Subjects = Microbiology
Microbiology

Isolation and molecular detection of Salmonella enterica serovars Typhimurium from poultry processing environments at wet markets in Sulaymaniyah Province, Iraq

Articles in Press, Accepted Manuscript, Available Online from 16 June 2026

Eman Dhahir Arif, Khoshi Ari Muhammed

Abstract Non-typhoidal Salmonella (NTS) is a predominant etiological agent of foodborne infections globally. Salmonella serovars are present throughout the chicken's digestive tract, particularly in the ceca. This study, conducted from October 2024 to April 2025, employed cultural methods to isolate and identify Salmonella from samples collected at the broiler chicken wet market in Sulaymaniyah province. The research additionally examined the prevalence of Salmonella enterica serovar Typhimurium in these samples by polymerase chain reaction (PCR). 210 samples were obtained from the cecum, cutting boards, knives, body swabs, workers' hands, and water. Salmonella was isolated from the samples and identified by culturing and molecular techniques. Consequently, 103 individuals (49%) tested positive for Salmonella via culture. The PCR results revealed that the contamination rate for Salmonella enterica was 74 (71.85%); 47 (63.51%) were S. Typhimurium, and 33 (70.22%) of S. Typhimurium possessed the hilA gene. The highest prevalence was observed in chopping boards, with 91.67% for S. enterica, whereas the maximum rate for S. Typhimurium was recorded in water, at 100%. The phylogenetic tree indicates that the Iraqi isolate with accession number PV250092 belongs to the principal group of isolates, exhibiting a bootstrap support value of 100%, signifying a robust genetic association with them. To conclude, this research demonstrated a notable prevalence of Salmonella in the broiler chicken processing environment, particularly a high incidence of S. Typhimurium isolates. The placement of the Iraqi isolate within the global isolate clade suggests a recent common ancestor with other isolates, indicating global transmission pathways.

Microbiology

Development of a recombinase polymerase amplification isothermal assay for rapid visual and lateral flow detection of porcine parvovirus-7

Volume 17, Issue 5, May 2026, Pages 305-313

Niharika Chahal, Sushila Maan, Kanisht Batra, Swati Sindhu, Narender Kumar, Ramandeep Kaur, Aman Kumar

Abstract Porcine parvoviruses (PPVs) are globally recognized as significant contributors to reproductive failure in swine, primarily due to their association with fetal death. Infection in pregnant sows can lead to severe reproductive disorders including stillbirth, mummification, embryonic death and infertility. A recombinase polymerase amplification assay targeting the variable region of the outer capsid protein gene of the PPV-7 genome was developed and systematically optimized under a range of reaction conditions. The assay showed optimal amplification at a constant temperature of 35.00 ˚C for 25 min, using 0.72 µM of each forward and reverse primer and 14.00 mM magnesium acetate. It demonstrated high sensitivity, reliably detecting as few as 2,050 copies of viral nucleic acids in both the conventional and fluorescent dye-based formats. The assay also showed high specificity, exhibiting no cross-reactivity with other common porcine pathogens such as porcine sapelovirus, porcine circovirus and classical swine fever virus. Of the 167 field samples tested, 23 were positive for PPV-7, corresponding to a positivity rate of 13.77%. Operating at a low and constant temperature, the assay eliminates the need for advanced laboratory equipment, making it highly suitable for pen-side application in field settings. In conclusion, this novel assay demonstrated strong potential for field-based detection of PPV-7 circulating within the swine population of Haryana, India, marking the first report of its kind from this region. Further validation using samples from clinically affected herds will strengthen its diagnostic applicability.

Microbiology

Pathological and molecular characterization of Mycobacterium tuberculosis complex in necropsied tissues of sambar deer (Rusa unicolor) and nilgai (Boselaphus tragocamelus) from Assam state, India

Volume 17, Issue 5, May 2026, Pages 333-338

Nur Abdul Kader, Nagendra Nath Barman, Durlav Prasad Bora, Arfan Ali, Rupam Dutta, Sophia Makdoh Gogoi, Pankaj Deka, Madhusmita Dehingia, Panchami Sharma, Abhijit Deka, Samir Das

Abstract Bovine tuberculosis is a chronic bacterial disease primarily caused by Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTBC), with significant zoonotic implications. This study aimed to detect MTBC in wildlife species, specifically nilgai (Boselaphus tragocamelus) and sambar deer (Rusa unicolor), using gross pathology, histopathology, acid-fast staining, and molecular confirmation. Necropsied tissue samples were collected during post-mortem examination of a nilgai and a sambar deer from the Assam State Zoo, Guwahati, India. Macroscopically, multiple granulomatous tubercles of varying sizes were observed in the lungs and liver, with creamy white caseous material marked upon sectioning. Ziehl-Neelsen staining of the tissue smears from granulomatous lesions confirmed the presence of acid-fast bacilli. Microscopic examination of tuberculosis granulomas revealed a central necrotic mass surrounded by inflammatory cell infiltration, including Langerhans-type giant cells. Molecular confirmation of MTBC infection was achieved by amplifying hsp65 and IS1081 in tissue samples, further validated by Basic Local Alignment Search Tool for nucleotide analysis following Sanger dideoxy sequencing. In conclusion, this study confirmed the presence of tuberculosis in these wildlife species through an integrated approach combining pathology, microbiology, and molecular diagnostics, highlighting the need to understand pathogen entry into the herd and prevent potential spillover.

Microbiology

In vitro synergistic efficacy of postbiotics and specific immunoglobulin Y antibodies against Mycobacterium avium subsp. paratuberculosis

Volume 17, Issue 4, April 2026, Pages 273-280

Mera Sharif, Naheed Mojgani, Nader Mosavari, Fattah Sotoodehnejad Nematalahi

Abstract Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne’s disease and a potential contributor to Crohn’s disease, presents a significant challenge due to its resistance to conventional antibiotics. This necessitates the development of innovative strategies for prevention and treatment. This study aimed to evaluate the anti-bacterial activity of pathogen-specific antibodies derived from chicken egg yolks (immunoglobulin Y [IgY]) and the postbiotics from lactic acid bacteria against MAP. Immunoglobulin Y antibodies were produced by immunizing hens with formalin-killed MAP strain antigens. The IgY was extracted and purified, and the anti-MAP titers were quantified by indirect enzyme-linked immunosorbent assay. The minimum inhibitory concentration of different concentrations of specific anti-MAP IgY and the mixture of postbiotics (from four different probiotic strains, including Lactobacillus reuteri, Lactobacillus rhamnosus, Lactobacillus acidophilus, and Pediococcus acidilactici) individually and in combination against MAP was determined at various time intervals. Anti-MAP IgY titers in egg yolks increased within 2 weeks of immunization, reaching peak levels at 6 weeks. Growth inhibition assays revealed that postbiotics concentration as low as 6.25 mg mL-1 effectively inhibited MAP growth. Anti-MAP IgY demonstrated anti-bacterial activity with a minimum inhibitory concentration of 50.00 mg mL-1, while the combined IgY-posbiotics treatment achieved MAP growth inhibition at a minimum inhibitory concentration of 3.125 mg mL-1. The findings of the study suggest that combination therapy with specific IgY and postbiotics may be a promising preventive strategy for controlling MAP infections. Further in vivo studies are needed to elucidate the underlying mechanisms and optimize the application of this approach for broader use in veterinary and human medicine.

Microbiology

Identification of Chlamydia abortus, Coxiella burnetii, and Brucella species from ruminant fetal abomasal contents using molecular methods

Volume 17, Issue 3, March 2026, Pages 153-160

Ayfer Güllü Yücetepe, Sadiye Dılşa Ateş, Osman Yaşar Tel, Özden Dellal, Oktay Keskin, Ahmet Murat Saytekin, Sibel Kızıl, Ufuk Ülker, Efsun Melike Çeçen, Sevil Erdenliğ Gürbilek

Abstract This study aimed to detect Coxiella burnetii, Chlamydia abortus, and Brucella species in the abomasal contents of aborted ruminant fetuses from the Central Anatolia region of Türkiye using PCR between 2020 and 2023. The abomasal contents of a total of 97 aborted fetuses from cattle, sheep, and goats with a history of abortion, collected between the years 2020 and 2023, were tested in this study. As a result of PCR analysis of 97 abomasal contents, four (4.10%; 95.00% confidence interval [CI]: 1.33 - 10.82) of them were C. abortus, including three sheep and one goat. Two (2.10%; 95.00% CI: 0.36 - 7.96) of them were C. burnetii, including one sheep and one cow. A total of 60 (61.90%; 95.00% CI: 51.40 - 71.37) samples from 47 cattle, nine sheep, and four goats were determined by Brucella genus-specific PCR. Following multiplex PCR analysis of the positive Brucella spp. samples, 39 (65.00%; 95.00% CI: 51.52 - 76.55) samples were identified as B. abortus, including two sheep, one goat, and 36 cattle. Additionally, 19 (31.70%; 95.00% CI: 20.60 - 45.09) isolates were identified as Brucella melitensis, including five sheep, two goats, and 12 cattle. In two sheep samples, both B. melitensis and C. abortus were identified from the same animals. In conclusion, Brucella spp. were the predominant abortion-causing pathogens, with C. abortus also contributing significantly. Effective control strategies under the One Health approach are essential to prevent the uncontrolled spread and inter-species transmission of these zoonotic agents in the region and country.

Microbiology

Molecular investigation of biofilm-forming genes in staphylococci isolated from dogs in Ilam, Iran

Volume 17, Issue 3, March 2026, Pages 191-197

Negar Soltani, Mostafa Nemati, Fazel Pourahmad

Abstract Biofilm formation is a key virulence factor in Staphylococcus aureus, contributing to bacterial persistence, antimicrobial resistance, and chronic infections. This study aimed to investigate the presence of biofilm-associated genes (fib, fnbA, fnbB, clfA, and clfB) in S. aureus isolates from dogs in Ilam, Iran. From December 2022 to September 2023, 250 swab samples were collected from nasal, oral, and rectal sites of dogs, yielding 81 S. aureus isolates confirmed by PCR amplification of the nuc gene. The prevalence of biofilm-associated genes varied, with clfA, clfB, and fnbA detected in 98.80% of isolates, fib in 63.00%, and fnbB in 16.00%. Notably, fnbA, clfA, and clfB were present in all rectal isolates, while fnbB was absent in this group. The findings highlighted the widespread presence of biofilm-related genes in S. aureus from dogs, suggesting their potential role in colonization and zoonotic transmission. The high prevalence of adhesion-associated genes underscored the need for monitoring biofilm-forming S. aureus in companion animals to mitigate antimicrobial resistance and public health risks.

Microbiology

Arctic-like lineage of rabies virus detected in Indian wild fox: a case study

Volume 17, Issue 2, February 2026, Pages 95-101

Vivekanandan Vinitha, Paramasivam Raja, Aravind Krishnan Unni, Ramasamy Bharathi, Prasanna Koovlamnikarthil Subhadra, Divya Chandran, Sathish Gopal, Chittibabu Yamini, Manoharan Parthiban, Sivamurthy Parthiban, Gopal Dhinakar Raj

Abstract Rabies is a viral disease affecting both land-dwelling and flying mammals. In India, dogs have been the primary source of rabies. This study aimed to investigate the role of wild animals in the transmission and persistence of the rabies virus and analyse the viral genome to understand its characteristics. In the present study, a brain sample from a fox (Vulpes vulpes) found dead in the free-ranging area of Mannamangalam forest station, Thrissur, Kerala state, India, was collected for rabies screening by fluorescent antibody staining and molecular techniques. Viral proteins and nucleic acids were detected and the samples were subsequently analyzed using next-generation sequencing for characterization. The genome analysis revealed that the virus belonged to the type I genotype of the arctic-like lineage. The phylogenetic analysis indicated that the fox virus strain shared close homology with all Indian isolates irrespective of the host species and was clustered in the same arctic-like lineage, denoting the distribution of a similar lineage and genotype across all regions of India. The deduced amino acid variations of nucleoprotein and glycoprotein genes also revealed a pattern of similarity amongst isolates of Indian origin and differed from isolates of other geographical locations and lineages. This study based on genome-wide surveillance could offer novel insights into the genetic makeup of currently circulating strains in the human-wildlife conflict and their continuing spread and persistence of rabies.

Microbiology

Determination of prevalence, virulence characterization, and antimicrobial resistance patterns of emerging methicillin- and vancomycin-resistant Staphylococcus aureus in frozen fish fillet and shrimp

Volume 17, Issue 1, January 2026, Pages 15-22

Reham M. EL-Tarabili, Sherief M. Abdel-Raheem, Mahmoud Ezzat, Mohamed Bolbol, Marwa E. Abo Hashem

Abstract Staphylococcus aureus is one of food poisoning bacteria. This study assessed the prevalence, virulence factors, and antimicrobial susceptibility profiles of S. aureus isolated from frozen fish and shrimp in Egypt. Ninety samples from frozen fish fillets and shrimps (45 for each) were examined for S. aureus prevalence using VITEK 2 compact system, followed by molecular confirmation by nuc gene, virulence characterization, and its resistance genes. The overall prevalence rate of S. aureus was 14.44% (13/90). Fish fillet had the highest mean total S. aureus count (9.50 ± 3.50 × 105 colony forming unit g-1), followed by shrimp (7.50 ± 3.30 × 105 colony-forming unit g-1), with a non-significant difference among fish fillet and shrimp. All confirmed S. aureus isolates were lecithinase producers and showed β-hemolysis, and coagulase positive, and confirmed molecularly coa gene positive. All isolates were resistant to ampicillin (100%), both erythromycin and clindamycin (69.23%), and tetracycline (61.53%), followed by vancomycin (46.15%). However, all isolates were sensitive to linezolid, tigecycline (84.70%), and trimethoprim/sulfamethoxazole (61.53%). Twelve (92.30%) phenotypically cefoxitin and oxacillin-resistant and molecularly mecA recovered S. aureus isolates were confirmed as methicillin-resistant S. aureus, while based on vancomycin-resistant pheno-typically, and molecularly vanA recovered S. aureus isolates were confirmed as vancomycin-resistant S. aureus. The emergence of multidrug-resistant methicillin-resistant S. aureus and vancomycin-resistant S. aureus in frozen fish fillets and shrimp indicates public health hazards, so there is a need for food safety measures alongside reliable detection methods of resistant bacteria along the food chain.

Microbiology

Production of recombinant goose parvovirus origin VP2 protein based on baculovirus expression system

Volume 17, Issue 1, January 2026, Pages 31-37

Remziye Özbek, Mustafa Ozan Atasoy, Turhan Turan, Hakan Işıdan, Hasan Abaylı, Kezban Şahna

Abstract Goose parvovirus causes major economic losses in the waterfowl industry due to the high mortality. Therefore, it is essential to establish protection/control objectives in the fight against the disease. The genome of goose parvovirus consists of three structural proteins, including VP1, VP2, and VP3. The VP2 is a candidate antigen in developing vaccines and diagnostic kits. This study aimed to produce the VP2 protein from a local goose parvovirus strain that causes serious infections in geese in Türkiye using the baculovirus expression vector system. To achieve this, the VP2 gene was first amplified by polymerase chain reaction, followed by purification and insertion into the pENTR™/TEV/D-TOPO™ entry vector. Then, the target gene in the pENTR™/TEV/D-TOPO™ vector was transferred to linear N-Term BaculoDirect™ DNA through LR recombination (site-specific recombination between attL and attR sites). The construct was transfected into Spodoptera frugiperda cells. To verify the production of baculoviral virions, a band of approximately 600 bp in length was obtained as a result of polymerase chain reaction amplification using external primer sets for both the VP2 gene and expression vector. The obtained band was purified and sequenced for confirmation. In addition, to confirm the production of the recombinant protein, western blot analysis was conducted utilizing the V5 epitope located at the N-terminus of the expressed protein, resulting in the detection of a ~65.00 kDa band corresponding to the VP2 gene. To detect protein expression in S. frugiperda cells infected with the recombinant baculovirus, immunofluorescence analysis was performed using the same epitope. 

Microbiology

Rotavirus infection in cattle

Volume 17, Issue 1, January 2026, Pages 63-65

Yahia Hassan Ali, Intisar Kamil Saeed, Muaz Magzoub Abdellatif, Amani Ahmed Ali, Alaa Ahmed Mustafa, Hind Abdel-Mageed Rikabi, Husham Mohammed Al-Hasssan Ataalfadeel

Abstract Rotavirus is one of the major causes of diarrhea in different animal species and has a bad economic impact due to the losses in neonates and productivity. To investigate the occurrence of this infection in bovine calves, three localities in Khartoum State, Sudan, were selected. A total of 200 fecal samples were collected from diarrheic calves; 100 from Khartoum and 50 from each of Khartoum Bahari and Omdurman provinces. Collected samples were screened for a group A rotavirus antigen using enzyme-linked immunosorbent assay (ELISA). Positive results were seen in 40.00% of samples; the highest prevalence of 42.00% was found in samples from Khartoum province. Five ELISA-positive samples were examined under electron microscope, and characteristic wheel-like appearance of rotavirus was visualized. Polyacrylamide gel electrophoresis was also applied on 15 of the positive samples; eight samples showed different polyacrylamide gel electrophoretic group A rotavirus long profile with different patterns. The results showed that the occurrence of rotavirus infection in cattle in Khartoum State is increasing.

Microbiology

In vitro physicochemical characterization of nephropathogenic strain of infectious bronchitis virus isolated from poultry

Volume 16, Issue 12, December 2025, Pages 675-680

Kamran Saaed, Faisal Ayub, Muhammad Arshad Durrani, Abdul Rafay, Mobashra Mustafa, Irtaqa Gull, Zahra Rafi, Muhammad Kashan Ansari, Muhammad Mubashar Beig, Abdul Razak, Hafiz Muhammad Moavia Atique

Abstract Infectious bronchitis virus (IBV) is an important pathogen in the poultry industry causing avian infectious bronchitis that is, an acute but highly contagious disease affecting the upper respiratory tract, kidneys and reproductive tract. The 3rd passage of a polymerase chain reaction confirmed nephropathogenic IBV isolate was used for this study. Heat stability for 5, 10, 15, 20, and 30 min at 56.00 ˚C, pH sensitivity at pH 3.00, 7.00, 9.00, and 11.00 ultraviolet (UV) irradiation for 10, 15, 20, and 30 min, and chloroform sensitivity were studied. The IBV isolate was found to be susceptible to a temperature of 56.00 ˚C for 5 min and above, UV irradiation within 10 min, chloroform treatment and to pH 11.00 while being resistant to pH 3.00 and 9.00. The second part of the study investigated in vitro effectiveness of the disinfection potential of several commercially used disinfectants in Pakistan against the IBV isolate. For this purpose, Virkon S, Bromosept, and Beloran were employed for the virus inactivation test. Following the IBV challenge for contact time of 1, 5, 10, and 30 min, we counted the number of embryos that died after incubation. Results showed that suitable dilution of disinfectant for the recommended contact period could kill the virus. The maximum susceptibility was seen in the case of Virkon S which killed the virus in just 1 min. Thus, IBV could be killed using commercially available Virkon S, Beloran, and Bromosept after being used in recommended concentrations for recommended contact time.

Microbiology

Comparative analysis of VP1 epitopic variation among different isolates of foot-and-mouth disease virus type-O during an outbreak in the Punjab province of Pakistan

Volume 16, Issue 11, November 2025, Pages 621-628

Atia Rasheed, Imran Altaf, Faisal Ayub, Arslan Rasheed, Rasheeda Bashir, Farheen Aslam, Iram Waqar, Hafsa Hamid, Abdul Razak, Kamran Saeed

Abstract Foot-and-mouth disease virus (FMDV) is a highly transmissible pathogen causing severe economic losses in the global livestock sector. Frequent outbreaks of FMDV type-O in Pakistan highlight the need for continuous genomic and antigenic surveillance to track its evolution. This study aimed to isolate and molecularly characterize FMDV type-O from an outbreak in the Punjab province of Pakistan using in vitro cell culture techniques. Samples were processed for viral isolation on a susceptible cell line, followed by RNA extraction. The VP1 gene, pivotal for antigenicity and immunogenicity, was amplified using a one-step polymerase chain reaction protocol. Purified amplicons underwent sequencing, and the nucleotide sequences were translated into amino acid sequences for further analysis. Protein three-dimensional modeling and in silico comparison were performed against the vaccinal seed strain PanAsia-2. The VP1 sequence analysis revealed notable genetic variability among the isolates, indicating adaptive evolution. Structural and antigenic modeling uncovered key differences between the field isolates and vaccinal strain, suggesting potential antigenic drift, which could undermine vaccine performance. The study underscores the dynamic evolution of FMDV type-O in Pakistan and the critical importance of ongoing genomic monitoring to refine vaccine strategies and enhance outbreak control.

Microbiology

Prevalence of bovine respiratory disease viruses in calves from the central desert of Iran

Volume 16, Issue 11, November 2025, Pages 647-654

Omid Karimi, Mehran Bakhshesh, Morteza Bitaraf Sani, Hamid Poormirzayee Tafti

Abstract Bovine respiratory disease (BRD) is a significant disease in the cattle industry worldwide. The interaction between environmental factors, hosts, livestock management, and viral and bacterial pathogens causes this disease. Viruses are crucial in the initiation and progression of BRD. This study was the first to investigate the prevalence of BRD viruses using the reverse transcription polymerase chain reaction method in nasal and eye conjunctival swabs and blood samples of 115 BRD calves in the central desert of Iran. At least one investigated virus was detected in 44 animals (38.26%). The detection rates of bovine viral diarrhea virus, bovine coronavirus, bovine adenovirus, bovine respiratory syncytial virus, bovine herpes virus-1, and bovine para influenza virus-3 were 20.00, 14.78, 5.21, 0.86, 0.00, and 0.00%, respectively. Three animals (2.60%) had a simultaneous infection with two viruses. Detection of bovine viral diarrhea virus, bovine coronavirus, and bovine adenovirus was correlated. The virus infection rates were 31.81 and 44.66% in five sampled cities. The virus detection rate in infected animals was related to the nose (26 animals; 50.09%), nose and eyes (seven animals; 15.90%), eyes (seven animals; 15.90%), nose, eyes, and blood (three animals; 6.81%), and blood (one animal; 2.27%) samples. The virus detection rate in different samples was in separate clusters. Monitoring and controlling the circulation of bovine viral diarrhea virus and bovine coronavirus in the central desert of Iran is vital due to the high detection rate. Our results highlight the necessity of investigating other viruses and bacterial agents related to the BRD in the study area.

Microbiology

Serological and molecular evidence of respiratory viral mixed infection in sheep and goats

Volume 16, Issue 9, September 2025, Pages 485-491

Yahia Hassan Ali, Intisar Kamil Saeed, Muaz Magzob Abdellatif, Alaa Mustafa, Hind AbdelMajeed Rikabi, Husham Mohammed AlHassan Attaalfadeel

Abstract Respiratory infections are considered within the major constraints of animal production; viruses are the major causing pathogens. This study aimed to elucidate the prevalence of parainfluenza virus-3 (PIV-3), bovine viral diarrhea virus, and respiratory syncytial virus (RSV) in sheep and goats and the existence of co-infections. A total of 270 sheep and 220 goat pneumonic lung tissues were collected from slaughterhouses in four different areas. Enzyme-linked immunosorbent assay was used to detect the antigen of the three viruses, fluorescent antibody technique and polymerase chain reaction confirmed enzyme-linked immuno-sorbent assay positive results. Prevalence detected for PIV-3 was 11.10% in sheep and 9.50% in goats, pestivirus was 10.40% in sheep and 7.70% in goats, and RSV was 17.80% in sheep and 5.00% in goats. Detected co-infections were 5.60% for PIV-3 and pestivirus in sheep and 4.00% in goats and pestivirus and RSV was observed only in goats (1.40%). Co-infection of the three viruses was detected in only one goat sample (1.00%). The existence of the three viruses in sheep and goats was confirmed. To our knowledge, this is the first report of the co-infections of PIV-3, pestivirus, and RSV in sheep and goats in the studied areas.

Microbiology

Molecular epizootiology of bovine ephemeral fever virus in Iran during 2015 to 2022

Volume 16, Issue 9, September 2025, Pages 529-535

Ali Naderian, Mehran Bakhshesh, Mohammad Hasan Ebrahimi-Jam

Abstract Bovine ephemeral fever (BEF) is a debilitating disease of cattle and water buffaloes. Bovine ephemeral fever viruses (BEFVs) form four phylogenetic lineages including the Middle East, East of Asia, Australia and Africa, while the exotic viral strains have also been detected in different geographic areas. We characterized eight BEFVs from different regions of Iran during a period of seven years from 2015 to 2022. Sequencing the entire length of the G gene, the BEFVs were classified in the Middle Eastern lineage with the maximum of 99.73% and minimum of 97.30% nucleotide identity. The all Iranian and Turkish BEFVs detected during the large epizootic in 2020 were clustered phylogenetically together. However, no amino acid variation was observed between the Iranian viruses detected in 2020 and those identified before 2020 in the Middle Eastern lineage suggesting that host, environmental and other genetic factor (s) might have involved in occurrence of the epizootic in 2020. Two BEFVs detected during 2022 outbreak from Kermanshah and Narmashir in the west and east of Iran, respectively, were clustered in two distinct groups as a novel amino acid substitution H51Y in the epitope G3 was also identified in Kermanshah 2022 sequence. These results imply that the Middle Eastern lineage replaced the previously circulated East Asian BEFVs in Iran during 2012 to 2013 and also signify the emergence of new BEFVs due to the intra-lineage evolution. Continuous monitoring of the circulating viruses and identifying the potential vector (s) and its biology help better understand epizootiology of BEFV in the high-risk region.

Microbiology

Coxiella burnetii in dogs and ticks from the Northeastern Anatolia region of Türkiye: serological and molecular findings

Volume 16, Issue 8, August 2025, Pages 431-437

Aliye Gülmez Sağlam, Elif Çelik, Fatih Büyük, Gencay Taşkın Taşçi, Seda Gökdemir, Nilgün Aydin, Eray Büyük, Salih Otlu

Abstract The Q fever is a zoonotic bacterial infection caused by an obligate intra-cellular bacterium, Coxiella burnetii. Members of the Canidae family (Mammalia), including dogs and foxes, are potential reservoirs of C. burnetii, which has a wide host range from mammals and birds to arthropods (primarily ticks). Infected dogs can transmit the disease to other animals and humans. This study aimed to investigate the presence of C. burnetii in dogs and ticks collected from infested dogs in the Kars, Ardahan, and Iğdir provinces of Türkiye by serological and molecular methods. Three hundred canine serum samples were analyzed for phase I and phase II C. burnetii antibodies using indirect enzyme-linked immunosorbent assay. Whole blood samples (n = 300) from the dogs sampled for sera and 184 ticks randomly collected from these dogs were also analyzed for C. burnetii with touch-down polymerase chain reaction. The ticks were classified according to the taxonomic characteristics. In result, 107 tick DNA samples collected from individual females and pooled males were evaluated. The C. burnetii was detected in 3.73% (of the tick samples. However, C. burnetii was not detected in any of the canine blood samples by polymerase chain reaction. Out of the 300 dogs, 18.33% presented antibodies against C. burnetii in their blood serum. When assessed for location, C. burnetii seropositivity was found to be significantly high especially in the Northeastern Anatolia region (18.33%). Study data highlighted the zoonotic risk of ticks, demonstrating that ticks on dogs can carry C. burnetii.

Microbiology

Prevalence and molecular characterization of resistant Staphylococcus aureus strains in bulk milk tanks of dairy cattle in Northern Egypt

Volume 16, Issue 6, June 2025, Pages 317-323

Walaa Abdallah Gad, Salama Ahmed Osman, Khaled Abd El-Hamid Abd El-Razik, Ashraf Hassan Soror, Yousef Adel Soliman, Ehab Ali Fouad

Abstract Bovine subclinical mastitis represents a major cause of severe economic losses in dairy farms. This research aimed to detect the antimicrobial resistance trends of Staphylococcus aureus and to determine the presence of mecA, mphC, lnuA, tetK and tetL antimicrobial resistance genes in raw bulk milk in the period between December 2023 and February 2024. One hundred raw bulk cow milk samples were gathered from different dairy farms in Egypt. The prevalence of subclinical bovine mastitis was 65.00% using California mastitis test. The prevalence of isolated S. aureus was 46.15% via bacterial culturing and all isolates (n = 30) were confirmed via hemolytic activity, catalase and coagulase test, and gram staining followed by polymerase chain reaction targeting nuc1 gene. Antimicrobial sensitivity test was applied on all confirmed S. aureus isolates utilizing the disk diffusion method on Mueller-Hinton agar. The highest resistance was verified for tetracycline at 100% followed by erythromycin and clindamycin at 56.66 and 16.66%, respectively. The highest sensitivity at 100% was verified for amikacin, ampicillin, amoxicillin plus clavulanic acid, ampicillin plus sulbactam, ciprofloxacin, colistin, gentamicin, imipenem, tobramycin, doxycycline and vancomycin. Multidrug resistance was found in 20.00% of the total isolates. Methicillin resistant S. aureus represented by mecA gene was identified in 83.33% of isolates. Macrolides resis­tant S. aureus represented by mphC gene was identified in 16.66% of isolates. Lincosamide resistant S. aureus represented by inuA gene was identified in 66.66% of isolates. Tetracycline resistant S. aureus represented by tetK and tetL genes was detected in 23.33 and 53.33% of isolates, respectively. This study provided antibiotic-resistant S. aureus profiles to dairy farms to avoid treatment failure, adverse effects on animal health and economic impact for the owner of the animal.

Microbiology

Molecular detection of the Escherichia coli heme-utilization gene A virulence factor in E. coli isolated from the feces of horses in Sumbawa island, Indonesia

Volume 16, Issue 6, June 2025, Pages 325-330

Kholik Kholik, Akhmad Sukri, Katty Hendriana Priscilia Riwu, Ieke Wulan Ayu, Ika Nurani Dewi

Abstract The transmission of Escherichia coli (E. coli) containing virulent genes from animals to humans and the environment poses significant public health challenges. This study aimed to detect the virulence factor of the E. coli heme-utilization gene A (chuA) in E. coli isolated from the feces of apparently healthy horses in the island of Sumbawa, Indonesia. The study utilized 52 fecal samples from a total horse population of 283, calculated using the disease detection formula. Fresh feces were collected immediately after excretion and placed in buffered peptone water for subsequent analysis. The samples were then isolated on eosin methylene blue media and identified using biochemical tests. Identified E. coli strains were further examined for detecting the chuA gene using polymerase chain reaction techniques. The E. coli was successfully isolated and identified in 11 (21.15%) of the 52 collected fecal samples. Polymerase chain reaction analysis detected the chuA gene in 8 (15.38%) E. coli isolates at 279 bp on gel electrophoresis. The close interaction between horses and humans in the island of Sumbawa,  Indonesia, may facilitate the spread of E. coli. Thus, surveillance is needed to employ a One Health approach to monitor E. coli strains encoding the chuA gene and other virulence factors to control their dissemination.

Microbiology

Conventional and molecular identification of Iranian Clostridia species associated with animal infection

Volume 16, Issue 6, June 2025, Pages 345-352

Lida Abdolmohammadi khiav, Anahita Emadi, Maryam Dadar

Abstract Clostridial disease causes severe economic losses in livestock by rapidly killing ruminants. Therefore, implementing effective control approaches to prevent this fatal disease is importance. The causative agent of this disease is Clostridium spp. Accurate identification of this microorganism is crucial for effectively managing clostridial diseases in farm. There are conventional methods for detecting the disease, including microbiological and biochemical tests, many of these tests are time-consuming and exhibit low sensitivity. So, this study aims to use conventional and molecular approaches to identify Iranian isolates associated with animal infections. To achieve this, 61 samples were collected from1984 to 2024 and cultured on liver media, and subsequently subjected to microbiological and biochemical tests. For molecular identification, the DNA of isolates was extracted, and the isolates were confirmed by polymerase chain reaction (PCR) using specific primers. The results of the conventional analysis revealed that all Iranian isolates were identified as C. perfringens and its type determined by PCR assay. According to our findings, C. perfringens type A is the most prevalent strain in Iran, which predominantly found in ostriches and bird samples, followed by type D. This study underscores the presence of C. perfringens types across variety hosts and geographic locations in Iran. In conclusion, the combining conventional methods with PCR helps reliably detecting Clostridium spp. This information holds the potential to significantly contribute to the development of preventive strategies against clostridial diseases in Iran.

Microbiology

First case of serpentovirus infection in a ball python (Python regius) in Thailand: a case report with molecular characterization

Volume 16, Issue 6, June 2025, Pages 361-364

Panithi Laoungbua, Nararat Laopichienpong, Apinya Longya, Lawan Chanhome, Taksa Vasaruchapong, Tanapong Tawan, Narongsak Chaiyabutr

Abstract The pet snake industry in Thailand has seen a significant rise in popularity, with the ball python (Python regius) becoming a frequently kept species. However, respiratory disease poses a notable health concern, and various viral pathogens, including serpentoviruses (formerly classified as nidoviruses), have been implicated. While serpentovirus infections have been reported globally in diverse snake species, no documented cases had previously been identified in Thailand. This case report describes a 9-month-old ball python presenting to the Reptile Science Clinic at the Queen Saovabha Memorial Institute in Bangkok, Thailand, with respiratory distress and emaciation. Despite veterinary intervention, the snake succumbed to the infection within two weeks. Post-mortem examination revealed marked mucus accumulation within the oral cavity and necrotic oral mucosa. Histopathological analysis demonstrated severe catarrhal pneumonia. Molecular investigations confirmed the presence of serpentovirus in the lung tissue of the affected python, with subsequent sequence analysis revealing close homology to known serpentoviruses in ball pythons. This report documents the first confirmed case of serpentovirus infection in a pet snake in Thailand.

Microbiology

Comparison of the efficacies of Rhodococcus equi recombinant vaccine in mice

Volume 16, Issue 5, May 2025, Pages 253-259

Gokcenur Sanioglu Golen, Osman Erganiş, Asli Balevi

Abstract Rhodococcus equi is an important bacterial pathogen and causes severe chronic granulomatous pneumonia in foals below 6 months of age. It has also become an opportunistic and emerging pathogen in immunocompromised humans. Vaccination is the most cost-effective strategy for controlling and preventing this infection. Although several potential virulence genes and candidate immunogens have been identified over the years, no effective vaccine is currently available to prevent R. equi disease in horses. Recently, bacterial vector vaccines have been shown to be promising for R. equi. In this study, the virulence-associated protein A (VapA) gene of R. equi was cloned into Protein Expression System small ubiquitin-related modifier (pET-SUMO) expression vectors and transferred into Escherichia coli BL21 (DE3). Also, adjuvant significantly affects the efficacy of recombinant vaccines. Therefore, native VapA and recombinant VapA were formulated with Immunostimuling Microparticle System (IMS 3012) or PetGel A (recommended for horses) and subcutaneously administered to mice. The immunization effect of four different vaccines was determined by assaying antibody titers and survival rates. The antibody response was slightly higher in the PetGel A formulations than IMS 3012. Survival rates were lower in the PetGel A formulations than IMS 3012. Given these results, recombinant VapA adjuvanted with PetGel A represents a promising formulation for developing new-generation R. equi vaccines.

Microbiology

In-vitro evaluation and efficacy of bacteriophage isolated from commercial poultry farms against Salmonella typhimurium

Volume 16, Issue 5, May 2025, Pages 267-275

Amina Zaib, Ali Ahmad Sheikh, Faisal Ayub, Muhammad Arshad Durrani, Mobashra Mustafa, Afifa Shahzad, Urooj Ejaz, Muhammad Zubair Latif, Chamman Zahra, Izza Izza, Fareeha Zaib, Husnain Ahmad, Muhammad Jawad Hafeez, Muhammad Mujahid, Hafiz Muhammad Moavia Atique

Abstract Avian Salmonellosis impacts the economy and public health, with chicken products being a major cause of gastroenteritis. Hygiene, immunization and medicines are all used as control techniques. Bacteriophages provide a safe, targeted alternative. In the present study in vitro evaluation of bacteriophages were done against Salmonella typhimurium. Lytic effect of bacteriophages isolated from poultry sludge was checked on culture of S. typhimurium. Stability study was checked at range of temperature and pH. The phages were stable at temperature (30.00 - 50.00 ˚C) and pH (5.00 - 9.00) where best activity was seen at 37.00 ˚C and pH 7.00. In vitro lytic activity was done at (optical density 600 nm) after exposure to bacterial host at different intervals. Multiplicity of Infection of 1.00 was used to check lytic activity of phages which indicated phages were potent enough to infect bacterial cells within their growth cycle. The percentage of unadsorbed phages was determined by bar chart analysis. The genome of three phages was treated with DNase I where they all were sensitive. Later the nucleic acid of phages was digested by restriction endonucleases (EcoRI and HindIII) both of the enzymes produced various restriction sites with different band. The present study proved that the application of bacteriophages in vitro into bacterial system i.e., S. typhimurium was an attractive method in diminishing infection in commercial poultry thus providing exceptional results that could be used on a large scale.

Microbiology

Proteomic profiling of pseudorabies virus-infected PK-15 cells based on 4D label free analysis

Volume 16, Issue 3, March 2025, Pages 141-147

Shuaiwei Wang, Xiaoyong Chen, Houqiang Luo, Meng Wang, Junyu Liu, Qingsong Han

Abstract Pseudorabies virus (PRV) heavily depends on host machinery to support its life cycle. Investigating the interaction between PRV and host could aid in the understandings of viral pathogenesis. In this study, we performed a 4D label free proteomic method to examine the differentially expressed proteins in porcine kidney PK-15 cells with PRV infection. The results showed that the levels of 661 proteins were significantly elevated and 693 proteins were markedly reduced. Furthermore, these altered proteins were primarily enriched in spliceosome, protein processing in endoplasmic reticulum (ER), RNA transport, and protein export. To ensure the reliability of the proteomic results, the protein levels of formin binding protein 11 and wolfram syndrome 1as components of spliceosome and ER were verified via western blotting and the results were consistent. Together, our data shed light on a new protein profiling induced by PRV infection and highlighted the importance of spliceosome and ER in PRV replication which could promote understandings of host-PRV interplay.

Microbiology

Genotyping and phylogenetic analysis of Mannheimia haemolytica isolates from cattle and buffaloes of West Azerbaijan, Iran

Volume 16, Issue 1, January 2025, Pages 11-18

Safa Farahmand-Azar, Amir Tukmechi, Abdolghaffar Ownagh

Abstract This study was conducted in West Azerbaijan province, Iran (37°27'18.022" N, 45°0'0" E) to investigate the genotyping and phylogenetic characterization of Mannheimia haemolytica in cattle and buffaloes from November 2022 to January 2024. Mannheimia haemolytica is a bacterium known to cause pasteurellosis pneumonia, a respiratory disease in ruminants, such as cattle and sheep. This is one of the main causes of economic losses in the feedlot industry. In addition to the deaths, treatment costs are also significant. The lung and nasal swab samples were collected from 378 cattle and buffaloes. The M. haemolytica was detected in 32 (8.46%) of the samples, with a notably higher isolation rate from lung tissue (56.25%; n = 18) compared to the nasal swabs (43.75%; n = 14). Interestingly, the study also revealed a seasonal pattern, with the highest isolation rates observed during January, February, and March. Multi-locus sequence typing demonstrated that all isolates belonged to sequence type 1 (ST1) within clonal complex 28. This finding is consistent with the global prevalence of ST1 in bovine isolates, indicating widespread distribution. Phylogenetic analysis revealed a strong correlation between ST1 and STs 30 and 54, highlighting the prevalence of ST1 in M. haemolytica among ruminants in West Azerbaijan, Iran. Further research is needed to investigate its potential for causing disease and its transmission pattern.

Microbiology

Molecular and histopathological characterization of fowl adenovirus serotype 4 in broiler chickens in Kashan, Iran: implications for disease control and prevention in the poultry industry

Volume 16, Issue 1, January 2025, Pages 19-25

Mohammadreza Ghorani, Amir Ali Shahbazfar, Mohsen Ghorbiani, Behzad Ghorbanzadeh, Rohollah Kamyabi

Abstract Fowl adenovirus (FAdV) is a DNA virus causing significant diseases, like inclusion body hepatitis, hydropericardium-hepatitis syndrome (HHS), and gizzard erosion. These diseases lead to severe economic losses in the poultry industry. Recent increases in HHS outbreaks in Iran, particularly among broilers, prompted this study to analyze FAdV isolates in Kashan, Iran. In December 2021, a high-mortality HHS outbreak in a Kashan broiler flock led to liver and heart samples being sent for analysis. Histopathological investigations revealed mononuclear hepatitis and intra-nuclear viral inclusion bodies in hepatocytes. Polymerase chain reaction and phylogenetic analyses confirmed the presence of FAdV-4 (accession number: PP856395), showing 99.99% identity with strains from Japan, the United Arab Emirates, Pakistan, and the United States. These findings highlight the genetic similarity and potential common origin of FAdV-4 strains. This study emphasizes the need for heightened biosecurity measures and effective vaccination strategies to mitigate the spread of FAdV-4. The confirmed presence of FAdV-4 in central Iran poses a significant threat to the poultry industry, necessitating prompt action to prevent substantial economic losses.