Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa.

Since its emergence in the beginning of the 90's, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1-4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

Antimicrobial resistance in the globalized food chain: a One Health perspective applied to the poultry industry.

Antimicrobial resistance (AMR) remains a major global public health crisis. The food animal industry will face escalating challenges to increase productivity while minimizing AMR, since the global demand for animal protein has been continuously increasing and food animals play a key role in the global food supply, particularly broiler chickens. As chicken products are sources of low-cost, high-quality protein, poultry production is an important economic driver for livelihood and survival in developed and developing regions. The globalization of the food supply, markedly in the poultry industry, is aligned to the globalization of the whole modern society, with an unprecedented exchange of goods and services, and transit of human populations among regions and countries. Considering the increasing threat posed by AMR, human civilization is faced with a complex, multifaceted problem compromising its future. Actions to mitigate antimicrobial resistance are needed in all sectors of the society at the human, animal, and environmental levels. This review discusses the problems associated with antimicrobial resistance in the globalized food chain, using the poultry sector as a model. We cover critical aspects of the emergence and dissemination of antimicrobial resistance in the poultry industry and their implications to public health in a global perspective. Finally, we provide current insights using the multidisciplinary One Health approach to mitigate AMR at the human-animal-environment interface.

Staphylococcus sciuri as a Reservoir of mecA to Staphylococcus aureus in Non-Migratory Seabirds from a Remote Oceanic Island.

Aim: Genomic analysis of a methicillin-resistant Staphylococcus aureus (MRSA) strain cultured from a non-migratory seabird at Fernando de Noronha Archipelago (Brazilian oceanic islands) was carried out to investigate the potential origin of MRSA genetic determinants in an ecological setting with minimal or absent antimicrobial selective pressure, and minimal interaction with humans and domestic animals. Results: The study determined mecA gene homology and the phylogenetic relatedness with mecA described in Staphylococcus sciuri, which was the major Staphylococcus spp. cultured from the birds. Our findings corroborate in silico assumptions that the mecA gene in MRSA strains clinically relevant for humans and animals originates from S. sciuri ancestors. Conclusion: Coagulase-negative staphylococci seem to be natural reservoirs of methicillin-resistant genes to S. aureus, even in environments with very low antimicrobial selection pressure.

Occurrence of KPC-Producing Escherichia coli in Psittaciformes Rescued from Trafficking in Paraíba, Brazil.

The emergence and spread of antimicrobial resistance pose a threat to public health globally. Antibiotic-resistant bacteria and genes can disseminate among environments, animals and humans. Therefore, investigation into potential reservoirs of multidrug-resistant bacteria is of great importance to the understanding of putative transmission routes of resistant bacteria and resistance genes. This study aimed to report the occurrence of Escherichia coli harboring the Klebsiella pneumoniae carbapenemase-producing gene (blaKPC) in Psittaciformes rescued from wildlife trafficking in Paraíba State, Brazil. Cloacal swabs were collected from thirty birds and cultured by conventional microbiology using MacConkey and serum tryptone glucose glycerol (STGG) media supplemented with selective antimicrobials. E. coli isolates (n = 43) were identified by phenotypic tests and confirmed by MALDI-TOF. Antimicrobial susceptibility profiles were determined by means of Kirby-Bauer test. All isolates were further screened for extended-spectrum beta-lactamase (ESBL) production, and putative genes encoding ESBL were investigated by PCR. Additionally, blaKPC-harboring strains were genotyped by REP-PCR. A total of 43 E. coli phenotypically resistant isolates were recovered. The highest resistance rate was observed against ciprofloxacin. Among the resistance genes, only blaKPC was found in seven different birds from three species. According to the genotyping, these seven isolates belonged to four different strains. To date, this is the first report on the occurrence of KPC-E. coli in Psittaciformes rescued from trafficking in Northeastern Brazil. Due to the high clinical importance of KPC-E. coli, our findings suggest that wild animals in captivity at wildlife rescue centers can play a role as reservoirs of bacteria that are resistance to Critically Important antimicrobials in human medicine.

Antimicrobial resistance and genotypic relatedness of environmental staphylococci in semi-extensive dairy farms.

This study aimed to investigate the occurrence, genotypic relatedness and antimicrobial resistance of Staphylococcus aureus and coagulase-negative Staphylococcus from milk and environmental sources in dairy herds. A total of 110 staphylococci recovered from 147 samples collected at 21 semi-extensive dairy farms in Northeastern Brazil were investigated. Staphylococcus aureus isolates were identified and screened for methicillin resistance by means of a duplex-PCR. The highest frequency of contamination by S. aureus was observed for milk samples (38.1%), while contamination by coagulase-negative staphylococci (CoNS) was most commonly detected in milkers' hand swabs (52.4%) and environmental samples (29.5%). Two mecA-positive Staphylococcus aureus (2/40; 5%) were detected, while the same gene was found in fourteen (14/70; 20%) CoNS. Clonally related isolates from milk and environmental sources, such as the surface of gates, were detected by PFGE. This study reports the occurrence of MRSA in dairy farms under semi-extensive production practices and reinforces the importance of environment as a source of Staphylococcus contamination in dairy herds.

Biofilm-forming and antimicrobial resistance traits of staphylococci isolated from goat dairy plants.

INTRODUCTION: Biofilm-associated antimicrobial resistance is of increasing importance to the maintenance and spread of foodborne pathogens in the food industry. This study aimed to investigate the ability to form biofilm and the antimicrobial resistance of staphylococci contaminating small-scale goat milk dairy plants. METHODOLOGY: Sixty isolates were tested for antimicrobial resistance against 20 drugs by the microdilution method. Biofilm-forming traits were assessed by the microtiter plate method (MtP), Congo red agar method (CRA), and icaD gene detection by polymerase chain reaction (PCR). RESULTS: High antimicrobial resistance to ampicillin (60/60; 100%), penicillin G (21/60; 35%), and erythromycin (15/60; 25%) was observed, but all isolates were susceptible to amoxicillin/K-clavulanate, ceftriaxone, ciprofloxacin, gentamicin, levofloxacin, linezolid, and moxifloxacin. No resistance to oxacillin or vancomycin was seen among Staphylococcus aureus. Twenty-seven isolates (27/60; 45%) were considered to form biofilm according to MtP, and similar biofilm-producing frequencies were observed in coagulase-negative staphylococci (CoNS) (20/44; 45.4%) and S. aureus (7/16; 43.7%). The icaD gene was observed only in S. aureus isolates. There was no association between biofilm production and antimicrobial resistance. A higher frequency of biofilm-producing staphylococci was found in isolates from bulk tank milk and hand swabs. On the other hand, isolates from pasteurized milk showed lower frequency of biofilm formation. CONCLUSIONS: Staphylococci contaminating goat dairy plants are potential biofilm producers. The results suggest no association between the ability to form biofilm and antimicrobial resistance.

Enterotoxin gene profile of Staphylococcus aureus isolates recovered from bovine milk produced in central Ethiopia.

INTRODUCTION: Staphylococcal food intoxication is dependent on the production of enterotoxins, the single most important virulence factors. Various studies conducted in Ethiopia have depicted the prevalence of S. aureus in bovine milk. However, there is no published data regarding the enterotoxin gene profile of S. aureus isolates in Ethiopia. The aim of this study was, therefore, to evaluate enterotoxin gene carriage profile of S. aureus isolates recovered from bovine milk samples from central Ethiopia. METHODOLOGY: In this study, 109 S. aureus isolates recovered from bovine milk were analyzed for carriage of the classical enterotoxin genes. Genomic DNA extraction was performed using a commercially available kit. Two sets of multiplex polymerase chain reaction (PCR) assays were used to detect the five classical enterotoxin-coding genes and the toxic shock syndrome toxin gene. RESULTS: At least one type of S. aureus enterotoxin gene (SE) was carried in 73 (66.9%) of the isolates. The most frequently encountered gene was sea (40; 36.7%) followed by seb (19; 17.4%), see (18; 16.5%), tst (16; 14.7%), sec-1 (12; 11.01%), and sed (7; 6.4%). Of the 73 S. aureus isolates harboring at least one of the enterotoxin genes, 26 (35.6%) strains harbored more than one enterotoxin gene. CONCLUSIONS: More than half of the S. aureus isolates harbored at least one of the enterotoxin coding genes, indicating milk specimens contaminated by S. aureus could have a high chance of causing food intoxication.

Prevalence of Listeria monocytogenes in raw bovine milk and milk products from central highlands of Ethiopia.

INTRODUCTION: Listeria monocytogenes is of major significance in human and veterinary medicine. Most human Listeria infections are foodborne and the association of contaminated milk and dairy produce consumption with human listeriosis is noteworthy. In Ethiopia, there is limited data regarding the prevalence of L. monocytogenes in raw bovine milk and dairy products. The aim of this study was, therefore, to determine the prevalence of L. monocytogenes in raw bovine milk and dairy produce. METHODOLOGY: A total of 443 milk and milk product samples were microbiologically analyzed following methods recommended by the U.S. Food and Drug Administration Bacteriological Analytical Manual to isolate Listeria spp. RESULTS: The overall prevalence of Listeria spp. was 28.4% and specifically that of L. monocytogenes was 5.6%. Taking the prevalence of Listeria spp. into consideration, cheese was found to be highly contaminated at 60%, followed by pasteurized milk samples (40%), raw milk (18.9%) and yoghurt (5%). Considering the prevalence of Listeria monocytogenes only, raw milk had the lowest contamination while cheese had the highest, followed by pasteurized milk and yoghurt. CONCLUSIONS: Raw milk and milk products produced in urban and peri-urban areas of central Ethiopia were contaminated with pathogenic bacteria, L. monocytogenes. The detection of this pathogen in raw milk and milk products warrants an urgent regulatory mechanism to be put in place and also the potential role of milk processing plants in the contamination of dairy products should be investigated.

Molecular characterization of multidrug-resistant Salmonella enterica subsp. enterica serovar Typhimurium isolates from swine.

As part of a longitudinal study of antimicrobial resistance among salmonellae isolated from swine, we studied 484 Salmonella enterica subsp. enterica serovar Typhimurium (including serovar Typhimurium var. Copenhagen) isolates. We found two common pentaresistant phenotypes. The first was resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (the AmCmStSuTe phenotype; 36.2% of all isolates), mainly of the definitive type 104 (DT104) phage type (180 of 187 isolates). The second was resistance to ampicillin, kanamycin, streptomycin, sulfamethoxazole, and tetracycline (the AmKmStSuTe phenotype; 44.6% of all isolates), most commonly of the DT193 phage type (77 of 165 isolates), which represents an unusual resistance pattern for DT193 isolates. We analyzed 64 representative isolates by amplified fragment length polymorphism (AFLP) analysis, which revealed DNA fingerprint similarities that correlated with both resistance patterns and phage types. To investigate the genetic basis for resistance among DT193 isolates, we characterized three AmKmStSuTe pentaresistant strains and one hexaresistant strain, which also expressed resistance to gentamicin (Gm phenotype), all of which had similar DNA fingerprints and all of which were collected during the same sampling. We found that the genes encoding the pentaresistance pattern were different from those from isolates of the DT104 phage type. We also found that all strains encoded all of their resistance genes on plasmids, unlike the chromosomally encoded genes of DT104 isolates, which could be transferred to Escherichia coli via conjugation, but that the plasmid compositions varied among the isolates. Two strains (strains UT08 and UT12) had a single, identical plasmid carrying bla(TEM) (which encodes ampicillin resistance), aphA1-Iab (which encodes kanamycin resistance), strA and strB (which encode streptomycin resistance), class B tetA (which encodes tetracycline resistance), and an unidentified sulfamethoxazole resistance allele. The third pentaresistant strain (strain UT20) was capable of transferring by conjugation two distinct resistance patterns, AmKmStSuTe and KmStSuTe, but the genes were carried on plasmids with slightly different restriction patterns (differing by a single band of 15 kb). The hexaresistant strain (strain UT30) had the same plasmid as strains UT08 and UT12, but it also carried a second plasmid that conferred the AmKmStSuGm phenotype. The second plasmid harbored the gentamicin resistance methylase (grm), which has not previously been reported in food-borne pathogenic bacteria. It also carried the sul1 gene for sulfamethoxazole resistance and a 1-kb class I integron bearing aadA for streptomycin resistance. We also characterized isolates of the DT104 phage type. We found a number of isolates that expressed resistance only to streptomycin and sulfamethoxazole (the StSu phenotype; 8.3% of serovar Typhimurium var. Copenhagen strains) but that had AFLP DNA fingerprints similar or identical to those of strains with genes encoding the typical AmCmStSuTe pentaresistance phenotype of DT104. These atypical StSu DT104 isolates were predominantly cultured from environmental samples and were found to carry only one class I integron of 1.0 kb, in contrast to the typical two integrons (InC and InD) of 1.0 and 1.2 kb, respectively, of the pentaresistant DT104 isolates. Our findings show the widespread existence of multidrug-resistant Salmonella strains and the diversity of multidrug resistance among epidemiologically related strains. The presence of resistance genes on conjugative plasmids and duplicate genes on multiple plasmids could have implications for the spread of resistance factors and for the stability of multidrug resistance among Salmonella serovar Typhimurium isolates.