Journal of Food & Industrial Microbiology

I am pleased to introduce the International Journal of Food & Industrial Microbiology (IJFIM) which is an open access Microbiology journal aiming to provide an online compendium for Food Microbiology, Pharmaceutical Sciences, Industrial Microbiology, Nano Microbiology and Pharmaceutical Microbiology. We have been started in year 2015 International Journal of Food & Industrial Microbiology (ISSN: 2572-4134) is growing continuously. It is our pleasure to announce that during year 2019, all issues of volume 5 were published online on time and the print issues were also brought out and dispatched within 30 days of publishing the issue online.

All published articles of this journal are included in the indexing and abstracting coverage of CAS Source Index (CASSI), Index Copernicus, Google Scholar, Sherpa Romeo, Academic Journals Database, GenamicsJournalSeek, JournalTOCs, CiteFactor, Electronic Journals Library, RefSeek, Hamdard University, EBSCO A-Z, Directory of Abstract Indexing for Journals, World Catalogue of Scientific Journals, OCLC- WorldCat, Scholarsteer, SWB online catalog, Virtual Library of Biology (vifabio), Publons, Dtufindit, Geneva Foundation for Medical Education and Research.

During the year 2019, International Journal of Food & Industrial Microbiology (IJFIM)  received a total of 16 papers, out of which 4 article was rejected in the preliminary screening due to plagiarism or being out of the format and peer review process. During 2019 around 4 articles were subjected for publication after they are accepted in the peer review process.

During the calendar year 2020, a total of two Editors, Fifteen Reviewers joined the board of IJFIM and contributed their valuable services towards contribution as well as publication of articles, and their valuable reviewer comments will beneficial to publish quality of article in the Journal.

I take this opportunity to acknowledge the contribution of Editor-in-chief and Associate Editor during the final editing of articles published and bringing out issues of International Journal of Food & Industrial Microbiology (IJFIM) in time. I would also like to express my gratitude to all the authors, reviewers, the publisher, language editor, honorary editors, the scientific advisory and the editorial board of IJFIM, the office bearers for their support in bringing out the new volume (Volume 6) of IJFIM for the calendar year 2020 and look forward to their unrelenting support further to release more issues for International Journal of Food & Industrial Microbiology (IJFIM) in scheduled time.

Whole genome sequencing analysis (WGSA) provides the best resolution for bacterial isolate typing and possesses the potential to identify transmission pathways. The aim of the study was to use WGSA to clarify possible transmission events involving two suspected outbreaks of the Staphylococcus aureus hospital in Ghana and to describe genomic characteristics of the S. Sampled aureus isolates in the outbreaks.

Introduction: Staphylococcus aureus causes a variety of serious infections including meningitis, septicemia, pneumonia, endocarditis, and osteomyelitis. Aureus (MRSA) is of particular concern because of its extensive antibiotic resistance and its association with persistent outbreaks in hospitals and in the community. Besides the relevance of MRSA to public health, methicillin-susceptible S. Aureus (MSSA) is commonly involved in bacteremia and inflammation of the skin and soft tissue (SSTI). The relative high prevalence of pvl genes, a pore-forming toxin associated with SSTI and severe necrotizing pneumonia is a striking feature of clinical MSSA isolates from Africa. This function of African MSSA isolates is of interest as the highly productive community-associated MRSA clones are also characterized by frequent pvl gene carriage.

With the advent of next generation sequencing technologies, the field of microbial genomics is progressing at a rapid pace. Whole genome sequencing analysis (WGSA) is superior to bacterial typing methods because it provides better resolution of bacterial isolates and is particularly suitable for highly clonal bacteria such as S. Aureus Aureus. WGSA had been applied to S in previous studies. Aureous and used to describe MRSA's intercontinental and local transmission, investigate outbreaks, predict antimicrobial resistance, and type bacterial strains. In general, WGSA's applications to research S. For several countries, aureus and other microbial pathogens were treated to a very small extent in many countries in Africa.

Methods: The research was performed at Korle-Bu Teaching Hospital and Lekma Hospital respectively where the alleged outbreaks occurred in 2012 and 2015. The S- There were three origins of aureus isolates obtained from the two hospitals, including transport, infectious disease, and the climate. The S complete genome sequencing. The aureus isolates is executed and the sequence reads mapped to the S. Auroreus strain reference genome USA300 FPR3757. A phylogenetic tree with a maximum likelihood was rebuilt. Multilocus sequence typing along with antimicrobial resistance analysis and virulence genes was performed using the SRST2 for fast reading mapping. 

Results: A reported outbreak of three S occurred in January 2012 at KBTH's Department of Child Welfare. Cases aureus. In case one, S. Aureus was removed from the blood of a 4-month-old baby girl admitted to the Emergency Ward. She had spent 5 days at the emergency ward and was then moved to another ward (designated P2), where she died. The second case was identified four days after the first case and was isolated from a 5-day old baby boy's cerebrospinal fluid, which was admitted to the emergency ward. Later, the child was moved to the ward P2. Two days on from the second case, S. Aureus was removed from a 4-month-old baby girl’s semen. Like the first two babies, this baby was admitted to the emergency ward and later moved to the ward P2.

KBTH's Infection Prevention and Control Unit called for an investigation into the situation after the baby's first case death. It has been identified as the babies from which S. Aureus shared the same breathing apparatus. Babies shared the same cot and were connected to one oxygen cylinder by tubes (giving set lines). Clinical staff confirmed that due to inadequate respiratory apparatus, they are resorting to this practice.

Following this development KBTH has taken steps to disinfect the deceased baby's materials (cot and bedding). Blood specimens for culture were collected from babies who were nearby and shared tubes with the deceased infant, but no bacteria developed in the specimens. A Nasal Carriage Test of S. Aureus was performed in the unit as well as environmental screening among babies, their mothers and health-care personnel. S carriage Nasal. Aureus and MRSA, respectively, were 49.7 per cent (88/147) and 4.8 per cent (7/147). Environmental specimens collected from equipment and surfaces in hospital wards yielded S. Prevalence of aureus and MRSA of 27.5 percent (39/142) and 11.3 percent (16/142), respectively. During this period, KBTH's bacteriology laboratory kept monitoring of S. Aureus isolates recovered from all hospital patients; an average of five S clinical isolates. The aureus are reported daily in this lab.

The S- The aureus isolates belonged to different types of sequences (STs) with the most common ST15 and ST152. All isolates carried the blaZ gene, and also observed low prevalence of tetK and dfrG genes. All the isolates were negative about mecA. The genes of the pvl were common and observed in distinct lines revealing diverse Sa2int phages. The genomics data at Korle-Bu Teaching Hospital revealed multiple transmission events involving S. Auroreus ST15 involves contamination of various surfaces in the emergency pediatric ward where the outbreak occurred.

Conclusion: Dissemination pattern of the ST15 clone in the Korle-Bu Teaching Hospital emergency ward illustrates a fundamental issue with the hospital's disinfection of environmental surfaces. Various phage populations rather than a single highly transmissible type of phage is likely to mediate the high prevalence of pvl genes among the genes S. aureus isolates. 

In China, since the 1990s, V. parahaemolyticus has been a leading cause of foodborne outbreaks and bacterial infectious diarrhea, and most infections are associated with the V. parahaemolyticus O3: K6 pandemic and its serovariants. There is nevertheless a lack of a detailed description of the sero-prevalence and genetic diversity of the V. parahaemolyticus pandemic clone in China. In this study, pandemic isolates in Chinese clinical and environmental samples obtained from multiple studies were analyzed to account for this deficiency. Significant serotypic diversity was observed primarily among isolates within the ST3 pandemic, which consisted of 21 O / K antigen combinations. The O3: K6 serotype pandemic exhibited a high degree of sequence diversity, shared by eight separate STs (ST3, ST227, ST431, ST435, ST487, ST489, ST526, and ST672). Testing of susceptibility to antimicrobials revealed that most isolates shared similar profiles of susceptibility to antibiotics. They were ampicillin resistant but susceptible to most other drugs studied. In conclusion, the high rates of serotypic and genetic diversity of the pandemic clone indicate that the regions concerned are significant reservoirs for the emergence of new pandemic strains. They stress the need for routine surveillance to prevent the infection with pandemic V. parahaemolyticus, which involves tracking antimicrobial responses to avoid unnecessary antibiotic violence. We also need further investigations to delineate the specific mechanisms underlying the possible seroconversion of pandemic isolates.

Introduction: The Gram-negative bacterium Vibrio parahaemolyticus is a natural inhabitant of the estuarine and coastal environments. This pathogen is a worldwide important cause of acute gastroenteritis in humans. It is a pathogenic bacteria of multiple serotypes, and can be classified into 13 O serotypes and 71 K serotypes based on somatic (O) antigens and capsular (K) antigens. The pandemic isolates, including serotype O3: K6 and their serovariants, have spread globally through either sporadic diarrhea or food-related contaminated outbreaks since 1997.

In this study, we identified the Chinese pandemic isolates V parahaemolyticus primarily from existing literature and re-analyzed the sero-prevalence and genetic diversity of these entire pandemic isolates. In our successful diarrheal infection studies, we isolated several of these pandemic isolates, and concentrated primarily on their antimicrobial responses in this research, which was not previously demonstrated. Overall, after the advent of this clone, our goal is to produce a detailed overview of the spread of the pandemic Vibrio parahaemolyticus O3: K6 and its serovariants.

Results: According to a detailed review, an extensive map of the dissemination of the pandemic serotypes detected in China was generated. The pandemic serotypes in nine coastal provinces and two inland provinces (Beijing and Sichuan) were highly abundant and variable, with 27 clinical and four environmental pandemic serotypes identified. O3: K6 (in 11 provinces) was the most widely disseminated serotype of clinical isolates, followed by O4: K68 (in eight provinces), O1: KUT (in five provinces), O1: K25 (in four provinces), and O1: K36 (in four). They identified the four environmental serotypes in Shanghai (O1: KUT, O3: K6), Jiangsu (O3: K6, O4: K48), Zhejiang (O3: K6), and Guangdong (O4: K9).

Discussion: The pandemic V. parahaemolyticus infection has attracted much attention from scientists as an emerging public health concern. This study gave an overview of the prevalence of V. parahaemolyticus pandemic isolates in both clinical and environmental samples collected from multiple Chinese studies. We have demonstrated a high serotypic and genetic diversity of these pandemic isolates. The pandemic isolates of O3: K6 (persistent from 2002 to 2012 for 11 years) spread through 11 provinces indicates that the pandemic clone has been endemically established in China. Continued monitoring of patterns of antibiotic resistance in pandemic isolates is urgently required to prevent excessive antibiotic misuse, though most of the isolates tested in this study showed only high ampicillin resistance.

The isolates analyzed in this study have been distributed to regions where the temperature differences and other environmental factors are vast. Therefore we suspect that in the transmission process the strains must adapt to different living environments by more frequently altering their biological properties. One of the most effective ways to accomplish this may be to make serological changes. Nevertheless, the specific serotype conversion mechanism is not yet known. Actually, the highest priority is to track the emergence of new serovariants constantly to prevent the pandemic strains from triggering coastal outbreaks and spreading to other countries and regions.

Another important aspect of this study was investigating the susceptibility of various pandemic isolates to antimicrobials. Our tests showed similar profiles of antibiotic susceptibility in ST3, ST88 and non-pandemic isolates. They concluded that the sampling location or month in which the samples were collected had no significant impact on patterns of resistance to V. parahaemolyticus, since isolates from both environmental and clinical sources shared similar profiles of resistance to antibiotics. Unsurprisingly, the majority of isolates tested in this study showed ampicillin resistance, which is very common in isolates recovered from various sources in V. parahaemolyticus.

Our findings represent a comprehensive review of the V. parahaemolyticus O3: K6 pandemic and its serovariants by thoroughly evaluating a comprehensive collection of pandemic isolates from multiple Chinese studies. The pandemic clone contains high levels of serotypic and genetic diversity, indicating that the regions involved are becoming important reservoirs for the emergence of new pandemic strains which potentially challenge the clinical management of the infection and its prevention. Thus, we emphasize the need for routine clinical and environmental monitoring to prevent infection and dissemination with pandemic V. parahaemolyticus, including monitoring antimicrobial response even though most of the current antimicrobial agents are effective in routine use. Extended research requires the process in which the isolates undergo seroconversion with pandemic genetic marks.

Antibiotic use in Egypt is largely under-regulated leading to the formation of resistant isolates. Carbapenems are last resort agents for treating infections of Acinetobacter baumannii that are resistant to other antibiotic classes. Alarmingly, however, carbapenem-resistant isolates are emerging. This research aimed at characterizing seventy-four carbapenem-unsusceptible A, both phenotypically and molecularly. Baumannii isolates from Egypt to detect the various enzymes responsible for the resistance to carbapenem.
Carbapenemase development was assessed using a variety of phenotypic methods: modified Hodge test (MHT), carbapenem inactivation (CIM), combined disk test (CDT), CarbAcineto NP test, and boronic acid testing. The polymerase chain reaction ( PCR) was used to test isolates for the existence of certain genes responsible for carbapenem resistance, as well as sequences for insertion.

Acinetobacter baumannii has become a pathogen which threatens life. It causes nosocomial infections worldwide, including infections of the skin and soft tissue, wound and bloodstream infections, infections of the urinary tract, meningitis, and ventilator-associated pneumonia, which is the most common and fatal infection from A. Bas-nii. These infections are especially dangerous owing to the ability of the pathogen to withstand the action of most antibacterial agents currently available, making A. Baumannii one of the most dangerous organisms in the ESKAPE. The number of community-acquired A, in addition. Infections of baumannii such as bacteremia, pneumonia, meningitis and endocarditis have been increasing progressively in the last few decades.

Resistance to Carbapenem in A. Baumannii strains are caused by loss or alteration of porins or, in some rare cases, by alteration of penicillin binding proteins. The key resistance mechanism, however, is the development of β-lactamase enzymes Four classes of molecular β-lactamase (A, B , C and D) were detected at A. Bas-nii. Just a few K. Pneumoniae carbapenemase (KPC) type enzymes of class A β-lactamases have an effect on carbapenems compared to those of class B and class D that act effectively on carbapenems. Class B β-lactamases are metallo-β-lactamases (MBL) needed for their catalytic activity by zinc ions.

Detection of carbapenemases is crucial to determine the extent of the problem and to guide the application of guidelines on antimicrobial stewardship to limit further production of carbapenem-resistant variants between A. They isolate the baumannii. The present study reports the prevalence of certain carbapenemases among CR-AB isolates from Alexandria, Egypt, in contrast to the various phenotypic and molecular techniques used in an Egyptian environment to detect these enzymes among CR-AB isolates.

Discussion: A. Baumannii is becoming a big concern due to the awful number of nosocomial infections caused by this pathogen, mainly at ICUs around the world. Moreover, A. Due to the excessive use of antibiotics, baumannii has become resistant to many groups of antimicrobials, contributing to the predominance of multidrug-resistant strains, especially in hospitals. What's more, A resistance to carbapenem. Baumannii isolates limits the clinical treatment choices for these infections that may lead to higher morbidity and mortality rates. A few earlier studies have commented on the prevalence of Egyptian A carbapenemases. Clinical isolates of the baumannii.

This research aimed to classify 74 Egyptian A, both phenotypically and molecularly. Baumannii isolates the various enzymes which are responsible for carbapenem resistance. Several phenotypic methods have been used including the testing of MHT, CIM, CDT, CarbAcineto NP and boronic acid discs. Phenotypic carbapenemase detection has the advantages of low cost, simplicity of operation and lack of complicated or costly equipment; however, it suffers from poor specificities and sensitivity. As a result, PCR screening was taken as the gold standard for some genes responsible for carbapenem resistance, as well as some insertion sequences to determine the sensitivity of the various phenotypic methods.

Comparing the results of the phenotypic tests with the results of carbapenemase molecular detection, the sensitivity of MHT, CIM, CDT, CarbAcineto NP, imipenem and meropenem boronic acid was 78.4, 68.9, 79.7, 95.9, 56.8 and 70.3 per cent respectively. Four isolates carrying blaOXA-51, blaOXA-23, blaVIM in the CarbAcineto NP test including isolate no. A81 which additionally carried blaOXA-58 developed the positive outcome in less than 15 min which could be attributed to the enzyme activity in these isolates. The false negative result observed with A2 carrying blaVIM, blaOXA-51 and blaOXA-23 could be explained by low concentration of zinc in the culture medium, or by very low activity of carbapenemase in the tested isolate. These findings are consistent with the previously reported high sensitivity of CarbAcineto NP in carbapenemase detection among Acinetobacter spp. Although only 21 isolates had positive allover tests, all nine isolates shown to be carrying NDM by PCR were also positively tested in MHT, CIM and CarbAcineto NP. sensitive to detect MBL 100%. On the other hand, in one isolate, CDT failed to detect NDM: A85 and boronic acid disc test with imipenem and meropenem failed to detect NDM in 2 isolates , respectively: A59 and A81 and A40 and A81. It is noteworthy that A81 was the only isolate shown to carry blaOXA-58.The insertion sequences may increase the production of β-lactamases when present upstream to CHDL encoding genes. The prevalence of ISAba1, ISAba2 and ISAba3, respectively, was 100, 2.7 and 4.1 percent in the current report. The occurrence of various sequences of insertion at A. Clinical isolates of Baumannii from Saudi Arabia were in agreement     with the findings of the current study.

Conclusions: With the exception of CarbAcineto NP which showed superior sensitivity approaching PCR findings, a combination of phenotypic tests, including MHT, CIM, CDT and boronic acid disk tests, seems to be necessary for the definitive detection of carbapenemases. NDM prevalence levels detected here are lower than previously reported from other parts of the country, suggesting the need for greater screening of different Egyptian governorates to determine the precise prevalence rate. Yet the prevalence levels of OXA-23 and VIM remain equally high.

For testing purposes 347 documented positive and negative serum samples were collected from large ruminants with a history of Brucella melitensis infection. The buffer acidified plate agglutination test (BAPA) achieved highest relative sensitivity. In the case of BAPA, Rose Bengal Plate (RBPT), indirect ELISA (iELISA) and rivanol (Riv. T) tests, the kappa (π) agreement assessed for both species indicated a substantial agreement (p possibly 0.05). The diagnostic performance of serological tests in cattle was arranged in descending order as follows, according to the data obtained from the receiver operating characteristic curves (ROCs), the area under the ROCs and the diagnostic odd ratio; BAPAT, Riv. T, RBPT, iELISA, EDTA-modified micro-agglutination test (EDTA-mMAT), and MAT. In buffaloes the equivalent picture was, Riv. T, RBPT, BAPAT, iELISA, EDTA-mMAT and MAT. Eleven Brucella field isolates have been recovered while four cattle areolates have been recognized as Brucella abortus biovar 1 and seven as Brucella melitensis biovar 3 from cattle and buffalo Usage of phenotypic sorting and molecular speciation of bacteria (Bruce-ladder PCR). Due to the improved diagnostic performance offered by EDTA-mMAT over MAT under investigation, the authors recommended switching from locally adopted MAT version to EDTA-mMAT, and to a limited extent, Riv. T could be used to validate established reactors via screening tests. Since Brucella melitensis is frequently isolated from the liver of slaughtered seropositive ruminants, The Ministerial Decree No 1329 of 1999 needs to be amended to include an explicit clause on liver condemnation, as it poses public health hazards.

Introduction: Brucellosis is the common name used by many species of the genus Brucella to cause animal and human infections (OIE, 2016). Brucellae displays a broad variety of preferences for the host. There are currently twelve species of Brucella, including three recorded in Egypt, viz. B. Aborto, B. Melitensis, and with B. Am I. B. In both the pathological and epidemiological perspectives, melitensis infection of small ruminants is fairly close to B. Infection of cattle with abort. The key signs of brucellosis in ruminants are reproductive disorders in the form of abortion or birth of non-surviving poor offsprings, low milk yield (reduction of 20-25 per cent), orchitis, epididymitis, and less common arthritis. B. Melitensis does not cause storms of abortion in pregnant livestock. In addition, brucellosis is known for its latent infection that hinders any programs of control. The diagnostic method providing conclusive evidence of brucellosis is the isolation and typing from the suspected animal of Brucella microorganisms. This method, however, has an inadequate sensitivity and also has a difficulty in applying control strategies on a wide scale (Gall and Nielsen, 2004). The most effective methods of diagnosis are still the identification of different immunoglobulins to Brucella in serum or milk samples. Usually screening all samples using an inexpensive and rapid test that is sensitive enough to detect a high proportion of infected animals is the most proficient and cost-effective approach. For the final diagnosis to be made, reactors to screening tests are then checked using normal, reliable and precise tests (Corbel, 2006). Serological findings must be measured against the circumstantial occurrence of disease, the degree of false positive serum reactions resulting from cross reactions with associated Gram-negative bacteria, or vaccination (Gall and Nielsen, 2004; Corbel, 2006). Brucella and sp. Buffalo infection has a course nearly similar to that of cattle and the same serological procedures adopted for cattle may be used for these animals, but each test should be validated for fitness (OIE, 2016). In this view, the current work was planned to detect the predominant species and biovars of Brucella isolates by traditional bacteriology and Bruce-Ladder PCR, which recovered from various large ruminant tissue samples, as well as to evaluate the diagnostic efficiency of some serological tests used to diagnose large brucellosis of ruminant.

Comprehensive Serological, Bacteriological, And Molecular Overview of Brucellosis In Cattle And Buffaloes In Some Governorates Page negative or vaccinated bacteria (Gall and Nielsen, 2004; Corbel, 2006) Brucella and sp. Buffalo infection has a course nearly similar to that of cattle and the same serological procedures adopted for cattle may be used for these animals, but each test should be validated for fitness (OIE, 2016). In this view, the current work was planned to detect the predominant species and biovars of Brucella isolates by traditional bacteriology and Bruce-Ladder PCR, which recovered from various large ruminant tissue samples, as well as to evaluate the diagnostic efficiency of some serological tests used to diagnose large brucellosis of ruminant.

Results: Validation is a process that determines the fitness of an assay for a planned purpose which has been properly established, optimized and standardized (OIE, 2013). All diagnostic immunoassays, either in the laboratory or in the field, should be checked for the species in which they are to be used or should provide diagnostic performance estimates for each test (OIE, 2013). Typically, bacteriological isolation cannot establish the sensitivity of a test as false negative culture results can occur for several reasons, including the absence of the micro-organism in the cultured tissues or insufficient numbers of the micro-organisms present to grow on different media. (Nielsen & Gall, 2004). In addition, inadequate tissue storage, failure to choose a suitable tissue variety or insufficient tissue material, and collection of samples from uninfected tissues.