., as well as an observation of the overall number of species. A snapshot of the relative abundances of the total number of species and the core species was made using a next-generation sequencing (NGS)-based metagenomic approach using the Illumina 2 × 250 bp paired-end platform. It was found that the two forms of anthropogenic pressure, the agricultural and the urban/industrial, have distinct effects, affecting different core genera and species. It was also demonstrated that both types of anthropogenic pressure cause a reduction in the overall number of bacterial species. Full article
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22 pages, 2099 KiB  
Article
Enterococcus faecium Isolates Present in Human Breast Milk Might Be Carriers of Multi-Antibiotic Resistance Genes
by Łukasz Wajda, Adam Ostrowski, Ewelina Błasiak and Patrycja Godowska
Bacteria 2022, 1(2), 66-87; https://doi.org/10.3390/bacteria1020007 - 25 Mar 2022
Cited by 6 | Viewed by 3484
Abstract
Using Enterococcus faecium strains as probiotics raises several controversies related to their antibiotic resistance (AR). In the current study, we examined isolates of E. faecium obtained from human breast milk. Catalase-negative and γ-haemolytic isolates were identified by analyzing the sequences of 16S rRNA [...] Read more.
Using Enterococcus faecium strains as probiotics raises several controversies related to their antibiotic resistance (AR). In the current study, we examined isolates of E. faecium obtained from human breast milk. Catalase-negative and γ-haemolytic isolates were identified by analyzing the sequences of 16S rRNA gene and their phenotypic resistance to antibiotics was investigated. We examined the expression of genes that were found on plasmids. The majority of isolates tested were resistant to erythromycin (96%), followed by trimethoprim (67%), tetracycline (57%), and gentamicin (55%). Ninety-seven percent of E. faecium isolates were resistant to at least two antibiotics. We detected the presence of the following genes on plasmids: ErmB (erythromycin), dfrA17 (trimethoprim), tetO, tetK (tetracycline), Aph(3′)-IIIa (neomycin), and marA (rifampicin). TetO was not expressed in all cases, dfrA14 was not expressed in CDCP1449, while tetK was only expressed in CDCP1128 and CDCP1331 isolates. In the majority of isolates, AR genes were located on chromosomes since they were not detected on plasmids. Our study shows that due to the spread of AR, human milk could be one of the first sources of the bacteria resistant to antimicrobials to infants. Full article
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